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  • 1201. Zhang, Guojie
    et al.
    Li, Cai
    Li, Qiye
    Li, Bo
    Larkin, Denis M.
    Lee, Chul
    Storz, Jay F.
    Antunes, Agostinho
    Greenwold, Matthew J.
    Meredith, Robert W.
    Ödeen, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Cui, Jie
    Zhou, Qi
    Xu, Luohao
    Pan, Hailin
    Wang, Zongji
    Jin, Lijun
    Zhang, Pei
    Hu, Haofu
    Yang, Wei
    Hu, Jiang
    Xiao, Jin
    Yang, Zhikai
    Liu, Yang
    Xie, Qiaolin
    Yu, Hao
    Lian, Jinmin
    Wen, Ping
    Zhang, Fang
    Li, Hui
    Zeng, Yongli
    Xiong, Zijun
    Liu, Shiping
    Zhou, Long
    Huang, Zhiyong
    An, Na
    Wang, Jie
    Zheng, Qiumei
    Xiong, Yingqi
    Wang, Guangbiao
    Wang, Bo
    Wang, Jingjing
    Fan, Yu
    da Fonseca, Rute R.
    Alfaro-Nunez, Alonzo
    Schubert, Mikkel
    Orlando, Ludovic
    Mourier, Tobias
    Howard, Jason T.
    Ganapathy, Ganeshkumar
    Pfenning, Andreas
    Whitney, Osceola
    Rivas, Miriam V.
    Hara, Erina
    Smith, Julia
    Farre, Marta
    Narayan, Jitendra
    Slavov, Gancho
    Romanov, Michael N.
    Borges, Rui
    Machado, Joao Paulo
    Khan, Imran
    Springer, Mark S.
    Gatesy, John
    Hoffmann, Federico G.
    Opazo, Juan C.
    Hastad, Olle
    Sawyer, Roger H.
    Kim, Heebal
    Kim, Kyu-Won
    Kim, Hyeon Jeong
    Cho, Seoae
    Li, Ning
    Huang, Yinhua
    Bruford, Michael W.
    Zhan, Xiangjiang
    Dixon, Andrew
    Bertelsen, Mads F.
    Derryberry, Elizabeth
    Warren, Wesley
    Wilson, Richard K.
    Li, Shengbin
    Ray, David A.
    Green, Richard E.
    O'Brien, Stephen J.
    Griffin, Darren
    Johnson, Warren E.
    Haussler, David
    Ryder, Oliver A.
    Willerslev, Eske
    Graves, Gary R.
    Alstroem, Per
    Fjeldsa, Jon
    Mindell, David P.
    Edwards, Scott V.
    Braun, Edward L.
    Rahbek, Carsten
    Burt, David W.
    Houde, Peter
    Zhang, Yong
    Yang, Huanming
    Wang, Jian
    Jarvis, Erich D.
    Gilbert, M. Thomas P.
    Wang, Jun
    Comparative genomics reveals insights into avian genome evolution and adaptation2014In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 346, no 6215, p. 1311-1320Article in journal (Refereed)
    Abstract [en]

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

  • 1202. Zhang, Qu
    et al.
    Hill, Geoffrey E
    Edwards, Scott V
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines.2014In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 15, article id 305Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: With its plumage color dimorphism and unique history in North America, including a recent population expansion and an epizootic of Mycoplasma gallisepticum (MG), the house finch (Haemorhous mexicanus) is a model species for studying sexual selection, plumage coloration and host-parasite interactions. As part of our ongoing efforts to make available genomic resources for this species, here we report a transcriptome assembly derived from genes expressed in spleen.

    RESULTS: We characterize transcriptomes from two populations with different histories of demography and disease exposure: a recently founded population in the eastern US that has been exposed to MG for over a decade and a native population from the western range that has never been exposed to MG. We utilize this resource to quantify conservation in gene expression in passerine birds over approximately 50 MY by comparing splenic expression profiles for 9,646 house finch transcripts and those from zebra finch and find that less than half of all genes expressed in spleen in either species are expressed in both species. Comparative gene annotations from several vertebrate species suggest that the house finch transcriptomes contain ~15 genes not yet found in previously sequenced vertebrate genomes. The house finch transcriptomes harbour ~85,000 SNPs, ~20,000 of which are non-synonymous. Although not yet validated by biological or technical replication, we identify a set of genes exhibiting differences between populations in gene expression (n = 182; 2% of all transcripts), allele frequencies (76 FST ouliers) and alternative splicing as well as genes with several fixed non-synonymous substitutions; this set includes genes with functions related to double-strand break repair and immune response.

    CONCLUSIONS: The two house finch spleen transcriptome profiles will add to the increasing data on genome and transcriptome sequence information from natural populations. Differences in splenic expression between house finch and zebra finch imply either significant evolutionary turnover of splenic expression patterns or different physiological states of the individuals examined. The transcriptome resource will enhance the potential to annotate an eventual house finch genome, and the set of gene-based high-quality SNPs will help clarify the genetic underpinnings of host-pathogen interactions and sexual selection.

  • 1203.
    Zhang, Zebin
    et al.
    China Agr Univ, Dept Anim Genet & Breeding, Coll Anim Sci & Technol, State Key Lab Anim Nutr,Natl Engn Lab Anim Breedi, Beijing, Peoples R China.
    Jia, Yaxiong
    Chinese Acad Agr Sci, Inst Anim Sci, Beijing, Peoples R China.
    Almeida, Pedro
    UCL, Dept Genet Evolut & Environm, London, England.
    Mank, Judith E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. UCL, Dept Genet Evolut & Environm, London, England.
    van Tuinen, Marcel
    Univ Groningen, Marine Evolut & Conservat Grp, Ctr Evolutionary & Ecol Studies, Groningen, Netherlands.
    Wang, Qiong
    China Agr Univ, Dept Anim Genet & Breeding, Coll Anim Sci & Technol, State Key Lab Anim Nutr,Natl Engn Lab Anim Breedi, Beijing, Peoples R China.
    Jiang, Zhihua
    Washington State Univ, Dept Anim Sci, Ctr Reprod Biol, Vet & Biomed Res Bldg, Pullman, WA 99164 USA.
    Chen, Yu
    Beijing Municipal Gen Stn Anim Sci, Beijing, Peoples R China.
    Zhan, Kai
    Anhui Acad Agr Sci, Inst Anim Husb & Vet Med, Hefei, Anhui, Peoples R China.
    Hou, Shuisheng
    Chinese Acad Agr Sci, Inst Anim Sci, Beijing, Peoples R China.
    Zhou, Zhengkui
    Chinese Acad Agr Sci, Inst Anim Sci, Beijing, Peoples R China.
    Li, Huifang
    Chinese Acad Agr Sci, Poultry Inst, Yangzhou, Jiangsu, Peoples R China.
    Yang, Fangxi
    Inst Pekin Duck, Beijing, Peoples R China.
    He, Yong
    Cherry Valley Farms Xianghe Co Ltd, Langfang, Peoples R China.
    Ning, Zhonghua
    China Agr Univ, Dept Anim Genet & Breeding, Coll Anim Sci & Technol, State Key Lab Anim Nutr,Natl Engn Lab Anim Breedi, Beijing, Peoples R China.
    Yang, Ning
    China Agr Univ, Dept Anim Genet & Breeding, Coll Anim Sci & Technol, State Key Lab Anim Nutr,Natl Engn Lab Anim Breedi, Beijing, Peoples R China.
    Qu, Lujiang
    China Agr Univ, Dept Anim Genet & Breeding, Coll Anim Sci & Technol, State Key Lab Anim Nutr,Natl Engn Lab Anim Breedi, Beijing, Peoples R China.
    Whole-genome resequencing reveals signatures of selection and timing of duck domestication2018In: GigaScience, ISSN 2047-217X, E-ISSN 2047-217X, Vol. 7, no 4, article id giy027Article in journal (Refereed)
    Abstract [en]

    Background: The genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic differences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new environments as well as the genetic basis of rapid phenotypic change. Here, we sequenced the whole genome of 78 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X per individual. Results: Our population and demographic analyses indicate a complex history of domestication, with early selection for separate meat and egg lineages. Genomic comparison of wild to domesticated populations suggests that genes that affect brain and neuronal development have undergone strong positive selection during domestication. Our F-ST analysis also indicates that the duck white plumage is the result of selection at the melanogenesis-associated transcription factor locus. Conclusions: Our results advance the understanding of animal domestication and selection for complex phenotypic traits.

  • 1204.
    Zhang, Zhifei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Holmer, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Wang, Haizhou
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Butler, Aodhán D.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    An early Cambrian agglutinated tubular lophophorate with brachiopod characters2014In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, p. 4682-Article in journal (Refereed)
    Abstract [en]

    The morphological disparity of lophotrochozoan phyla makes it difficult to predict the morphology of the last common ancestor. Only fossils of stem groups can help discover the morphological transitions that occurred along the roots of these phyla. Here, we describe a tubular fossil Yuganotheca elegans gen.et sp. nov. from the Cambrian (Stage 3) Chengjiang Lagerstätte (Yunnan, China) that exhibits an unusual combination of phoronid, brachiopod and tommotiid (Cambrian problematica) characters, notably a pair of agglutinated valves, enclosing a horseshoe-shaped lophophore, supported by a lower bipartite tubular attachment structure with a long coelomic pedicle providing anchorage. The discovery has important implications for the early evolution of lophotrochozoans, suggesting rooting of brachiopods into the sessile lophotrochozoans and the origination of their bivalved bauplan preceding the biomineralization of shell valves in crown brachiopods.

  • 1205. Zhao, Lei
    et al.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Overall, Andrew D. J.
    Waxman, David
    The characteristic trajectory of a fixing allele: a consequence of fictitious selection that arises from conditioning2013In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 195, no 2, p. 993-1006Article in journal (Refereed)
    Abstract [en]

    This work is concerned with the historical progression, to fixation, of an allele in a finite population. This progression is characterized by the average frequency trajectory of alleles that achieve fixation before a given time, T. Under a diffusion analysis, the average trajectory, conditional on fixation by time T, is shown to be equivalent to the average trajectory in an unconditioned problem involving additional selection. We call this additional selection “fictitious selection”; it plays the role of a selective force in the unconditioned problem but does not exist in reality. It is a consequence of conditioning on fixation. The fictitious selection is frequency dependent and can be very large compared with any real selection that is acting. We derive an approximation for the characteristic trajectory of a fixing allele, when subject to real additive selection, from an unconditioned problem, where the total selection is a combination of real and fictitious selection. Trying to reproduce the characteristic trajectory from the action of additive selection, in an infinite population, can lead to estimates of the strength of the selection that deviate from the real selection by >1000% or have the opposite sign. Strong evolutionary forces may be invoked in problems where conditioning has been carried out, but these forces may largely be an outcome of the conditioning and hence may not have a real existence. The work presented here clarifies these issues and provides two useful tools for future analyses: the characteristic trajectory of a fixing allele and the force that primarily drives this, namely fictitious selection. These should prove useful in a number of areas of interest including coalescence with selection, experimental evolution, time series analyses of ancient DNA, game theory in finite populations, and the historical dynamics of selected alleles in wild populations.

  • 1206.
    Zhao, Lei
    et al.
    Fudan Univ, Ctr Computat Syst Biol, 220 Handan Rd, Shanghai 200433, Peoples R China..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Fudan Univ, Ctr Computat Syst Biol, 220 Handan Rd, Shanghai 200433, Peoples R China..
    Waxman, David
    Fudan Univ, Ctr Computat Syst Biol, 220 Handan Rd, Shanghai 200433, Peoples R China..
    An informational transition in conditioned Markov chains: Applied to genetics and evolution2016In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 402, p. 158-170Article in journal (Refereed)
    Abstract [en]

    In this work we assume that we have some knowledge about the state of a population at two known times, when the dynamics is governed by a Markov chain such as a Wright-Fisher model. Such knowledge could be obtained, for example, from observations made on ancient and contemporary DNA, or during laboratory experiments involving long term evolution. A natural assumption is that the behaviour of the population, between observations, is related to (or constrained by) what was actually observed. The present work shows that this assumption has limited validity. When the time interval between observations is larger than a characteristic value, which is a property of the population under consideration, there is a range of intermediate times where the behaviour of the population has reduced or no dependence on what was observed and an equilibrium-like distribution applies. Thus, for example, if the frequency of an allele is observed at two different times, then for a large enough time interval between observations, the population has reduced or no dependence on the two observed frequencies for a range of intermediate times. Given observations of a population at two times, we provide a general theoretical analysis of the behaviour of the population at all intermediate times, and determine an expression for the characteristic time interval, beyond which the observations do not constrain the population's behaviour over a range of intermediate times. The findings of this work relate to what can be meaningfully inferred about a population at intermediate times, given knowledge of terminal states.

  • 1207.
    Zhao, Weizhou
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Evolution of streamlined genomes in ultra-small aquatic bacteria2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis investigates the evolutionary processes of streamlined genomes from aquatic bacteria adapting to different salinities, using two groups of ultra-small aquatic bacteria (LD12 Alphaproteobacteria and acI Actinobacteria). Due to difficulties in obtaining pure cultures of these bacteria, culture-free approaches (single-cell genomics and metagenomics) were used to construct and compare genomes, and to study the mechanisms and selective forces of adaptation to freshwater, brackish, and marine ecosystems.

    A study of single-cell amplified genomes (SAGs) from freshwater LD12 Alphaproteobacteria revealed that LD12 forms a clade embedded within the globally dominant marine Alphaproteobacteria SAR11, and subclades were organized into distinct microclusters. LD12 genomes had a very low ratio of recombination to point mutations, in contrast to their marine relatives which had a very high ratio of recombination to mutation. We suggested that the transition from marine to freshwater was a bottleneck event, resulting in reduced opportunities for recombination.

    In a separate study, we analyzed complete genomes and SAGs from acI Actinobacteria abundant in freshwater ecosystems, and found overall low rates of sequence divergence with however a dramatic acceleration near genomic island 1 (GI-1). We also identified a type IV topoisomerase, the delta subunit of DNA polymerase, and an RNA polymerase sigma factor near GI-1. Based on these results, we proposed a model for the evolution and expression of novel genes in these genomes.

    We also isolated and analyzed the genomes of single cells from a marine Actinobacteria (subclass Candidatus Actinomarinidae). These were not related to acI, but to Acidimicrobiia, which suggested salinity barriers have been crossed several times by Actinobacteria.

    To further understand the transition to different salinities, we obtained acI SAGs from three different intermediate-salinity Baltic Sea locations. We took sequence reads from 21 metagenomes taken along the salinity gradient, and recruited these fragments to both the freshwater and brackish acI reference genomes. These results indicated that transitions between fresh and brackish waters have occurred multiple times in acI Actinobacteria and some of these strains are globally present in coastal waters.

    List of papers
    1. Single cell genomics reveals low recombination frequencies in freshwater bacteria of the SAR11 clade
    Open this publication in new window or tab >>Single cell genomics reveals low recombination frequencies in freshwater bacteria of the SAR11 clade
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    2013 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 14, no 11, article id R130Article in journal (Refereed) Published
    Abstract [en]

    Background: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt-and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. Results: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. Conclusions: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host.

    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-206203 (URN)10.1186/gb-2013-14-11-r130 (DOI)000330616200009 ()24286338 (PubMedID)
    Funder
    Swedish Research Council, 349-2007-831 621-2008-3259 621-2011-4669-4669 2009-3784 2008-1923 2012-3892EU, European Research CouncilGöran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of TechnologyKnut and Alice Wallenberg Foundation, KAW-2011.0148 KAW-2012.0075Swedish National Infrastructure for Computing (SNIC), p2006019 p2009043
    Available from: 2013-09-03 Created: 2013-08-29 Last updated: 2019-09-20Bibliographically approved
    2. Rapid diversification of functional homologs in replacement genomic islands of freshwater Actinobacteria
    Open this publication in new window or tab >>Rapid diversification of functional homologs in replacement genomic islands of freshwater Actinobacteria
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-393357 (URN)
    Available from: 2019-09-19 Created: 2019-09-19 Last updated: 2019-09-26
    3. Evolution of subclass Candidatus Actinomarinidae inferred from single-cell amplified genomes of saltwater Actinobacteria
    Open this publication in new window or tab >>Evolution of subclass Candidatus Actinomarinidae inferred from single-cell amplified genomes of saltwater Actinobacteria
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-393359 (URN)
    Available from: 2019-09-19 Created: 2019-09-19 Last updated: 2019-09-23
    4. A phylometagenomic study based on single-cell amplified genomes from Actinobacteria in the brackish waters of the Baltic Sea
    Open this publication in new window or tab >>A phylometagenomic study based on single-cell amplified genomes from Actinobacteria in the brackish waters of the Baltic Sea
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-393361 (URN)
    Available from: 2019-09-19 Created: 2019-09-19 Last updated: 2019-09-26
  • 1208.
    Zhao, Weizhou
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Garcia, Sarahi L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andersson, Siv G.E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Rapid diversification of functional homologs in replacement genomic islands of freshwater ActinobacteriaManuscript (preprint) (Other academic)
  • 1209.
    Zhao, Weizhou
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Garcia, Sarahi L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Evolution of subclass Candidatus Actinomarinidae inferred from single-cell amplified genomes of saltwater ActinobacteriaManuscript (preprint) (Other academic)
  • 1210.
    Zhao, Weizhou
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Garcia, Sarahi L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Grossart, Hans-Peter
    Leibniz Institute for Freshwater Ecology and Inland Fisheries.
    Wannicke, Nicola
    Leib­niz In­sti­tu­te for Plas­ma Sci­ence and Tech­no­lo­gy.
    McMahon, Katherine D
    Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin, Madison.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    A phylometagenomic study based on single-cell amplified genomes from Actinobacteria in the brackish waters of the Baltic SeaManuscript (preprint) (Other academic)
  • 1211.
    Zhu, Min
    et al.
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.;Univ Chinese Acad Sci, Coll Earth Sci, Beijing 100049, Peoples R China..
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Pan, Zhaohui
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.;Univ Chinese Acad Sci, Coll Earth Sci, Beijing 100049, Peoples R China..
    Zhu, Youan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Qiao, Tuo
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China..
    Zhao, Wenjin
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China..
    Jia, Liantao
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China..
    Lu, Jing
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China..
    A Silurian maxillate placoderm illuminates jaw evolution2016In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 354, no 6310, p. 334-336Article in journal (Refereed)
    Abstract [en]

    The discovery of Entelognathus revealed the presence of maxilla, premaxilla, and dentary, supposedly diagnostic osteichthyan bones, in a Silurian placoderm. However, the relationship between these marginal jaw bones and the gnathal plates of conventional placoderms, thought to represent the inner dental arcade, remains uncertain. Here we report a second Silurian maxillate placoderm, which bridges the gnathal and maxillate conditions. We propose that the maxilla, premaxilla, and dentary are homologous to the gnathal plates of placoderms and that all belong to the same dental arcade. The gnathal-maxillate transformation occurred concurrently in upper and lower jaws, predating the addition of infradentary bones to the lower jaw.

  • 1212.
    Zhu, Min
    et al.
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.;Univ Chinese Acad Sci, Coll Earth Sci, Beijing 100049, Peoples R China..
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Zhao, Wen-Jin
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.;Univ Chinese Acad Sci, Coll Earth Sci, Beijing 100049, Peoples R China..
    Jia, Lian-Tao
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China..
    A Devonian tetrapod-like fish reveals substantial parallelism in stem tetrapod evolution2017In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 1, no 10, p. 1470-1476Article in journal (Refereed)
    Abstract [en]

    The fossils assigned to the tetrapod stem group document the evolution of terrestrial vertebrates from lobe-finned fishes. During the past 18 years the phylogenetic structure of this stem group has remained remarkably stable, even when accommodating new discoveries such as the earliest known stem tetrapod Tungsenia and the elpistostegid (fish-tetrapod intermediate) Tiktaalik. Here we present a large lobe-finned fish from the Late Devonian period of China that disrupts this stability. It combines characteristics of rhizodont fishes (supposedly a basal branch in the stem group, distant from tetrapods) with derived elpistostegid-like and tetrapod-like characters. This melange of characters may reflect either detailed convergence between rhizodonts and elpistostegids plus tetrapods, under a phylogenetic scenario deduced from Bayesian inference analysis, or a previously unrecognized close relationship between these groups, as supported by maximum parsimony analysis. In either case, the overall result reveals a substantial increase in homoplasy in the tetrapod stem group. It also suggest that ecological diversity and biogeographical provinciality in the tetrapod stem group have been underestimated.

  • 1213.
    Zielinski, P.
    et al.
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland..
    Nadachowska-Brzyska, Krystyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dudek, K.
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland..
    Babik, W.
    Jagiellonian Univ, Inst Environm Sci, Gronostajowa 7, PL-30387 Krakow, Poland..
    Divergence history of the Carpathian and smooth newts modelled in space and time2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 16, p. 3912-3928Article in journal (Refereed)
    Abstract [en]

    Information about demographic history is essential for the understanding of the processes of divergence and speciation. Patterns of genetic variation within and between closely related species provide insights into the history of their interactions. Here, we investigated historical demography and genetic exchange between the Carpathian (Lissaritan montandoni, Lm) and smooth (L. vulgaris, Lv) newts. We combine an extensive geographical sampling and multilocus nuclear sequence data with the approximate Bayesian computation framework to test alternative scenarios of divergence and reconstruct the temporal and spatial pattern of gene flow between species. A model of recent (last glacial period) interspecific gene flow was favoured over alternative models. Thus, despite the relatively old divergence (4-6 mya) and presumably long periods of isolation, the species have retained the ability to exchange genes. Nevertheless, the low migration rates (ca. 10 per gene copy per generation) are consistent with strong reproductive isolation between the species. Models allowing demographic changes were favoured, suggesting that the effective population sizes of both species at least doubled as divergence reaching the current ca. 0.2 million in Lm and 1 million in Lv. We found asymmetry in rates of interspecific gene flow between Lm and one evolutionary lineage of Lv. We suggest that intraspecific polymorphism for hybrid incompatibilities segregating within Lv could explain this pattern and propose further tests to distinguish between alternative explanations. Our study highlights the importance of incorporating intraspecific genetic structure into the models investigating the history of divergence.

  • 1214.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Pérez-Huerta, Alberto
    University of Alabama.
    Goujet, Daniel
    Muséum national d'histoire naturelle.
    Vertebrate Microfossils as Tools in Stratigraphy: A Study of the LowerDevonian Andrée Land Group Spitsbergen2014In: Springer Geology, p. 1167-1171Article in journal (Refereed)
    Abstract [en]

    We have studied vertebrate microremains from the Lower to Middle Devonian of the Andrée Land Group, comprising the Wood Bay and Grey Hoek formations. We have defined two new thelodont assemblages, which represent different depositional phases during the late Early to early Middle Devonian formation of the Andrée Land Group. The definition of these two new thelodont assemblages allows us to precisely establish the relative ages of the Lower–Middle Devonian strata. Rare earth element (REE) abundances were measured in a number of thelodont and chondrichthyan microfossil dental tissue biominerals, using laser ablation inductively coupled plasma mass spectrometry (LA–ICP–MS). The evaluation of fossil preservation level was performed using semiquantitative spot-geochemistry analyses on finely polished thelodont scale thin-sections using Energy Dispersive X-ray Spectroscopy (EDS), and Electron Backscattering Diffractometry (EBSD) was applied to detect recrystallization. Stable oxygen isotope measurements (δ18O) of bulk biominerals were conducted in parallel, and showed lower heavy oxygen values in the fossil tissues with stronger visible alteration, such as those from the Grey Hoek Formation. Our results suggest that certain lithostratigraphic units of the Andrée Land Group must be regarded as contemporaneous lithofacies subjected to different sedimentary environments, rather than as separate stratigraphic members.

  • 1215.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Fadel, Alexander
    University of Lille-1.
    Qvarnström, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Pérez-Huerta, Alberto
    University of Alabama.
    Jeffries, Teresa
    London Natural History Museum.
    Early vertebrate microremains as proxies to palaeoenvironment: rare earth elements in dermal scale biominerals from the Silurian and Lower Devonian2016In: Thansactions of the Society of Micropalaeontology, 2016Conference paper (Other academic)
  • 1216.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Fadel, Alexander
    University of Lille-1.
    Qvarnström, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Pérez-Huerta, Alberto
    University of Alabama.
    Jeffries, Teresa
    London Natural History Museum.
    Early vertebrate microremains as proxies to palaeornvironment :: rare earth elements ind ermal scale biominerals from the Silurian and Lower Devonian2018In: Résumés de la 26-eme RST 2018, 2018, Vol. 3, p. 301-301Conference paper (Refereed)
  • 1217.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Jeffries, Teresa
    London Natural History Museum.
    Qvarnström, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Pérez-Huerta, Alberto
    University of Alabama.
    Distribution histologique des terres rares (REE) dans des microrestes de vertébrés du Paléozoique Inférieur2016Conference paper (Refereed)
  • 1218.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Karatajute-Talimaa, Valentina
    Vilnius University.
    Aspidin or galeaspidin: new early vertebrate histology from the Lower Silurian of Southern Siberia2011In: Program and Abstracts: 71st Annual Meeting Society of Vertebrate Paleontology, 2011, p. Sec1: 221-Conference paper (Refereed)
  • 1219.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Karatajute-Talimaa, Valentina
    Vilnius University.
    Goujet, Daniel
    Museum national d'histoire naturelle.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Thelodont scales from the Lower and Middle Devonian Andree Land Group, Spitsbergen2013In: GFF, ISSN 1103-5897, E-ISSN 2000-0863, Vol. 135, no 1, p. 57-73Article in journal (Refereed)
    Abstract [en]

    Scales of six thelodont taxa are described from the Devonian of Spitsbergen. Numerous samples from localities widely dispersed on Spitsbergen yield several assemblages considered to represent different depositional phases of the late Lower lower Middle Devonian of the Andrée Land Group, but also support the view that certain lithostratigraphic units of the Andrée Land Group should be regarded as contemporaneous lithofacies subjected to different sedimentary environments, rather than as separate stratigraphic members. The description of Woodfjordia collisa gen. et sp. nov., Talivalia svalbardia sp. nov., Canonia cf. C. grossi, Amaltheolepis montiwatsonia sp. nov., Amaltheolepis winsnesi and Amaltheolepis austfjordia sp. nov. also allows for a comparison with similar faunas from other regions of the Northern Hemisphere and motivates further elaboration of Early-Middle Devonian thelodont biostratigraphy.

  • 1220.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Karatajute-Talimaa, Valentina
    Vilnius University.
    Joachimski, Michael M.
    University of Erlangen Nuremberg.
    Jeffries, Teresa
    London Natural History Museum.
    Silurian vertebrates from northern Mongolia:: diversity, ecology and environment2014Conference paper (Refereed)
  • 1221.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Pérez-Huerta, Alberto
    University of Alabama.
    Fadel, Alexander
    University of Lille-1.
    Jeffries, Teresa
    London Natural History Museum.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Goujet, Daniel
    Muséum national d'histoire naturelle.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Andrée Land of Spitsbergen:: Devonian vertebrate diversity and palaeoenvironments2018Conference paper (Refereed)
  • 1222.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Richter, Martha
    Natural History Museum.
    Karatajute-Talimaa, Valentina
    Vilnius University.
    Meredith Smith, Moya
    King's College London, Dental Institute.
    Tissue diversity and evolutionary trends of the dermal skeleton of Silurian thelodonts2013In: Historical Biology, ISSN 0891-2963, E-ISSN 1029-2381, Vol. 25, no 2, p. 143-154Article in journal (Refereed)
    Abstract [en]

    Previously described scale morphotypes of Silurian thelodonts, constrained by their representation as isolated dermaldenticles are reassessed to provide a more robust character basis for their inclusion in future phylogenetic studies. Asrelatively common microfossils, thelodonts are important biostratigraphical markers, but their interrelationships withgeologically younger species known by complete skeletons are still unresolved. We examined scales of 21 knownmorphotypes from north-eastern Europe, Siberia and central Asia and described their distinct tissue arrangementsconsidering (1) thickness and direction of dentine tubules, (2) presence or absence of a pulp canal, (3) number and positionof pulp canals, (4) the presence or absence of a distinct outer crown layer and (5) the extent of Sharpey’s fibres penetratingthe scale base. We correlated the traditional thelodont scale type morphologies with these distinct scale histologies, as foundin Silurian thelodonts. In addition, a new histological type for thelodont scales, the Talimaalepis type, is described torepresent a new taxon, from the Early-Mid Silurian. Our study suggests that, through time, there is a general trend ofincreasing complexity in thelodont dermal tissue structures. Three types of dentine and internal scale organisations weredistinguished in Silurian species studied, namely (1) irregular, thin tubular dentine; (2) irregular, thick tubular dentine, withtwo subtypes as a function of pulp canal development and (3) regular, tubular dentine (orthodentine).

  • 1223.
    Zigaite, Zivile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Whitehouse, Martin
    Naturhistoriska Riksmuseet Stockholm.
    Joachimski, Michael M.
    University of Erlangen Nuremberg.
    Sansom, Ivan
    University of Birmingham.
    Ahlberg, Per Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Oxygen isotopes in modern and fossil ecosystems: model and case study overview2016Conference paper (Other academic)
  • 1224.
    Zu, Pengjuan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Effects of Nectar Production and Pollinator Assemblies on Mating Patterns in Orchids2011Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Pollinator visitation patterns should affect pollination success and mating patterns in flowering species. In the orchid family, about one third of the species do not provide any reward for their pollinators. Pollination by deceit is typically associated with low fruit set but may increase the chance of cross-pollination since the pollinator should soon leave the individual plant when there is no reward in the flowers. This may be beneficial if self-fertilisation results in inbreeding depression. I studied the mating patterns of one rewarding and one deceptive orchid in two closely related genera by tracking the fate of stained pollinia. I also conducted controlled crosses to estimate inbreeding depression. The results show that the deceptive orchid Dactylorhiza lapponica has lower pollination success, but higher cross-pollination rate (ca. 90%) than the nectariferous orchid Gymnadenia conopsea (ca. 18% cross-pollination). The results further suggest that in G. conopsea, nocturnal visitors mediate higher geitonogamous pollination rate (ca. 100%) than diurnal visitors (ca. 60%). In both study species, fruits produced from cross-pollination were heavier than fruits produced from selfing. Inbreeding depression for fruit mass did not differ significantly between the two species (δ = 0.21 in D. lapponica and δ = 0.29 in G. conopsea). These data support the hypothesis that pollination by deceit can enhance cross-pollination. A literature study including several rewarding and non-rewarding orchid species indicated lower geitonogamy in the deceptive orchids, but the difference was not statistically significant. 

  • 1225. Zuccolo, Andrea
    et al.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    De Paoli, Emanuele
    Morgante, Michele
    The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution2015In: Gene, ISSN 0378-1119, E-ISSN 1879-0038, Vol. 568, no 1, p. 89-99Article in journal (Refereed)
    Abstract [en]

    Long Terminal Repeat retroelements (LTR-RTs) are a major component of many plant genomes. Although well studied and described in angiosperms, their features and dynamics are poorly understood in gymnosperms. Representative complete copies of a Ty1-copia element isolate in Picea abies and named PARTC were identified in six other conifer species (Picea glauca, Pinus sylvestris, Pinus taeda, Abies sibirica, Taxus baccata and Juniperus communis) covering more than 200 million years of evolution. Here we characterized the structure of this element, assessed its abundance across conifers, studied the modes and timing of its amplification, and evaluated the degree of conservation of its extant copies at nucleotide level over distant species. We demonstrated that the element is ancient, abundant, widespread and its paralogous copies are present in the genera Picea, Pinus and Abies as an LTR-RT family. The amplification leading to the extant copies of PARTC occurred over long evolutionary times spanning 10 s of MY and mostly took place after the speciation of the conifers analyzed. The level of conservation of PARTC is striking and may be explained by low substitution rates and limited removal mechanisms for LTR-RTs. These PARTC features and dynamics are representative of a more general scenario for LTR-RTs in gymnosperms quite different from that characterizing the vast majority of LTR-RT elements in angiosperms. (C) 2015 Elsevier B.V. All rights reserved.

  • 1226.
    Zumberge, J. Alex
    et al.
    Univ Calif Riverside, Dept Earth Sci, Riverside, CA 92521 USA.
    Love, Gordon D.
    Univ Calif Riverside, Dept Earth Sci, Riverside, CA 92521 USA.
    Cárdenas, Paco
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Sperling, Erik A.
    Stanford Univ, Dept Geol Sci, Stanford, CA 94305 USA.
    Gunasekera, Sunithi
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Rohrssen, Megan
    Cent Michigan Univ, Dept Earth & Atmospher Sci, Mt Pleast, MI USA.
    Grosjean, Emmanuelle
    Geosci Australia, Canberra, ACT, Australia.
    Grotzinger, John P.
    CALTECH, Div Geol & Planetary Sci, Pasadena, CA USA.
    Summons, Roger E.
    MIT, Dept Earth Atmospher & Planetary Sci, Cambridge, MA USA.
    Demosponge steroid biomarker 26-methylstigmastane provides evidence for Neoproterozoic animals2018In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, no 11, p. 1709-1714Article in journal (Refereed)
    Abstract [en]

    Sterane biomarkers preserved in ancient sedimentary rocks hold promise for tracking the diversification and ecological expansion of eukaryotes. The earliest proposed animal biomarkers from demosponges (Demospongiae) are recorded in a sequence around 100 Myr long of Neoproterozoic-Cambrian marine sedimentary strata from the Huqf Supergroup, South Oman Salt Basin. This C-30 sterane biomarker, informally known as 24-isopropylcholestane (24-ipc), possesses the same carbon skeleton as sterols found in some modern-day demosponges. However, this evidence is controversial because 24-ipc is not exclusive to demosponges since 24-ipc sterols are found in trace amounts in some pelagophyte algae. Here, we report a new fossil sterane biomarker that co-occurs with 24-ipc in a suite of late Neoproterozoic-Cambrian sedimentary rocks and oils, which possesses a rare hydrocarbon skeleton that is uniquely found within extant demosponge taxa. This sterane is informally designated as 26-methylstigmastane (26-mes), reflecting the very unusual methylation at the terminus of the steroid side chain. It is the first animal-specific sterane marker detected in the geological record that can be unambiguously linked to precursor sterols only reported from extant demosponges. These new findings strongly suggest that demosponges, and hence multicellular animals, were prominent in some late Neoproterozoic marine environments at least extending back to the Cryogenian period.

  • 1227.
    Zwoinska, Martyna K.
    et al.
    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.
    Cortazar-Chinarro, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ramsden, Mark
    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.
    Selection on learning performance results in the correlated evolution of sexual dimorphism in life history2016In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, no 2, p. 342-357Article in journal (Refereed)
    Abstract [en]

    The evolution of learning can be constrained by trade-offs. As male and female life histories often diverge, the relationship between learning and fitness may differ between the sexes. However, because sexes share much of their genome, intersexual genetic correlations can prevent males and females from reaching their sex-specific optima resulting in intralocus sexual conflict (IaSC). To investigate if IaSC constraints sex-specific evolution of learning, we selected Caenorhabditis remanei nematode females for increased or decreased olfactory learning performance and measured learning, life span (in mated and virgin worms), reproduction, and locomotory activity in both sexes. Males from downward-selected female lines had higher locomotory activity and longer virgin life span but sired fewer progeny than males from upward-selected female lines. In contrast, we found no effect of selection on female reproduction and downward-selected females showed higher locomotory activity but lived shorter as virgins than upward-selected females. Strikingly, selection on learning performance led to the reversal of sexual dimorphism in virgin life span. We thus show sex-specific trade-offs between learning, reproduction, and life span. Our results support the hypothesis that selection on learning performance can shape the evolution of sexually dimorphic life histories via sex-specific genetic correlations.

  • 1228.
    Åberg, Emma
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Anderssson, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jemth, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Conservation and divergence in the evolution of binding affinity between p53 and MDM2Manuscript (preprint) (Other academic)
  • 1229.
    Åberg, Emma
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Saccoccia, Fulvio
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Grabherr, Manfred
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ore, Wai Ying Josefin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jemth, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Hultqvist, Greta
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Evolution of the p53-MDM2 pathway2017In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, article id 177Article in journal (Refereed)
    Abstract [en]

    Background: The p53 signalling pathway, which controls cell fate, has been extensively studied due to its prominent role in tumor development. The pathway includes the tumor supressor protein p53, its vertebrate paralogs p63 and p73, and their negative regulators MDM2 and MDM4. The p53/p63/p73-MDM system is ancient and can be traced in all extant animal phyla. Despite this, correct phylogenetic trees including both vertebrate and invertebrate species of the p53/p63/p73 and MDM families have not been published. Results: Here, we have examined the evolution of the p53/p63/p73 protein family with particular focus on the p53/ p63/p73 transactivation domain (TAD) and its co-evolution with the p53/p63/p73- binding domain (p53/p63/p73BD) of MDM2. We found that the TAD and p53/p63/p73BD share a strong evolutionary connection. If one of the domains of the protein is lost in a phylum, then it seems very likely to be followed by loss of function by the other domain as well, and due to the loss of function it is likely to eventually disappear. By focusing our phylogenetic analysis to p53/p63/ p73 and MDM proteins from phyla that retain the interaction domains TAD and p53/p63/p73BD, we built phylogenetic trees of p53/p63/p73 and MDM based on both vertebrate and invertebrate species. The trees follow species evolution and contain a total number of 183 and 98 species for p53/p63/p73 and MDM, respectively. We also demonstrate that the p53/p63/p73 and MDM families result from whole genome duplications. Conclusions: The signaling pathway of the TAD and p53/p63/p73BD in p53/p63/p73 and MDM, respectively, dates back to early metazoan time and has since then tightly co-evolved, or disappeared in distinct lineages.

  • 1230.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Pollinators, herbivores, and the evolution of floral traits2019In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 364, no 6436, p. 122-123Article in journal (Other academic)
  • 1231.
    Ågren, Jon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Oakley, Christopher G.
    Michigan State Univ, Dept Plant Biol, E Lansing, MI 48824 USA. WWF Norway, Postboks 6784, N-0130 Oslo, Norway..
    Lundemo, Sverre
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Schemske, Douglas W.
    Michigan State Univ, Dept Plant Biol, E Lansing, MI 48824 USA.;Michigan State Univ, WK Kellogg Biol Stn, E Lansing, MI 48824 USA..
    Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: Estimates of selection and QTL mapping2017In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 71, no 3, p. 550-564Article in journal (Refereed)
    Abstract [en]

    To identify the ecological and genetic mechanisms of local adaptation requires estimating selection on traits, identifying their genetic basis, and evaluating whether divergence in adaptive traits is due to conditional neutrality or genetic trade-offs. To this end, we conducted field experiments for three years using recombinant inbred lines (RILs) derived from two ecotypes of Arabidopsis thaliana (Italy, Sweden), and at each parental site examined selection on flowering time and mapped quantitative trait loci (QTL). There was strong selection for early flowering in Italy, but weak selection in Sweden. Eleven distinct flowering time QTL were detected, and for each the Italian genotype caused earlier flowering. Twenty-seven candidate genes were identified, two of which (FLC and VIN3) appear under major flowering time QTL in Italy. Seven of eight QTL in Italy with narrow credible intervals colocalized with previously reported fitness QTL, in comparison to three of four in Sweden. The results demonstrate that the magnitude of selection on flowering time differs strikingly between our study populations, that the genetic basis of flowering time variation is multigenic with some QTL of large effect, and suggest that divergence in flowering time between ecotypes is due mainly to conditional neutrality.

  • 1232.
    Ålund, Murielle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Gametes and speciation: from prezygotic to postzygotic isolation2012Report (Other academic)
    Abstract [en]

    Speciation lies at the heart of evolutionary biology and researchers have been trying to understand the mechanisms leading to the evolution of reproductive isolation since over 250 years. Premating barriers (i.e. barriers preventing heterospecific individuals to mate with each other) and extrinsic postzygotic isolation (i.e. environmental factors affecting the fitness of hybrid individuals) have been studied in many taxa. However, little is known about what is happening at the gametic level, both before heterospecific fertilization (i.e. postmating prezygotic or gametic isolation) and in hybrid individuals (i.e. intrinsic postzygotic incompatibilities). In this essay, I will give an overview of the role gametes play in the evolution of reproductive isolation. I conclude that gametes and reproductive proteins evolve quickly, under strong influence of sexual and sexually antagonistic selection. Gametes are very diverse between species and sperm competition and female cryptic choice can lead to higher fertilization success of sperm from conspecific males. In the hybrid offspring, spermatogenesis can be easily disturbed by small differences in gene expression and this leads to a greater number of genes causing hybrid sterility compared to hybrid inviability among taxa. Following Haldane’s rule, the heterogametic sex is the first to be affected by hybrid incompatibilities, but different mechanisms seem to cause inviability and sterility and taxa with heterogametic males or heterogametic females might be affected differently. I end this review by focusing on one particular model system for studying speciation: the Ficedula flycatchers. Much is known about the ecological factors affecting speciation and hybridization between pied and collared flycatchers and new molecular data give insights into the genetics of speciation, but the role of gametes has not been studied in this system. Studies on gamete divergence and hybrid gamete production in the flycatchers will allow us to get a better idea of the role of gametes in speciation in a wild organism with homogametic males.

  • 1233.
    Ålund, Murielle
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Michigan State Univ, Dept Integrat Biol, Giltner Hall 362, E Lansing, MI 48825 USA.
    Persson Schmiterlöw, Siri
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    McFarlane, S. Eryn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Edinburgh, Inst Evolutionary Biol, Charlotte Auerbach Rd, Edinburgh EH9 3FL, Midlothian, Scotland.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Optimal sperm length for high siring success depends on forehead patch size in collared flycatchers2018In: Behavioral Ecology, ISSN 1045-2249, E-ISSN 1465-7279, Vol. 29, no 6, p. 1436-1443Article in journal (Refereed)
    Abstract [en]

    Dominance over rivals, sexual attractiveness, and highly efficient ejaculates are 3 important contributors of male fertilization success but theories about how primary and secondary sexual characters may co-evolve largely remain to be tested. We investigated how variation in a sexual signal (forehead patch size) and sperm morphology jointly affected siring success of 70 males in a natural population of collared flycatchers. We show that the optimal sperm length to attain high relative fertilization success depended on the size of a male's secondary sexual character. Males with small forehead patches sired more offspring in their nest when they produced long sperm and vice-versa. These results are not compatible with theories based on simple relationships between display traits and sperm "quality" but imply that the optimal fertilization strategy (and hence optimal sperm traits) differs between males even in a predominantly socially monogamous population with moderate extra-pair paternity rates. Thus, a better knowledge of the complex chain of behavioural interactions between the sexes and their gametes is needed for a complete understanding of how sexual selection operates in nature.

  • 1234.
    Ålund, Murielle
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Persson-Schmitterlöw, Siri
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    McFarlane, S. Eryn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Revisiting the definition of “sperm quality”: selection on sperm length depends on a male’s attractiveness and dominance in wild collared flycatchersManuscript (preprint) (Other academic)
    Abstract [en]

    Dominance over rivals, sexual attractiveness and highly efficient ejaculates are all known to be essential for male fertilization success but the theories of how primary and secondary sexual characters may co-evolve largely remain to be tested. Here, we measure sperm morphology in 131 wild-caught collared flycatchers over a four-year period and investigate the links between male display traits, sperm characteristics and siring success among 425 offspring sired by 71 of these males. We show that the optimal sperm length to attain high relative fertilization success depends on the size of a male’s secondary sexual character. Males with small ornaments sire more offspring in their own nest when they produce long sperm and vice-versa. These results are not compatible with theories based on simple relationships between secondary sexual traits and sperm “quality” but imply that the optimal fertilization strategy (and hence optimal sperm traits) differ between males even in a predominantly socially monogamous population with moderate extra-pair copulation rates. Thus, a better knowledge of the complex chain of behavioural interactions between the sexes and their gametes is needed for a complete understanding of how sexual selection operates in nature.

  • 1235.
    Ålund, Murielle
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Whittington, Emma
    Center for Reproductive Evolution, 248 Life Sciences Complex, Syracuse, NY 13244, USA.
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Borziak, Kirill
    Center for Reproductive Evolution, 248 Life Sciences Complex, Syracuse, NY 13244, USA.
    Jones, Williams
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    McFarlane, S. Eryn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Mugal, Carina F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Wang, Mi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Wheatcroft, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Xu, Luohao
    University of Vienna, Austria.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Immler, Simone
    School of Biological Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
    Dorus, Steve
    Center for Reproductive Evolution, 248 Life Sciences Complex, Syracuse, NY 13244, USA.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Reproductive -omics of a wild avian speciation model unveils candidate genes for gamete interactionManuscript (preprint) (Other academic)
    Abstract [en]

    The complex nature of interspecific interactions contributing to reproductive isolation means that we still know little about their molecular basis. Male reproductive traits are notorious for their fast evolution at the phenotypic and genotypic level, and divergence in components of the ejaculate can lead to incompatibilities between closely related species. Making use of recent advances of molecular tools and the extensive knowledge on the biology and ecology of young sister species, here the pied (Ficedula hypoleuca) and collared flycatcher (F. albicollis), allows the identification of candidate phenotypes and the underlying genotypes maintaining species boundaries. Pied flycatcher females can avoid costly production of sterile hybrids when mated to collared flycatchers by cryptically favouring conspecific sperm. Here, we describe the testes transcriptome and sperm proteome of both species, confirm the complexity of avian sperm development and functions and identify several candidate genes for interactions between sperm and the female reproductive tract, using multiple independent measures of divergence between the species. We show that divergence at the transcriptional and translational levels can potentially lead to the evolution of reproductive incompatibilities despite low levels of sequence divergence, and suggest that integrating several -omics techniques with knowledge of the biology of naturally hybridizing species will greatly improve our understanding of the molecular basis of speciation in the near future. 

  • 1236.
    Ålund née Podevin, Murielle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sex, Sperm and Speciation: On sexual selection and fertility in hybridizing flycatchers2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Sexual reproduction entails complex co-evolution between the sexes, necessary for successful fertilization, ensuring individual and population-level fitness. Interfertility is the main criterion for species definition and understanding speciation requires detailed studies of reproductive barriers. However, many studies on reproductive barriers are constrained to infer evolutionary processes from patterns. In this thesis, I focus on a hybrid zone between collared and pied flycatchers (Ficedula albicollis and hypoleuca) on the island of Öland, and a trait that is essential for fertilization: sperm. Long-term monitoring of these species, combined with recent advances in molecular tools, allow me to study how complex on-going intersexual and interspecific interactions influence reproductive isolation in this young hybrid zone. I start by exploring the links between pre- and postmating sexual selection within collared flycatchers (paper I and II). I show that secondary sexual characters and indirect mate-choice benefits are tightly linked to physiology (paper I), and that a male’s attractiveness and dominance status dictate which sperm traits are optimal, as a male’s fertilization success depends on an interaction between sperm and display traits (paper II). I then report a source of strong postzygotic isolation between recently diverged collared and pied flycatchers: impaired spermatogenesis resulting in absence of mature sperm cells in hybrid males (paper III). I show however that pied flycatcher females, who are most exposed to hybridization, can mitigate these costs through mechanisms of cryptic female choice impairing heterospecific sperm performance, allowing them to bias paternity towards pure-species offspring (paper IV). Finally, by exploring the testes transcriptomes and sperm proteomes of both species, I highlight the importance of gene and protein regulation mechanisms in facilitating phenotypic divergence between these species (paper V). Thus, my thesis reveals complex interactions between primary and secondary sexual characters in a wild bird and suggests that mechanisms of sexual selection are tightly linked to essential physiological functions. I also show that genetic incompatibilities can evolve rapidly despite low genome-wide levels of divergence but that divergence in regulatory regions and proteins potentially allows fast evolution of molecular mechanisms impairing or preventing costly heterospecific fertilization. 

    List of papers
    1. Sexual selection affects climate adaptation in collared flycatchers
    Open this publication in new window or tab >>Sexual selection affects climate adaptation in collared flycatchers
    2017 (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The role of sexual selection in climate adaptation is debated. We tested whether sexual selection has the potential to speed up adaptation to thermal conditions in a natural population of collared flycatchers. Based on a three-year cross-fostering experiment, we found that the size of a sexually selected trait predicted offspring metabolic rate: male collared flycatchers with large forehead patches sired offspring with low metabolic rate regardless of the ambient temperature. Thus, there was a stable significant relationship between forehead patch size of genetic fathers and offspring metabolic rate. Nestlings with high metabolic rate experienced a survival advantage when growing under warm temperatures, while the opposite was true in cold environments. Our study shows that females can modulate their offspring’s physiology through mate choice, and that sexual selection can thus affect climate adaptation.

    Keywords
    sexual selection, climate adaptation, resting metabolic rate, Ficedula flycatcher, secondary sexual character, physiology
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-322788 (URN)
    Available from: 2017-07-30 Created: 2017-07-30 Last updated: 2017-07-30
    2. Revisiting the definition of “sperm quality”: selection on sperm length depends on a male’s attractiveness and dominance in wild collared flycatchers
    Open this publication in new window or tab >>Revisiting the definition of “sperm quality”: selection on sperm length depends on a male’s attractiveness and dominance in wild collared flycatchers
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Dominance over rivals, sexual attractiveness and highly efficient ejaculates are all known to be essential for male fertilization success but the theories of how primary and secondary sexual characters may co-evolve largely remain to be tested. Here, we measure sperm morphology in 131 wild-caught collared flycatchers over a four-year period and investigate the links between male display traits, sperm characteristics and siring success among 425 offspring sired by 71 of these males. We show that the optimal sperm length to attain high relative fertilization success depends on the size of a male’s secondary sexual character. Males with small ornaments sire more offspring in their own nest when they produce long sperm and vice-versa. These results are not compatible with theories based on simple relationships between secondary sexual traits and sperm “quality” but imply that the optimal fertilization strategy (and hence optimal sperm traits) differ between males even in a predominantly socially monogamous population with moderate extra-pair copulation rates. Thus, a better knowledge of the complex chain of behavioural interactions between the sexes and their gametes is needed for a complete understanding of how sexual selection operates in nature.

    Keywords
    sperm morphology, secondary sexual character, mating strategy, fertilization success, Ficedula flycatcher, extra-pair copulation
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-326808 (URN)
    Available from: 2017-07-30 Created: 2017-07-30 Last updated: 2017-07-30
    3. Low fertility of wild hybrid male flycatchers despite recent divergence
    Open this publication in new window or tab >>Low fertility of wild hybrid male flycatchers despite recent divergence
    2013 (English)In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 9, no 3, article id 20130169Article in journal (Refereed) Published
    Abstract [en]

    Postzygotic isolation may be important for maintaining species boundaries, particularly when premating barriers are incomplete. Little is known about the course of events leading from minor environmental mismatches affecting hybrid fitness to severe genetic incompatibilities causing sterility or inviability. We investigated whether reduced reproductive success of hybrid males was caused by suboptimal sperm traits or by more severe genetic incompatibilities in a hybrid zone of pied (Ficedula hypoleuca) and collared flycatchers (F. albicollis) on the island of Oland, Sweden. About 4 per cent hybridization is observed in this population and all female hybrids are sterile. We found no sperm in the ejaculates of most sampled hybrid males, and sperm with abnormal morphology in two hybrids. Furthermore, none of the hybrids sired any offspring because of high levels of hatching failure and extra-pair paternity in their nests. These results from a natural hybrid zone suggest that the spermatogenesis of hybrid males may become disrupted despite little genetic divergence between the parental species.

    Keywords
    hybrid, sterility-infertility, flycatcher, sperm, postzygotic incompatibility
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-202341 (URN)10.1098/rsbl.2013.0169 (DOI)000318762300035 ()
    Available from: 2013-06-24 Created: 2013-06-24 Last updated: 2017-12-06Bibliographically approved
    4. Females discriminate against heterospecific sperm in a natural hybrid zone
    Open this publication in new window or tab >>Females discriminate against heterospecific sperm in a natural hybrid zone
    Show others...
    2016 (English)In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, no 8, p. 1844-1855Article in journal (Refereed) Published
    Abstract [en]

    When hybridization is maladaptive, species-specific mate preferences are selectively favored, but low mate availability may constrain species-assortative pairing. Females paired to heterospecifics may then benefit by copulating with multiple males and subsequently favoring sperm of conspecifics. Whether such mechanisms for biasing paternity toward conspecifics act as important reproductive barriers in socially monogamous vertebrate species remains to be determined. We use a combination of long-term breeding records from a natural hybrid zone between collared and pied flycatchers (Ficedula albicollis and F. hypoleuca), and an in vitro experiment comparing conspecific and heterospecific sperm performance in female reproductive tract fluid, to evaluate the potential significance of female cryptic choice. We show that the females most at risk of hybridizing (pied flycatchers) frequently copulate with multiple males and are able to inhibit heterospecific sperm performance. The negative effect on heterospecific sperm performance was strongest in pied flycatcher females that were most likely to have been previously exposed to collared flycatcher sperm. We thus demonstrate that a reproductive barrier acts after copulation but before fertilization in a socially monogamous vertebrate. While the evolutionary history of this barrier is unknown, our results imply that there is opportunity for it to be accentuated via a reinforcement-like process.

    Keywords
    Cryptic female choice, hybrid zones, postcopulatory prezygotic barriers, reinforcement, speciation, sexual selection
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-303102 (URN)10.1111/evo.12986 (DOI)000381205700013 ()
    Funder
    Swedish Research Council, 621-2012-3722The Royal Swedish Academy of Sciences
    Available from: 2016-10-05 Created: 2016-09-15 Last updated: 2018-08-10Bibliographically approved
    5. Reproductive -omics of a wild avian speciation model unveils candidate genes for gamete interaction
    Open this publication in new window or tab >>Reproductive -omics of a wild avian speciation model unveils candidate genes for gamete interaction
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The complex nature of interspecific interactions contributing to reproductive isolation means that we still know little about their molecular basis. Male reproductive traits are notorious for their fast evolution at the phenotypic and genotypic level, and divergence in components of the ejaculate can lead to incompatibilities between closely related species. Making use of recent advances of molecular tools and the extensive knowledge on the biology and ecology of young sister species, here the pied (Ficedula hypoleuca) and collared flycatcher (F. albicollis), allows the identification of candidate phenotypes and the underlying genotypes maintaining species boundaries. Pied flycatcher females can avoid costly production of sterile hybrids when mated to collared flycatchers by cryptically favouring conspecific sperm. Here, we describe the testes transcriptome and sperm proteome of both species, confirm the complexity of avian sperm development and functions and identify several candidate genes for interactions between sperm and the female reproductive tract, using multiple independent measures of divergence between the species. We show that divergence at the transcriptional and translational levels can potentially lead to the evolution of reproductive incompatibilities despite low levels of sequence divergence, and suggest that integrating several -omics techniques with knowledge of the biology of naturally hybridizing species will greatly improve our understanding of the molecular basis of speciation in the near future. 

    Keywords
    Reproductive isolation, cryptic female choice, sperm, proteomics, transcriptomics, Ficedula flycatchers
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-326809 (URN)
    Available from: 2017-07-30 Created: 2017-07-30 Last updated: 2017-07-30
  • 1237.
    Ödeen, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Håstad, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Alström, Per
    Evolution of ultraviolet vision in the largest avian radiation: the passerines2011In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 11, p. 313-Article in journal (Refereed)
    Abstract [en]

    Background: Interspecific variation in avian colour vision falls into two discrete classes: violet sensitive (VS) and ultraviolet sensitive (UVS). They are characterised by the spectral sensitivity of the most shortwave sensitive of the four single cones, the SWS1, which is seemingly under direct control of as little as one amino acid substitution in the cone opsin protein. Changes in spectral sensitivity of the SWS1 are ecologically important, as they affect the abilities of birds to accurately assess potential mates, find food and minimise visibility of social signals to predators. Still, available data have indicated that shifts between classes are rare, with only four to five independent acquisitions of UV sensitivity in avian evolution. Results: We have classified a large sample of passeriform species as VS or UVS from genomic DNA and mapped the evolution of this character on a passerine phylogeny inferred from published molecular sequence data. Sequencing a small gene fragment has allowed us to trace the trait changing from one stable state to another through the radiation of the passeriform birds. Their ancestor is hypothesised to be UVS. In the subsequent radiation, colour vision changed between UVS and VS at least eight times. Conclusions: The phylogenetic distribution of SWS1 cone opsin types in Passeriformes reveals a much higher degree of complexity in avian colour vision evolution than what was previously indicated from the limited data available. Clades with variation in the colour vision system are nested among clades with a seemingly stable VS or UVS state, providing a rare opportunity to understand how an ecologically important trait under simple genetic control may co-evolve with, and be stabilised by, associated traits in a character complex.

  • 1238.
    Östman, Örjan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Wengström, Åsa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Gradin, Ulf
    Wissman, Jorgen
    Schafer, Martina
    Lundström, Jan O.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lower abundance of flood water mosquito larvae in managed wet meadows in the lower Dalalven floodplains, Sweden2015In: Wetlands Ecology and Management, ISSN 0923-4861, E-ISSN 1572-9834, Vol. 23, no 2, p. 257-267Article in journal (Refereed)
    Abstract [en]

    To investigate the effect of vegetation management on mosquito abundance on the floodplains of the River Dalalven, central Sweden, we studied abundance of floodwater mosquito larvae (mainly Aedes sticticus) using a paired design, comparing flooded wet meadows that were mowed or grazed by cattle to those that were unmanaged. Two floods occurred during the study year (2012), the first in conjunction with the spring flood in May and the second after heavy rainfall in July. We used the standard mosquito dipper to estimate mosquito larval abundance along transects from the shore towards permanent water on each meadow. The number of mosquito larvae was on average lower in each managed wet meadow compared to the corresponding unmanaged meadow, both in May (71 % reduction, SD = 28 %) and in July (35 % reduction, SD = 79 %). However, there was substantial variation in the difference between managed and unmanaged meadows among pairs. We measured water depth, temperature, estimated proportion of open water surface, soil nutrient levels and micro-topology. Some of the variation in larval abundance could be explained by differences in local conditions. Mosquito larval abundance increased with nutrient levels and occurrence of tussocks, and decreased with water depth and percentage open water surface, especially among unmanaged wetlands. This study suggests that mowing or grazing may reduce the abundance of floodwater mosquito larvae in flooded wet meadows. In addition, vegetation management seem to have the greatest effect on mosquito larval abundance in nutrient-rich wet meadows where tussocks are abundant.

  • 1239.
    Šupraha, Luka
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Phenotypic evolution and adaptive strategies in marine phytoplankton (Coccolithophores)2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Coccolithophores are biogeochemically important marine algae that interact with the carbon cycle through photosynthesis (CO2 sink), calcification (CO2 source) and burial of carbon into oceanic sediments. The group is considered susceptible to the ongoing climate perturbations, in particular to ocean acidification, temperature increase and nutrient limitation. The aim of this thesis was to investigate the adaptation of coccolithophores to environmental change, with the focus on temperature stress and nutrient limitation. The research was conducted in frame of three approaches: experiments testing the physiological response of coccolithophore species Helicosphaera carteri and Coccolithus pelagicus to phosphorus limitation, field studies on coccolithophore life-cycles with a method comparison and an investigation of the phenotypic evolution of the coccolithophore genus Helicosphaera over the past 15 Ma. Experimental results show that the physiology and morphology of large coccolithophores are sensitive to phosphorus limitation, and that the adaptation to low-nutrient conditions can lead to a decrease in calcification rates. Field studies have contributed to our understanding of coccolithophore life cycles, revealing complex ecological patterns within the Mediterranean community which are seemingly regulated by seasonal, temperature-driven environment changes. In addition, the high-throughput sequencing (HTS) molecular method was shown to provide overall good representation of coccolithophore community composition. Finally, the study on Helicosphaera evolution showed that adaptation to decreasing CO2 in higher latitudes involved cell and coccolith size decrease, whereas the adaptation in tropical ecosystems also included a physiological decrease in calcification rates in response to nutrient limitation. This thesis advanced our understanding of coccolithophore adaptive strategies and will improve our predictions on the fate of the group under ongoing climate change.

    List of papers
    1. Eco-physiological adaptation shapes the response of calcifying algae to nutrient limitation
    Open this publication in new window or tab >>Eco-physiological adaptation shapes the response of calcifying algae to nutrient limitation
    2015 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 16499Article in journal (Refereed) Published
    Abstract [en]

    The steady increase in global ocean temperature will most likely lead to nutrient limitation in the photic zone. This will impact the physiology of marine algae, including the globally important calcifying coccolithophores. Understanding their adaptive patterns is essential for modelling carbon production in a low-nutrient ocean. We investigated the physiology of Helicosphaera carteri, a representative of the abundant but under-investigated flagellated functional group of coccolithophores. Two strains isolated from contrasting nutrient regimes (South Atlantic and Mediterranean Sea) were grown in phosphorus-replete and phosphorus-limited batch cultures. While growing exponentially in a phosphorus-replete medium, the Mediterranean strain exhibited on average 24% lower growth rate, 36% larger coccosphere volume and 21% lower particulate inorganic carbon (PIC) production than the Atlantic strain. Under phosphorus limitation, the same strain was capable of reaching a 2.6 times higher cell density than the Atlantic strain due to lower phosphorus requirements. These results suggest that local physiological adaptation can define the performance of this species under nutrient limitation.

    National Category
    Ecology Cell Biology Evolutionary Biology Earth and Related Environmental Sciences
    Identifiers
    urn:nbn:se:uu:diva-253354 (URN)10.1038/srep16499 (DOI)000364487200001 ()26560531 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationThe Royal Swedish Academy of Sciences
    Available from: 2015-05-26 Created: 2015-05-26 Last updated: 2017-12-04Bibliographically approved
    2. High temperature decreases the PIC/POC ratio and increases phosphorus requirements in Coccolithus pelagicus (Haptophyta)
    Open this publication in new window or tab >>High temperature decreases the PIC/POC ratio and increases phosphorus requirements in Coccolithus pelagicus (Haptophyta)
    Show others...
    2014 (English)In: Biogeosciences, ISSN 1726-4170, E-ISSN 1726-4189, Vol. 11, p. 3531-3545Article in journal (Refereed) Published
    Abstract [en]

    Rising ocean temperatures will likely increase stratification of the water column and reduce nutrient input into the photic zone. This will increase the likelihood of nutrient limitation in marine microalgae, leading to changes in the abundance and composition of phytoplankton communities, which in turn will affect global biogeochemical cycles. Calcifying algae, such as coccolithophores, influence the carbon cycle by fixing CO2 into particulate organic carbon through photosynthesis (POC production) and into particulate inorganic carbon through calcification (PIC production). As calcification produces a net release of CO2, the ratio of PIC to POC production determines whether coccolithophores act as a source (high PIC / POC) or a sink (low PIC / POC) of atmospheric CO2. We studied the effect of phosphorus (P-) limitation and high temperature on the physiology and the PIC / POC ratio of two subspecies of Coccolithus pelagicus. This large and heavily calcified species is a major contributor to calcite export from the photic zone into deep-sea reservoirs. Phosphorus limitation did not influence exponential growth rates in either subspecies, but P-limited cells had significantly lower cellular P-content. One of the subspecies was subjected to a 5 °C temperature increase from 10 °C to 15 °C, which did not affect exponential growth rates either, but nearly doubled cellular P-content under both high and low phosphate availability. This temperature increase reduced the PIC / POC ratio by 40–60%, whereas the PIC / POC ratio did not differ between P-limited and nutrient-replete cultures when the subspecies were grown near their respective isolation temperature. Both P-limitation and elevated temperature significantly increased coccolith malformations. Our results suggest that a temperature increase may intensify P-limitation due to a higher P-requirement to maintain growth and POC production rates, possibly reducing abundances in a warmer ocean. Under such a scenario C. pelagicus may decrease its calcification rate relative to photosynthesis, thus favouring CO2 sequestration over release. It seems unlikely that P-limitation by itself causes changes in the PIC / POC ratio in this species.

    Keywords
    coccolithophores, culture experiments, phosphate limitation, calcification
    National Category
    Natural Sciences
    Research subject
    Biology; Earth Science with specialization in Environmental Analysis
    Identifiers
    urn:nbn:se:uu:diva-220830 (URN)10.5194/bg-11-3531-2014 (DOI)000339265800008 ()
    Available from: 2014-03-20 Created: 2014-03-20 Last updated: 2017-12-05Bibliographically approved
    3. Phosphorus availability modifies carbon production in Coccolithus pelagicus (Haptophyta)
    Open this publication in new window or tab >>Phosphorus availability modifies carbon production in Coccolithus pelagicus (Haptophyta)
    Show others...
    2015 (English)In: Journal of Experimental Marine Biology and Ecology, ISSN 0022-0981, E-ISSN 1879-1697, Vol. 472, p. 24-31Article in journal (Refereed) Published
    Abstract [en]

    Abstract The coccolithophore Coccolithus pelagicus (Wallich) Schiller fixes CO2 into particulate organic carbon (POC) through photosynthesis and into particulate inorganic carbon (PIC) in the form of calcite. To examine the role of phosphorus (P) availability in the production of POC and PIC, C. pelagicus subsp. braarudii (Gaarder) Geisen et al. was grown in semi-continuous cultures at three initial phosphate concentrations (P-replete, 1, and 0.5 μM [P]). Reduced P-availability (1 and 0.5 μM [P]) decreased POC production, while PIC production only decreased when phosphate concentrations became growth limiting (0.5 μM [P]). This decrease has not been observed previously in batch cultures, highlighting the inadequacy of the batch culture approach with regard to determining carbon production. The reduction in growth rate by 50% at 0.5 μM [P] was accompanied by a doubling in cell volume (and POC). PIC production was halved, resulting in a lowered PIC to POC ratio. The average number of coccoliths per cell (and PIC content) remained the same among treatments, despite the significant change in cell size. Our data suggest that POC production in C. pelagicus is more sensitive towards a moderate reduction in phosphorus availability than PIC production. Once phosphorus availability limits cell division, however, phosphorus resources are invested into POC rather than PIC production. This reduces cell density and sinking rates, indicating that coccoliths do not act as ballast for reaching deeper nutrient-rich layers under nutrient limitation.

    Keywords
    Calcification, Carbon production, Coccolithus pelagicus, Phosphorus limitation, Semi-continuous culture
    National Category
    Microbiology Cell Biology
    Identifiers
    urn:nbn:se:uu:diva-301334 (URN)
    Available from: 2016-08-19 Created: 2016-08-19 Last updated: 2017-11-28
    4. Observations on the life cycle and ecology of Acanthoica quattrospina Lohmann from a Mediterranean estuary
    Open this publication in new window or tab >>Observations on the life cycle and ecology of Acanthoica quattrospina Lohmann from a Mediterranean estuary
    2014 (English)In: Journal of Nannoplankton Research, ISSN 1210-8049, Vol. 34, no SI, p. 49-56Article in journal (Refereed) Published
    National Category
    Ecology Biological Systematics
    Identifiers
    urn:nbn:se:uu:diva-253353 (URN)
    Conference
    INA Workshop on Extant Coccolithophores research
    Available from: 2015-05-26 Created: 2015-05-26 Last updated: 2016-09-13Bibliographically approved
    5. Coccolithophore life-cycle dynamics in a coastal Mediterranean ecosystem: seasonality and species-specific patterns
    Open this publication in new window or tab >>Coccolithophore life-cycle dynamics in a coastal Mediterranean ecosystem: seasonality and species-specific patterns
    2016 (English)In: Journal of Plankton Research, ISSN 0142-7873, E-ISSN 1464-3774, Vol. 38, no 5, p. 1178-1193Article in journal (Refereed) Published
    Abstract [en]

    Coccolithophores (calcifying haptophyte algae) commonly exhibit a heteromorphic life cycle, alternating between morphologically distinct heterococcolith (diploid) and holococcolith (haploid) phases. The prevalence of each life phase in a coccolithophore community defines its overall ecological and biogeochemical performance due to differences in physiology, biomass and calcification. The main drivers of life-cycle dynamics and ecological preferences of the two life-phases are still unclear and field data of high taxonomic resolution are needed. We investigated the distribution and abundance patterns of the life-phases of 14 coccolithophore species. The study was conducted along the strong environmental gradients of the Krka River estuary (Eastern Adriatic Sea) during winter (February) and summer (July) 2013. The results reveal characteristic life-phase seasonality with an overall dominance of the heterococcolith phase during winter and a holococcolith phase during summer. However, we also detected exceptions to the strictly seasonal patterns as well as species-specific ecological preferences. Our findings provide new insights into coccolithophore life-phase dynamics in the Mediterranean Sea that will further advance the understanding of ecology and evolution of the group.

    National Category
    Earth and Related Environmental Sciences Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-302897 (URN)10.1093/plankt/fbw061 (DOI)000384135000004 ()
    Available from: 2016-09-12 Created: 2016-09-12 Last updated: 2019-01-25Bibliographically approved
    6. Haptophyte diversity and vertical distribution explored by 18S and 28S ribosomal RNA gene metabarcoding and scanning electron microscopy
    Open this publication in new window or tab >>Haptophyte diversity and vertical distribution explored by 18S and 28S ribosomal RNA gene metabarcoding and scanning electron microscopy
    2017 (English)In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 64, no 4, p. 514-532Article in journal (Refereed) Published
    Abstract [en]

    Haptophyta encompasses more than 300 species of mostly marine pico- and nanoplanktonic flagellates. Our aims were to investigate the Oslofjorden haptophyte diversity and vertical distribution by metabarcoding, and to improve the approach to study haptophyte community composition, richness and proportional abundance by comparing two rRNA markers and scanning electron microscopy (SEM). Samples were collected in August 2013 at the Outer Oslofjorden, Norway. Total RNA/cDNA was amplified by haptophyte-specific primers targeting the V4 region of the 18S, and the D1-D2 region of the 28S rRNA. Taxonomy was assigned using curated haptophyte reference databases and phylogenetic analyses. Both marker genes showed Chrysochromulinaceae and Prymnesiaceae to be the families with highest number of Operational Taxonomic Units (OTUs), as well as proportional abundance. The 18S rRNA data setalso contained OTUs assigned to eight supported and defined clades consisting of environmental sequences only, possibly representing novel lineages from family to class. We also recorded new species for the area. Comparing coccolithophores by SEM with metabarcoding shows a good correspondence with the 18S rRNA gene proportional abundances. Our results contribute to link morphological and molecular data and 28S to 18S rRNA gene sequences of haptophytes without cultured representatives, and to improve metabarcoding methodology.

    Keywords
    Abundance, coccolithophores, high-throughput sequencing, Oslofjorden, phylogeny, richness
    National Category
    Biological Sciences Biological Systematics Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-302898 (URN)10.1111/jeu.12388 (DOI)000406102000010 ()27973742 (PubMedID)
    Note

    De två första författarna delar förstaförfattarskapet.

    Available from: 2016-09-12 Created: 2016-09-12 Last updated: 2017-11-02Bibliographically approved
    7. Nutrient availability modified the evolution of calcifying algae during the past 15 million years
    Open this publication in new window or tab >>Nutrient availability modified the evolution of calcifying algae during the past 15 million years
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology Earth and Related Environmental Sciences
    Identifiers
    urn:nbn:se:uu:diva-302900 (URN)
    External cooperation:
    Available from: 2016-09-12 Created: 2016-09-12 Last updated: 2016-09-13
  • 1240.
    Šupraha, Luka
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Gerecht, Andrea C.
    Probert, Ian
    Henderiks, Jorijntje
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    The adaptive strategies of coccolithophores and their biogeochemical implications2016Conference paper (Refereed)
  • 1241.
    Šupraha, Luka
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Gerecht, Andrea Cornelia
    Probert, Ian
    Henderiks, Jorijntje
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Eco-physiological adaptation shapes the response of calcifying algae to nutrient limitation2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 16499Article in journal (Refereed)
    Abstract [en]

    The steady increase in global ocean temperature will most likely lead to nutrient limitation in the photic zone. This will impact the physiology of marine algae, including the globally important calcifying coccolithophores. Understanding their adaptive patterns is essential for modelling carbon production in a low-nutrient ocean. We investigated the physiology of Helicosphaera carteri, a representative of the abundant but under-investigated flagellated functional group of coccolithophores. Two strains isolated from contrasting nutrient regimes (South Atlantic and Mediterranean Sea) were grown in phosphorus-replete and phosphorus-limited batch cultures. While growing exponentially in a phosphorus-replete medium, the Mediterranean strain exhibited on average 24% lower growth rate, 36% larger coccosphere volume and 21% lower particulate inorganic carbon (PIC) production than the Atlantic strain. Under phosphorus limitation, the same strain was capable of reaching a 2.6 times higher cell density than the Atlantic strain due to lower phosphorus requirements. These results suggest that local physiological adaptation can define the performance of this species under nutrient limitation.

  • 1242.
    Šupraha, Luka
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Henderiks, Jorijntje
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Nutrient availability modified the evolution of calcifying algae during the past 15 million yearsManuscript (preprint) (Other academic)
22232425 1201 - 1242 of 1242
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