Evolution Letters最新文献

{"title":"Parallel and convergent evolution in genes underlying seasonal migration.","authors":"Luz E Zamudio-Beltrán, Christen M Bossu, Alfredo A Bueno-Hernández, Peter O Dunn, Nicholas D Sly, Christine Rayne, Eric C Anderson, Blanca E Hernández-Baños, Kristen C Ruegg","doi":"10.1093/evlett/qrae064","DOIUrl":"10.1093/evlett/qrae064","url":null,"abstract":"<p><p>Seasonal migration has fascinated scientists and natural historians for centuries. While the genetic basis of migration has been widely studied across different taxa, there is little consensus regarding which genomic regions play a role in the ability to migrate and whether they are similar across species. Here, we examine the genetic basis of intraspecific variation within and between distinct migratory phenotypes in a songbird. We focus on the Common Yellowthroat (<i>Geothlypis trichas</i>) as a model system because the polyphyletic origin of eastern and western clades across North America provides a strong framework for understanding the extent to which there has been parallel or convergent evolution in the genes associated with migratory behavior. First, we investigate genome-wide population genetic structure in the Common Yellowthroat in 196 individuals collected from 22 locations across breeding range. Then, to identify candidate genes involved in seasonal migration, we identify signals of putative selection in replicate comparisons between resident and migratory phenotypes within and between eastern and western clades. Overall, we find wide-spread support for parallel evolution at the genic level, particularly in genes that mediate biological timekeeping. However, we find little evidence of parallelism at the individual SNP level, supporting the idea that there are multiple genetic pathways involved in the modulation of migration.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 2","pages":"189-208"},"PeriodicalIF":3.4,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143796781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hiding in plain sight: the Y chromosome and its reinvigorated role in evolutionary processes.","authors":"Wouter van der Bijl, Judith E Mank","doi":"10.1093/evlett/qrae065","DOIUrl":"10.1093/evlett/qrae065","url":null,"abstract":"<p><p>Recent methodological approaches have expanded our understanding of Y chromosome sequence, revealed unexpected Y diversity, and sparked a growing realization of its importance in evolutionary processes. To fully understand the diversity and importance of the Y chromosome, we suggest the need to move from a holotype Y chromosome sequence, based on a single individual and meant to represent the species, to a thorough understanding of Y chromosome haplotype diversity, its phenotypic implications, and its phylogeographic distribution. Additionally, the Y chromosome may play an important role in two key rules of speciation that have otherwise been attributed to the X, namely Haldane's Rule and the Large-X Effect. Emerging genomic tools and analytical approaches are just now giving us the means to ask how important this small, often forgotten region of the genome is in evolutionary processes.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 2","pages":"165-171"},"PeriodicalIF":3.4,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143796775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heritability and age-dependent changes in genetic variation of telomere length in a wild house sparrow population.","authors":"Heung Ying Janet Chik, Aaron Sibma, Maria-Elena Mannarelli, Natalie Dos Remedios, Mirre J P Simons, Terry Burke, Hannah L Dugdale, Julia Schroeder","doi":"10.1093/evlett/qrae055","DOIUrl":"10.1093/evlett/qrae055","url":null,"abstract":"<p><p>Telomere length (TL) and/or its rate of change are popular biomarkers of senescence, as telomere dynamics are linked with survival and lifespan. However, the evolutionary potential of telomere dynamics has received mixed support in natural populations. To better understand how telomere dynamics evolve, it is necessary to quantify genetic variation in TL and how such variation changes with age. Here, we analyzed 2,083 longitudinal samples from 1,225 individuals across 16 years, collected from a wild, insular house sparrow (<i>Passer domesticus</i>) population with complete life history and genetic relatedness data. Using a series of \"animal\" models, we confirmed that TL changes with age, reflecting senescence in this population. We found TL to be repeatable (14.0%, 95% CrI: 9.1%-19.9%) and heritable (12.3%, 95% CrI: 7.5%-18.2%); and detected a genotype-by-age interaction, meaning that genotypes differ in their rate of change of TL, and additive genetic variance increases at older ages. Our findings provide empirical evidence from a wild population that supports hypotheses explaining the evolution of senescence and highlight the importance of telomere dynamics as a key biomarker of body physiology for the evolution of senescence.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 2","pages":"209-220"},"PeriodicalIF":3.4,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143796772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomics resolves key relationships in <i>Rumex</i> and uncovers a dynamic history of independently evolving sex chromosomes.","authors":"Mark S Hibbins, Joanna L Rifkin, Baharul I Choudhury, Olena Voznesenska, Bianca Sacchi, Meng Yuan, Yunchen Gong, Spencer C H Barrett, Stephen I Wright","doi":"10.1093/evlett/qrae060","DOIUrl":"10.1093/evlett/qrae060","url":null,"abstract":"<p><p>Sex chromosomes have evolved independently many times across eukaryotes. Despite a considerable body of literature on sex chromosome evolution, the causes and consequences of variation in their formation, degeneration, and turnover remain poorly understood. Chromosomal rearrangements are thought to play an important role in these processes by promoting or extending the suppression of recombination on sex chromosomes. Sex chromosome variation may also contribute to barriers to gene flow, limiting introgression among species. Comparative approaches in groups with sexual system variation can be valuable for understanding these questions. <i>Rumex</i> is a diverse genus of flowering plants harboring significant sexual system and karyotypic variation, including hermaphroditic and dioecious clades with XY (and XYY) sex chromosomes. Previous disagreement in the phylogenetic relationships among key species has rendered the history of sex chromosome evolution uncertain. Resolving this history is important for investigating the interplay of chromosomal rearrangements, introgression, and sex chromosome evolution in the genus. Here, we use new transcriptome assemblies from 11 species representing major clades in the genus, along with a whole-genome assembly generated for a key hermaphroditic species. Using phylogenomic approaches, we find evidence for the independent evolution of sex chromosomes across two major clades, and introgression from unsampled lineages likely predating the formation of sex chromosomes in the genus. Comparative genomic approaches revealed high rates of chromosomal rearrangement, especially in dioecious species, with evidence for a complex origin of the sex chromosomes through multiple chromosomal fusions. However, we found no evidence of elevated rates of fusion on the sex chromosomes in comparison with autosomes, providing no support for an adaptive hypothesis of sex chromosome expansion due to sexually antagonistic selection. Overall, our results highlight a complex history of karyotypic evolution in <i>Rumex</i>, raising questions about the role that chromosomal rearrangements might play in the evolution of large heteromorphic sex chromosomes.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 2","pages":"221-235"},"PeriodicalIF":3.4,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143796784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shared genetic architecture links energy metabolism, behavior and starvation resistance along a power-endurance axis.","authors":"Berra Erkosar, Cindy Dupuis, Loriane Savary, Tadeusz J Kawecki","doi":"10.1093/evlett/qrae062","DOIUrl":"10.1093/evlett/qrae062","url":null,"abstract":"<p><p>Shared developmental, physiological, and molecular mechanisms can generate strong genetic covariances across suites of traits, constraining genetic variability, and evolvability to certain axes in multivariate trait space (\"variational modules\" or \"syndromes\"). Such trait suites will not only respond jointly to selection; they will also covary across populations that diverged from one another by genetic drift. We report evidence for such a genetically correlated trait suite that links traits related to energy metabolism along a \"power-endurance\" axis in <i>Drosophila melanogaster.</i> The \"power\" pole of the axis is characterized by high potential for energy generation and expenditure-high expression of glycolysis and TCA cycle genes, high abundance of mitochondria, and high spontaneous locomotor activity. The opposite \"endurance\" pole is characterized by high triglyceride (fat) reserves, locomotor endurance, and starvation resistance (and low values of traits associated with the \"power\" pole). This trait suite also aligns with the first principal component of metabolome; the \"power\" direction is characterized by low levels of trehalose (blood sugar) and high levels of some amino acids and their derivatives, including creatine, a compound known to facilitate energy production in muscles. Our evidence comes from six replicate \"Selected\" populations adapted to a nutrient-poor larval diet regime during 250 generations of experimental evolution and six \"Control\" populations evolved in parallel on a standard diet regime. We found that, within each of these experimental evolutionary regimes, the above traits strongly covaried along this \"power-endurance\" axis across replicate populations which diversified by drift, indicating a shared genetic architecture. The two evolutionary regimes also drove divergence along this axis, with Selected populations on average displaced towards the \"power\" direction compared to Controls. Aspects of this \"power-endurance\" axis resemble the \"pace of life\" syndrome and the \"thrifty phenotype\"; it may have evolved as part of a coordinated organismal response to nutritional conditions.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 1","pages":"150-162"},"PeriodicalIF":3.4,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11790217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Does metabolic rate influence genome-wide amino acid composition in the course of animal evolution?","authors":"Wei Wang, De-Xing Zhang","doi":"10.1093/evlett/qrae061","DOIUrl":"10.1093/evlett/qrae061","url":null,"abstract":"<p><p>Natural selection is believed to shape amino acid usage of the proteome by minimizing the energy cost of protein biosynthesis. Although this hypothesis explains well the amino acid frequency (AA_frequency) difference among the 20 common amino acids within a given genome (species), whether it is applicable to cross-species difference remains to be inspected. Here, we proposed and tested a \"metabolic rate hypothesis,\" which suggests that metabolic rate impacts genome-wide AA_frequency, considering that the energy allocated to protein biosynthesis is under selection pressure due to metabolic rate constraint. We performed integrated phylogenetic comparative analyses on proteomic sequence and metabolic rate data of 166 species covering 130 eumetazoan orders. We showed that resting metabolic rate (RMR) was significantly linked to AA_frequency variation across animal lineages, with a contribution comparable to or greater than genomic traits such as GC content and codon usage bias. Consistent with the metabolic rate hypothesis, low-energy-cost amino acids are observed to be more likely at higher frequency in animal species with high (residual) metabolic rate. Correlated evolution of RMR and AA_frequency was further inferred being driven by adaptation. The relationship between RMR and AA_frequency varied greatly among amino acids, most likely reflecting a trade-off among various interacting factors. Overall, there exists no \"one-size-fits-all\" predictor for AA_frequency, and integrated investigation of multilevel traits is indispensable for a fuller understanding of AA_frequency variation and evolution in animal.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 1","pages":"137-149"},"PeriodicalIF":3.4,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11790228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anisogamy and sex roles: a commentary.","authors":"Judit Mokos, István Scheuring, András Liker, Robert P Freckleton, Tamás Székely","doi":"10.1093/evlett/qrae058","DOIUrl":"10.1093/evlett/qrae058","url":null,"abstract":"<p><p>The origin and maintenance of sex differences in reproductive behavior (often labeled sex roles) have remained controversial topics, and recent meta-analyses and theoretical models have helped to elucidate the processes that generate diverse sex roles. We are glad to see that our study (Mokos et al., 2021) generated a healthy debate, and in agreement with recent commentaries (Janicke, 2024; Lehtonen & Parker, 2024) we call for a more comprehensive approach to understanding sex role evolution.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"8 6","pages":"761-763"},"PeriodicalIF":3.4,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11641848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A shared developmental genetic basis for sexually antagonistic male and female adaptations in the toothed water strider.","authors":"Claudia Pruvôt, David Armisén, Pascale Roux, Göran Arnqvist, Locke Rowe, Arild Husby, Abderrahman Khila","doi":"10.1093/evlett/qrae056","DOIUrl":"10.1093/evlett/qrae056","url":null,"abstract":"<p><p>Sexual conflict can drive the divergence of male and female phenotypes and cross-species comparative analyses have documented patterns of correlated evolution of sex-specific traits that promote the evolutionary interests of the sexes. However, male-female coevolution can be highly dynamic, particularly if the male and female traits share an underlying genetic program. Here, we use water striders, a well-studied model system for sexually antagonistic coevolution, and ask whether sex-specific phenotypic adaptations covary across populations and whether they share a common developmental genetic basis. Using comparative analyses both at the population and species levels, we document an association between a derived male mate-grasping trait and a putative female antigrasping counteradaptation in the toothed water strider <i>Gerris odontogaster</i>. Interestingly, in several populations where males have partly lost their derived grasping trait, females have also reduced their antigrasping adaptation. We used RNAi to show that these male and female traits are both linked to a common developmental genetic program involving Hox- and sex-determination genes, despite the fact that they are different structures on different abdominal segments. Our work illustrates the dynamic nature of sexually antagonistic coevolution and suggests that the pleiotropic nature of developmental genetic programs can blur the distinction between inter- and intralocus genetic conflict.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 1","pages":"13-23"},"PeriodicalIF":3.4,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11790218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterizing the evolution of defense in a tripartite marine symbiosis using adaptive dynamics.","authors":"Prerna Singh, Marjolein Bruijning, Gavriela D Carver, Mohamed S Donia, Charlotte Jessica E Metcalf","doi":"10.1093/evlett/qrae052","DOIUrl":"10.1093/evlett/qrae052","url":null,"abstract":"<p><p>The evolution and maintenance of symbiotic systems remains a fascinating puzzle. While the coevolutionary dynamics of bipartite (host-symbiont) systems are well-studied, the dynamics of more complex systems have only recently garnered attention with increasing technological advances. We model a tripartite system inspired by the marine symbiotic relationship between the alga <i>Bryopsis</i> sp., its intracellular defensive bacterial symbiont \"<i>Candidatus</i> Endobryopsis kahalalidifaciens,\" which produces a toxin that protects the alga against fish herbivores, and the sea-slug <i>Elysia rufescens</i> (Zan et al., 2019), which is not deterred by the toxin. We disentangle the role of selection on different actors within this system by investigating evolutionary scenarios where defense evolves as (i) a host-controlled trait that reduces algal reproductive ability; (ii) a symbiont-controlled trait that impacts symbiont transmission; and (iii) a trait jointly controlled by both host and symbiont. Optimal investment in defensive toxins varies based on the characteristics of the host, symbiont, and sea slug; and evolutionary trajectories are modulated by trade-off shape, i.e., a strongly decelerating trade-off between defense and symbiont transmission can drive symbiont diversification via evolutionary branching. Increasing slug herbivory reduces host investment in defense to favor reproduction, while symbiont investment in defense first declines and then increases as host density declines to the degree that horizontal symbiont transmission is no longer beneficial. Increasing vertical transmission selects for reduced defense by the host when it evolves as a jointly controlled trait, as a result of investment by the symbiont. Our theoretical exploration of the evolution of defensive symbiosis in scenarios involving interactions with multiple herbivores provides a first window into the origin and maintenance of the <i>Bryopsis</i> sp. system, and adds another piece to the puzzle of the evolution of symbiotic systems.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 1","pages":"105-114"},"PeriodicalIF":3.4,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11790223/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic structure and common ancestry expose the dingo-dog hybrid myth.","authors":"Andrew R Weeks, Peter Kriesner, Nenad Bartonicek, Anthony van Rooyen, Kylie M Cairns, Collin W Ahrens","doi":"10.1093/evlett/qrae057","DOIUrl":"10.1093/evlett/qrae057","url":null,"abstract":"<p><p>The evolutionary history of canids has been shown to be complex, with hybridization and domestication confounding our understanding of speciation among various canid lineages. The dingo is a recent canid lineage that was completely isolated from other canids for over 5000 years on the Australian mainland, but the introduction of domestic dogs in 1788 has placed doubt on its independence, with recent studies highlighting hybridization between dingoes and domestic dogs. Using genomic single nucleotide polymorphism data from 434 Australian canid samples, we explicitly test for introgression between closely related canid groups and dingoes. We found no evidence of introgression between dingoes and domestic dogs and show that previous work has likely mischaracterized shared ancestral genetic variation as evidence for hybridization. Further, New Guinea Singing Dogs are the only canid group that significantly shared genetic variation with dingoes, which fits with our understanding of previous phylogenetic analyses. Despite more recent sympatric distributions with dogs, dingoes have likely maintained their independence since their arrival in Australia, even in areas with high lethal control, indicating that their evolutionary trajectory is currently being conserved. The future conservation of the dingo lineage will require policies that promote coexistence pathways between humans and dingoes that protect rangeland systems and the dingoes' evolutionary future.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"9 1","pages":"1-12"},"PeriodicalIF":3.4,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11790216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}