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Signatures of convergence in Neotropical cichlid fish 新热带慈鲷的趋同特征
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2024-09-16 DOI: 10.1111/mec.17524
Mariana Leal-Cardín, Seraina E. Bracamonte, Javier Aldegunde, Isabel S. Magalhaes, Claudia Patricia Ornelas-García, Marta Barluenga
{"title":"Signatures of convergence in Neotropical cichlid fish","authors":"Mariana Leal-Cardín,&nbsp;Seraina E. Bracamonte,&nbsp;Javier Aldegunde,&nbsp;Isabel S. Magalhaes,&nbsp;Claudia Patricia Ornelas-García,&nbsp;Marta Barluenga","doi":"10.1111/mec.17524","DOIUrl":"10.1111/mec.17524","url":null,"abstract":"<p>Convergent evolution of similar phenotypes suggests some predictability in the evolutionary trajectories of organisms, due to strong and repeated selective pressures, and/or developmental constraints. In adaptive radiations, particularly in cichlid fish radiations, convergent phenotypes are commonly found within and across geographical settings. Cichlids show major repeated axes of morphological diversification. Recurrent changes in body patterns reveal adaption to alternative habitats, and modifications of the trophic apparatus respond to the exploitation of different food resources. Here we compare morphologically and genetically two Neotropical cichlid assemblages, the Mexican desert cichlid and the Nicaraguan Midas cichlid, with similar polymorphic body and trophic adaptations despite their independent evolution. We found a common morphological axis of differentiation in trophic structures in both cichlid radiations, but two different axes of differentiation in body shape, defining two alternative limnetic body patterns. Adaptation to limnetic habitats implied regulation of immune functions in the Midas cichlid, while morphogenesis and metabolic functions in the desert cichlid. Convergent phenotypic adaptions could be associated to divergent gene regulation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 19","pages":""},"PeriodicalIF":4.5,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17524","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269061","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}
引用次数: 0
Sexually selected differences in warbler plumage are related to a putative inversion on the Z chromosome 莺羽色的性别差异与 Z 染色体上的假定倒位有关
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2024-09-13 DOI: 10.1111/mec.17525
Peter O. Dunn, Nicholas D. Sly, Corey R. Freeman-Gallant, Amberleigh E. Henschen, Christen M. Bossu, Kristen C. Ruegg, Piotr Minias, Linda A. Whittingham
{"title":"Sexually selected differences in warbler plumage are related to a putative inversion on the Z chromosome","authors":"Peter O. Dunn,&nbsp;Nicholas D. Sly,&nbsp;Corey R. Freeman-Gallant,&nbsp;Amberleigh E. Henschen,&nbsp;Christen M. Bossu,&nbsp;Kristen C. Ruegg,&nbsp;Piotr Minias,&nbsp;Linda A. Whittingham","doi":"10.1111/mec.17525","DOIUrl":"10.1111/mec.17525","url":null,"abstract":"<p>Large structural variants in the genome, such as inversions, may play an important role in producing population structure and local adaptation to the environment through suppression of recombination. However, relatively few studies have linked inversions to phenotypic traits that are sexually selected and may play a role in reproductive isolation. Here, we found that geographic differences in the sexually selected plumage of a warbler, the common yellowthroat (<i>Geothlypis trichas</i>), are largely due to differences in the Z (sex) chromosome (males are ZZ), which contains at least one putative inversion spanning 40% (31/77 Mb) of its length. The inversions on the Z chromosome vary dramatically east and west of the Appalachian Mountains, which provides evidence of cryptic population structure within the range of the most widespread eastern subspecies (<i>G. t. trichas</i>). In an eastern (New York) and western (Wisconsin) population of this subspecies, female prefer different male ornaments; larger black facial masks are preferred in Wisconsin and larger yellow breasts are preferred in New York. The putative inversion also contains genes related to vision, which could influence mating preferences. Thus, structural variants on the Z chromosome are associated with geographic differences in male ornaments and female choice, which may provide a mechanism for maintaining different patterns of sexual selection in spite of gene flow between populations of the same subspecies.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 21","pages":""},"PeriodicalIF":4.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Habitat fragmentation strongly restricts gene flow in endangered ectomycorrhizal fungal populations: Evidence from Rhizopogon togasawarius, specific to Pseudotsuga japonica, across the entire distribution range 生境破碎化严重限制了濒危外生菌根真菌种群的基因流动:在整个分布范围内,红豆杉特有的Rhizopogon togasawarius提供的证据
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2024-09-12 DOI: 10.1111/mec.17533
Hiroshi Abe, Lu Gan, Masao Murata, Kazuhide Nara
{"title":"Habitat fragmentation strongly restricts gene flow in endangered ectomycorrhizal fungal populations: Evidence from Rhizopogon togasawarius, specific to Pseudotsuga japonica, across the entire distribution range","authors":"Hiroshi Abe,&nbsp;Lu Gan,&nbsp;Masao Murata,&nbsp;Kazuhide Nara","doi":"10.1111/mec.17533","DOIUrl":"10.1111/mec.17533","url":null,"abstract":"<p>Habitat fragmentation reduces gene flow, causing genetic differentiation and diversity loss in endangered species through genetic drift and inbreeding. However, the impact of habitat fragmentation on ectomycorrhizal (ECM) fungi remains unexplored, despite their critical roles in forest ecosystems. Here, we investigated the population genetic structure and the demographic history of <i>Rhizopogon togasawarius</i>, the ECM fungus specifically colonizing the host tree <i>Pseudotsuga japonica</i>, across its entire distribution range (&gt;200 km). These two species are designated as endangered species on the IUCN Red List since they are found only in small, fragmented forests in Japan. We analysed 236 <i>R. togasawarius</i> individuals from five remaining populations across the Kii Peninsula and the Shikoku Island, separated by a sea channel. Simple sequence repeat analyses using 20 loci revealed strong genetic differentiation among populations (<i>F</i><sub>ST</sub> = 0.255), even significant in the nearest population pair separated by a distance of only 8 km (<i>F</i><sub>ST</sub> = 0.075), indicating extremely limited gene flow between populations. DIYABC-RF analyses implied that population divergence occurred approximately 6000 generations ago between the two regions, and nearly 1500 generations ago between the nearest populations within Shikoku Island, related to past climate events. Because of prolonged genetic isolation, significant inbreeding was confirmed in four of five populations, where effective population sizes became very small (<i>N</i><sub>e</sub> = 9.0–58.0). Although evaluation of extinction risks for microorganisms is challenging, our conservation genetic results indicated that habitat fragmentation increases extinction risk through population genetic mechanisms, and therefore should not be overlooked in biodiversity conservation efforts.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 19","pages":""},"PeriodicalIF":4.5,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17533","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226242","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}
引用次数: 0
A sex chromosome polymorphism maintains divergent plumage phenotypes between extensively hybridizing yellowhammers (Emberiza citrinella) and pine buntings (E. leucocephalos) 性染色体多态性维持了广泛杂交的黄椋鸟(Emberiza citrinella)和松鹀(E. leucocephalos)之间不同的羽色表型
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2024-09-11 DOI: 10.1111/mec.17526
Ellen Nikelski, Alexander S. Rubtsov, Darren Irwin
{"title":"A sex chromosome polymorphism maintains divergent plumage phenotypes between extensively hybridizing yellowhammers (Emberiza citrinella) and pine buntings (E. leucocephalos)","authors":"Ellen Nikelski,&nbsp;Alexander S. Rubtsov,&nbsp;Darren Irwin","doi":"10.1111/mec.17526","DOIUrl":"10.1111/mec.17526","url":null,"abstract":"<p>Under allopatric speciation, populations of a species become isolated by a geographic barrier and develop reproductive isolation through genetic differentiation. When populations meet in secondary contact, the strength of evolved reproductive barriers determines the extent of hybridization and whether the populations will continue to diverge or merge together. The yellowhammer (<i>Emberiza citrinella</i>) and pine bunting (<i>E. leucocephalos</i>) are avian sister species that diverged in allopatry on either side of Eurasia during the Pleistocene glaciations. Though they differ greatly in plumage and form distinct genetic clusters in allopatry, these taxa show negligible mitochondrial DNA differentiation and hybridize extensively where they overlap in central Siberia, lending uncertainty to the state of reproductive isolation in the system. To assess the strength of reproductive barriers between taxa, we examined genomic differentiation across the system. We found that extensive admixture has occurred in sympatry, indicating that reproductive barriers between taxa are weak. We also identified a putative Z chromosome inversion region that underlies plumage variation in the system, with the ‘pine bunting’ haplotype showing dominance over the ‘yellowhammer’ haplotype. Our results suggest that yellowhammers and pine buntings are currently at a crossroads and that evolutionary forces may push this system towards either continued differentiation or population merging. However, even if these taxa merge, recombination suppression between putative chromosome Z inversion haplotypes may maintain divergent plumage phenotypes within the system. In this way, our findings highlight the important role hybridization plays in increasing the genetic and phenotypic variation as well as the evolvability of a system.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 19","pages":""},"PeriodicalIF":4.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17526","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205176","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}
引用次数: 0
Population genomics of seal lice provides insights into the postglacial history of northern European seals 海豹虱的种群基因组学为了解北欧海豹的冰川后历史提供了线索。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2024-09-09 DOI: 10.1111/mec.17523
Ludmila Sromek, Kevin P. Johnson, Mervi Kunnasranta, Eeva Ylinen, Stephany Virrueta Herrera, Elena Andrievskaya, Vyacheslav Alexeev, Olga Rusinek, Aqqalu Rosing-Asvid, Tommi Nyman
{"title":"Population genomics of seal lice provides insights into the postglacial history of northern European seals","authors":"Ludmila Sromek,&nbsp;Kevin P. Johnson,&nbsp;Mervi Kunnasranta,&nbsp;Eeva Ylinen,&nbsp;Stephany Virrueta Herrera,&nbsp;Elena Andrievskaya,&nbsp;Vyacheslav Alexeev,&nbsp;Olga Rusinek,&nbsp;Aqqalu Rosing-Asvid,&nbsp;Tommi Nyman","doi":"10.1111/mec.17523","DOIUrl":"10.1111/mec.17523","url":null,"abstract":"<p>Genetic analyses of host-specific parasites can elucidate the evolutionary histories and biological features of their hosts. Here, we used population-genomic analyses of ectoparasitic seal lice (<i>Echinophthirius horridus</i>) to shed light on the postglacial history of seals in the Arctic Ocean and the Baltic Sea region. One key question was the enigmatic origin of relict landlocked ringed seal populations in lakes Saimaa and Ladoga in northern Europe. We found that that lice of four postglacially diverged subspecies of the ringed seal (<i>Pusa hispida</i>) and Baltic gray seal (<i>Halichoerus grypus</i>), like their hosts, form genetically differentiated entities. Using coalescent-based demographic inference, we show that the sequence of divergences of the louse populations is consistent with the geological history of lake formation. In addition, local effective population sizes of the lice are generally proportional to the census sizes of their respective seal host populations. Genome-based reconstructions of long-term effective population sizes revealed clear differences among louse populations associated with gray versus ringed seals, with apparent links to Pleistocene and Holocene climatic variation as well as to the isolation histories of ringed seal subspecies. Interestingly, our analyses also revealed ancient gene flow between the lice of Baltic gray and ringed seals, suggesting that the distributions of Baltic seals overlapped to a greater extent in the past than is the case today. Taken together, our results demonstrate how genomic information from specialized parasites with higher mutation and substitution rates than their hosts can potentially illuminate finer scale population genetic patterns than similar data from their hosts.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 20","pages":""},"PeriodicalIF":4.5,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17523","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142152730","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}
引用次数: 0
Repeatome evolution across space and time: Unravelling repeats dynamics in the plant genus Erythrostemon Klotzsch (Leguminosae Juss). 跨越时空的重复序列进化:解开植物 Erythrostemon Klotzsch 属(豆科 Juss)的重复动态。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2024-09-09 DOI: 10.1111/mec.17510
Natália Castro, Bruno Vilela, Yennifer Mata-Sucre, André Marques, Edeline Gagnon, Gwilym P Lewis, Lucas Costa, Gustavo Souza
{"title":"Repeatome evolution across space and time: Unravelling repeats dynamics in the plant genus Erythrostemon Klotzsch (Leguminosae Juss).","authors":"Natália Castro, Bruno Vilela, Yennifer Mata-Sucre, André Marques, Edeline Gagnon, Gwilym P Lewis, Lucas Costa, Gustavo Souza","doi":"10.1111/mec.17510","DOIUrl":"https://doi.org/10.1111/mec.17510","url":null,"abstract":"<p><p>Fluctuations in genomic repetitive fractions (repeatome) are known to impact several facets of evolution, such as ecological adaptation and speciation processes. Therefore, investigating the divergence of repetitive elements can provide insights into an important evolutionary force. However, it is not clear how the different repetitive element clades are impacted by the different factors such as ecological changes and/or phylogeny. To discuss this, we used the Neotropical legume genus Erythrostemon (Caesalpinioideae) as a model, given its ancient origin (~33 Mya), lineage-specific niche conservatism, macroecological heterogeneity, and disjunct distribution in Meso- and South American (MA and SA respectively) lineages. We performed a comparative repeatomic analysis of 18 Erythrostemon species to test the impact of environmental variables over repeats diversification. Overall, repeatome composition was diverse, with high abundances of satDNAs and Ty3/gypsy-Tekay transposable elements, predominantly in the MA and SA lineages respectively. However, unexpected repeatome profiles unrelated to the phylogeny/biogeography were found in a few MA (E. coccineus, E. pannosus and E. placidus) and SA (E. calycinus) species, related to reticulate evolution and incongruence between nuclear and plastid topology, suggesting ancient hybridizations. The plesiomorphic Tekay and satDNA pattern was altered in the MA-sensu stricto subclade with a striking genomic differentiation (expansion of satDNA and retraction of Tekay) associated with the colonization of a new environment in Central America around 20 Mya. Our data reveal that the current species-specific Tekay pool was the result of two bursts of amplification probably in the Miocene, with distinct patterns for the MA and SA repeatomes. This suggests a strong role of the Tekay elements as modulators of the genome-environment interaction in Erythrostemon, providing macroevolutionary insights about mechanisms of repeatome differentiation and plant diversification across space and time.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17510"},"PeriodicalIF":4.5,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142152731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
36-year study reveals stability of a wild wheat population across microhabitats 长达 36 年的研究揭示了野生小麦种群在不同微生境中的稳定性。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2024-09-01 DOI: 10.1111/mec.17512
Tal Dahan-Meir, Thomas James Ellis, Fabrizio Mafessoni, Hanan Sela, Ori Rudich, Jacob Manisterski, Naomi Avivi-Ragolsky, Amir Raz, Moshe Feldman, Yehoshua Anikster, Magnus Nordborg, Avraham A. Levy
{"title":"36-year study reveals stability of a wild wheat population across microhabitats","authors":"Tal Dahan-Meir,&nbsp;Thomas James Ellis,&nbsp;Fabrizio Mafessoni,&nbsp;Hanan Sela,&nbsp;Ori Rudich,&nbsp;Jacob Manisterski,&nbsp;Naomi Avivi-Ragolsky,&nbsp;Amir Raz,&nbsp;Moshe Feldman,&nbsp;Yehoshua Anikster,&nbsp;Magnus Nordborg,&nbsp;Avraham A. Levy","doi":"10.1111/mec.17512","DOIUrl":"10.1111/mec.17512","url":null,"abstract":"<p>Long-term genetic studies of wild populations are very scarce, but are essential for connecting ecological and population genetics models, and for understanding the dynamics of biodiversity. We present a study of a wild wheat population sampled over a 36-year period at high spatial resolution. We genotyped 832 individuals from regular sampling along transects during the course of the experiment. Genotypes were clustered into ecological microhabitats over scales of tens of metres, and this clustering was remarkably stable over the 36 generations of the study. Simulations show that it is difficult to determine whether this spatial and temporal stability reflects extremely limited dispersal or fine-scale local adaptation to ecological parameters. Using a common-garden experiment, we showed that the genotypes found in distinct microhabitats differ phenotypically. Our results provide a rare insight into the population genetics of a natural population over a long monitoring period.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 19","pages":""},"PeriodicalIF":4.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17512","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142102702","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}
引用次数: 0
Genetic adaptation despite high gene flow in a range-expanding population. 在一个范围不断扩大的种群中,尽管基因流动频繁,但仍能实现遗传适应。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2024-08-31 DOI: 10.1111/mec.17511
Andy Lee, Benjamin N Daniels, William Hemstrom, Cataixa López, Yuki Kagaya, Daisuke Kihara, Jean M Davidson, Robert J Toonen, Crow White, Mark R Christie
{"title":"Genetic adaptation despite high gene flow in a range-expanding population.","authors":"Andy Lee, Benjamin N Daniels, William Hemstrom, Cataixa López, Yuki Kagaya, Daisuke Kihara, Jean M Davidson, Robert J Toonen, Crow White, Mark R Christie","doi":"10.1111/mec.17511","DOIUrl":"https://doi.org/10.1111/mec.17511","url":null,"abstract":"<p><p>Signals of natural selection can be quickly eroded in high gene flow systems, curtailing efforts to understand how and when genetic adaptation occurs in the ocean. This long-standing, unresolved topic in ecology and evolution has renewed importance because changing environmental conditions are driving range expansions that may necessitate rapid evolutionary responses. One example occurs in Kellet's whelk (Kelletia kelletii), a common subtidal gastropod with an ~40- to 60-day pelagic larval duration that expanded their biogeographic range northwards in the 1970s by over 300 km. To test for genetic adaptation, we performed a series of experimental crosses with Kellet's whelk adults collected from their historical (HxH) and recently expanded range (ExE), and conducted RNA-Seq on offspring that we reared in a common garden environment. We identified 2770 differentially expressed genes (DEGs) between 54 offspring samples with either only historical range (HxH offspring) or expanded range (ExE offspring) ancestry. Using SNPs called directly from the DEGs, we assigned samples of known origin back to their range of origin with unprecedented accuracy for a marine species (92.6% and 94.5% for HxH and ExE offspring, respectively). The SNP with the highest predictive importance occurred on triosephosphate isomerase (TPI), an essential metabolic enzyme involved in cold stress response. TPI was significantly upregulated and contained a non-synonymous mutation in the expanded range. Our findings pave the way for accurately identifying patterns of dispersal, gene flow and population connectivity in the ocean by demonstrating that experimental transcriptomics can reveal mechanisms for how marine organisms respond to changing environmental conditions.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17511"},"PeriodicalIF":4.5,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142102705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Selection on genome-wide gene expression plasticity of rice in wet and dry field environments. 水稻在干湿田间环境中全基因组基因表达可塑性的选择。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2024-08-30 DOI: 10.1111/mec.17522
Elena Hamann, Simon C Groen, Taryn S Dunivant, Irina Ćalić, Colleen Cochran, Rachel Konshok, Michael D Purugganan, Steven J Franks
{"title":"Selection on genome-wide gene expression plasticity of rice in wet and dry field environments.","authors":"Elena Hamann, Simon C Groen, Taryn S Dunivant, Irina Ćalić, Colleen Cochran, Rachel Konshok, Michael D Purugganan, Steven J Franks","doi":"10.1111/mec.17522","DOIUrl":"https://doi.org/10.1111/mec.17522","url":null,"abstract":"<p><p>Gene expression can be highly plastic in response to environmental variation. However, we know little about how expression plasticity is shaped by natural selection and evolves in wild and domesticated species. We used genotypic selection analysis to characterize selection on drought-induced plasticity of over 7,500 leaf transcripts of 118 rice accessions (genotypes) from different environmental conditions grown in a field experiment. Gene expression plasticity was neutral for most gradually plastic transcripts, but transcripts with discrete patterns of expression showed stronger selection on expression plasticity. Whether plasticity was adaptive and co-gradient or maladaptive and counter-gradient varied among varietal groups. No transcripts that experienced selection for plasticity across environments showed selection against plasticity within environments, indicating a lack of evidence for costs of adaptive plasticity that may constrain its evolution. Selection on expression plasticity was influenced by degree of plasticity, transcript length and gene body methylation. We observed positive selection on plasticity of co-expression modules containing transcripts involved in photosynthesis, translation and responsiveness to abiotic stress. Taken together, these results indicate that patterns of selection on expression plasticity were context-dependent and likely associated with environmental conditions of varietal groups, but that the evolution of adaptive plasticity would likely not be constrained by opposing patterns of selection on plasticity within compared to across environments. These results offer a genome-wide view of patterns of selection and ecological constraints on gene expression plasticity and provide insights into the interplay between plastic and evolutionary responses to drought at the molecular level.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17522"},"PeriodicalIF":4.5,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142102707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Towards the conservation of the crucian carp in Europe: Prolific hybridization but no evidence for introgression between native and non-native taxa 保护欧洲鲫鱼:本地与非本地类群之间杂交繁盛,但无证据表明存在引种现象。
IF 4.5 1区 生物学
Molecular Ecology Pub Date : 2024-08-30 DOI: 10.1111/mec.17515
Daniel L. Jeffries, Lori Lawson-Handley, Dunja K. Lamatsch, K. Håkan Olsén, Carl D. Sayer, Bernd Hänfling
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