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  • 101.
    Baião, Guilherme Costa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Genomic and transcriptomic investigation of reproductive incompatibility in Drosophila2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Both nuclear and cytoplasmic elements can contribute to the emergence of reproductive incompatibilities that influence evolution and speciation. In the projects that compose this thesis, we use genomics and transcriptomics to study some of those elements in Drosophila.

    In the first study, we show that Wolbachia, an endosymbiotic bacterium known to cause reproductive alterations in its hosts, influences gene expression in D. paulistorum. Affected genes were associated with biological functions such as metabolism, immunity, reproduction, and chemical communication. Our results indicate that Wolbachia accentuates the differences in expression profiles between semispecies and suggest that the symbiont influences host pre-and postmating isolation.

    In the second paper, we uncover widespread persistent heteroplasmy in D. paulistorum. We reveal that D. paulistorum mitochondria are polyphyletic, with two divergent mitotypes, and that the heteroplasmy likely originated through introgression. One of the mitotypes shows biparental inheritance, non-responsiveness to host energy demands and rapid titer increase in the early embryo. We hypothesize that such selfish traits evolved in response to competition between mitotypes.

    In the third project, we show that differentially expressed genes between D. paulistorum semispecies are associated with a variety of biological processes, especially broad regulatory functions that occur via variability in transcription, translation and ubiquitination of post-translational modification. We reveal that the expression profile of F1 inter-semispecies hybrids is markedly similar to that of the maternal line, and that Wolbachia has a small but potentially significant interaction with genes that are differentially expressed in semispecies and F1 hybrids.

    Finally, we use comparative genomics to study the evolution of closely related Wolbachia strains with known reproductive phenotypes. We confirm previous observations that Wolbachia genomes are very dynamic and that phage-associated regions are particularly variable and likely involved in horizontal transfer of genes linked to reproductive phenotypes. An in-depth screen for genetic elements potentially involved in Wolbachia-induced cytoplasmic incompatibility recovers genes previously known to be involved in the phenotype and novel candidates.

    In conclusion, this thesis contributes to our understanding of genetic factors that affect Drosophila evolution, particularly those leading to reproductive incompatibility in D. paulistorum and associated with Wolbachia.

    List of papers
    1. The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation
    Open this publication in new window or tab >>The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation
    2019 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 20, article id 465Article in journal (Refereed) Published
    Abstract [en]

    Background: The Neotropical fruit fly Drosophila paulistorum (Diptera: Drosophilidae) is a species complex in statu nascendi comprising six reproductively isolated semispecies, each harboring mutualistic Wolbachia strains. Although wild type flies of each semispecies are isolated from the others by both pre- and postmating incompatibilities, mating between semispecies and successful offspring development can be achieved once flies are treated with antibiotics to reduce Wolbachia titer. Here we use RNA-seq to study the impact of Wolbachia on D. paulistorum and investigate the hypothesis that the symbiont may play a role in host speciation. For that goal, we analyze samples of heads and abdomens of both sexes of the Amazonian, Centro American and Orinocan semispecies of D. paulistorum.

    Results: We identify between 175 and 1192 differentially expressed genes associated with a variety of biological processes that respond either globally or according to tissue, sex or condition in the three semispecies. Some of the functions associated with differentially expressed genes are known to be affected by Wolbachia in other species, such as metabolism and immunity, whereas others represent putative novel phenotypes involving muscular functions, pheromone signaling, and visual perception.

    Conclusions: Our results show that Wolbachia affect a large number of biological functions in D. paulistorum, particularly when present in high titer. We suggest that the significant metabolic impact of the infection on the host may cause several of the other putative and observed phenotypes. We also speculate that the observed differential expression of genes associated with chemical communication and reproduction may be associated with the emergence of pre- and postmating barriers between semispecies, which supports a role for Wolbachia in the speciation of D. paulistorum.

    Keywords
    Speciation, symbiosis, Wolbachia, transcriptome, Drosophila paulistorum, host-symbiont interactions
    National Category
    Genetics Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-389597 (URN)10.1186/s12864-019-5816-9 (DOI)000470715200001 ()31174466 (PubMedID)
    Funder
    Swedish Research Council, 2014-4353
    Available from: 2019-07-24 Created: 2019-07-24 Last updated: 2020-03-12Bibliographically approved
    2. Persistence of high-level heteroplasmy through biparental transmission of a selfish mitochondrion in Drosophila paulistorum
    Open this publication in new window or tab >>Persistence of high-level heteroplasmy through biparental transmission of a selfish mitochondrion in Drosophila paulistorum
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Heteroplasmy, or the coexistence of multiple mitotypes in an individual, has during recent years been shown to be more common in animals than previously anticipated. However, cases of stable, high-titer heteroplasmy are still relatively rare, as are systems with consistent paternal mitochondrial inheritance. In this study, we sequenced and assembled the full mitochondrial genomes of 23 Neotropical Drosophila lines belonging to six species of the willistoni group and three of the saltans group and discovered that 40% the 13 sequenced Drosophila paulistorum lines, are persistently heteroplasmic. We further showed that the mitochondria of D. paulistorum are polyphyletic, forming two clades, a and b, and that mitochondria of the a2 clade are exclusively found in heteroplasmic flies. Genomic analysis indicates that a2 is a functional mitochondrion, with no signs of loss of function mutations. Even so, our results demonstrate that a2 displays unusual features, including lack of titer response to energetic demands, higher titer in males than females, and consistent biparental transmission due to rapid replication during early embryo development. Together these features indicate that a2 might be a selfish mitochondrion that persists due to efficient biparental transmission.

    Using the assembled genomes, we reconstructed the evolutionary history of mitochondria in the willistoni subgroup and identified signs of multiple mitochondrial losses, gains and introgressions. The data indicated an a-like mitochondrial ancestor in the willistoni subgroup, with the b mitochondrion likely being acquired through introgression from an unidentified donor. We hypothesize that the selfish characteristics of a2 might have emerged as a response to competition for inheritance with the introgressed b

    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Molecular Evolution
    Identifiers
    urn:nbn:se:uu:diva-406755 (URN)
    Available from: 2020-03-11 Created: 2020-03-11 Last updated: 2020-03-12
    3. Differential gene expression in semispecies and hybrids of Drosophila paulistorum
    Open this publication in new window or tab >>Differential gene expression in semispecies and hybrids of Drosophila paulistorum
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Gene expression divergence is correlated with and can be either a cause or a consequence of species divergence. Studying gene expression differences between closely related species, and their hybrid offspring, can thus give us clues about genes and mechanisms associated with reproductive isolation (RI) between them and allow us to better understand early stages of speciation. In this study, we use RNA-Seq to investigate gene expression divergence between the Amazonian, Centro-American and Orinocan semispecies of Drosophila paulistorum, a species cluster in statu nascendi, and between inter-semispecies hybrids and their parents. We uncover a large number of genes with varying expression between semispecies, with the highest numbers in male abdomens. The differentially expressed genes are associated with a range of biological functions, but especially with broad, regulatory functions, that are governed by transcription, translation, post-translational modifications and induced by signal transduction. We found that the expression pattern of hybrids was much more similar to the maternal line and that very few genes have a different expression than both of their parents. When comparing the differentially expressed genes in semispecies and hybrids to gene affected by Wolbachia in D. paulistorum, we see a small overlap. However, especially in hybrids, some of the overlapping genes appear to be highly relevant. Our study provides insights about expression differences associated with RI in D. paulistorum, and the impact of Wolbachia on the divergence of semispecies and hybrid sterility.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-406757 (URN)
    Available from: 2020-03-11 Created: 2020-03-11 Last updated: 2020-03-12
    4. Comparative genomics of closely related Wolbachia strains infecting Drosophila
    Open this publication in new window or tab >>Comparative genomics of closely related Wolbachia strains infecting Drosophila
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Cytoplasmic incompatibility (CI) is the most common form of reproductive manipulation induced by the vertically inherited endosymbiont Wolbachia. The phenotype causes partial or complete sterility in crosses between infected males and non-infected females, thus benefiting infected females in the population and the spread of the bacteria. Because of these properties, CI-inducing Wolbachia has been implicated as a mean for biological pest control. Although CI has been known for several decades, the first CI-associated genes, cifA and cifB, were only recently discovered. In this study, we sequenced five complete Wolbachia genomes (wSan, wYak, wTei, wAu, wMa,) and performed comparative genomic analyses between these and four previously published complete Wolbachia genomes (wRi, wNo, wHa, wMel), that have all had their CI properties tested in the same genetic host background, Drosophila simulans STC. Using these genomes, we investigate what types of genes differ between closely related Wolbachia strains and compare the sequences from some of the strains in their natural host vs. after transfer to D. simulans STC. We find that phage-associated and hypothetical genes are likely to vary more between genomes and that very few mutations have occurred when strains were transferred to D. simulans. Furthermore, we investigate the evolution of the known CI genes and take advantage of the highly similar genomes of some strains as well as their complex CI properties to identify further genes associated with both mod and resc functions of CI.

    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Molecular Evolution
    Identifiers
    urn:nbn:se:uu:diva-406756 (URN)
    Available from: 2020-03-11 Created: 2020-03-11 Last updated: 2020-03-12
  • 102. Bajdek, Piotr
    et al.
    Owocki, Krzysztof
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Putative dicynodont coprolites from the Upper Triassic of Poland2014In: Palaeogeography, Palaeoclimatology, Palaeoecology, ISSN 0031-0182, E-ISSN 1872-616X, Vol. 411, p. 1-17Article in journal (Refereed)
    Abstract [en]

    A significant number (more than 100) of brownto dark and silty, carbonate or pyrite-mineralized, in part organic carbon-rich, spherical or oval-shaped structures have been collected fromthe Upper Triassic (uppermost NorianlowerRhaetian) sediments of the Lipie Śląskie clay-pit at Lisowice near Lubliniec town, Poland. Their geological context, morphology, content, geochemistry and association with skeletal remains suggest they are fecal masses of a sizable herbivorous tetrapod. The only large herbivore known from the site is a giant 5 meter-long dicynodont (Synapsida: Anomodontia), represented by numerous bones and also by large, oval-shaped footprints. The putative dicynodont coprolites were collected from mudstone and siltstone with numerous organic remains that were deposited in anoxic conditions. In addition, REEs and other trace element concentrations suggest that the burial environment and diagenesis of these coprolites were under anoxic conditions. SEM and thin section images of the coprolite matrix show numerous nests with pyrite (probably bacterial in origin) and large amount of mineral particles. The putative dicynodont coprolites contain also amorphous, dark organic matter, poorly preserved palynomorphs, small fragments of plant cuticle. Detailed characteristic of these coprolites reveals possible implications for the ecology and physiology of the source animal species. The δ 13C values of the gymnospermcuticle and dark organic matter measured in three coprolites are −23.4‰, −21.2‰and −20.3‰, all average. The evidence from these coprolites suggests that dicynodonts processed plant soft elements into very small pieces, but wood fragments were found also in a mass accumulation in two coprolites.

  • 103.
    Bajdek, Piotr
    et al.
    Aleja Najswieztszej Maryi Panny 20-20A, PL-42200 Czestochowa, Poland..
    Qvarnström, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Owocki, Krzysztof
    Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland..
    Sulej, Tomasz
    Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland..
    Sennikov, Andrey G.
    Russian Acad Sci, Borissiak Paleontol Inst, Profsoyuznaya 123, Moscow 117997, Russia.;Kazan Fed Univ, Kremlyovskaya 18, Kazan 420008, Russia..
    Golubev, Valeriy K.
    Russian Acad Sci, Borissiak Paleontol Inst, Profsoyuznaya 123, Moscow 117997, Russia.;Kazan Fed Univ, Kremlyovskaya 18, Kazan 420008, Russia..
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Microbiota and food residues including possible evidence of pre-mammalian hair in Upper Permian coprolites from Russia2016In: Lethaia: an international journal of palaeontology and stratigraphy, ISSN 0024-1164, E-ISSN 1502-3931, Vol. 49, no 4, p. 455-477Article in journal (Refereed)
    Abstract [en]

    Coprolites (fossil faeces) provide direct evidence on the diet of its producer and unique insights on ancient food webs and ecosystems. We describe the contents of seven coprolites, collected from the Late Permian Vyazniki site of the European part of Russia. Two coprolite morphotypes (A, B) contain remains of putative bacteria, cyanobacteria, fungi, protists, invertebrate eggs, arthropod elements, undigested bone and tooth fragments, fish scales and elongated hair-like structures with hollow interiors. Content, size and shape of the coprolites together with the associated body fossil record suggest that the most probable scat-producers were carnivorous tetrapods; the bone-rich morphotype A reveals short food retention time and a fast metabolism and is therefore assigned to therapsid carnivores whereas morphotype B with rarer and degraded bones are assigned to archosauromorphs or other non-therapsid carnivores. The general coprolite matrix contains abundant micron-sized spheres and thin-walled vesicles which are interpreted as oxide and phosphatic pseudomorphs after microbial cells. From analyses of the undigested bones, we infer that they represent remains of actinopterygian fish, a therapsid and unrecognizable parts of amphibians and/or reptiles. Additionally, hair-like structures found in one coprolite specimen occur as diagenetically altered (oxide-replaced) structures and moulds (or partly as pseudomorphs) in a microcrystalline carbonate-fluoride-bearing calcium phosphate. This suggests that the latest Permian therapsids probably were equipped with hair-like integument or hairsuit. If true, this is by far the oldest evidence of this mammalian character in the stem group of mammals.

  • 104.
    BALTEKIN, ÖZDEN
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Experimental Evolution of Persister Fractions in Escherichia coli2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 105. Baltscheffsky, Herrick
    et al.
    Persson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    On an Early Gene for Membrane-Integral Inorganic Pyrophosphatase in the Genome of an Apparently Pre-LUCA Extremophile, the Archaeon Candidatus Korarchaeum cryptofilum2014In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 78, no 2, p. 140-147Article in journal (Refereed)
    Abstract [en]

    A gene for membrane-integral inorganic pyrophosphatase (miPPase) was found in the composite genome of the extremophile archaeon Candidatus Korarchaeum cryptofilum (CKc). This korarchaeal genome shows unusual partial similarity to both major archaeal phyla Crenarchaeota and Euryarchaeota. Thus this Korarchaeote might have retained features that represent an ancestral archaeal form, existing before the occurrence of the evolutionary bifurcation into Crenarchaeota and Euryarchaeota. In addition, CKc lacks five genes that are common to early genomes at the LUCA border. These two properties independently suggest a pre-LUCA evolutionary position of this extremophile. Our finding of the miPPase gene in the CKc genome points to a role for the enzyme in the energy conversion of this very early archaeon. The structural features of its miPPase indicate that it can pump protons through membranes. An miPPase from the extremophile bacterium Caldicellulosiruptor saccharolyticus also has a sequence indicating a proton pump. Recent analysis of the three-dimensional structure of the miPPase from Vigna radiata has resulted in the recognition of a strongly acidic substrate (orthophosphate: Pi, pyrophosphate: PPi) binding pocket, containing 11 Asp and one Glu residues. Asp (aspartic acid) is an evolutionarily very early proteinaceous amino acid as compared to the later appearing Glu (glutamic acid). All the Asp residues are conserved in the miPPase of CKc, V. radiata and other miPPases. The high proportion of Asp, as compared to Glu, seems to strengthen our argument that biological energy conversion with binding and activities of orthophosphate (Pi) and energy-rich pyrophosphate (PPi) in connection with the origin and early evolution of life may have started with similar or even more primitive acidic peptide funnels and/or pockets.

  • 106.
    Barbosa, Camilo
    et al.
    Univ Kiel, Dept Evolutionary Ecol & Genet, Kiel, Germany.
    Römhild, Roderich
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Univ Kiel, Dept Evolutionary Ecol & Genet, Kiel, Germany;Max Planck Inst Evolutionary Biol, Plon, Germany.
    Rosenstiel, Philip
    UKSH, Inst Clin Mol Biol, Kiel, Germany.
    Schulenburg, Hinrich
    Univ Kiel, Dept Evolutionary Ecol & Genet, Kiel, Germany;Max Planck Inst Evolutionary Biol, Plon, Germany.
    Evolutionary stability of collateral sensitivity to antibiotics in the model pathogen Pseudomonas aeruginosa2019In: eLIFE, E-ISSN 2050-084X, Vol. 8, article id e51481Article in journal (Refereed)
    Abstract [en]

    Evolution is at the core of the impending antibiotic crisis. Sustainable therapy must thus account for the adaptive potential of pathogens. One option is to exploit evolutionary trade-offs, like collateral sensitivity, where evolved resistance to one antibiotic causes hypersensitivity to another one. To date, the evolutionary stability and thus clinical utility of this trade-off is unclear. We performed a critical experimental test on this key requirement, using evolution experiments with Pseudomonas aeruginosa, and identified three main outcomes: (i) bacteria commonly failed to counter hypersensitivity and went extinct; (ii) hypersensitivity sometimes converted into multidrug resistance; and (iii) resistance gains frequently caused re-sensitization to the previous drug, thereby maintaining the trade-off. Drug order affected the evolutionary outcome, most likely due to variation in the effect size of collateral sensitivity, epistasis among adaptive mutations, and fitness costs. Our finding of robust genetic trade-offs and drug-order effects can guide design of evolution-informed antibiotic therapy.

  • 107.
    Barnaby, Jonathan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Cooperative Breeding in the Southern Anteater-Chat: Sexual Disparity, Survival and Dispersal2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Group-living sets the scene for complex social behaviours such as cooperative breeding, and exploring the factors that shape group-living is crucial in understanding these behaviours. This thesis explores the ecology of a population of the facultative cooperative breeding southern anteater-chat (Myrmecocichla formicivora), a group-living bird species endemic to southern Africa. It reveals a breeding system based around a breeding pair and up to three auxiliary males. Despite equal numbers of males and females produced as fledglings there was a surplus of adult males, which remained philopatric. Dispersal was strongly female biased. Females dispersed within their first year, they dispersed further than males, and they lost the benefits of the natal site. The sex skew in the population suggested that these factors drive differential mortality, with juvenile females having much lower annual survival than juvenile males. Adult survival was higher, with female survival only slightly lower than male survival. Dispersal distances suggested that males selected the breeding location, nearer to their natal site. There was no evidence of surplus non-breeding females. On the loss of a breeding female there was no replacement until new females entered the population, yet if a breeding male disappeared the female promptly re-paired with a male from another group. There was no indication of birds floating in the population, and if males were orphaned or widowed they joined other groups as unrelated helpers in preference to floating. There was no sign of inter-group or individual aggression among chats, and unrelated helpers were peacefully accepted into groups, suggesting mutual benefits. In fact all birds in a group helped raise offspring of the breeding pair, and groups with more helpers fledged more offspring, which implies that both direct and indirect fitness benefits can be gained through joining a group and helping. There was surprisingly little inheritance of breeding position by auxiliaries, and strikingly low levels of extra-pair paternity. This study suggests that the Southern anteater-chat group structure arises through male philopatry due to a shortage of breeding females, the benefits of remaining on the natal site and helping, and the potentially high costs of living alone.

    List of papers
    1. Group-living in the southern anteater-chat Myrmecocichla formicivora.
    Open this publication in new window or tab >>Group-living in the southern anteater-chat Myrmecocichla formicivora.
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Group-living sets the scene for complex social behaviours such as cooperative breeding, and exploring the factors that shape group-living is crucial in understanding these behaviours. Here we describe some aspects of the ecology of a population of the facultative cooperative breeding southern anteater-chat (Myrmecocichla formicivora), a group living bird species endemic to southern Africa. We used data from a four year study of individually marked birds, with pedigrees completed using microsatellite genotyping. Southern anteater-chats live in groups of 2-5 individuals - a breeding pair and up to three additional none-breeders. These auxiliary birds were either retained offspring or unrelated individuals, and all birds in a group assisted by feeding at the nest. Our population had a skewed sex ratio of approximately 58% males to 42% females, yet the sex ratio of fledglings was equal, suggesting sex-biased mortality. Helpers were predominantly retained male offspring; however 21% of helpers were unrelated to either of the breeding pair. Southern anteater-chats appear to be non-territorial, with an apparent lack of aggression both within and between groups. Our study confirms that the southern anteater-chat is a facultative cooperative breeder, with both pair breeders and groups with helpers capable of fledging youngsters. We provide evidence suggesting that the breeding system of the southern anteater-chat is based on prompt female dispersal, and male philopatry due to an apparent shortage of mates, potential benefits of the natal site and possible high costs of floating. It appears that ecological constraints promoting delayed dispersal are reinforced by benefits gained from remaining philopatric.

    Keywords
    Southern anteater-chat, cooperative breeding, social evolution, behavioural ecology, delayed dispersal, family living, Africa
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-179071 (URN)
    Available from: 2012-08-13 Created: 2012-08-07 Last updated: 2012-09-05
    2. Sex specific survival in the southern anteater-chat Mymecocichla formicivora.
    Open this publication in new window or tab >>Sex specific survival in the southern anteater-chat Mymecocichla formicivora.
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Survival is a key factor behind life-history variation both between and within species. It is also a major influence on sociality in species which delay dispersal and live in family groups. Knowledge of differential survival rates between males and females and juveniles and adults give insights into the costs and benefits of different behavioural and life-history strategies. Here we investigate patterns of survival in a population of the southern anteater-chat (Myrmecocichla formicivora), a facultative cooperatively breeding passerine of southern Africa. Using data from a 9-year mark-capture-recapture study, we examined juvenile and adult sex related variation in survival, and the role of environmental variables (rainfall, temperature) for survival patterns in the population. Annual adult survival probability (mean ± SE) was 0.71 ± 0.03 for males and 0.60 ± 0.04 for females. Juvenile survival was lower for each sex, with juvenile female survival (0.36 ± 0.04) being 35% lower than juvenile male survival (0.55 ± 0.04). Using these estimates we calculated the mean life span (MLS) in years for male southern anteater-chat to be 4.0 ± 0.7, considerably higher than for females at 2.0 ± 0.4. These figures closely matched the population-age structure of the study area, and could explain the high male biased sex skew of adult birds in this population. Higher annual mean temperature was associated with higher survival, whereas higher annual rainfall was associated with lower survival for both sex and age classes. Female survival, particularly female juvenile survival, may be reduced due to prompt dispersal and longer dispersal distances, and the additional costs of breeding early in life. Differential survival can promote male philopatry and this in turn could well encourage the cooperative breeding we see in the southern anteater-chat.

    Keywords
    Southern anteater-chat, cooperative breeding, social evolution, behavioural ecology, delayed dispersal, family living, Africa
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-179072 (URN)
    Available from: 2012-08-13 Created: 2012-08-07 Last updated: 2012-09-05
    3. The rarer sex - female natal dispersal and breeder replacement in the southern anteater-chat Myrmecocichla formicivora.
    Open this publication in new window or tab >>The rarer sex - female natal dispersal and breeder replacement in the southern anteater-chat Myrmecocichla formicivora.
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Sex biased dispersal is a crucial factor in understanding the mechanism of family dynamics in many cooperative breeders. Female biased dispersal occurs in many cooperatively breeding birds. It is often associated with females dispersing earlier and further, and a male biased sex skew in the population. Here we investigated female dispersal in the southern anteater-chat, a facultative cooperatively breeding passerine of southern Africa. Our study population had a male biased sex skew, and females had lower annual survival than males. Dispersal was strongly female biased, with females dispersing within their first year whereas many males remained philopatric beyond the next breeding season. Breeding females were on average younger than breeding males, and also dispersed further. Each breeding group contained only one female. No females were found floating in the population, and all females were associated with one or more males in a breeding group. It appears that all females disperse in their first year directly to a breeding position. If a female disappeared in the breeding season they were not replaced until new females matured and dispersed the following season, yet if a male breeder disappeared during the breeding season he was almost immediately replaced, indicating that there are no surplus females.

    Keywords
    Southern anteater-chat, cooperative breeding, social evolution, behavioural ecology, delayed dispersal, family living, Africa
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-179073 (URN)
    Available from: 2012-08-13 Created: 2012-08-07 Last updated: 2012-09-05
    4. From helping to breeding – male choice in the southern anteater-chats Myrmecocichla formicivora.
    Open this publication in new window or tab >>From helping to breeding – male choice in the southern anteater-chats Myrmecocichla formicivora.
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Dispersal choice is important in understanding population structure and dynamics. Here we examine male choice in the facultative cooperative breeding southern anteater-chat Myrmecocichla formicivora based on a four year study in South Africa. The sex ratio in our study population was male biased, with many males remaining philopatric. All groups consisted of one or more adult males associated with one adult female. We found a significant positive effect of auxiliary number on group productivity (both number of young fledged, and first year survival), while controlling for potentially confounding variables (territory and breeder identity). The majority of auxiliaries, 54%, were related to both birds in the breeding pair, with another 25% related to one member of the pair, and 21% related to neither of the breeders. There was no evidence of males floating within our study population, and it appears that if males lose their family due to mortality they join other groups as unrelated non-breeding auxiliaries rather than float. No aggression was observed between individual southern anteater-chats, and unrelated group members helped rear offspring in the group they had joined. Despite the presence of, and helping by unrelated group members there was very little evidence of breeding position inheritance (1/24 auxiliaries unrelated to the breeding female) or extra-pair paternity (2.4% of fledglings). This study suggests that the southern anteater-chat group structure arises through male philopatry due to a lack of breeding females and potentially high costs of living alone.

    Keywords
    Southern anteater-chat, cooperative breeding, social evolution, behavioural ecology, delayed dispersal, family living, Africa
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-179074 (URN)
    Available from: 2012-08-13 Created: 2012-08-07 Last updated: 2012-09-05
    5. Development of a suit of microsatellite markers for the southern anteater-chat Myrmecocichla formicivora.
    Open this publication in new window or tab >>Development of a suit of microsatellite markers for the southern anteater-chat Myrmecocichla formicivora.
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    We tested the cross amplification of 37 microsatellite markers for their suitability in genotyping the southern anteater-chat Myrmecocichla formicivora, an opportunistic cooperatively breeding passerine bird endemic to southern Africa. Fourteen microsatellite markers were identified as having suitable characteristics, with minor deviation from Hardy-Weinberg equilibrium and little evidence of null alleles. These 14 Primer pairs were combined in 4 multiplexes and run on 183 individual samples from our study population of southern anteater-chat on Benfontein Nature Reserve, near Kimberley in central South Africa. The loci ranged from 3-34 alleles per locus, and observed heterozygosity ranged from 0.45 -0.93. We then tested these 14 microsatellites for their use in examining paternity in a population of southern anteater-chat being studied on Benfontein Nature Reserve, near Kimberley in South Africa. Of the population of 183 individuals (the 2011 population) 93% of the offspring could be allocated a mother, 97% a father, and 87% a parent pair with 95% confidence. The remainder could be allocated at the 80% confidence level. Where mothers could be assigned from observations this was in 100% agreement with the microsatellite results, giving us good support for the accurate assignment of parentage in our population.

    Keywords
    Southern anteater-chat, cooperative breeding, social evolution, microsatellites, genotyping, cross-amplification, behavioural ecology, delayed dispersal, family living, Africa
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-179075 (URN)
    Available from: 2012-08-13 Created: 2012-08-07 Last updated: 2012-09-05
  • 108.
    Barnaby, Jonathan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Ekman, Jan
    From helping to breeding – male choice in the southern anteater-chats Myrmecocichla formicivora.Manuscript (preprint) (Other academic)
    Abstract [en]

    Dispersal choice is important in understanding population structure and dynamics. Here we examine male choice in the facultative cooperative breeding southern anteater-chat Myrmecocichla formicivora based on a four year study in South Africa. The sex ratio in our study population was male biased, with many males remaining philopatric. All groups consisted of one or more adult males associated with one adult female. We found a significant positive effect of auxiliary number on group productivity (both number of young fledged, and first year survival), while controlling for potentially confounding variables (territory and breeder identity). The majority of auxiliaries, 54%, were related to both birds in the breeding pair, with another 25% related to one member of the pair, and 21% related to neither of the breeders. There was no evidence of males floating within our study population, and it appears that if males lose their family due to mortality they join other groups as unrelated non-breeding auxiliaries rather than float. No aggression was observed between individual southern anteater-chats, and unrelated group members helped rear offspring in the group they had joined. Despite the presence of, and helping by unrelated group members there was very little evidence of breeding position inheritance (1/24 auxiliaries unrelated to the breeding female) or extra-pair paternity (2.4% of fledglings). This study suggests that the southern anteater-chat group structure arises through male philopatry due to a lack of breeding females and potentially high costs of living alone.

  • 109.
    Barnaby, Jonathan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Ekman, Jan
    The rarer sex - female natal dispersal and breeder replacement in the southern anteater-chat Myrmecocichla formicivora.Manuscript (preprint) (Other academic)
    Abstract [en]

    Sex biased dispersal is a crucial factor in understanding the mechanism of family dynamics in many cooperative breeders. Female biased dispersal occurs in many cooperatively breeding birds. It is often associated with females dispersing earlier and further, and a male biased sex skew in the population. Here we investigated female dispersal in the southern anteater-chat, a facultative cooperatively breeding passerine of southern Africa. Our study population had a male biased sex skew, and females had lower annual survival than males. Dispersal was strongly female biased, with females dispersing within their first year whereas many males remained philopatric beyond the next breeding season. Breeding females were on average younger than breeding males, and also dispersed further. Each breeding group contained only one female. No females were found floating in the population, and all females were associated with one or more males in a breeding group. It appears that all females disperse in their first year directly to a breeding position. If a female disappeared in the breeding season they were not replaced until new females matured and dispersed the following season, yet if a male breeder disappeared during the breeding season he was almost immediately replaced, indicating that there are no surplus females.

  • 110.
    Barnaby, Jonathan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Fletcher, Kevin
    Ekman, Jan
    Development of a suit of microsatellite markers for the southern anteater-chat Myrmecocichla formicivora.Manuscript (preprint) (Other academic)
    Abstract [en]

    We tested the cross amplification of 37 microsatellite markers for their suitability in genotyping the southern anteater-chat Myrmecocichla formicivora, an opportunistic cooperatively breeding passerine bird endemic to southern Africa. Fourteen microsatellite markers were identified as having suitable characteristics, with minor deviation from Hardy-Weinberg equilibrium and little evidence of null alleles. These 14 Primer pairs were combined in 4 multiplexes and run on 183 individual samples from our study population of southern anteater-chat on Benfontein Nature Reserve, near Kimberley in central South Africa. The loci ranged from 3-34 alleles per locus, and observed heterozygosity ranged from 0.45 -0.93. We then tested these 14 microsatellites for their use in examining paternity in a population of southern anteater-chat being studied on Benfontein Nature Reserve, near Kimberley in South Africa. Of the population of 183 individuals (the 2011 population) 93% of the offspring could be allocated a mother, 97% a father, and 87% a parent pair with 95% confidence. The remainder could be allocated at the 80% confidence level. Where mothers could be assigned from observations this was in 100% agreement with the microsatellite results, giving us good support for the accurate assignment of parentage in our population.

  • 111.
    Barnaby, Jonathan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Fletcher, Kevin
    Ekman, Jan
    Group-living in the southern anteater-chat Myrmecocichla formicivora. Manuscript (preprint) (Other academic)
    Abstract [en]

    Group-living sets the scene for complex social behaviours such as cooperative breeding, and exploring the factors that shape group-living is crucial in understanding these behaviours. Here we describe some aspects of the ecology of a population of the facultative cooperative breeding southern anteater-chat (Myrmecocichla formicivora), a group living bird species endemic to southern Africa. We used data from a four year study of individually marked birds, with pedigrees completed using microsatellite genotyping. Southern anteater-chats live in groups of 2-5 individuals - a breeding pair and up to three additional none-breeders. These auxiliary birds were either retained offspring or unrelated individuals, and all birds in a group assisted by feeding at the nest. Our population had a skewed sex ratio of approximately 58% males to 42% females, yet the sex ratio of fledglings was equal, suggesting sex-biased mortality. Helpers were predominantly retained male offspring; however 21% of helpers were unrelated to either of the breeding pair. Southern anteater-chats appear to be non-territorial, with an apparent lack of aggression both within and between groups. Our study confirms that the southern anteater-chat is a facultative cooperative breeder, with both pair breeders and groups with helpers capable of fledging youngsters. We provide evidence suggesting that the breeding system of the southern anteater-chat is based on prompt female dispersal, and male philopatry due to an apparent shortage of mates, potential benefits of the natal site and possible high costs of floating. It appears that ecological constraints promoting delayed dispersal are reinforced by benefits gained from remaining philopatric.

  • 112.
    Barnaby, Jonathan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Griesser, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    The role of nepotism, cooperation, and competition in the avian families2010Book (Refereed)
    Abstract [en]

    A large number of bird species live in stable groups, and this sets the scene for complex social behaviours, such as cooperative breeding. The vast majority of groups consist of families which arise when young postpone dispersal and remain with their parents beyond independence. However, the factors selecting for the evolution of families and thus also cooperative breeding among birds, are still a challenging puzzle. The currently accepted key explanation for the evolution of families and cooperative breeding focuses on dispersal constraints. While constraints successfully explain within‐population dispersal decisions, they fail as an ultimate explanation because offspring in the majority of species face some sort of dispersal constraint, yet still disperse promptly. Recent alternative explanations focus on the role of philopatry and nepotism, and emphasise a key role of life‐history for the evolution of families. Phylogenetic analyses and field studies have indicated that living in family groups is far more widespread among long‐lived species than short‐lived ones. A long lifespan gives parents the opportunity to invest in their offspring for a prolonged period, while this option is less viable for short‐lived species. Thus, living with nepotistic parents provides offspring with direct fitness benefits that can select for the evolution of family living beyond independence. Nevertheless this generalisation is brought into question since many long‐lived bird species do not live in family groups. An alternative approach attempts to explain family living through the variation in territory quality. Here the incentive to remain with the parents is created by the availability of resources on the natal territory independent of parental nepotism. However, there is not only cooperation, conflicts are also common place in families. Living with independent, sexually mature offspring can lead to conflicts through a change in resource availability or the death of aparent. Therefore families can be expected to be dynamic societies where both parent and offspring decisions depend on each other, and family maintenance depends upon the current ecological conditions. Based on  this background, here we review recent studies that have investigated the processes that facilitate family formation, and which highlight both cooperation and conflict that arises from living in family groups. We examine the strengths of current models and explore ideas for a more coherent framework in which to understand prolonged family association in birds. We argue that two paths lead to family living, depending on the life-history. In medium-short lived species where the postponement of independent reproduction comes at a high cost, offspring can benefit from an association with their parents until the next breeding season. In longer-lived species, offspring actually benefit from postponing the onset of independent reproduction, making family living beyond the first year of life an adaptive strategy, and giving the option for cooperative breeding. These processes are illustrated by 5 species-specific case studies. We then finally suggest a number of key questions to developing a deeper understanding of the evolution of family living in birds.

  • 113.
    Barnaby, Jonathan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Herrmann, Eric
    Ekman, Jan
    Sex specific survival in the southern anteater-chat Mymecocichla formicivora. Manuscript (preprint) (Other academic)
    Abstract [en]

    Survival is a key factor behind life-history variation both between and within species. It is also a major influence on sociality in species which delay dispersal and live in family groups. Knowledge of differential survival rates between males and females and juveniles and adults give insights into the costs and benefits of different behavioural and life-history strategies. Here we investigate patterns of survival in a population of the southern anteater-chat (Myrmecocichla formicivora), a facultative cooperatively breeding passerine of southern Africa. Using data from a 9-year mark-capture-recapture study, we examined juvenile and adult sex related variation in survival, and the role of environmental variables (rainfall, temperature) for survival patterns in the population. Annual adult survival probability (mean ± SE) was 0.71 ± 0.03 for males and 0.60 ± 0.04 for females. Juvenile survival was lower for each sex, with juvenile female survival (0.36 ± 0.04) being 35% lower than juvenile male survival (0.55 ± 0.04). Using these estimates we calculated the mean life span (MLS) in years for male southern anteater-chat to be 4.0 ± 0.7, considerably higher than for females at 2.0 ± 0.4. These figures closely matched the population-age structure of the study area, and could explain the high male biased sex skew of adult birds in this population. Higher annual mean temperature was associated with higher survival, whereas higher annual rainfall was associated with lower survival for both sex and age classes. Female survival, particularly female juvenile survival, may be reduced due to prompt dispersal and longer dispersal distances, and the additional costs of breeding early in life. Differential survival can promote male philopatry and this in turn could well encourage the cooperative breeding we see in the southern anteater-chat.

  • 114. Barrett, Paul M.
    et al.
    Evans, David C.
    Campione, Nicolas E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Evolution of dinosaur epidermal structures2015In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 11, no 6, article id 20150229Article in journal (Refereed)
    Abstract [en]

    Spectacularly preserved non-avian dinosaurs with integumentary filaments/feathers have revolutionized dinosaur studies and fostered the suggestion that the dinosaur common ancestor possessed complex integumentary structures homologous to feathers. This hypothesis has major implications for interpreting dinosaur biology, but has not been tested rigorously. Using a comprehensive database of dinosaur skin traces, we apply maximum-likelihood methods to reconstruct the phylogenetic distribution of epidermal structures and interpret their evolutionary history. Most of these analyses find no compelling evidence for the appearance of protofeathers in the dinosaur common ancestor and scales are usually recovered as the plesiomorphic state, but results are sensitive to the outgroup condition in pterosaurs. Rare occurrences of ornithischian filamentous integument might represent independent acquisitions of novel epidermal structures that are not homologous with theropod feathers.

  • 115.
    Bartoszek, Krzysztof
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Applied Mathematics and Statistics.
    Phylogenetic effective sample size2016In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 407, p. 371-386Article in journal (Refereed)
    Abstract [en]

    In this paper I address the question—how large is a phylogenetic sample? I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein-Uhlenbeck processes-the regression effective sample size. I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AICc is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations.

  • 116.
    Bartoszek, Krzysztof
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg.
    Quantifying the effects of anagenetic and cladogenetic evolution2014In: Mathematical Biosciences, ISSN 0025-5564, E-ISSN 1879-3134, Vol. 254, p. 42-57Article in journal (Refereed)
    Abstract [en]

    An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both types of change, quantify the effects of speciational change via the correlation between species and attribute the proportion of change to each type. I discuss results of parameter estimation of Hominoid body size in this light. I derive mathematical formulae related to this problem, the probability generating functions of the number of speciation events along a randomly drawn lineage and from the most recent common ancestor of two randomly chosen tip species for a conditioned Yule tree. Additionally I obtain in closed form the variance of the distance from the root to the most recent common ancestor of two randomly chosen tip species.

  • 117.
    Bartoszek, Krzysztof
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg.
    The Laplace Motion in Phylogenetic Comparative Methods2012In: Proceedings of the XVIII National Conference on Applications of Mathematics in Biology and Medicine, 2012, p. 25-30Conference paper (Refereed)
    Abstract [en]

    The majority of current phylogenetic comparative methods assume that the stochastic evolutionaryprocess is homogeneous over the phylogeny or offer relaxations of this in rather limited and usually parameter expensive ways. Here we make a preliminary investigation, bymeans of a numerical experiment, whether the Laplace motion process can offer an alternative approach.

  • 118.
    Bartoszek, Krzysztof
    et al.
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg.
    Jones, Graham
    Oxelman, Bengt
    University of Gothenburg.
    Sagitov, Serik
    Chalmers University of Technology and the University of Gothenburg.
    Time to a single hybridization event in a group of species with unknown ancestral history2013In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 322, p. 1-6Article in journal (Refereed)
    Abstract [en]

    We consider a stochastic process for the generation of species which combines a Yule process with a simple model for hybridization between pairs of co-existent species. We assume that the origin of the process, when there was one species, occurred at an unknown time in the past, and we condition the process on producing n species via the Yule process and a single hybridization event. We prove results about the distribution of the time of the hybridization event. In particular we calculate a formula for all moments, and show that under various conditions, the distribution tends to an exponential with rate twice that of the birth rate for the Yule process.

  • 119.
    Bartoszek, Krzysztof
    et al.
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg.
    Krzeminski, Michal
    Gdansk University of Technology.
    Critical case stochastic phylogenetic tree model via the Laplace transform2014In: Demonstratio Matematicae, ISSN 0420-1213, Vol. 47, no 2, p. 474-481Article in journal (Refereed)
    Abstract [en]

    Birth-and-death models are now a common mathematical tool to describe branching patterns observed in real-world phylogenetic trees. Liggett and Schinazi (2009) is one such example. The authors propose a simple birth-and-death model that is compatible with phylogenetic trees of both in uenza and HIV, depending on the birth rate parameter. An interesting special case of this model is the critical case where the birth rate equals the death rate. This is a non-trivial situation and to study its asymptotic behaviour we employed the Laplace transform. With this we correct the proof of Liggett and Schinazi (2009) in the critical case.

  • 120.
    Bartoszek, Krzysztof
    et al.
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg.
    Pienaar, J.
    Mostad, P.
    Chalmers University of Technology and the University of Gothenburg.
    Andersson, S.
    University of Gothenburg.
    Hansen, T. F.
    Oslo University.
    A phylogenetic comparative method for studying multivariate adaptation2012In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 314, p. 204-215Article in journal (Refereed)
    Abstract [en]

    Phylogenetic comparative methods have been limited in the way they model adaptation. Although some progress has been made, there are still no methods that can fully account for coadaptationbetween traits. Based on Ornstein-Uhlenbeck (OU) models of adaptive evolution, we present a method,with R implementation, in which multiple traits evolve both in response to each other and, as inprevious OU models, to fixed or randomly evolving predictor variables. We present the interpretation ofthe model parameters in terms of evolutionary and optimal regressions enabling the study of allometric and adaptive relationships between traits. To illustrate the method we reanalyze a data set of antlerand body-size evolution in deer (Cervidae).

  • 121.
    Bartoszek, Krzysztof
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Applied Mathematics and Statistics.
    Pietro, Lio'
    Cambridge University.
    A novel algorithm to reconstruct phylogenies using gene sequences and expression data2014In: International Proceedings of Chemical, Biological & Environmental Engineering; Environment, Energy and Biotechnology III, 2014, p. 8-12Conference paper (Refereed)
    Abstract [en]

    Phylogenies based on single loci should be viewed with caution and the best approach for obtaining robust trees is to examine numerous loci across the genome. It often happens that for the same set of species trees derived from different genes are in conflict between each other. There are several methods that combine information from different genes in order to infer the species tree. One novel approach is to use informationfrom different -omics. Here we describe a phylogenetic method based on an Ornstein–Uhlenbeck process that combines sequence and gene expression data. We test our method on genes belonging to the histidine biosynthetic operon. We found that the method provides interesting insights into selection pressures and adaptive hypotheses concerning gene expression levels.

  • 122.
    Bartoszek, Krzysztof
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Applied Mathematics and Statistics.
    Sagitov, Serik
    A consistent estimator of the evolutionary rate2015In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 371, p. 69-78Article in journal (Refereed)
    Abstract [en]

    We consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate 2, conditioned on the observed number of particles to be equal to n. Particles are assumed to move independently on the real line according to the Brownian motion with the local variance sigma(2). In this paper we treat n particles as a sample of related species. The spatial Brownian motion of a particle describes the development of a trait value of interest (e.g. log-body-size). We propose an unbiased estimator 4 of the evolutionary rate rho(2) - sigma(2)/lambda. The estimator R-n(2) is proportional to the sample variance S-n(2) computed from n trait values. We find an approximate formula for the standard error of R-n(2), based on a neat asymptotic relation for the variance of S-n(2). (C) 2015 Elsevier Ltd. All rights reserved.

  • 123.
    Bartoszek, Krzysztof
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Applied Mathematics and Statistics.
    Sagitov, Serik
    Chalmers University of Technology and the University of Gothenburg.
    A consistent estimator of the evolutionary rate2015In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 371, p. 69-78Article in journal (Refereed)
    Abstract [en]

    We consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate λ, conditioned on the observed number of particles to be equal to n. Particles are assumed to move independently on the real line according to the Brownian motion with the local variance σ2. In this paper we treat n particles as a sample of related species. The spatial Brownian motion of a particle describes the development of a trait value of interest (e.g. log-body-size). We propose an unbiased estimator Rn2 of the evolutionary rate ρ22/λ. The estimator Rn2 is proportional to the sample variance Sn2 computed from n trait values. We find an approximate formula for the standard error of Rn2 based on a neat asymptotic relation for the variance of Sn2.

  • 124.
    Bartoszek, Krzysztof
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Applied Mathematics and Statistics.
    Sagitov, Serik
    Chalmers University of Technology and the Unversity of Gothenburg.
    Phylogenetic confidence intervals for the optimal trait value2015In: Journal of Applied Probability, ISSN 0021-9002, E-ISSN 1475-6072, Vol. 52, no 4, p. 1115-1132Article in journal (Refereed)
    Abstract [en]

    We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree ismodelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to evolve along lineages as an Ornstein–Uhlenbeck process. As a result, the trait values of the n species form a sample with dependent observations. We establish three limit theorems for the samplemean corresponding to three domains for the adaptation rate. In the case of fast adaptation, we show that for large n the normalized sample mean isapproximately normally distributed. Using these limit theorems, we develop novel confidence interval formulae for the optimal trait value.

  • 125.
    Baruch, Zdravko
    et al.
    Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia.
    Jones, Alice R.
    Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia.
    Hill, Kathryn E.
    Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia.
    McInerney, Francesca A.
    Univ Adelaide, Sch Phys Sci, Adelaide, SA 5005, Australia;Univ Adelaide, Sprigg Geobiol Ctr, Adelaide, SA 5005, Australia.
    Blyth, Colette
    Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia.
    Caddy-Retalic, Stefan
    Univ Adelaide, Sch Phys Sci, Adelaide, SA 5005, Australia;Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Sprigg Geobiol Ctr, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia.
    Christmas, Matthew J.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia.
    Gellie, Nicholas J. C.
    Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia.
    Lowe, Andrew J.
    Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia.
    Martin-Fores, Irene
    Spanish Natl Res Council, Natl Museum Nat Sci, Madrid 28006, Spain;Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia.
    Nielson, Kristine E.
    Univ Adelaide, Sch Phys Sci, Adelaide, SA 5005, Australia;Univ Adelaide, Sprigg Geobiol Ctr, Adelaide, SA 5005, Australia.
    Breed, Martin F.
    Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia.
    Functional acclimation across microgeographic scales in Dodonaea viscosa2018In: AoB Plants, ISSN 2041-2851, E-ISSN 2041-2851, Vol. 10, no 3, article id ply029Article in journal (Refereed)
    Abstract [en]

    Intraspecific plant functional trait variation provides mechanistic insight into persistence and can infer population adaptive capacity. However, most studies explore intraspecific trait variation in systems where geographic and environmental distances co-vary. Such a design reduces the certainty of trait-environment associations, and it is imperative for studies that make trait-environment associations be conducted in systems where environmental distance varies independently of geographic distance. Here we explored trait variation in such a system, and aimed to: (i) quantify trait variation of parent and offspring generations, and associate this variation to parental environments; (ii) determine the traits which best explain population differences; (iii) compare parent and offspring trait-trait relationships. We characterized 15 plant functional traits in eight populations of a shrub with a maximum separation ca. 100 km. Populations differed markedly in aridity and elevation, and environmental distance varied independently of geographic distance. We measured traits in parent populations collected in the field, as well as their offspring reared in greenhouse conditions. Parent traits regularly associated with their environment. These associations were largely lost in the offspring generation, indicating considerable phenotypic plasticity. An ordination of parent traits showed clear structure with strong influence of leaf area, specific leaf area, stomatal traits, isotope delta C-13 and delta N-15 ratios, and N-area, whereas the offspring ordination was less structured. Parent trait-trait correlations were in line with expectations from the leaf economic spectrum. We show considerable trait plasticity in the woody shrub over microgeographic scales (<100 km), indicating it has the adaptive potential within a generation to functionally acclimate to a range of abiotic conditions. Since our study shrub is commonly used for restoration in southern Australia and local populations do not show strong genetic differentiation in functional traits, the potential risks of transferring seed across the broad environmental conditions are not likely to be a significant issue.

  • 126.
    Bastiaans, Eric
    et al.
    Laboratory of Genetics, Wageningen University, Wageningen.
    Debets, Alfons J. M.
    Aanen, Duur K.
    Experimental demonstration of the benefits of somatic fusion and the consequences for allorecognition2015In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 69, no 4, p. 1091-1099Article in journal (Refereed)
    Abstract [en]

    Allorecognition, the ability to distinguish “self” from “nonself” based on allelic differences at allorecognition loci, is common in all domains of life. Allorecognition restricts the opportunities for social parasitism, and is therefore crucial for the evolution of cooperation. However, the maintenance of allorecognition diversity provides a paradox. If allorecognition is costly relative to cooperation, common alleles will be favored. Thus, the cost of allorecognition may reduce the genetic variation upon which allorecognition crucially relies, a prediction now known as “Crozier’s paradox.” We establish the relative costs of allorecognition, and their consequences for the short-term evolution of recognition labels theoretically predicted by Crozier. We use fusion among colonies of the fungus Neurospora crassa, regulated by highly variable allorecognition genes, as an experimental model system. We demonstrate that fusion among colonies is mutually beneficial, relative to absence of fusion upon allorecognition. This benefit is due not only to absence of mutual antagonism, which occurs upon allorecognition, but also to an increase in colony size per se. We then experimentally demonstrate that the benefit of fusion selects against allorecognition diversity, as predicted by Crozier. We discuss what maintains allorecognition diversity.

  • 127.
    Bastiaans, Eric
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Wageningen University.
    Debets, Alfons J. M.
    Aanen, Duur K.
    Experimental evolution reveals that high relatedness protects multicellular cooperation from cheaters2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 11435Article in journal (Refereed)
    Abstract [en]

    In multicellular organisms, there is a potential risk that cheating mutants gain access to the germline. Development from a single-celled zygote resets relatedness among cells to its maximum value each generation, which should accomplish segregation of cheating mutants from non-cheaters and thereby protect multicellular cooperation. Here we provide the crucial direct comparison between high- and low-relatedness conditions to test this hypothesis. We allow two variants of the fungus Neurospora crassa to evolve, one with and one without the ability to form chimeras with other individuals, thus generating two relatedness levels. While multicellular cooperation remains high in the high-relatedness lines, it significantly decreases in all replicate low-relatedness lines, resulting in an average threefold decrease in spore yield. This reduction is caused by cheating mutants with reduced investment in somatic functions, but increased competitive success when fusing with non-cheaters. Our experiments demonstrate that high-genetic relatedness is crucial to sustain multicellular cooperation.

  • 128.
    Bauerfeind, Stephanie S.
    et al.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurer Str 190, CH-8057 Zurich, Switzerland.
    Sorensen, Jesper G.
    Univ Aarhus, Sect Genet Ecol & Evolut, Dept Biosci, DK-8000 Aarhus C, Denmark.
    Loeschcke, Volker
    Univ Aarhus, Sect Genet Ecol & Evolut, Dept Biosci, DK-8000 Aarhus C, Denmark.
    Berger, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurer Str 190, CH-8057 Zurich, Switzerland.
    Broder, E. Dale
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurer Str 190, CH-8057 Zurich, Switzerland;Univ Denver, Interdisciplinary Res Incubator Study InEqual, Denver, CO 80208 USA.
    Geiger, Madeleine
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurer Str 190, CH-8057 Zurich, Switzerland.
    Ferrari, Manuela
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurer Str 190, CH-8057 Zurich, Switzerland.
    Blanckenhorn, Wolf U.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurer Str 190, CH-8057 Zurich, Switzerland.
    Geographic variation in responses of European yellow dung flies to thermal stress2018In: Journal of Thermal Biology, ISSN 0306-4565, E-ISSN 1879-0992, Vol. 73, p. 41-49Article in journal (Refereed)
    Abstract [en]

    Climatic conditions can be very heterogeneous even over small geographic scales, and are believed to be major determinants of the abundance and distribution of species and populations. Organisms are expected to evolve in response to the frequency and magnitude of local thermal extremes, resulting in local adaptation. Using replicate yellow dung fly (Scathophaga stercoraria; Diptera: Scathophagidae) populations from cold (northern Europe) and warm climates (southern Europe), we compared 1) responses to short-term heat and cold shocks in both sexes, 2) heat shock protein (Hsp70) expression in adults and eggs, and 3) female reproductive traits when facing short-term heat stress during egg maturation. Contrary to expectations, thermal traits showed minor geographic differentiation, with weak evidence for greater heat resistance of southern flies but no differentiation in cold resistance. Hsp70 protein expression was little affected by heat stress, indicating systemic rather than induced regulation of the heat stress response, possibly related to this fly group's preference for cold climes. In contrast, sex differences were pronounced: males (which are larger) endured hot temperatures longer, while females featured higher Hsp70 expression. Heat stress negatively affected various female reproductive traits, reducing first clutch size, overall reproductive investment, egg lipid content, and subsequent larval hatching. These responses varied little across latitude but somewhat among populations in terms of egg size, protein content, and larval hatching success. Several reproductive parameters, but not Hsp70 expression, exhibited heritable variation among full-sib families. Rather than large-scale clinal geographic variation, our study suggests some local geographic population differentiation in the ability of yellow dung flies to buffer the impact of heat stress on reproductive performance.

  • 129.
    Baur, Julian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland.
    Roy, Jeannine
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland.
    Schafer, Martin A.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland.
    Puniamoorthy, Nalini
    Natl Univ Singapore, Dept Biol Sci, Singapore, Singapore.
    Blanckenhorn, Wolf U. B.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland.
    Rohner, Patrick T.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland;Indiana Univ, Dept Biol, 915 East Third St,102 Myers Hall, Bloomington, IN 47405 USA.
    Intraspecific mating system evolution and its effect on complex male secondary sexual traits: Does male-male competition increase selection on size or shape?2020In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 33, no 3, p. 297-308Article in journal (Refereed)
    Abstract [en]

    Sexual selection is generally held responsible for the exceptional diversity in secondary sexual traits in animals. Mating system evolution is therefore expected to profoundly affect the covariation between secondary sexual traits and mating success. Whereas there is such evidence at the interspecific level, data within species remain scarce. We here investigate sexual selection acting on the exaggerated male fore femur and the male wing in the common and widespread dung flies Sepsis punctum and S. neocynipsea (Diptera: Sepsidae). Both species exhibit intraspecific differences in mating systems and variation in sexual size dimorphism (SSD) across continents that correlates with the extent of male-male competition. We predicted that populations subject to increased male-male competition will experience stronger directional selection on the sexually dimorphic male foreleg. Our results suggest that fore femur size, width and shape were indeed positively associated with mating success in populations with male-biased SSD in both species, which was not evident in conspecific populations with female-biased SSD. However, this was also the case for wing size and shape, a trait often assumed to be primarily under natural selection. After correcting for selection on overall body size by accounting for allometric scaling, we found little evidence for independent selection on any of these size or shape traits in legs or wings, irrespective of the mating system. Sexual dimorphism and (foreleg) trait exaggeration is therefore unlikely to be driven by direct precopulatory sexual selection, but more so by selection on overall size or possibly selection on allometric scaling.

  • 130.
    Bazyan, Saloume
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Sexual selection and extinction in deer2013Independent thesis Advanced level (degree of Master (Two Years)), 80 credits / 120 HE creditsStudent thesis
    Abstract [en]

    By performing a comparative analysis and using phylogenetic relationships of the Cervidaefamily this study aimed to address whether or not sexual selection may play a role in the extinctionof species by making species more vulnerable to extinction. The role of sexual selection in makingspecies more vulnerable to extinction is largely unexplored, and several factors such as ecologicaland life history traits may increase the risk of extinction.In all species of the family Cervidae (Gilbert et al. 2006, Geist 1998,Groves and Grubb2011,Meijaardand Groves2004,Price et al. 2005, Goss 1983) sexually selected characters plays amain role in determining species status and thus potentially their probability of extinction. In thisstudy the intensity of sexual selection (measured as sexual size dimorphism, antler size and matingsystem) and the rate of extinction (IUCN classification and anthropogenic effect) were counted asfactors to determine the role of sexual selection intensity in both species-rich and species-poorclades.By using the programme MESQUITE and phylogenetic trees, the results show an associationbetween species with larger body size and dimorphism, living in open habitats and having largerantler size expanded to more than three tines; such species are mostly non-territorial and formharems during the rutting season. The small species are territorial, live in closed habitats, aremonomorphic and have small antler size limited to two tines or less. Moreover species that aremore subjected to habitat degradation and anthropogenic effects tend to become smaller in size.Extinction risk for the species-rich clades with small sized, territorial and small antler sizedspecies is lower than for those consisting of species with larger antler size, larger body size, livingin open habitats and using harems as mating system.To sum up, the intensity of sexual selection in larger species in deer family put them in risk ofextinction; but on the other site, small species are more adapted to the environment by choosingdifferent strategy in mating system, and reducing antler and body size thus diminishing theextinction risk.

  • 131.
    Bazzi, Mohamad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Kear, Benjamin P.
    Uppsala University, Music and Museums, Museum of Evolution.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Campione, Nicolas E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology. Univ New England, Sch Environm & Rural Sci, Palaeosci Res Ctr, Armidale, NSW 2351, Australia.
    Static Dental Disparity and Morphological Turnover in Sharks across the End-Cretaceous Mass Extinction2018In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 28, no 16, p. 2607-2615Article in journal (Refereed)
    Abstract [en]

    The Cretaceous-Palaeogene (K-Pg) mass extinction profoundly altered vertebrate ecosystems and prompted the radiation of many extant clades [1, 2]. Sharks (Selachimorpha) were one of the few larger-bodied marine predators that survived the K-Pg event and are represented by an almost-continuous dental fossil record. However, the precise dynamics of their transition through this interval remain uncertain [3]. Here, we apply 2D geometric morphometrics to reconstruct global and regional dental morphospace variation among Lamniformes (Mackerel sharks) and Carch-arhiniformes (Ground sharks). These clades are prevalent predators in today's oceans, and were geographically widespread during the late Cretaceous-early Palaeogene. Our results reveal a decoupling of morphological disparity and taxonomic richness. Indeed, shark disparity was nearly static across the K-Pg extinction, in contrast to abrupt declines among other higher-trophic-level marine predators [4, 5]. Nevertheless, specific patterns indicate that an asymmetric extinction occurred among lamniforms possessing lowcrowned/triangular teeth and that a subsequent proliferation of carcharhiniforms with similar tooth morphologies took place during the early Paleocene. This compositional shift in post-Mesozoic shark lineages hints at a profound and persistent K-Pg signature evident in the heterogeneity of modern shark communities. Moreover, such wholesale lineage turnover coincided with the loss of many cephalopod [6] and pelagic amniote [5] groups, as well as the explosive radiation of middle trophic-level teleost fishes [1]. We hypothesize that a combination of prey availability and post-extinction trophic cascades favored extant shark antecedents and laid the foundation for their extensive diversification later in the Cenozoic [7-10].

  • 132. Beaumont, Mark A
    et al.
    Nielsen, Rasmus
    Robert, Christian
    Hey, Jody
    Gaggiotti, Oscar
    Knowles, Lacey
    Estoup, Arnaud
    Panchal, Mahesh
    Corander, Jukka
    Hickerson, Mike
    Sisson, Scott A
    Fagundes, Nelson
    Chikhi, Lounès
    Beerli, Peter
    Vitalis, Renaud
    Cornuet, Jean-Marie
    Huelsenbeck, John
    Foll, Matthieu
    Yang, Ziheng
    Rousset, Francois
    Balding, David
    Excoffier, Laurent
    In defence of model-based inference in phylogeography.2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 3, p. 436-446Article in journal (Refereed)
    Abstract [en]

    Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics.

  • 133.
    Beekman, Madeleine
    et al.
    Univ Sydney, Sch Life & Environm Sci, Sydney, NSW 2006, Australia..
    Nieuwenhuis, Bart
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ortiz-Barrientos, Daniel
    Univ Queensland, Sch Biol Sci, St Lucia, Qld, Australia..
    Evans, Jonathan P.
    Univ Western Australia, Sch Anim Biol, Ctr Evolutionary Biol, Nedlands, WA 6009, Australia..
    Sexual selection in hermaphrodites, sperm and broadcast spawners, plants and fungi2016In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 371, no 1706, article id 20150541Article, review/survey (Refereed)
    Abstract [en]

    Darwin was the first to recognize that sexual selection is a strong evolutionary force. Exaggerated traits allow same-sex individuals to compete over access to mates and provide a mechanism by which mates are selected. It is relatively easy to appreciate how inter-and intrasexual selection work in organisms with the sensory capabilities to perceive physical or behavioural traits that signal mate quality or mate compatibility, and to assess the relative quality of competitors. It is therefore not surprising that most studies of sexual selection have focused on animals with separate sexes and obvious adaptations that function in the context of reproductive competition. Yet, many sexual organisms are both male and female at the same time, often lack sexual dimorphism and never come into direct contact at mating. How does sexual selection act in such species, and what can we learn from them? Here, we address these questions by exploring the potential for sexual selection in simultaneous hermaphrodites, sperm-and broadcast spawners, plants and fungi. Our reviewreveals a range of mechanisms of sexual selection, operating primarily after gametes have been released, which are common in many of these groups and also quite possibly in more familiar (internally fertilizing and sexually dimorphic) organisms. This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.

  • 134. Bella, Eleni
    et al.
    Liepelt, Sascha
    Parducci, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Drouzas, Andreas D.
    Genetic insights into the hybrid origin of Abies borisii-regis Mattf.2015In: Plant Systematics and Evolution, ISSN 0378-2697, E-ISSN 1615-6110, Vol. 301, no 2, p. 749-759Article in journal (Refereed)
    Abstract [en]

    Abies × borisii-regis Mattf. (King Boris fir) is a taxon endemic to the southern Balkan Peninsula, described as a hybrid between the widespread A. alba Mill. (Silver fir) and the Greek endemic A. cephalonica Loud (Greek fir). Even though A. × borisii-regis has attracted much research attention in the past, its origin, geographical distribution and taxonomic status are not fully elucidated and molecular evidence for hybridization is missing. To shed more light on this issue, we analyzed representative populations from these three Abies taxa using paternally inherited (chloroplast) and maternally inherited (mitochondrial) DNA markers. Both Silver and Greek fir could be clearly distinguished using mitochondrial markers, while we observed a mixture of maternal lineages in theA. × borisii-regis populations. In contrast, using chloroplast markers, we could not identify species-specific haplotypes, but a neighbor-joining analysis of population genetic distances revealed two separate clusters for the Silver fir and the Greek fir, while the A. × borisii-regis populations were placed in intermediate positions. Our results are in agreement with the hypothesis that the A. ×borisii-regis populations investigated are a result of hybridization between A. cephalonica and A. alba.

  • 135. Bellis, Emily S
    et al.
    Kelly, Elizabeth A
    Lorts, Claire M
    Gao, Huirong
    DeLeo, Victoria L
    Rouhan, Germinal
    Budden, Andrew
    Bhaskara, Govinal B
    Hu, Zhenbin
    Muscarella, Robert
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Timko, Michael P
    Nebie, Baloua
    Runo, Steven M
    Chilcoat, N Doane
    Juenger, Thomas E
    Morris, Geoffrey P
    dePamphilis, Claude W
    Lasky, Jesse R
    Genomics of sorghum local adaptation to a parasitic plant2020In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 117, no 8, p. 4243-4251Article in journal (Refereed)
    Abstract [en]

    Host-parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR-Cas9-edited sorghum further indicate that the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.

  • 136.
    Benson, Roger B. J.
    et al.
    Univ Oxford, Dept Earth Sci, S Parks Rd, Oxford OX2 3AN, England..
    Hunt, Gene
    Smithsonian Inst, Natl Museum Nat Hist, Dept Paleobiol, POB 37012,MRC 121, Washington, DC 20560 USA..
    Carrano, Matthew T.
    Smithsonian Inst, Natl Museum Nat Hist, Dept Paleobiol, POB 37012,MRC 121, Washington, DC 20560 USA..
    Campione, Nicolas E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Cope's rule and the adaptive landscape of dinosaur body size evolution2018In: Palaeontology, ISSN 0031-0239, E-ISSN 1475-4983, Vol. 61, no 1, p. 13-48Article, review/survey (Refereed)
    Abstract [en]

    The largest known dinosaurs weighed at least 20million times as much as the smallest, indicating exceptional phenotypic divergence. Previous studies have focused on extreme giant sizes, tests of Cope's rule, and miniaturization on the line leading to birds. We use non-uniform macroevolutionary models based on Ornstein-Uhlenbeck and trend processes to unify these observations, asking: what patterns of evolutionary rates, directionality and constraint explain the diversification of dinosaur body mass? We find that dinosaur evolution is constrained by attraction to discrete body size optima that undergo rare, but abrupt, evolutionary shifts. This model explains both the rarity of multi-lineage directional trends, and the occurrence of abrupt directional excursions during the origins of groups such as tiny pygostylian birds and giant sauropods. Most expansion of trait space results from rare, constraint-breaking innovations in just a small number of lineages. These lineages shifted rapidly into novel regions of trait space, occasionally to small sizes, but most often to large or giant sizes. As with Cenozoic mammals, intermediate body sizes were typically attained only transiently by lineages on a trajectory from small to large size. This demonstrates that bimodality in the macroevolutionary adaptive landscape for land vertebrates has existed for more than 200million years.

  • 137.
    Berg, Elena C.
    et al.
    Amer Univ Paris, Dept Comp Sci Math & Environm Sci, Paris, France.
    Lind, Martin I.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Monahan, Shannon
    Amer Univ Paris, Dept Comp Sci Math & Environm Sci, Paris, France.
    Bricout, Sophie
    Amer Univ Paris, Dept Comp Sci Math & Environm Sci, Paris, France.
    Maklakov, Alexei A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kin but less than kind: within-group male relatedness does not increase female fitness in seed beetles2019In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 286, no 1910, p. 1471-2954, article id 20191664Article in journal (Refereed)
    Abstract [en]

    Theory maintains within-group male relatedness can mediate sexual conflict by reducing male-male. competition and collateral harm to females. We tested whether male relatedness can lessen female harm in the seed beetle Callosobruchus maculatus. Male relatedness did not influence female lifetime reproductive success or individual fitness across two different ecologically relevant scenarios of mating competition. However, male relatedness marginally improved female survival. Because male relatedness improved female-survival in late life when C. maculatus females are no longer producing offspring, our results do not provide support for the role of within-group male relatedness in mediating sexual conflict. The fact that male relatedness improves the post-reproductive part of the female life cycle strongly suggests that the effect is non-adaptive. We discuss adaptive and non-adaptive mechanisms that could result in reduced female harm in this and previous studies, and suggest that cognitive error is a likely explanation.

  • 138.
    Berger, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Berg, Elena C
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Widegren, William
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Maklakov, Alexei A
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Multivariate intralocus sexual conflict in seed beetles2014In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 68, no 12, p. 3457-69Article in journal (Refereed)
    Abstract [en]

    Intralocus sexual conflict (IaSC) is pervasive because males and females experience differences in selection but share much of the same genome. Traits with integrated genetic architecture should be reservoirs of sexually antagonistic genetic variation for fitness, but explorations of multivariate IaSC are scarce. Previously, we showed that upward artificial selection on male life span decreased male fitness but increased female fitness compared with downward selection in the seed beetle Callosobruchus maculatus. Here, we use these selection lines to investigate sex-specific evolution of four functionally integrated traits (metabolic rate, locomotor activity, body mass, and life span) that collectively define a sexually dimorphic life-history syndrome in many species. Male-limited selection for short life span led to correlated evolution in females toward a more male-like multivariate phenotype. Conversely, males selected for long life span became more female-like, implying that IaSC results from genetic integration of this suite of traits. However, while life span, metabolism, and body mass showed correlated evolution in the sexes, activity did not evolve in males but, surprisingly, did so in females. This led to sexual monomorphism in locomotor activity in short-life lines associated with detrimental effects in females. Our results thus support the general tenet that widespread pleiotropy generates IaSC despite sex-specific genetic architecture.

  • 139.
    Berger, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Grieshop, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lind, Martin I.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Goenaga, Julieta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Maklakov, Alexei A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Intralocus Sexual Conflict and Environmental Stress2014In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 68, no 8, p. 2184-2196Article in journal (Refereed)
    Abstract [en]

    Intralocus sexual conflict (IaSC) occurs when selection at a given locus favors different alleles in males and females, placing a fundamental constraint on adaptation. However, the relative impact of IaSC on adaptation may become reduced in stressful environments that expose conditionally deleterious mutations to selection. The genetic correlation for fitness between males and females (r(MF)) provides a quantification of IaSC across the genome. We compared IaSC at a benign (29 degrees C) and a stressful (36 degrees C) temperature by estimating r(MF)s in two natural populations of the seed beetle Callosobruchus maculatus using isofemale lines. In one population, we found substantial IaSC under benign conditions signified by a negative r(MF) (-0.51) and, as predicted, a significant reduction of IaSC under stress signified by a reversed and positive r(MF) (0.21). The other population displayed low IaSC at both temperatures (r(MF): 0.38; 0.40). In both populations, isofemale lines harboring alleles beneficial to males but detrimental to females at benign conditions tended to show overall low fitness under stress. These results offer support for low IaSC under stress and suggest that environmentally sensitive and conditionally deleterious alleles that are sexually selected in males mediate changes in IaSC. We discuss implications for adaptive evolution in sexually reproducing populations.

  • 140.
    Berger, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Stångberg, Josefine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Grieshop, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Martinossi-Allibert, Ivain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Temperature effects on life-history trade-offs, germline maintenance and mutation rate under simulated climate warming2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1866, article id 20171721Article in journal (Refereed)
    Abstract [en]

    Mutation has a fundamental influence over evolutionary processes, but how evolutionary processes shape mutation rate remains less clear. In asexual unicellular organism, increased mutation rates have been observed in stressful environments and the reigning paradigm ascribes this increase to selection for evolvability. However, this explanation does not apply in sexually reproducing species, where little is known about how the environment affects mutation rate. Here we challenged experimental lines of seed beetle, evolved at ancestral temperature or under simulated climate warming, to repair induced mutations at ancestral and stressful temperature. Results show that temperature stress causes individuals to pass on a greater mutation load to their grand-offspring. This suggests that stress-induced mutation rates, in unicellular and multicellular organisms alike, can result from compromised germline DNA repair in low condition individuals. Moreover, lines adapted to simulated climate warming had evolved increased longevity at the cost of reproduction, and this allocation decision improved germline repair. These results suggest that mutation rates can be modulated by resource allocation trade-offs encompassing life-history traits and the germline and have important implications for rates of adaptation and extinction as well as our understanding of genetic diversity in multicellular organisms.

  • 141.
    Berger, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Walters, R. J.
    Blanckenhorn, W. U.
    Experimental evolution for generalists and specialists reveals multivariate genetic constraints on thermal reaction norms2014In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 27, no 9, p. 1975-1989Article in journal (Refereed)
    Abstract [en]

    Theory predicts the emergence of generalists in variable environments and antagonistic pleiotropy to favour specialists in constant environments, but empirical data seldom support such generalist-specialist trade-offs. We selected for generalists and specialists in the dung fly Sepsis punctum (Diptera: Sepsidae) under conditions that we predicted would reveal antagonistic pleiotropy and multivariate trade-offs underlying thermal reaction norms for juvenile development. We performed replicated laboratory evolution using four treatments: adaptation at a hot (31 degrees C) or a cold (15 degrees C) temperature, or under regimes fluctuating between these temperatures, either within or between generations. After 20 generations, we assessed parental effects and genetic responses of thermal reaction norms for three correlated life-history traits: size at maturity, juvenile growth rate and juvenile survival. We find evidence for antagonistic pleiotropy for performance at hot and cold temperatures, and a temperature-mediated trade-off between juvenile survival and size at maturity, suggesting that trade-offs associated with environmental tolerance can arise via intensified evolutionary compromises between genetically correlated traits. However, despite this antagonistic pleiotropy, we found no support for the evolution of increased thermal tolerance breadth at the expense of reduced maximal performance, suggesting low genetic variance in the generalist-specialist dimension.

  • 142.
    Berger, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    You, Tao
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Minano, Maravillas R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Grieshop, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lind, Martin I.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Maklakov, Alexei A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sexually antagonistic selection on genetic variation underlying both male and female same-sex sexual behavior2016In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 16, article id 88Article in journal (Refereed)
    Abstract [en]

    Background: Intralocus sexual conflict, arising from selection for different alleles at the same locus in males and females, imposes a constraint on sex-specific adaptation. Intralocus sexual conflict can be alleviated by the evolution of sex-limited genetic architectures and phenotypic expression, but pleiotropic constraints may hinder this process. Here, we explored putative intralocus sexual conflict and genetic (co)variance in a poorly understood behavior with near male-limited expression. Same-sex sexual behaviors (SSBs) generally do not conform to classic evolutionary models of adaptation but are common in male animals and have been hypothesized to result from perception errors and selection for high male mating rates. However, perspectives incorporating sex-specific selection on genes shared by males and females to explain the expression and evolution of SSBs have largely been neglected.

    Results: We performed two parallel sex-limited artificial selection experiments on SSB in male and female seed beetles, followed by sex-specific assays of locomotor activity and male sex recognition (two traits hypothesized to be functionally related to SSB) and adult reproductive success (allowing us to assess fitness consequences of genetic variance in SSB and its correlated components). Our experiments reveal both shared and sex-limited genetic variance for SSB. Strikingly, genetically correlated responses in locomotor activity and male sex-recognition were associated with sexually antagonistic fitness effects, but these effects differed qualitatively between male and female selection lines, implicating intralocus sexual conflict at both male-and female-specific genetic components underlying SSB.

    Conclusions: Our study provides experimental support for the hypothesis that widespread pleiotropy generates pervasive intralocus sexual conflict governing the expression of SSBs, suggesting that SSB in one sex can occur due to the expression of genes that carry benefits in the other sex.

  • 143.
    Berglund, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    The ups and downs of parental care2013In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 28, no 7, p. 387-388Article, book review (Other academic)
  • 144.
    Berglund, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Why are sexually selected weapons almost absent in females?2013In: Current Zoology, ISSN 1674-5507, Vol. 59, no 4, p. 564-568Article in journal (Refereed)
    Abstract [en]

    In sex role reversed species, predominantly females evolve sexually selected traits, such as ornaments and/or weapons. Female ornaments are common and their function well documented in many species, whether sex role reversed or not. However, sexually selected female weapons seem totally absent except for small wing spurs in three jacana species, present in both males and females. This poor female weaponry is in sharp contrast to the situation in species with conventional sex roles: males commonly have evolved sexually selected weapons as well as ornaments. At the same time, females in many taxa have naturally selected weapons, used in competition over resources or in predator defence. Why are sexually selected weapons then so rare, almost absent, in females? Here I briefly review weaponry in females and the function of these weapons, conclude that the near absence of sexually selected weapons begs an explanation, and suggest that costs of sexually selected weapons may exceed costs of ornaments. Females are more constrained when evolving sexually selected traits compared to males, at least compared to those males that do not provide direct benefits, as trait costs reduce a female’s fecundity. I suggest that this constraining trade-off between trait and fecundity restricts females to evolve ornaments but rarely weapons. The same may apply to paternally investing males. Whether sexually selected weapons actually are more costly than sexually selected ornaments remains to be investigated.

  • 145.
    Berglund, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Meiotic Recombination in Human and Dog: Targets, Consequences and Implications for Genome Evolution2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Understanding the mechanism of recombination has important implications for genome evolution and genomic variability. The work presented in this thesis studies the properties of recombination by investigating the effects it has on genome evolution in humans and dogs.

    Using alignments of human genes with chimpanzee and macaque orthologues we studied substitution patterns along the human lineage and scanned for evidence of positive selection. The properties mirror the situation in human non-coding sequences with the fixation bias ‘GC-biased gene conversion’ (gBGC) as a driving force in the most rapidly evolving regions. By assigning candidate genes to distinct classes of evolutionary forces we quantified the extent of those genes affected by gBGC to 20%. This suggests that human-specific characters can be prompted by the fixation bias of gBGC, which can be mistaken for selection.

    The gene PRDM9 controls recombination in most mammals, but is lacking in dogs. Using whole-genome alignments of dog with related species we examined the effects of PRDM9 inactivation. Additionally, we analyzed genomic variation in the genomes of several dog breeds. We identified that non-allelic homologous recombination (NAHR) via sequence identity, often GC-rich, creates structural variants of genomic regions. We show that these regions, which are also found in dog recombination hotspots, are a subset of unmethylated CpG-islands (CGIs). We inferred that CGIs have experienced a drastic increase in biased substitution rates, concurrent with a shift of recombination to target these regions. This enables recurrent episodes of gBGC to shape their distribution.

    The work presented in this thesis demonstrates the importance of meiotic recombination on patterns of molecular evolution and genomic variability in humans and dogs. Bioinformatic analyses identified mechanisms that regulate genome composition. gBGC is presented as an alternative to positive selection and is revealed as a major factor affecting allele configuration and the emergence of accelerated evolution on the human lineage. Characterization of recombination-induced sequence patterns highlights the potential of non-methylation and establishes unmethylated CGIs as targets of meiotic recombination in dogs. These observations describe recombination as an interesting process in genome evolution and provide further insights into the mechanisms of genomic variability.

    List of papers
    1. Hotspots of biased nucleotide substitutions in human genes
    Open this publication in new window or tab >>Hotspots of biased nucleotide substitutions in human genes
    2009 (English)In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 7, no 1, p. e26-Article in journal (Refereed) Published
    Abstract [en]

    Genes that have experienced accelerated evolutionary rates on the human lineage during recent evolution are candidates for involvement in human-specific adaptations. To determine the forces that cause increased evolutionary rates in certain genes, we analyzed alignments of 10,238 human genes to their orthologues in chimpanzee and macaque. Using a likelihood ratio test, we identified protein-coding sequences with an accelerated rate of base substitutions along the human lineage. Exons evolving at a fast rate in humans have a significant tendency to contain clusters of AT-to-GC (weak-to-strong) biased substitutions. This pattern is also observed in noncoding sequence flanking rapidly evolving exons. Accelerated exons occur in regions with elevated male recombination rates and exhibit an excess of nonsynonymous substitutions relative to the genomic average. We next analyzed genes with significantly elevated ratios of nonsynonymous to synonymous rates of base substitution (dN/dS) along the human lineage, and those with an excess of amino acid replacement substitutions relative to human polymorphism. These genes also show evidence of clusters of weak-to-strong biased substitutions. These findings indicate that a recombination-associated process, such as biased gene conversion (BGC), is driving fixation of GC alleles in the human genome. This process can lead to accelerated evolution in coding sequences and excess amino acid replacement substitutions, thereby generating significant results for tests of positive selection.

    National Category
    Medical and Health Sciences Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
    Identifiers
    urn:nbn:se:uu:diva-119520 (URN)10.1371/journal.pbio.1000026 (DOI)000262811000008 ()19175294 (PubMedID)
    Available from: 2010-02-26 Created: 2010-02-26 Last updated: 2017-12-12Bibliographically approved
    2. Detecting positive selection within genomes: the problem of biased gene conversion
    Open this publication in new window or tab >>Detecting positive selection within genomes: the problem of biased gene conversion
    Show others...
    2010 (English)In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 365, no 1552, p. 2571-2580Article in journal (Refereed) Published
    Abstract [en]

    The identification of loci influenced by positive selection is a major goal of evolutionary genetics. A popular approach is to perform scans of alignments on a genome-wide scale in order to find regions evolving at accelerated rates on a particular branch of a phylogenetic tree. However, positive selection is not the only process that can lead to accelerated evolution. Notably, GC-biased gene conversion (gBGC) is a recombination-associated process that results in the biased fixation of G and C nucleotides. This process can potentially generate bursts of nucleotide substitutions within hotspots of meiotic recombination. Here, we analyse the results of a scan for positive selection on genes on branches across the primate phylogeny. We show that genes identified as targets of positive selection have a significant tendency to exhibit the genomic signature of gBGC. Using a maximum-likelihood framework, we estimate that more than 20 per cent of cases of significantly elevated non-synonymous to synonymous substitution rates ratio (d(N)/d(S)), particularly in shorter branches, could be due to gBGC. We demonstrate that in some cases, gBGC can lead to very high d(N)/d(S) (more than 2). Our results indicate that gBGC significantly affects the evolution of coding sequences in primates, often leading to patterns of evolution that can be mistaken for positive selection.

    Keywords
    biased gene conversion, selection, recombination
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-135631 (URN)10.1098/rstb.2010.0007 (DOI)000280097000017 ()20643747 (PubMedID)
    Available from: 2010-12-07 Created: 2010-12-07 Last updated: 2017-12-11Bibliographically approved
    3. Novel origins of copy number variation in the dog genome
    Open this publication in new window or tab >>Novel origins of copy number variation in the dog genome
    Show others...
    2012 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 13, no 8, p. R73-Article in journal (Refereed) Published
    Abstract [en]

    BACKGROUND: Copy number variants (CNVs) account for substantial variation between genomes and are a major source of normal and pathogenic phenotypic differences. The dog is an ideal model to investigate mutational mechanisms that generate CNVs as its genome lacks a functional ortholog of the PRDM9 gene implicated in recombination and CNV formation in humans. Here we comprehensively assay CNVs using high-density array comparative genomic hybridization in 50 dogs from 17 dog breeds and 3 gray wolves. RESULTS: We use a stringent new method to identify a total of 430 high-confidence CNV loci, which range in size from 9 kb to 1.6 Mb and span 26.4 Mb, or 1.08%, of the assayed dog genome, overlapping 413 annotated genes. Of CNVs observed in each breed, 98% are also observed in multiple breeds. CNVs predicted to disrupt gene function are significantly less common than expected by chance. We identify a significant overrepresentation of peaks of GC content, previously shown to be enriched in dog recombination hotspots, in the vicinity of CNV breakpoints. CONCLUSIONS: A number of the CNVs identified by this study are candidates for generating breed-specific phenotypes. Purifying selection seems to be a major factor shaping structural variation in the dog genome, suggesting that many CNVs are deleterious. Localized peaks of GC content appear to be novel sites of CNV formation in the dog genome by non-allelic homologous recombination, potentially activated by the loss of PRDM9. These sequence features may have driven genome instability and chromosomal rearrangements throughout canid evolution.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-194244 (URN)10.1186/gb-2012-13-8-r73 (DOI)000315867500007 ()22916802 (PubMedID)
    Note

    Additional author: The LUPA Consortium (www.eurolupa.org)

    Available from: 2013-02-11 Created: 2013-02-11 Last updated: 2017-12-06Bibliographically approved
    4. Germline Metyhlation Patterns Determine The Distribution Of Recombination Events In The Dog Genome
    Open this publication in new window or tab >>Germline Metyhlation Patterns Determine The Distribution Of Recombination Events In The Dog Genome
    (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653Article in journal (Refereed) Submitted
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-233190 (URN)
    Available from: 2014-09-30 Created: 2014-09-30 Last updated: 2017-12-05Bibliographically approved
  • 146. Berlin, S.
    et al.
    Trybush, S. O.
    Fogelqvist, J.
    Gyllenstrand, N.
    Hallingbaeck, H. R.
    Ahman, I.
    Nordh, N-E
    Shield, I.
    Powers, S. J.
    Weih, M.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Roennberg-Waestljung, A-C
    Karp, A.
    Hanley, S. J.
    Genetic diversity, population structure and phenotypic variation in European Salix viminalis L. (Salicaceae)2014In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 10, no 6, p. 1595-1610Article in journal (Refereed)
    Abstract [en]

    To investigate the potential of association genetics for willow breeding, Salix viminalis germplasm was assembled from UK and Swedish collections (comprising accessions from several European countries) and new samples collected from nature. A subset of the germplasm was planted at two sites (UK and Sweden), genotyped using 38 SSR markers and assessed for phenological and biomass traits. Population structure, genetic differentiation (F-ST) and quantitative trait differentiation (Q(ST)) were investigated. The extent and patterns of trait adaptation were assessed by comparing F-ST and Q(ST) parameters. Of the 505 genotyped diploid accessions, 27 % were not unique. Genetic diversity was high: 471 alleles was amplified; the mean number of alleles per locus was 13.46, mean observed heterozygosity was 0.55 and mean expected heterozygosity was 0.62. Bayesian clustering identified four subpopulations which generally corresponded to Western Russia, Western Europe, Eastern Europe and Sweden. All pairwise F-ST values were highly significant (p<0.001) with the greatest genetic differentiation detected between the Western Russian and the Western European subpopulations (F-ST = 0.12), and the smallest between the Swedish and Eastern European populations (F-ST = 0.04). The Swedish population also had the highest number of identical accessions, supporting the view that S. viminalis was introduced into this country and has been heavily influenced by humans. Q(ST) values were high for growth cessation and leaf senescence, and to some extent stem diameter, but low for bud burst time and shoot number. Overall negative clines between longitudinal coordinates and leaf senescence, bud burst and stem diameter were also found.

  • 147.
    Berlin, Sofia
    et al.
    Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences.
    Fogelqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Rönnberg-Wästljung, Ann Christin
    Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences.
    Polymorphism and divergence of two willow species, Salix viminalis L. and Salix schwerinii E. Wolf2011In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 1, no 5, p. 387-400Article in journal (Refereed)
    Abstract [en]

    We investigated species divergence, present and past gene flow, levels of nucleotide polymorphism, and linkage disequilibrium in two willows from the plant genus Salix. Salix belongs together with Populus to the Salicaceae family; however, most population genetic studies of Salicaceae have been performed in Populus, the model genus in forest biology. Here we present a study on two closely related willow species Salix viminalis and S. schwerinii, in which we have resequenced 33 and 32 nuclear gene segments representing parts of 18 nuclear loci in 24 individuals for each species. We used coalescent simulations and estimated the split time to around 600,000 years ago and found that there is currently limited gene flow between the species. Mean intronic nucleotide diversity across gene segments was slightly higher in S. schwerinii (πi = 0.00849) than in S. viminalis (πi = 0.00655). Compared with other angiosperm trees, the two willows harbor intermediate levels of silent polymorphisms. The decay of linkage disequilibrium was slower in S. viminalis compared with S. schwerinii, and we speculate that this is due to different demographic histories as S. viminalis has been partly domesticated in Europe.

  • 148. Bernander, Rolf
    et al.
    Lind, Anders E
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Ettema, Thijs J G
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    An archaeal origin for the actin cytoskeleton: Implications for eukaryogenesis.2011In: Communicative & Integrative Biology, ISSN 1942-0889, E-ISSN 1942-0889, Vol. 4, no 6, p. 664-7Article in journal (Refereed)
    Abstract [en]

    A hallmark of the eukaryotic cell is the actin cytoskeleton, involved in a wide array of processes ranging from shape determination and phagocytosis to intracellular transport and cytokinesis. Recently, we reported the discovery of an actin-based cytoskeleton also in Archaea. The archaeal actin ortholog, Crenactin, was shown to belong to a conserved operon, Arcade (actin-related cytoskeleton in Archaea involved in shape determination), encoding an additional set of cytoskeleton-associated proteins. Here, we elaborate on the implications of these findings for the evolutionary relation between archaea and eukaryotes, with particular focus on the possibility that eukaryotic actin and actin-related proteins have evolved from an ancestral archaeal actin gene. Archaeal actin could thus have played an important role in cellular processes essential for the origin and early evolution of the eukaryotic lineage. Further exploration of uncharacterized archaeal lineages is necessary to find additional missing pieces in the evolutionary trajectory that ultimately gave rise to present-day organisms.

  • 149.
    Bernander, Rolf
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Lind, Anders E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Ettema, Thijs J.G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    An archaeal origin for the actin cytoskeleton: implications for eukaryogenesis2011In: Communicative & Integrative Biology, ISSN 1942-0889, E-ISSN 1942-0889, Vol. 4, no 6, p. 664-667Article in journal (Refereed)
    Abstract [en]

    A hallmark of the eukaryotic cell is the actin cytoskeleton, involved in a wide array of processes ranging from shape determination and phagocytosis to intracellular transport and cytokinesis. Recently, we reported the discovery of an actin-based cytoskeleton also in Archaea. The archaeal actin ortholog, Crenactin, was shown to belong to a conserved operon, Arcade (actin-related cytoskeleton in Archaea involved in shape determination), encoding an additional set of cytoskeleton-associated proteins. Here, we elaborate on the implications of these findings for the evolutionary relation between archaea and eukaryotes, with particular focus on the possibility that eukaryotic actin and actin-related proteins have evolved from an ancestral archaeal actin gene. Archaeal actin could thus have played an important role in cellular processes essential for the origin and early evolution of the eukaryotic lineage. Further exploration of uncharacterized archaeal lineages is necessary to find additional missing pieces in the evolutionary trajectory that ultimately gave rise to present-day organisms.

  • 150.
    Berner, D.
    et al.
    Univ Basel, Inst Zool, CH-4051 Basel, Switzerland..
    Thibert-Plante, Xavier
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Univ Tennessee, Natl Inst Math & Biol Synth, Knoxville, TN USA.;Umea Univ, Dept Ecol & Environm Sci, Umea, Sweden.;Umea Univ, IceLab, Umea, Sweden..
    How mechanisms of habitat preference evolve and promote divergence with gene flow2015In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 28, no 9, p. 1641-1655Article in journal (Refereed)
    Abstract [en]

    Habitat preference may promote adaptive divergence and speciation, yet the conditions under which this is likely are insufficiently explored. We use individual-based simulations to study the evolution and consequence of habitat preference during divergence with gene flow, considering four different underlying genetically based behavioural mechanisms: natal habitat imprinting, phenotype-dependent, competition-dependent and direct genetic habitat preference. We find that the evolution of habitat preference generally requires initially high dispersal, is facilitated by asymmetry in population sizes between habitats, and is hindered by an increasing number of underlying genetic loci. Moreover, the probability of habitat preference to emerge and promote divergence differs greatly among the underlying mechanisms. Natal habitat imprinting evolves most easily and can allow full divergence in parameter ranges where no divergence is possible in the absence of habitat preference. The reason is that imprinting represents a one-allele mechanism of assortative mating linking dispersal behaviour very effectively to local selection. At the other extreme, direct genetic habitat preference, a two-allele mechanism, evolves under restricted conditions only, and even then facilitates divergence weakly. Overall, our results indicate that habitat preference can be a strong reproductive barrier promoting divergence with gene flow, but that this is highly contingent on the underlying preference mechanism.

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