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  • 201.
    Näslund, Kalle
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    von Salomé, Jenny
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Bergström, Tomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jareborg, Niclas
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Genome-wide prediction of human VNTRs2005In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646, Vol. 85, no 1, p. 24-35Article in journal (Refereed)
    Abstract [en]

    Polymorphic minisatellites, also known as variable number of tandem repeats (VNTRs), are tandem repeat regions that show variation in the number of repeat units among chromosomes in a population. Currently, there are no general methods for predicting which minisatellites have a high probability of being polymorphic, given their sequence characteristics. An earlier approach has focused on potentially highly polymorphic and hypervariable minisatellites, which make up only a small fraction of all minisatellites in the human genome. We have developed a model, based on available minisatellite and VNTR sequence data, that predicts the probability that a minisatellite (unit size > or = 6 bp) identified by the computer program Tandem Repeats Finder is polymorphic (VNTR). According to the model, minisatellites with high copy number and high degree of sequence similarity are most likely to be VNTRs. This approach was used to scan the draft sequence of the human genome for VNTRs. A total of 157,549 minisatellite repeats were found, of which 29,224 are predicted to be VNTRs. Contrary to previous results, VNTRs appear to be widespread and abundant throughout the human genome, with an estimated density of 9.1 VNTRs/Mb.

  • 202.
    Padial, Jose M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Castroviejo-Fisher, Santiago
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Köhler, Jörn
    Domic, Enrique
    De la Riva, Ignacio
    Systematics of the Eleutherodactylus fraudator species group (Anura : Brachycephalidae)2007In: Herpetological Monographs, ISSN 0733-1347, E-ISSN 1938-5137, Vol. 21, no 1, p. 213-240Article in journal (Refereed)
    Abstract [en]

    Members of the Eleutherodactylus fraudator species group occur in Bolivia and Peru. This group has not been reviewed since its proposal and description. Its putative monophyly has not been tested and its phylogenetic relationships are still unresolved. It was included in the Central American genus Craugastor based on a putative morphological synapomorphy, but this hypothesis of relationship is doubtful. Its alpha-diversity is unknown and some putative members have still not been studied in detail. To assess the taxonomic status and phylogenetic relationships of this species group, we applied a taxonomic integrative approach based on comparisons of morphological characters (external and internal), bioacoustics (based on advertisement calls) and phylogenetic analyses of partial 16S mitochondrial gene (560 bp). We redescribe Eleutheroductylus bisignatus (Werner, 1899) and include it together with E. mercedesae in the group. Molecular, bioacoustical and morphological characters support the taxonomic status of all the species. Maximum parsimony, Bayesian and neighbor-joining phylogenetic analyses of the partial mitochondrial gene as well as the presence of a new condition of the mandibular ramus of the trigeminal nerve and two bioacoustical characters, support the monophyly of this group. Moreover, our data suggest the nonmonophyly of the subgenus Eleutherodactylus and the monophyly of the genus Craugastor when the C. bufonifermas species group is excluded. We redescribe the crown clade formed by members of the E. fraudator group and name it as the subgenus Yunganastes, which contains Eleutherodactylus ashkapara Kohler, 2000, E. bisignatus (Werner, 1899), E. frandator Lynch and McDiarmid, 1987, E. mercedesae Lynch and McDiarmid, 1987 and E. pluvicanorus De la Riva and Lynch, 1997. We describe the advertisement call of E. bisignatus for the first time and compare it with available calls of E. ashkapara and E. pluvicanorus. We suggest the common structure of the advertisement calls and the aggressive calls of the species belonging to Yunganastes (single melodic whistles with frequency modulation and no pulses) as synapomorphic for the new subgenus. We exclude members of Yunganastes from the Middle American genus Craugastor, to which it was previously tied by the presence of the putative synapomorphic "E" condition of the trigeminal nerve of the mandibular ramus of the abductor muscle. We describe a new condition of the trigeminal nerve and consider it synapomorphic for Yunganastes. Members of this subgenus are endemic to the cloud forests and humid montane forests of the Cordillera Oriental of the Andes in Bolivia and southern Peru.

  • 203.
    Padial, Jose M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Luis Telleria, Jose
    Observations of the Felou gundi (Felovia vae Lataste, 1886) in central Mauritania (Rodentia: Ctenodactylidae)2009In: Mammalia (Paris), ISSN 0025-1461, E-ISSN 1864-1547, Vol. 73, no 2, p. 153-154Article in journal (Refereed)
  • 204.
    Padial, José M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Castroviejo-Fisher, Santiago
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Köhler, Jörn
    Vilà, Carles
    Chaparro, Juan C.
    De la Riva, Ignacio
    Deciphering the products of evolution at the species level: the need for an integrative taxonomy2009In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 38, no 4, p. 431-447Article in journal (Refereed)
    Abstract [en]

    Progress in molecular techniques together with the incorporation of phylogenetic analyses of DNA into taxonomy have caused an increase in the number of species' discoveries in groups with morphological characters that are difficult to study or in those containing polytypic species. But some emerged criticisms plead for a taxonomic conservatism grounded either on the requirement of providing evidences of morphological distinctiveness or reproductive barriers to erect new species names. In a case study of taxonomic research on Neotropical frogs, we combine several lines of evidence (morphological characters, prezygotic reproductive isolation and phylogenetic analyses of mitochondrial DNA) to test the status of 15 nominal species and to assess the degree of agreement of the different lines of evidence. Our study reveals that morphology alone is not sufficient to uncover all species, as there is no other single line of evidence independently. Full congruence between lines of evidence is restricted to only four out of the 15 species. Five species show congruence of two lines of evidence, whereas the remaining six are supported by only one. The use of divergence in morphological characters seems to be the most conservative approach to delineate species boundaries because it does not allow the identification of some sibling reciprocally monophyletic species differing in their advertisement calls. The separate analysis of differences in advertisement calls (evidence of reproductive isolation) or of phylogenetic data alone also shows limitations, because they do not support some morphological species. Our study shows that only an integrative approach combining all sources of evidence provides the necessary feedback to evaluate the taxonomic status of existing species and to detect putative new ones. Furthermore, the application of integrative taxonomy enables the identification of hypotheses about the existence of species that will probably be rejected or changed, and those that can be expected to persist.

  • 205. Pemberton, Trevor J.
    et al.
    Sandefur, Conner I.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Rosenberg, Noah A.
    Sequence determinants of human microsatellite variability2009In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 10, p. e612-Article, review/survey (Refereed)
    Abstract [en]

    Background

    Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database.

    Results

    Calibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length), under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity.

    Conclusions

    These results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability.

  • 206. Preece, Paul
    et al.
    Virley, David J
    Costandi, Moheb
    Coombes, Robert
    Moss, Stephen J
    Mudge, Anne W
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Cairns, Nigel J
    Amyloid precursor protein mRNA levels in Alzheimer's disease brain2004In: Brain Research. Molecular Brain Research, ISSN 0169-328X, E-ISSN 1872-6941, Vol. 122, no 1, p. 1-9Article in journal (Refereed)
    Abstract [en]

    Insoluble beta-amyloid deposits in Alzheimer's disease (AD) brain are proteolytically derived from the membrane bound amyloid precursor protein (APP). The APP gene is differentially spliced to produce isoforms that can be classified into those containing a Kunitz-type serine protease inhibitor domain (K(+), APP(751), APP(770), APRP(365) and APRP(563)), and those without (K(-), APP(695) and APP(714)). Given the hypothesis that Abeta is a result of aberrant catabolism of APP, differential expression of mRNA isoforms containing protease inhibitors might play an active role in the pathology of AD. We took 513 cerebral cortex samples from 90 AD and 81 control brains and quantified the mRNA isoforms of APP with TaqMan real-time RT-PCR. After adjustment for age at death, brain pH and gender we found a change in the ratio of KPI(+) to KPI(-) mRNA isoforms of APP. Three separate probes, designed to recognise only KPI(+) mRNA species, gave increases of between 28% and 50% in AD brains relative to controls (p=0.002). There was no change in the mRNA levels of KPI-(APP 695) (p=0.898). Therefore, whilst KPI-mRNA levels remained stable the KPI(+) species increased specifically in the AD brains.

  • 207. Preece, Paul
    et al.
    Virley, David J
    Costandi, Moheb
    Coombes, Robert
    Moss, Stephen J
    Mudge, Anne W
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Cairns, Nigel J
    An optimistic view for quantifying mRNA in post-mortem human brain2003In: Brain Research. Molecular Brain Research, ISSN 0169-328X, E-ISSN 1872-6941, Vol. 116, no 1-2, p. 7-16Article in journal (Refereed)
    Abstract [en]

    Quantitative human mRNA data are derived from post-mortem or biopsied tissue. RNA degradation, poor replication, a large mRNA variance and confounding factors such as brain pH and age of death are often cited, however, as objections to the data's reliability. A central question is whether post-mortem human mRNA can be treated as a statistically ordered system. TaqMan real-time RT-PCR was used to measure seven mRNAs in 513 cortical samples taken from 90 Alzheimer's disease and 81 control brains. Despite a high mRNA variance strong correlations were found between the mRNA transcripts in a single brain. Where a brain has a high/low level of one mRNA, the same brain invariably has a high/low level of other mRNAs; correlated order is present and allows removal of that source of variation common to all genes. Although levels of mRNA are highly variable between subjects (>1000-fold), quantitative order is present in post-mortem human mRNA, allowing effects due to pathology or gender to be isolated and tested for significance.

  • 208. Preece, Paul
    et al.
    Virley, David J
    Costandi, Moheb
    Coombes, Robert
    Moss, Stephen J
    Mudge, Anne W
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Cairns, Nigel J
    Beta-secretase (BACE) and GSK-3 mRNA levels in Alzheimer's disease2003In: Brain Research. Molecular Brain Research, ISSN 0169-328X, E-ISSN 1872-6941, Vol. 116, no 1-2, p. 155-158Article in journal (Refereed)
    Abstract [en]

    Beta-secretase (BACE) and glycogen synthase kinase (GSK 3) are two enzymes thought to play a role in Alzheimer's disease. We extracted mRNA from 90 Alzheimer and 81 control brains. Levels of mRNA were quantified for BACE and GSK 3 with TaqMan real-time RT-PCR. We found no change in the Alzheimer's disease brains relative to controls for either the BACE or the GSK 3alpha mRNA levels.

  • 209.
    Qvarnstrom, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Haavie, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Saether, S. A.
    Eriksson, D.
    Part, T.
    Song similarity predicts hybridization in flycatchers2006In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 19, no 4, p. 1202-1209Article in journal (Refereed)
    Abstract [en]

    Given that population divergence in sexual signals is an important prerequisite for reproductive isolation, a key prediction is that cases of signal convergence should lead to hybridization. However, empirical studies that quantitatively demonstrate links between phenotypic characters of individuals and their likelihood to hybridize are rare. Here we show that song convergence between sympatric pied (Ficedula hypoleuca) and collared flycatchers (F. albicollis) influence social and sexual interactions between the two species. In sympatry, the majority of male pied flycatchers (65%) include various parts of collared flycatcher song in their song repertoire (but not vice versa). Playback experiments on male interactions demonstrate that male collared flycatchers respond similarly to this 'mixed' song as to conspecific song. Long-term data on pairing patterns show that males singing a converged song attract females of the other species: female collared flycatchers only pair with male pied flycatchers if the males sing the mixed song type. From the perspective of a male pied flycatcher, singing a mixed song type is associated with 30% likelihood of hybridization. This result, combined with our estimates of the frequency of mixed singers, accurately predicts the observed occurrence of hybridization among male pied flycatchers in our study populations (20.45% of 484 pairs; predicted 19.5%). Our results support the suggestion that song functions as the most important prezygotic isolation mechanism in many birds.

  • 210.
    Qvarnström, A
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Haavie, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Saether, S A
    Eriksson, D
    Pärt, T
    Song similarity predicts hybridization in flycatchers.2006In: J Evol Biol, ISSN 1010-061X, Vol. 19, no 4, p. 1202-9Article in journal (Refereed)
    Abstract [en]

    Given that population divergence in sexual signals is an important prerequisite for reproductive isolation, a key prediction is that cases of signal convergence should lead to hybridization. However, empirical studies that quantitatively demonstrate links between phenotypic characters of individuals and their likelihood to hybridize are rare. Here we show that song convergence between sympatric pied (Ficedula hypoleuca) and collared flycatchers (F. albicollis) influence social and sexual interactions between the two species. In sympatry, the majority of male pied flycatchers (65%) include various parts of collared flycatcher song in their song repertoire (but not vice versa). Playback experiments on male interactions demonstrate that male collared flycatchers respond similarly to this 'mixed' song as to conspecific song. Long-term data on pairing patterns show that males singing a converged song attract females of the other species: female collared flycatchers only pair with male pied flycatchers if the males sing the mixed song type. From the perspective of a male pied flycatcher, singing a mixed song type is associated with 30% likelihood of hybridization. This result, combined with our estimates of the frequency of mixed singers, accurately predicts the observed occurrence of hybridization among male pied flycatchers in our study populations (20.45% of 484 pairs; predicted 19.5%). Our results support the suggestion that song functions as the most important prezygotic isolation mechanism in many birds.

  • 211. Ramirez, O.
    et al.
    Altet, L.
    Enseñat, C.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Sanchez, A.
    Ruiz, A.
    Genetic assessment of the Iberian wolf Canis lupus signatus captive breeding program2006In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 7, no 6, p. 861-878Article in journal (Refereed)
    Abstract [en]

    The main goal of ex situ conservation programs is to improve the chances of long term survival of natural populations by founding and managing captive colonies that can serve as a source of individuals for future reintroductions or to reinforce existing populations. The degree in which a captive breeding program has captured the genetic diversity existing in the source wild population has seldom been evaluated. In this study we evaluate the genetic diversity in wild and captive populations of the Iberian wolf, Canis lupus signatus, in order to assess how much genetic diversity is being preserved in the ongoing ex situ conservation program for this subspecies. A sample of domestic dogs was also included in the analysis for comparison. Seventy-four wolves and 135 dogs were genotyped at 13 unlinked microsatellite loci. The results show that genetic diversity in Iberian wolves is comparable in magnitude to that of other wild populations of gray wolf. Both the wild and the captive Iberian wolf populations have a similarly high genetic diversity indicating that no substantial loss of diversity has occurred in the captive-breeding program. The effective number of founders of the program was estimated as similar to 16, suggesting that all founders in the studbook pedigree were genetically independent. Our results emphasize also the genetic divergence between wolves and domestic dogs and indicate that our set of 13 microsatellite loci provide a powerful diagnostic test to distinguish wolves, dogs and their hybrids.

  • 212.
    Robert Piotr, Olinski
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Neuroscience. Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Genome duplication-driven evolution of gene families: insights from the formation of the insulin family.2005Conference proceedings (editor) (Refereed)
  • 213. Roed, Knut H.
    et al.
    Flagstad, Oystein
    Nieminen, Mauri
    Holand, Oystein
    Dwyer, Mark J.
    Rov, Nils
    Vila, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Genetic analyses reveal independent domestication origins of Eurasian reindeer2008In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 275, no 1645, p. 1849-1855Article in journal (Refereed)
    Abstract [en]

    Although there is little doubt that the domestication of mammals was instrumental for the modernization of human societies, even basic features of the path towards domestication remain largely unresolved for many species. Reindeer are considered to be in the early phase of domestication with wild and domestic herds still coexisting widely across Eurasia. This provides a unique model system for understanding how the early domestication process may have taken place. We analysed mitochondrial sequences and nuclear microsatellites in domestic and wild herds throughout Eurasia to address the origin of reindeer herding and domestication history. Our data demonstrate independent origins of domestic reindeer in Russia and Fennoscandia. This implies that the Saami people of Fennoscandia domesticated their own reindeer independently of the indigenous cultures in western Russia. We also found that augmentation of local reindeer herds by crossing with wild animals has been common. However, some wild reindeer populations have not contributed to the domestic gene pool, suggesting variation in domestication potential among populations. These differences may explain why geographically isolated indigenous groups have been able to make the technological shift from mobile hunting to large-scale reindeer pastoralism independently.

  • 214. Rosenberg, Noah A.
    et al.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    The relationship between homozygosity and the frequency of the most frequent allele2008In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 179, no 4, p. 2027-2036Article in journal (Refereed)
    Abstract [en]

    Homozygosity is a commonly used summary of allele-frequencydistributions at polymorphic loci. Because high-frequency allelescontribute disproportionately to the homozygosity of a locus,it often occurs that most homozygotes are homozygous for themost frequent allele. To assess the relationship between homozygosityand the highest allele frequency at a locus, for a given homozygosityvalue, we determine the lower and upper bounds on the frequencyof the most frequent allele. These bounds suggest tight constraintson the frequency of the most frequent allele as a function ofhomozygosity, differing by at most and having an average difference of 2/18 0.1184. The close connection between homozygosityand the frequency of the most frequent allele—which weillustrate using allele frequencies from human populations—hasthe consequence that when one of these two quantities is known,considerable information is available about the other quantity.This relationship also explains the similar performance of statisticaltests of population-genetic models that rely on homozygosityand those that rely on the frequency of the most frequent allele,and it provides a basis for understanding the utility of extendedhomozygosity statistics in identifying haplotypes that havebeen elevated to high frequency as a result of positive selection.

  • 215.
    Saether, Stein Are
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Saetre, Glenn-Peter
    Borge, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Wiley, Chris J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Svedin, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Andersson, G.
    Veen, T.
    Haavie, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Servedio, M.R.
    Bures, S.
    Kral, M.
    Hjernqvist, Mårten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Sex chromosome-linked species recognition and evolution of reproductive isolation in flycatchers2007In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 318, no 5847, p. 95-97Article in journal (Refereed)
    Abstract [en]

    Interbreeding between species (hybridization) typically produces unfit offspring. Reduced hybridization should therefore be favored by natural selection. However, this is difficult to accomplish because hybridization also sets the stage for genetic recombination to dissociate species-specific traits from the preferences for them. Here we show that this association is maintained by physical linkage (on the same chromosome) in two hybridizing Ficedula flycatchers. By analyzing the mating patterns of female hybrids and cross-fostered offspring, we demonstrate that species recognition is inherited on the Z chromosome, which is also the known location of species-specific male plumage traits and genes causing low hybrid fitness. Limited recombination on the Z chromosome maintains associations of Z-linked genes despite hybridization, suggesting that the sex chromosomes may be a hotspot for adaptive speciation.

  • 216.
    Saetre, Peter
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Lindberg, Julia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Leonard, Jennifer A
    Olsson, Kerstin
    Petterson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology, Medical Genetics.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Bergström, Tomas F
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology, Medical Genetics.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    From wild wolf to domestic dog: gene expression changes in the brain2004In: Brain Research. Molecular Brain Research, ISSN 0169-328X, E-ISSN 1872-6941, Vol. 126, no 2, p. 198-206Article in journal (Refereed)
    Abstract [en]

    Despite the relatively recent divergence time between domestic dogs (Canis familiaris) and gray wolves (Canis lupus), the two species show remarkable behavioral differences. Since dogs and wolves are nearly identical at the level of DNA sequence, we hypothesize that the two species may differ in patterns of gene expression.

    We compare gene expression patterns in dogs, wolves and a close relative, the coyote (Canis latrans), in three parts of the brain: hypothalamus, amygdala and frontal cortex, with microarray technology. Additionally, we identify genes with region-specific expression patterns in all three species. Among the wild canids, the hypothalamus has a highly conserved expression profile. This contrasts with a marked divergence in domestic dogs. Real-time PCR experiments confirm the altered expression of two neuropeptides, CALCB and NPY. Our results suggest that strong selection on dogs for behavior during domestication may have resulted in modifications of mRNA expression patterns in a few hypothalamic genes with multiple functions. This study indicates that rapid changes in brain gene expression may not be exclusive to the development of human brains. Instead, they may provide a common mechanism for rapid adaptive changes during speciation, particularly in cases that present strong selective pressures on behavioral characters.

  • 217. Saetre, Peter
    et al.
    Lindberg, Julia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Wirén, Anna
    Holm, Karl
    Bakken, Morten
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Genetic alterations in haemoglobin levels and behaviour in mice selected for high litter sizeManuscript (Other academic)
  • 218.
    Saetre, Peter
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Stark, John M
    Microbial dynamics and carbon and nitrogen cycling following re-wetting of soils beneath two semi-arid plant species.2005In: Oecologia, ISSN 0029-8549, Vol. 142, no 2, p. 247-60Article in journal (Refereed)
    Abstract [en]

    Sporadic summer rainfall in semi-arid ecosystems can provide enough soil moisture to drastically increase CO(2) efflux and rates of soil N cycling. The magnitudes of C and N pulses are highly variable, however, and the factors regulating these pulses are poorly understood. We examined changes in soil respiration, bacterial, fungal and microfaunal populations, and gross rates of N mineralization, nitrification, and NH(4) (+) and NO(3) (-) immobilization during the 10 days following wetting of dry soils collected from stands of big sagebrush (Artemisia tridentata) and cheatgrass (Bromus tectorum) in central Utah. Soil CO(2) production increased more than tenfold during the 17 h immediately following wetting. The labile organic C pool released by wetting was almost completely respired within 2-3 days, and was nearly three times as large in sagebrush soil as in cheatgrass. In spite of larger labile C pools beneath sagebrush, microbial and microfaunal populations were nearly equal in the two soils. Bacterial and fungal growth coincided with depletion of labile C, and populations peaked in both soils 2 days after wetting. Protozoan populations, whose biomass was nearly 3,000-fold lower than bacteria and fungi, peaked after 2-4 days. Gross N mineralization and nitrification rates were both faster in cheatgrass soil than in sagebrush, and caused greater nitrate accumulation in cheatgrass soil. Grazing of bacteria and fungi by protozoans and nematodes could explain neither temporal trends in N mineralization rates nor differences between soil types. However, a mass balance model indicated that the initial N pulse was associated with degradation of microbial substrates that were rich in N (C:N <8.3), and that microbes had shifted to substrates with lower N contents (C:N =15-25) by day 7 of the incubation. The model also suggested that the labile organic matter in cheatgrass soil had a lower C:N ratio than in sagebrush, and this promoted faster N cycling rates and greater N availability. This study provides evidence that the high N availability often associated with wetting of cheatgrass soils is a result of cheatgrass supplying substrates to microbes that are of high decomposability and N content.

  • 219.
    Sallares, R.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Bouwman, A.
    Anderung, C.
    The spread of malaria to southern Europe in antiquity:: New approaches to old problems.2004In: Medical History, ISSN 0025-7273, no 48, p. 311-328Article in journal (Refereed)
  • 220.
    SANMARTIN, ISABEL
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. SYSTEMATIC ZOOLOGY.
    BIOGEOGRAPHY: AN ECOLOGICAL AND EVOLUTIONARY APPROACH: 7TH EDITION ( C. BARRY COX AND PETER D. MOORE)2006In: SYSTEMATIC BIOLOGY, ISSN 1063-5157, Vol. 55, no 2, p. 361-363Article, book review (Refereed)
  • 221.
    SANMARTIN, ISABEL
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. SYSTEMATIC ZOOLOGY.
    Biogeography in a Changing World2006In: Event-Based Biogeography: Integrating patterns, processes, and time, CRC Press (Taylor & Francis Group) , 2006, p. 135-156Chapter in book (Refereed)
    Abstract [en]

    Cladistic biogeography searches for general patterns of distribution among multiple organisms as evidence of a common biogeographic history, but does not explicitly consider the evolutionary processes that created such patterns or the timing of divergence of the organisms studied. This makes biogeographic results often difficult to interpret. Here, I review recent methodological developments on biogeographic analysis based on the recognition of processes (“the event based approach”), which have led to an extraordinary revolution in biogeographic studies. Event-based methods explicitly include all biogeographic processes into the analysis as possible explanations for the observed biogeographic pattern. Each process (vicariance, duplication, extinction, and dispersal) is associated with a cost inversely related to its likelihood. The optimal biogeographic reconstruction is the one that minimizes the total cost of the implied events (most parsimonious). Significance of results can be assessed by comparing them with those derived from random data sets under the null hypothesis that distributions are not phylogenetically constrained. I compare two event-based methods, dispersal-vicariance analysis and parsimony-based tree fitting in relation to alternative biogeographic scenarios: hierarchical vs reticulate, widespread vs. endemic, etc. I describe recent studies in which event-based methods, combined with large data sets of phylogenies and estimates of divergence times, have been used to test large-scale biogeographic patterns on the Holarctic and Southern Hemisphere biotas. Despite claims by cladistic biogeography that dispersal is a random, stochastic event, these studies show that dispersal can also generate congruent distribution patterns among multiple taxa if coordinated in direction, e.g., by prevailing winds and ocean currents (“concerted dispersal”). They also suggest major biogeographic differences between animal and plants, with plant patterns more influenced by recent dispersal.

  • 222.
    Sanmartin, Isabel
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Zoology. Systematic Zoology.
    Integrating processes, time, and patterns: The event-based approach to historical biogeography2005In: The Systematics Association 5th Biennial Meeting, 2005Conference paper (Other scientific)
    Abstract [en]

    Traditional cladistic biogeographic methods search for concordance between phylogenetic and distribution patterns of different organisms as evidence of a common history of geological isolation events (vicariance). However, these methods are flawed because they only focus on “topological congruence”, overlooking other important sources of information. Biogeographic processes such as dispersal and extinction are not incorporated directly into the analysis, which makes cladistic results very difficult to interpret. Similarly, integration of timing of species divergences is needed if we want to discriminate between alternative biogeographic scenarios, or to exclude “pseudo-congruence”, i.e., congruent patterns that originated at different times. Finally, cladistic methods do not directly attempt to test the statistical significance of results. In this paper, I review recent developments on biogeographic analysis designed to overcome these problems, and illustrate them with case studies. Event-based parsimony methods, such as dispersal-vicariance analysis or parsimony-based tree fitting, are derived from explicit process models and reconstruct both ancestral distributions and biogeographic events. Each process is associated with a cost that should be inversely related to its likelihood, with the most parsimonious explanation of the data being the one of minimum cost. Using large data sets of phylogenies and permutation tests, event-based methods have been used, for example, to study directions of dispersal and test alternative diversification hypotheses in the Holarctic fauna, or to identify patterns of concerted dispersal in the Southern Hemisphere. Other more probabilistic methods include the application of Bayesian Inference to biogeographic analysis, in which dispersal and extinction can be introduced as random parameters in the model. This method is currently under development and would be applied to infer colonization patterns in the Canary Archipelago.

  • 223.
    Sanmartin, Isabel
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Systematic Zoology.
    Phylogenies and the radiation of animals around the Northern and Southern Hemispheres2005In: DIVERSITAS Open Science Conference 2005: Integrating biodiversity science for human well-being, 2005, p. 39-Conference paper (Other scientific)
    Abstract [en]

    Historical, phylogeny-based biogeography plays a crucial role in understanding how present-day biodiversity has been generated. Biogeographic reconstructions can be used to identify “relict” biotas, whose long-term survival is threatened, or to predict the response of species to long-term climatic changes.

    So far, however, the role of historical biogeography in conservation decisions has been limited by the lack of an appropriate method of biogeographic analysis. Traditional (cladistic) methods search for general patterns of distribution as evidence of a common biogeographic history, but ignore the evolutionary processes creating such patterns, or the time of origin and ecology of the organisms studied. Moreover, biogeographic analyses are usually restricted to one or few organisms, making them of limited value for conservation policies.

    Recently, new methods of biogeographic analysis have been developed that allow incorporating processes into the analysis (the “event-based approach”). Here, I describe how these methods, together with large data sets of phylogenies and statistical evaluation of results, allow us for the first time to test specific biogeographic hypotheses at a large, intercontinental scale. For example, comparison of a large dated set of Holarctic animal phylogenies reveals that faunal migration over the Bering Bridge was controlled by the prevailing climatic conditions, so its importance as a dispersal route changed considerably over time. Phylogeny-based estimates of species richness among Holarctic infraregions suggest that the higher extant diversity of the Asian fauna was probably the result of higher diversification rates during the Tertiary. Although patterns of diversity in the Southern Hemisphere are usually attributed to vicariant events associated to Gondwana’s break-up, a recent meta-analysis of plant and animal phylogenies suggests that long-distance dispersal has played a major role in the radiation of Southern Hemisphere plants.

  • 224.
    Schielzeth, Holger
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Bolund, Elisabeth
    Patterns of conspecific brood parasitism in zebra finches2010In: Animal Behaviour, ISSN 0003-3472, E-ISSN 1095-8282, Vol. 79, no 6, p. 1329-1337Article in journal (Refereed)
    Abstract [en]

    Conspecific brood parasitism (CBP) brings the obvious fitness advantage of decreased breeding costs. However, the successful development of parasitic eggs depends on appropriate timing in relation to the host's own eggs. A detailed documentation of CBP requires full knowledge of parentage. We achieved this in a captive population of zebra finches, Taeniopygia guttata, breeding in aviaries. The overall frequency of CBP was relatively high (21% of all host clutches, 5.4% of all eggs in host clutches) and comparable to what has been found in the wild in this species. A large proportion of paired females adopted a mixed strategy, laying one or two additional eggs in other nests before initiating their own clutches. Females showed a high individual consistency in whether they adopted a pure nonparasitic strategy or a mixed strategy, which is indicative of individual specialization. About 38% of all eggs laid outside a pair's own nest were incubated by host pairs and can thus be considered successfully parasitic. No paired females were purely parasitic but unpaired females used CBP as a best of a bad job strategy. Hosts were targeted during the early phase of clutch initiation with the majority of parasitic eggs laid 0-5 days before the onset of incubation and usually before the host commenced egg laying. We did not find evidence that particular types of host females were targeted. The within-female repeatability of being a host was estimated to be negative. Overall, the systematic temporal patterns indicate targeted CBP behaviour in zebra finches.

  • 225.
    Schielzeth, Holger
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Kamp, Johannes
    Eichhorn, Goetz
    Heincke, Thomas
    Koshkin, Maxim A.
    Lachmann, Lars
    Sheldon, Robert D.
    Koshkin, Alexej V.
    Wader, gull and tern population estimates for a key breeding and stopover site in Central Kazakhstan2010In: Bird conservation international, ISSN 0959-2709, E-ISSN 1474-0001, Vol. 20, no 2, p. 186-199Article in journal (Refereed)
    Abstract [en]

    Population size estimates of waders, gulls and terns passing through or breeding in Central Asia are very scarce, although highly important for global flyway population estimates as well as for targeting local conservation efforts. The Tengiz-Korgalzhyn region is one of the largest wetland complexes in Central Asia. We conducted surveys in this region between 1999 and 2008 and present estimates of population size as well as information on phenology and age structure for 50 species of Charadriiformes. The Tengiz-Korgalzhyn wetlands are especially important for Red-necked Phalaropes Phalaropus lobatus and Ruffs Philomachus pugnax with, respectively, 41% and 13% of their flyway populations using the area during spring migration. The region is also an important post-breeding moulting site for Pied Avocets Recurvirostra avosetta and Black-tailed Godwits Limosa limosa used by, respectively, 5% and 4% of their flyway populations. Besides its key importance as a migratory stopover site, the study area is a key breeding site for the Critically Endangered Sociable Lapwing Vanellus gregarius, the Near Threatened Black-winged Pratincole Glare la nordmanni and for Pallas's Gull Larus ichthyaetus with 16%, 6% and 5% of their world populations, respectively. We identified 29 individual sites that held more than 1% of the relevant flyway populations of at least one species of Charadriiformes. Including data on other species of waterbirds (mainly waterfowl), there were 93 sites that qualify for Important Bird Areas (IBA). About half of them are protected in a state nature reserve, while an additional 20% are recognised as IBAs. Nevertheless, 28 important sites are currently not recognised as IBAs nor are they protected by other conservation means. These sites require conservation attention.

  • 226.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Issues raised by use of ethnic-group names in genome study2010In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 464, no 7288, p. 487-487Article in journal (Refereed)
  • 227. Schroeder, Kari B.
    et al.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Crawford, Michael H.
    Schurr, Theodore G.
    Boca, Simina M.
    Conrad, Donald F.
    Tito, Raul Y.
    Osipova, Ludmilla P.
    Tarskaia, Larissa A.
    Zhadanov, Sergey I.
    Wall, Jeffrey D.
    Pritchard, Jonathan K.
    Malhi, Ripan S.
    Smith, David G.
    Rosenberg, Noah A.
    Haplotypic background of a private allele at high frequency in the Americas2009In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 26, no 5, p. 995-1016Article, review/survey (Refereed)
    Abstract [en]

    Recently, the observation of a high-frequency private allele,the 9-repeat allele at microsatellite D9S1120, in all sampledNative American and Western Beringian populations has been interpretedas evidence that all modern Native Americans descend primarilyfrom a single founding population. However, this inference assumedthat all copies of the 9-repeat allele were identical by descentand that the geographic distribution of this allele had notbeen influenced by natural selection. To investigate whetherthese assumptions are satisfied, we genotyped 34 single nucleotidepolymorphisms across 500 kilobases (kb) around D9S1120 in 21Native American and Western Beringian populations and 54 otherworldwide populations. All chromosomes with the 9-repeat alleleshare the same haplotypic background in the vicinity of D9S1120,suggesting that all sampled copies of the 9-repeat allele areidentical by descent. Ninety-one percent of these chromosomesshare the same 76.26 kb haplotype, which we call the "AmericanModal Haplotype" (AMH). Three observations lead us to concludethat the high frequency and widespread distribution of the 9-repeatallele are unlikely to be the result of positive selection:1) aside from its association with the 9-repeat allele, theAMH does not have a high frequency in the Americas, 2) the AMHis not unusually long for its frequency compared with otherhaplotypes in the Americas, and 3) in Latin American mestizopopulations, the proportion of Native American ancestry at D9S1120is not unusual compared with that observed at other genomewidemicrosatellites. Using a new method for estimating the timeto the most recent common ancestor (MRCA) of all sampled copiesof an allele on the basis of an estimate of the length of thegenealogy descended from the MRCA, we calculate the mean timeto the MRCA of the 9-repeat allele to be between 7,325 and 39,900years, depending on the demographic model used. The resultssupport the hypothesis that all modern Native Americans andWestern Beringians trace a large portion of their ancestry toa single founding population that may have been isolated fromother Asian populations prior to expanding into the Americas.

  • 228. Seddon, J M
    et al.
    Parker, H G
    Ostrander, E A
    Ellegren, H
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    SNPs in ecological and conservation studies: a test in the Scandinavian wolf population.2005In: Mol Ecol, ISSN 0962-1083, Vol. 14, no 2, p. 503-11Article in journal (Refereed)
    Abstract [en]

    Single nucleotide polymorphisms (SNPs) have the potential to become the genetic marker of choice in studies of the ecology and conservation of natural populations because of their capacity to access variability across the genome. In this study, we provide one of the first demonstrations of SNP discovery in a wild population in order to address typical issues of importance in ecology and conservation in the recolonized Scandinavian and neighbouring Finnish wolf Canis lupus populations. Using end sequence from BAC (bacterial artificial chromosome) clones specific for dogs, we designed assays for 24 SNP loci, 20 sites of which had previously been shown to be polymorphic in domestic dogs and four sites were newly identified as polymorphic in wolves. Of the 24 assayed loci, 22 SNPs were found to be variable within the Scandinavian population and, importantly, these were able to distinguish individual wolves from one another (unbiased probability of identity of 4.33 x 10(-8)), providing equivalent results to that derived from 12 variable microsatellites genotyped in the same population. An assignment test shows differentiation between the Scandinavian and neighbouring Finnish wolf populations, although not all known immigrants are accurately identified. An exploration of the misclassification rates in the identification of relationships shows that neither 22 SNP nor 20 microsatellite loci are able to discriminate across single order relationships. Despite the remaining obstacle of SNP discovery in nonmodel organisms, the use of SNPs in ecological and conservation studies is encouraged by the advent of large scale screening methods. Furthermore, the ability to amplify extremely small fragments makes SNPs of particular use for population monitoring, where faecal and other noninvasive samples are routinely used.

  • 229.
    Seddon, Jennifer
    et al.
    University of Queensland.
    Berggren, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Fleeman, Linda
    University of Sydney.
    Evolutionary history of DLA class II haplotypes in canine diabetes mellitus through single nucleotide polymorphism genotyping2010In: Tissue Antigens, ISSN 0001-2815, E-ISSN 1399-0039, Vol. 75, no 3, p. 218-226Article in journal (Refereed)
    Abstract [en]

    Strong linkage disequilibrium (LD) is a characteristic of the major histocompatibility complex (MHC) region, as well as the genome in general in dogs as a consequence of demographic changes with domestication. Disease association studies of MHC haplotypes may be affected by high LD and the resultant shared genetic backgrounds of haplotypes giving associations with linked but non-causative mutations, and also by convergent haplotypes, in which combinations of alleles have arisen independently. This study provides preliminary tools for dog leukocyte antigen (DLA) class II haplotype analysis with 102 single nucleotide polymorphisms (SNPs) identified in 14.6 kb and genotyping of 20 of these SNPs to tag haplotypes in 60 dogs with diabetes mellitus and in 49 non-diabetic dogs. The pattern of LD and analysis of SNP patterns indicated combinations of exon 2 alleles have arisen through both recombination and convergence. For exon 2 haplotypes associated with susceptibility or protection from diabetes mellitus, a region of fixed differences in SNPs across the DQ region was observed, suggesting a region outside exon 2 may be implicated in disease association. Four new DQB1 promoter alleles restricted to diabetic dogs were identified, as well as a substitution difference in the X1 box of the DQB1 promoter that will potentially modify the effect of the protective haplotypes within diabetic dogs

  • 230.
    Seddon, J.M.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Canid-specific primers for molecular sexing using tissue or non-invasive samples.2005In: Conservation Genetics, no 6, p. 147-149Article in journal (Refereed)
  • 231. Seddon, J.M.
    et al.
    Ellegren, H.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    A temporal analysis shows MHC loci in the Scandivavian wolf population are consistent with neutral evolution.2004In: Proceedings of the Royal Society London: Series B, no 271, p. 2283-2291Article in journal (Refereed)
  • 232. Seddon, JM
    et al.
    Sundqvist, AK
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Björnerfeldt, S
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Ellegren, H
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Genetic identification of immigrants in the Scandinavian wolf population.2006In: Conservation Genetics, no 7, p. 225-230Article in journal (Refereed)
  • 233.
    Skoglund, Pontus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Sequence Polymorphism in Candidate Genes for Differences in Winter Plumage between Scottish and Scandinavian Willow Grouse (Lagopus lagopus)2010In: PLoS one, ISSN 1932-6203, Vol. 5, no 4, p. e10334-Article in journal (Refereed)
    Abstract [en]

    Background: Population variation in the degree of seasonal polymorphism is rare in birds, and the genetic basis of this phenomenon remains largely undescribed. Both sexes of Scandinavian and Scottish Willow grouse (Lagopus lagopus) display marked differences in their winter phenotypes, with Scottish grouse retaining a pigmented plumage year-round and Scandinavian Willow grouse molting to a white morph during winter. A widely studied pathway implicated in vertebrate pigmentation is the melanin system, for which functional variation has been characterised in many taxa. Methodology/Principal Findings: We sequenced coding regions from four genes involved in melanin pigmentation (DCT, MC1R, TYR and TYRP1), and an additional control involved in the melanocortin pathway (AGRP), to investigate the genetic basis of winter plumage in Lagopus. Despite the well documented role of the melanin system in animal coloration, we found no plumage-associated polymorphism or evidence for selection in a total of similar to 2.6 kb analysed sequence. Conclusions/Significance: Our results indicate that the genetic basis of alternating between pigmented and unpigmented seasonal phenotypes is more likely explained by regulatory changes controlling the expression of these or other loci in the physiological pathway leading to pigmentation.

  • 234. Smith, N.G.
    et al.
    Brandström, M.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Ellegren, H.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Evidence for turnover of functional noncoding DNA in mammalian genome evolution.2004In: Genomics, no 84, p. 806-813Article in journal (Refereed)
  • 235.
    Smith, Nick G.C.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Brandström, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Evidence for turnover of functional noncoding DNA in mammalian genome evolution2004In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646, Vol. 84, no 5, p. 806-813Article in journal (Refereed)
    Abstract [en]

    The vast majority of the mammalian genome does not code for proteins, and a fundamental question in genomics is: What proportion of the noncoding mammalian genome is functional? Most attempts to address this issue use sequence comparisons between highly diverged mammals such as human and mouse to identify conservation due to negative selection. But such comparisons will underestimate the true proportion of functional noncoding DNA if there is turnover, if patterns of negative selection change over time. Here we test whether the inferred level of negative selection differs between different pairwise species comparisons. Using a multiple alignment of more than a megabase of contiguous sequence from eight mammalian species, we find a strong negative relationship between inferred levels of negative selection and pairwise divergence using 21 pairwise comparisons. This result suggests that there is a high rate of turnover of functional noncoding elements in the mammalian genome, so measures of functional constraint based on human–mouse comparisons may seriously underestimate the true value.

  • 236. Snoejis, Pauli
    et al.
    Wänstrand, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Pinto, Ernani
    Barros, Marcelo Paes de
    Colepicolo, Pio
    Pedersén, Marianne
    Thiamine (vitamin B1) dynamics in phytoplankton and copepods is regulated by inorganic nutrient supplyArticle in journal (Refereed)
  • 237. Strandberg, E
    et al.
    Jacobsson, J
    Saetre, P
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Direct and maternal gentic effects on behaviour in German Shepherd dogs in Sweden.2005In: Livestock Production Science, no 93, p. 33-42Article in journal (Other (popular scientific, debate etc.))
  • 238. Sundberg, Rolf
    et al.
    Castensson, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Statistical methodology in case-control 5'-nuclease assays: statistical design, modelling and inference for identification of differentially expressed genesManuscript (Other academic)
  • 239. Sundberg, Rolf
    et al.
    Castensson, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Statistical modeling in case-control real-time RT-PCR assays, for identification of differentially expressed genes in schizophrenia2006In: Biostatistics, ISSN 1465-4644, E-ISSN 1468-4357, Vol. 7, no 1, p. 130-144Article in journal (Refereed)
    Abstract [en]

    Aspects of experimental design, statistical modeling, and statistical inference in case-control real-time reverse transcription-polymerase chain reaction (RT-PCR) assays are discussed. The background is mRNA expression data from an investigation of genes previously suggested to be schizophrenia related. Real-time RT-PCR allows large samples of individuals. However, with more individuals than positions per plate, incomplete designs are required. A basic multivariate (for several genes jointly) random-effects analysis of covariance model, incorporating heterogeneity both between and within individuals, is formulated. The use of reference genes to form additional regressors is found to be highly efficient. Because regressions between and within individuals are usually different, it is important first to average over the intraindividual replicates. This has consequences for the influence of plate effects. Topics also discussed are testing for a significant mean disease effect, differential coregulation, and the difficulty of identifying genes affected in only a subgroup of cases.

  • 240.
    Sundqvist, A-K
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Björnerfeldt, S
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Leonard, J A
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Hailer, F
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Hedhammar, A
    Ellegren, H
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    VilÃ, C
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Unequal contribution of sexes in the origin of dog breeds.2006In: Genetics, ISSN 0016-6731, Vol. 172, no 2, p. 1121-8Article in journal (Refereed)
    Abstract [en]

    Department of Evolutionary Biology, Uppsala University, Sweden. anna-karin.sundqvist@ebc.uu.se

    Dogs (Canis familiaris) were domesticated from the gray wolf (Canis lupus) at least 14,000 years ago, and there is evidence of dogs with phenotypes similar to those in modern breeds 4000 years ago. However, recent genetic analyses have suggested that modern dog breeds have a much more recent origin, probably <200 years ago. To study the origin of contemporaneous breeds we combined the analysis of paternally inherited Y chromosome markers with maternally inherited mitochondrial DNA and biparentally inherited autosomal microsatellite markers in both domestic dogs and their wild ancestor, the gray wolf. Our results show a sex bias in the origin of breeds, with fewer males than females contributing genetically, which clearly differs from the breeding patterns in wild gray wolf populations where both sexes have similar contributions. Furthermore, a comparison of mitochondrial DNA and Y chromosome diversity in dog groups recognized by the World Canine Organization, as well as in groups defined by the breeds' genetic composition, shows that paternal lineages are more differentiated among groups than maternal lineages. This demonstrates a lower exchange of males than of females between breeds belonging to different groups, which illustrates how breed founders may have been chosen.

  • 241. Sundqvist, Anna-Karin
    et al.
    Björnerfeldt, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Leonard, Jennifer
    Hailer, Frank
    Hedhammar, Åke
    Ellegren, Hans
    Vilà, Carles
    Unequal contribution of sexes in the origin of dog breeds2006In: Genetics, ISSN 0016-6731, Vol. 172, no 2, p. 1121–1128-Article in journal (Refereed)
  • 242.
    Sundqvist, Anna-Karin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Wolf or dog? Genetic identification of predator from saliva collected around bite wounds on prey2008In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 9, no 5, p. 1275-1279Article in journal (Refereed)
    Abstract [en]

    Wolf predation on livestock is a management problem in many areas and is often used to justify control measures against the wolves. However, wolves coexist with dogs across their range, and dogs could be responsible for attacks blamed on wolves. In this study we evaluate the possibility of obtaining sufficient DNA for species identification of the predator from saliva remaining close to bite wounds following a canid attack. Predator DNA of reasonably high quality was successfully extracted from bite wounds on two sheep that had been attacked on a farm and were genotyped using six informative microsatellite markers. A single consensus genotype could be constructed from the bite wounds of both sheep which we compared to genotypes obtained from Scandinavian wolves and dogs. The results clearly showed that the saliva sampled originated from a single dog. This report thus demonstrates the feasibility of predator species identification from bite wounds and also illustrates that it can not be taken for granted that wolves are responsible for canid livestock kills.

  • 243.
    Svensson, Emma
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Axelsson, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Vretemark, Maria
    Västergötlands länsmuseum.
    Makowiecki, Daniel
    Laboratory for Natural Environment Reconstruction.
    Gilbert, M Thomas P
    Centre for GeoGenetics, Natural History Museum of Denmark.
    Willerslev, Eske
    Centre for GeoGenetics, Natural History Museum of Denmark.
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Insights into Y chromosomal genetic variation and effective population size in the extinct European aurochs Bos primigeniusManuscript (preprint) (Other academic)
  • 244.
    Svensson, Emma
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Vretemark, Maria
    Västergötlands länsmuseum.
    Telldahl, Ylva
    Osteoarchaeological Research Laboratory.
    Persson, Per
    Kulturhistorisk Museum, Universitet i Oslo.
    Malmborg, Gustav
    Högskolan på gotland.
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Signs of contrasting selection in medieval and modern North European cattleManuscript (preprint) (Other academic)
  • 245.
    Svensson, Emma M
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Detecting Sex and Selection in Ancient Cattle Remains Using Single Nucleotide Polymorphisms2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    All contemporary taurine cattle originated some 10,000 years ago when their wild ancestor, the aurochs, was domesticated in the Near East. Although the aurochs was widespread also in Europe, there is no evidence for a local domestication. The aurochs has been extinct since 1627 and therefore little is known about its biology. Following domestication, cattle were selected for traits of interest to humans. All modern cattle breeds were developed in the 19th century and the only sources of information about prehistoric breeding practices, and breeds, come from a few ancient Roman Empire and medieval European written accounts.

    The aim for this thesis was to investigate the effects early selection may have had on the cattle genome and to investigate genetic variation in European aurochs. Using second-generation sequencing and coalescent simulation analyses of aurochs Y chromosomal DNA, I estimated effective population size to between 20,000-80,000 aurochs bulls, indicating that a large population was present when domestic cattle entered Europe. A Y chromosomal SNP revealed that the two male lineages present in modern cattle were also present in European aurochs, and that the frequency of these lineages in domestic cattle fluctuated over time. This indicates that cattle were mobile and that bottlenecks, possibly due to selective breeding, occurred. I used nuclear SNPs to trace genetic variation in North European cattle through time and show that when genetics is combined with archaeology and osteology, even small but notable changes in the use of cattle can be detected. There has been a significant decrease in genetic variation over time, with the most dramatic changes associated with the formation of breeds during the 19th century.

    List of papers
    1. Insights into Y chromosomal genetic variation and effective population size in the extinct European aurochs Bos primigenius
    Open this publication in new window or tab >>Insights into Y chromosomal genetic variation and effective population size in the extinct European aurochs Bos primigenius
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    (English)Manuscript (preprint) (Other academic)
    Keywords
    aurochs, effective population size, Y-chromosome
    National Category
    Genetics
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-123260 (URN)
    Available from: 2010-04-27 Created: 2010-04-27
    2. Temporal fluctuations of Y-chromosomal variation in Bos taurus
    Open this publication in new window or tab >>Temporal fluctuations of Y-chromosomal variation in Bos taurus
    2008 (English)In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 4, no 6, p. 752-754Article in journal (Refereed) Published
    Abstract [en]

    Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.

    Keywords
    ancient DNA, Bos taurus, single nucleotide polymorphism, Y chromosome
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-107102 (URN)10.1098/rsbl.2008.0342 (DOI)000260719800040 ()
    Available from: 2009-07-16 Created: 2009-07-16 Last updated: 2017-12-13Bibliographically approved
    3. A DNA test for sex identification in cattle confirms osteometric results
    Open this publication in new window or tab >>A DNA test for sex identification in cattle confirms osteometric results
    2008 (English)In: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 35, no 4, p. 942-946Article in journal (Refereed) Published
    Abstract [en]

    It is of vital importance to be able to sex identify cattle remains to understand the strategies and importance of cattle husbandry in an ancient society. This is usually done from osteoarchaeological assemblages and often relies on measurements of metapodials. The breadth measurement of the distal trochlea is considered an easy way to identify the sex. Bones from males appears to be easily distinguishable from female counterparts, although it has been complicated to find an external control for the morphological results. Here we investigate the reliability of these particular morphometrics for sex identifying cattle bones with molecular genetics. We use a sex discriminating single nucleotide polymorphism in the ZFXY gene and we apply it to DNA from the bones. To keep the fragment size short and suitable for ancient DNA we base the test on a SNP. The test confirms the osteological sex identification in all cases were DNA could be retrieved. This molecular method can also be used when no fragments suitable for osteological sex identification can be found or when the measurements are non-conclusive.

    Keywords
    ancient nuclear DNA, cattle, sex identification, SNP
    National Category
    Archaeology Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-106383 (URN)10.1016/j.jas.2007.06.021 (DOI)000253824100012 ()
    Available from: 2009-06-22 Created: 2009-06-22 Last updated: 2017-12-13Bibliographically approved
    4. Typing Late Prehistoric Cows and Bulls: Osteology and Genetics of Cattle at the Eketorp Fortification and Settlement on Öland, Sweden
    Open this publication in new window or tab >>Typing Late Prehistoric Cows and Bulls: Osteology and Genetics of Cattle at the Eketorp Fortification and Settlement on Öland, Sweden
    (English)Manuscript (preprint) (Other academic)
    Keywords
    Ancient DNA, Domestic cattle, Cattle breeding, Osteometry, Eketorp fortification and settlement, Iron Age, Middle Ages, SNP, Working animals
    National Category
    Archaeology Genetics
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-123258 (URN)
    Available from: 2010-04-27 Created: 2010-04-27
    5. Tracing genetic change over time using nuclear SNPs in ancient and modern cattle
    Open this publication in new window or tab >>Tracing genetic change over time using nuclear SNPs in ancient and modern cattle