Evolutionary Applications最新文献

{"title":"Climate change vulnerability and conservation strategies for tertiary relict tree species: Insights from landscape genomics of Taxus cuspidata","authors":"Yanjun Luo,&nbsp;Wei Qin,&nbsp;Yu Yan,&nbsp;Kangquan Yin,&nbsp;Runguo Zang,&nbsp;Fang K. Du","doi":"10.1111/eva.13686","DOIUrl":"10.1111/eva.13686","url":null,"abstract":"<p>The unprecedented habitat fragmentation or loss has threatened the existence of many species. Therefore, it is essential to understand whether and how these species can pace with the environmental changes. Recent advantages in landscape genomics enabled us to identify molecular signatures of adaptation and predict how populations will respond to changing environments, providing new insights into the conservation of species. Here, we investigated the pattern of neutral and putative adaptive genetic variation and its response to changing environments in a tertiary relict tree species, <i>Taxus cuspidata</i> Sieb. et Zucc, which is distributed in northeast China and adjacent regions. We investigated the pattern of genetic diversity and differentiation using restriction site-associated DNA sequencing (RAD-seq) and seven nuclear microsatellites (nSSRs) datasets. We further explored the endangered mechanism, predicted its vulnerability in the future, and provided guidelines for the conservation and management of this species. RAD-seq identified 16,087 single nucleotide polymorphisms (SNPs) in natural populations. Both the SNPs and nSSRs datasets showed high levels of genetic diversity and low genetic differentiation in <i>T. cuspidata</i>. Outlier detection by <i>F</i>_ST outlier analysis and genotype-environment associations (GEAs) revealed 598 outlier SNPs as putative adaptive SNPs. Linear redundancy analysis (RDA) and nonlinear gradient forest (GF) showed that the contribution of climate to genetic variation was greater than that of geography, and precipitation played an important role in putative adaptive genetic variation. Furthermore, the genetic offset and risk of non-adaptedness (RONA) suggested that the species at the northeast edge may be more vulnerable in the future. These results suggest that although the species has maintained high current genetic diversity in the face of recent habitat loss and fragmentation, future climate change is likely to threaten the survival of the species. Temperature (Bio03) and precipitation (Prec05) variables can be potentially used as predictors of response of <i>T. cuspidata</i> under future climate. Together, this study provides a theoretical framework for conservation and management strategies for wildlife species in the context of future climate change.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11375028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142152717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the Genetic Landscape: Insights Into the Genomic Signatures of Changle Goose","authors":"Hao Chen,&nbsp;Yan Wu,&nbsp;Yihao Zhu,&nbsp;Keyi Luo,&nbsp;Sumei Zheng,&nbsp;Hongbo Tang,&nbsp;Rui Xuan,&nbsp;Yuxuan Huang,&nbsp;Jiawei Li,&nbsp;Rui Xiong,&nbsp;Xinyan Fang,&nbsp;Lei Wang,&nbsp;Yujie Gong,&nbsp;Junjie Miao,&nbsp;Jing Zhou,&nbsp;Hongli Tan,&nbsp;Yanan Wang,&nbsp;Liping Wu,&nbsp;Jing Ouyang,&nbsp;Min Huang,&nbsp;Xueming Yan","doi":"10.1111/eva.13768","DOIUrl":"10.1111/eva.13768","url":null,"abstract":"<p>The Changle goose (CLG), a Chinese indigenous breed, is celebrated for its adaptability, rapid growth, and premium meat quality. Despite its agricultural value, the exploration of its genomic attributes has been scant. Our study entailed whole-genome resequencing of 303 geese across CLG and five other Chinese breeds, revealing distinct genetic diversity metrics. We discovered significant migration events from Xingguo gray goose to CLG and minor gene flow between them. We identified genomic regions through selective sweep analysis, correlating with CLG's unique traits. An elevated inbreeding coefficient in CLG, alongside reduced heterozygosity and rare single nucleotide polymorphisms (R_SNPs), suggests a narrowed genetic diversity. Genomic regions related to reproduction, meat quality, and growth were identified, with the <i>GATA3</i> gene showing strong selection signals for meat quality. A non-synonymous mutation in the <i>Sloc2a1</i> gene, which is associated with reproductive traits in the CLG, exhibited significant differences in allelic frequency. The roles of <i>CD82</i>, <i>CDH8</i>, and <i>PRKAB1</i> in growth and development, alongside <i>FABP4</i>, <i>FAF1</i>, <i>ESR1</i>, and <i>AKAP12</i> in reproduction, were highlighted. Additionally, <i>Cdkal1</i> and <i>Mfsd14a</i> may influence meat quality. This comprehensive genetic analysis underpins the unique genetic makeup of CLG, providing a basis for its conservation and informed breeding strategies.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11340016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142034662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Linked Selection and Gene Density Shape Genome-Wide Patterns of Diversification in Peatmosses","authors":"Olena Meleshko,&nbsp;Michael D. Martin,&nbsp;Kjell Ivar Flatberg,&nbsp;Hans K. Stenøien,&nbsp;Thorfinn Sand Korneliussen,&nbsp;Péter Szövényi,&nbsp;Kristian Hassel","doi":"10.1111/eva.13767","DOIUrl":"10.1111/eva.13767","url":null,"abstract":"<p>Genome evolution under speciation is poorly understood in nonmodel and nonvascular plants, such as bryophytes—the largest group of nonvascular land plants. Their genomes are structurally different from angiosperms and likely subjected to stronger linked selection pressure, which may have profound consequences on genome evolution in diversifying lineages, even more so when their genome architecture is conserved. We use the highly diverse, rapidly radiated group of peatmosses (<i>Sphagnum</i>) to characterize the processes affecting genome diversification in bryophytes. Using whole-genome sequencing data from populations of 12 species sampled at different phylogenetic and geographical scales, we describe high correlation of the genomic landscapes of differentiation, divergence, and diversity in <i>Sphagnum</i>. Coupled with evidence from the patterns of covariation among different measures of genetic diversity, phylogenetic discordance, and gene density, this provides strong support that peatmoss genome evolution has been shaped by the long-term effects of linked selection, constrained by distribution of selection targets in the genome. Thus, peatmosses join the growing number of animal and plant groups where functional features of the genome, such as gene density, and linked selection drive genome evolution along predetermined and highly similar routes in different species. Our findings demonstrate the great potential of bryophytes for studying the genomics of speciation and highlight the urgent need to expand the genomic resources in this remarkable group of plants.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11333200/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142007949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing genotype–environment interactions in Atlantic salmon reared in freshwater loch and recirculating systems","authors":"Mette J. Tollervey,&nbsp;Michaël Bekaert,&nbsp;Agustín Barría González,&nbsp;Saif Agha,&nbsp;Ross D. Houston,&nbsp;Andrea Doeschl-Wilson,&nbsp;Ashie Norris,&nbsp;Herve Migaud,&nbsp;Alejandro P. Gutierrez","doi":"10.1111/eva.13751","DOIUrl":"10.1111/eva.13751","url":null,"abstract":"<p>The interest in recirculating aquaculture systems (RAS) is growing due to their benefits such as increased productivity, better control over animal care, reduced environmental effects, and less water consumption. However, in some regions of the world, traditional aquaculture methods remain prevalent, and selective breeding has often been designed for performance within these systems. Therefore, it is important to evaluate how current fish populations fare in RAS to guide future breeding choices. In a commercial setting, we explore the genetic structure of growth characteristics, measure genotype–environment interactions (GxE) in salmon smolts, and examine genetic markers related to growth in freshwater lochs and RAS. Young salmon were raised together until they reached the parr stage, after which they were divided equally between freshwater net-pens and RAS. After an 8-week period, we sampled fish from each environment and genotyped them. Our findings revealed that fish reared in RAS were generally smaller in weight and length but exhibited a higher condition factor and uniformity. We found a notably smaller component of unexplained variance in the RAS, leading to higher heritability estimates. We observed a low GxE effect for length and condition factor, but significant re-ranking for whole-body weight, as well as noticeable differences in trait associations across environments. Specifically, a segment of chromosome 22 was found to be linked with the condition factor in the RAS population only. Results suggests that if the use of RAS continues to expand, the efficiency of existing commercial populations may not reach its full potential unless breeding programs specific to RAS are implemented.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11310769/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141915599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Niche breadth and divergence in sympatric cryptic coral species (Pocillopora spp.) across habitats within reefs and among algal symbionts","authors":"Scott C. Burgess,&nbsp;Alyssa M. Turner,&nbsp;Erika C. Johnston","doi":"10.1111/eva.13762","DOIUrl":"10.1111/eva.13762","url":null,"abstract":"<p>While the presence of morphologically cryptic species is increasingly recognized, we still lack a useful understanding of what causes and maintains co-occurring cryptic species and its consequences for the ecology, evolution, and conservation of communities. We sampled 724 <i>Pocillopora</i> corals from five habitat zones (the fringing reef, back reef, and fore reef at 5, 10, and 20 m) at four sites around the island of Moorea, French Polynesia. Using validated genetic markers, we identified six sympatric species of <i>Pocillopora</i>, most of which cannot be reliably identified based on morphology: <i>P. meandrina</i> (42.9%), <i>P. tuahiniensis</i> (25.1%), <i>P. verrucosa</i> (12.2%), <i>P. acuta</i> (10.4%), <i>P. grandis</i> (7.73%), and <i>P.</i> cf. <i>effusa</i> (2.76%). For 423 colonies (58% of the genetically identified hosts), we also used <i>psbA</i>^ncr or ITS2 markers to identify symbiont species (Symbiodiniaceae). The relative abundance of <i>Pocillopora</i> species differed across habitats within the reef. Sister taxa <i>P. verrucosa</i> and <i>P. tuahiniensis</i> had similar niche breadths and hosted the same specialist symbiont species (mostly <i>Cladocopium pacificum</i>) but the former was more common in the back reef and the latter more common deeper on the fore reef. In contrast, sister taxa <i>P. meandrina</i> and <i>P. grandis</i> had the highest niche breadths and overlaps and tended to host the same specialist symbiont species (mostly <i>C. latusorum</i>). <i>Pocillopora acuta</i> had the narrowest niche breadth and hosted the generalist, and more thermally tolerant, <i>Durusdinium gynnii</i>. Overall, there was a positive correlation between reef habitat niche breadth and symbiont niche breadth—<i>Pocillopora</i> species with a broader habitat niche also had a broader symbiont niche. Our results show how fine-scale variation within reefs plays an important role in the generation and coexistence of cryptic species. The results also have important implications for how niche differences affect community resilience, and for the success of coral restoration practices, in ways not previously appreciated.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11294925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141887765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The many dimensions of combination therapy: How to combine antibiotics to limit resistance evolution","authors":"Christin Nyhoegen,&nbsp;Sebastian Bonhoeffer,&nbsp;Hildegard Uecker","doi":"10.1111/eva.13764","DOIUrl":"10.1111/eva.13764","url":null,"abstract":"<p>In combination therapy, bacteria are challenged with two or more antibiotics simultaneously. Ideally, separate mutations are required to adapt to each of them, which is a priori expected to hinder the evolution of full resistance. Yet, the success of this strategy ultimately depends on how well the combination controls the growth of bacteria with and without resistance mutations. To design a combination treatment, we need to choose drugs and their doses and decide how many drugs get mixed. Which combinations are good? To answer this question, we set up a stochastic pharmacodynamic model and determine the probability to successfully eradicate a bacterial population. We consider bacteriostatic and two types of bactericidal drugs—those that kill independent of replication and those that kill during replication. To establish results for a null model, we consider non-interacting drugs and implement the two most common models for drug independence—Loewe additivity and Bliss independence. Our results show that combination therapy is almost always better in limiting the evolution of resistance than administering just one drug, even though we keep the total drug dose constant for a ‘fair’ comparison. Yet, exceptions exist for drugs with steep dose–response curves. Combining a bacteriostatic and a bactericidal drug which can kill non-replicating cells is particularly beneficial. Our results suggest that a 50:50 drug ratio—even if not always optimal—is usually a good and safe choice. Applying three or four drugs is beneficial for treatment of strains with large mutation rates but adding more drugs otherwise only provides a marginal benefit or even a disadvantage. By systematically addressing key elements of treatment design, our study provides a basis for future models which take further factors into account. It also highlights conceptual challenges with translating the traditional concepts of drug independence to the single-cell level.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11297101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141887677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The complex effects of modern oncogenic environments on the fitness, evolution and conservation of wildlife species","authors":"Antoine M. Dujon,&nbsp;Beata Ujvari,&nbsp;Sophie Tissot,&nbsp;Jordan Meliani,&nbsp;Océane Rieu,&nbsp;Nikita Stepanskyy,&nbsp;Rodrigo Hamede,&nbsp;Jácint Tokolyi,&nbsp;Aurora Nedelcu,&nbsp;Frédéric Thomas","doi":"10.1111/eva.13763","DOIUrl":"10.1111/eva.13763","url":null,"abstract":"<p>Growing evidence indicates that human activities are causing cancer rates to rise in both human and wildlife populations. This is due to the inability of ancestral anti-cancer defences to cope with modern environmental risks. The evolutionary mismatch between modern oncogenic risks and evolved cancer defences has far-reaching effects on various biological aspects at different timeframes, demanding a comprehensive study of the biology and evolutionary ecology of the affected species. Firstly, the increased activation of anti-cancer defences leads to excessive energy expenditure, affecting other biological functions and potentially causing health issues like autoimmune diseases. Secondly, tumorigenesis itself can impact important fitness-related parameters such as competitiveness, predator evasion, resistance to parasites, and dispersal capacity. Thirdly, rising cancer risks can influence the species' life-history traits, often favoring early reproduction to offset fitness costs associated with cancer. However, this strategy has its limits, and it may not ensure the sustainability of the species if cancer risks continue to rise. Lastly, some species may evolve additional anti-cancer defences, with uncertain consequences for their biology and future evolutionary path. In summary, we argue that the effects of increased exposure to cancer-causing substances on wildlife are complex, ranging from immediate responses to long-term evolutionary changes. Understanding these processes, especially in the context of conservation biology, is urgently needed.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11294924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141887766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotyping-by-sequencing informs conservation of Andean palms sources of non-timber forest products","authors":"Nicolás Peñafiel Loaiza,&nbsp;Abigail H. Chafe,&nbsp;Mónica Moraes R,&nbsp;Nora H. Oleas,&nbsp;Julissa Roncal","doi":"10.1111/eva.13765","DOIUrl":"10.1111/eva.13765","url":null,"abstract":"<p>Conservation and sustainable management of lineages providing non-timber forest products are imperative under the current global biodiversity loss. Most non-timber forest species, however, lack genomic studies that characterize their intraspecific variation and evolutionary history, which inform species' conservation practices. Contrary to many lineages in the Andean biodiversity hotspot that exhibit high diversification, the genus <i>Parajubaea</i> (Arecaceae) has only three species despite the genus' origin 22 million years ago. Two of the three palm species, <i>P. torallyi</i> and <i>P. sunkha</i>, are non-timber forest species endemic to the Andes of Bolivia and are listed as IUCN endangered. The third species, <i>P. cocoides</i>, is a vulnerable species with unknown wild populations. We investigated the evolutionary relationships of <i>Parajubaea</i> species and the genetic diversity and structure of wild Bolivian populations. Sequencing of five low-copy nuclear genes (3753 bp) challenged the hypothesis that <i>P. cocoides</i> is a cultigen that originated from the wild Bolivian species. We further obtained up to 15,134 de novo single-nucleotide polymorphism markers by genotyping-by-sequencing of 194 wild <i>Parajubaea</i> individuals. Our total DNA sequencing effort rejected the taxonomic separation of the two Bolivian species. As expected for narrow endemic species, we observed low genetic diversity, but no inbreeding signal. We found three genetic clusters shaped by geographic distance, which we use to propose three management units. Different percentages of missing genotypic data did not impact the genetic structure of populations. We use the management units to recommend in situ conservation by creating new protected areas, and ex situ conservation through seed collection.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11291087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141873716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 evidence of a hybrid swarm between Alpine ibex (Capra ibex) and domestic goat (C. hircus)","authors":"Alice Brambilla,&nbsp;Noel Zehnder,&nbsp;Bruno Bassano,&nbsp;Luca Rossi,&nbsp;Christine Grossen","doi":"10.1111/eva.13761","DOIUrl":"10.1111/eva.13761","url":null,"abstract":"<p>Improving the understanding of the causes and effects of anthropogenic hybridization is fundamental to ensure species conservation, particularly in the case of hybridization between wild species and their domestic relatives. Knowledge is missing for many species also because of a lack of appropriate tools for hybrid identification. Here, coupling genotype and phenotype analysis, we carried out an extensive investigation of ongoing hybridization in Alpine ibex <i>Capra ibex</i>, a mountain ungulate of conservation concern from a genetic perspective. By genotyping 63 diagnostic and 465 neutral SNPs, 20 suspected hybrids and 126 Alpine ibex without suspicious phenotype, representing 8 populations across a major part of the species distribution, we found evidence for ongoing hybridization between Alpine ibex and domestic goat. We identified different levels of hybridization including backcrosses into both Alpine ibex and domestic goat. Our results suggest a lack of reproductive barriers between the two species and good survival and reproductive success of the hybrids. Hybridization was locally intense, like a hybrid swarm, but not spread across the rest of the species distribution. Most of the hybrids were discovered in two locations in the north-west of Italy, while random sampling of individuals from different areas did not provide evidence of recent hybridization. Our method, based on amplicon sequencing of 63 diagnostic SNPs specifically developed for this purpose, allowed us to identify hybrids and backcrosses up to the fourth to fifth generations and was suitable for genetic samples of different quality, although with varying levels of certainty regarding the exact number of generations passed since hybridization. Based on the paired analysis of genotype and phenotype, we provide guidelines for the first identification of hybrids in the field and suggest a procedure for the reliable identification of hybrids.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11284124/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The evolutionary consequences of interactions between the epigenome, the genome and the environment","authors":"Pierre Baduel,&nbsp;Iris Sammarco,&nbsp;Rowan Barrett,&nbsp;Marta Coronado-Zamora,&nbsp;Amélie Crespel,&nbsp;Bárbara Díez-Rodríguez,&nbsp;Janay Fox,&nbsp;Dario Galanti,&nbsp;Josefa González,&nbsp;Alexander Jueterbock,&nbsp;Eric Wootton,&nbsp;Ewan Harney","doi":"10.1111/eva.13730","DOIUrl":"10.1111/eva.13730","url":null,"abstract":"<p>The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11266121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}