Jeffrey W Streicher, Shea M Lambert, Fausto R Méndez de la Cruz, Norberto Martínez-Méndez, Uri Omar García-Vázquez, Adrián Nieto Montes de Oca, John J Wiens
The processes that restrict gene flow between populations are fundamental to speciation. Here, we develop a simple framework for studying whether divergence in morphology, climatic niche, time and space contribute to reduced gene flow among populations and species. We apply this framework to a model system involving a clade of spiny lizards (Sceloporus) occurring mostly in northeastern Mexico, which show striking variation in morphology and habitat among closely related species and populations. We developed a new time-calibrated phylogeny for the group using RADseq data from 152 individuals. This phylogeny identified 12 putative species-level clades, including at least two undescribed species. We then estimated levels of gene flow among 21 geographically adjacent pairs of species and populations. We also estimated divergence in morphological and climatic niche variables among these same pairs, along with divergence times and geographic distances. Using Bayesian generalised linear models, we found that gene flow between pairs of lineages is negatively related to divergence time and morphological divergence among them (which are uncorrelated), and not to geographic distance or climatic divergence. The framework used here can be applied to study speciation in many other organisms having genomic data but lacking direct data on reproductive isolation. We also found several other intriguing patterns in this system, including the parallel evolution of a strikingly similar montane blue-red morph from more dull-coloured desert ancestors within two different, nonsister species.
{"title":"What Predicts Gene Flow During Speciation? The Relative Roles of Time, Space, Morphology and Climate.","authors":"Jeffrey W Streicher, Shea M Lambert, Fausto R Méndez de la Cruz, Norberto Martínez-Méndez, Uri Omar García-Vázquez, Adrián Nieto Montes de Oca, John J Wiens","doi":"10.1111/mec.17580","DOIUrl":"10.1111/mec.17580","url":null,"abstract":"<p><p>The processes that restrict gene flow between populations are fundamental to speciation. Here, we develop a simple framework for studying whether divergence in morphology, climatic niche, time and space contribute to reduced gene flow among populations and species. We apply this framework to a model system involving a clade of spiny lizards (Sceloporus) occurring mostly in northeastern Mexico, which show striking variation in morphology and habitat among closely related species and populations. We developed a new time-calibrated phylogeny for the group using RADseq data from 152 individuals. This phylogeny identified 12 putative species-level clades, including at least two undescribed species. We then estimated levels of gene flow among 21 geographically adjacent pairs of species and populations. We also estimated divergence in morphological and climatic niche variables among these same pairs, along with divergence times and geographic distances. Using Bayesian generalised linear models, we found that gene flow between pairs of lineages is negatively related to divergence time and morphological divergence among them (which are uncorrelated), and not to geographic distance or climatic divergence. The framework used here can be applied to study speciation in many other organisms having genomic data but lacking direct data on reproductive isolation. We also found several other intriguing patterns in this system, including the parallel evolution of a strikingly similar montane blue-red morph from more dull-coloured desert ancestors within two different, nonsister species.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142589946","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}
Emmanouil Meramveliotakis, Joaquín Ortego, Ioannis Anastasiou, Alfried P Vogler, Anna Papadopoulou
Habitat association has been proposed to affect evolutionary dynamics through its control on dispersal propensity, which is considered a key trait for lineage survival in habitats of low durational stability. The Habitat Constraint hypothesis predicts different micro- and macroevolutionary patterns for stable versus dynamic habitat specialists, but the empirical evidence remains controversial and in insects mostly derives from winged lineages. We here use genome-wide SNP data to assess the effect of habitat association on the population dynamics of two closely related flightless lineages of the genus Eutagenia (Coleoptera: Tenebrionidae), which are co-distributed across the Cyclades islands in the Eastern Mediterranean but are associated with habitat types of different presumed stability: the psammophilous lineage is associated with dynamic sandy coastal habitats, while the geophilous lineage is associated with comparatively stable compact soil habitats. Our comparative population genomic and demographic analyses support higher inter-island gene flow in the psammophilous lineage, presumably due to the physical properties of dynamic sand-dune habitats that promote passive dispersal. We also find consistent bottlenecks in the psammophilous demes, suggesting that lineage evolution in the dynamic habitat is punctuated by local extinction and recolonisation events. The inferred demographic processes are surprisingly uniform among psammophilous demes, but vary considerably among geophilous demes depending on historical island connectivity, indicating more stringent constraints on the dynamic habitat lineage. This study extends the Habitat Constraint hypothesis by demonstrating that selection on dispersal traits is not the only mechanism that can drive consistent differences in evolutionary dynamics between stable versus dynamic habitat specialists.
栖息地关联被认为是低持续稳定性栖息地中物种生存的关键特征,它通过控制扩散倾向影响进化动态。栖息地约束假说预测了稳定栖息地专家与动态栖息地专家不同的微观和宏观进化模式,但实证证据仍然存在争议,而且在昆虫中主要来自有翅类群。我们在本文中利用全基因组 SNP 数据评估了生境关联对 Eutagenia 属(鞘翅目:Tenebrionidae)两个密切相关的不会飞的品系种群动态的影响,这两个品系共同分布于东地中海的基克拉迪群岛,但与假定稳定性不同的生境类型相关:嗜沙品系与动态沙质沿海生境相关,而嗜地品系与相对稳定的紧密土壤生境相关。我们的种群基因组和人口比较分析表明,嗜沙系的岛屿间基因流动较高,这可能是由于动态沙丘栖息地的物理特性促进了被动扩散。我们还在嗜栉水母种群中发现了一致的瓶颈现象,这表明在动态栖息地中的种系进化会受到局部灭绝和重新定居事件的干扰。推断出的人口统计过程在嗜棘皮动物种群中惊人地一致,但在嗜地动物种群中却因历史上岛屿的连通性而有很大差异,这表明动态栖息地的世系受到了更严格的限制。这项研究扩展了 "生境限制假说",证明对扩散特征的选择并不是唯一的机制,它可以驱动稳定生境专家与动态生境专家之间进化动态的一致差异。
{"title":"Habitat Association Predicts Population Connectivity and Persistence in Flightless Beetles: A Population Genomics Approach Within a Dynamic Archipelago.","authors":"Emmanouil Meramveliotakis, Joaquín Ortego, Ioannis Anastasiou, Alfried P Vogler, Anna Papadopoulou","doi":"10.1111/mec.17577","DOIUrl":"https://doi.org/10.1111/mec.17577","url":null,"abstract":"<p><p>Habitat association has been proposed to affect evolutionary dynamics through its control on dispersal propensity, which is considered a key trait for lineage survival in habitats of low durational stability. The Habitat Constraint hypothesis predicts different micro- and macroevolutionary patterns for stable versus dynamic habitat specialists, but the empirical evidence remains controversial and in insects mostly derives from winged lineages. We here use genome-wide SNP data to assess the effect of habitat association on the population dynamics of two closely related flightless lineages of the genus Eutagenia (Coleoptera: Tenebrionidae), which are co-distributed across the Cyclades islands in the Eastern Mediterranean but are associated with habitat types of different presumed stability: the psammophilous lineage is associated with dynamic sandy coastal habitats, while the geophilous lineage is associated with comparatively stable compact soil habitats. Our comparative population genomic and demographic analyses support higher inter-island gene flow in the psammophilous lineage, presumably due to the physical properties of dynamic sand-dune habitats that promote passive dispersal. We also find consistent bottlenecks in the psammophilous demes, suggesting that lineage evolution in the dynamic habitat is punctuated by local extinction and recolonisation events. The inferred demographic processes are surprisingly uniform among psammophilous demes, but vary considerably among geophilous demes depending on historical island connectivity, indicating more stringent constraints on the dynamic habitat lineage. This study extends the Habitat Constraint hypothesis by demonstrating that selection on dispersal traits is not the only mechanism that can drive consistent differences in evolutionary dynamics between stable versus dynamic habitat specialists.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575190","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}
Kamil Konowalik, Salvatore Tomasello, Jacek Urbaniak
Climate change and human influence are transforming mountain ecosystems, significantly impacting species distributions and biodiversity. Among these changes, the upward migration of lowland species into mountain regions stands out. This study examines the ecogeographical niche overlap and genetic diversity among three Leucanthemum species distributed along an altitudinal gradient in the Carpathian Mountains: the lowland L. ircutianum (4x), the montane L. rotundifolium (2x) and the alpine L. gaudinii (2x). By genotyping over 600 individuals using SNP analysis, followed by principal coordinate analysis (PCoA), Neighbour-Net Network and Structure clustering, we reveal not just distinct genetic groups but also hybridisation across all species, suggesting the potential for triple hybrids. Genetic admixture is further supported by environmental background and niche overlap analyses that reveal substantial overlap among species, particularly in line with their vertical distribution. Climate envelope plots indicate a likely reduction in available habitat for mountainous species due to climate change, leading to an increase in competition and an intensification of hybridisation. Anthropogenic influences are further intensifying these hybridisation trends. Among the studied species, L. gaudinii is most at risk of overwhelming hybridisation, whereas L. ircutianum may experience habitat expansion. By providing a comprehensive genetic and ecological overview, our research highlights the significance of hybridisation in biodiversity conservation and the challenges posed by environmental changes and anthropogenic activities in mountain environments. This study not only contributes to the understanding of genetic diversity in the Carpathians but also underscores the broader implications for molecular ecology and conservation strategies in mountain ecosystems.
气候变化和人类影响正在改变山区生态系统,对物种分布和生物多样性产生重大影响。在这些变化中,低地物种向山区的上移尤为突出。本研究考察了沿喀尔巴阡山脉海拔梯度分布的三个白头翁物种的生态位重叠和遗传多样性:低地白头翁(4x)、山地白头翁(2x)和高山白头翁(2x)。通过使用 SNP 分析对 600 多个个体进行基因分型,然后进行主坐标分析(PCoA)、邻接网络分析和结构聚类分析,我们不仅发现了不同的遗传群体,而且还发现了所有物种之间的杂交,这表明存在三系杂交的可能性。环境背景和生态位重叠分析进一步证实了基因掺杂,这些分析表明物种之间存在大量重叠,尤其是在垂直分布方面。气候包络图显示,由于气候变化,山区物种的可用栖息地可能会减少,从而导致竞争加剧和杂交加剧。人类活动的影响进一步加剧了这些杂交趋势。在所研究的物种中,L. gaudinii面临的杂交风险最大,而L. ircutianum则可能经历栖息地扩张。通过提供全面的遗传和生态概述,我们的研究强调了杂交在生物多样性保护中的重要性,以及山区环境变化和人类活动带来的挑战。这项研究不仅有助于了解喀尔巴阡山脉的遗传多样性,还强调了分子生态学和山区生态系统保护策略的广泛意义。
{"title":"Genetic Diversity and Ecogeographical Niche Overlap Among Hybridising Ox-Eye Daisies (Leucanthemum, Asteraceae) in the Carpathian Mountains: The Impact of Anthropogenic Disturbances.","authors":"Kamil Konowalik, Salvatore Tomasello, Jacek Urbaniak","doi":"10.1111/mec.17581","DOIUrl":"https://doi.org/10.1111/mec.17581","url":null,"abstract":"<p><p>Climate change and human influence are transforming mountain ecosystems, significantly impacting species distributions and biodiversity. Among these changes, the upward migration of lowland species into mountain regions stands out. This study examines the ecogeographical niche overlap and genetic diversity among three Leucanthemum species distributed along an altitudinal gradient in the Carpathian Mountains: the lowland L. ircutianum (4x), the montane L. rotundifolium (2x) and the alpine L. gaudinii (2x). By genotyping over 600 individuals using SNP analysis, followed by principal coordinate analysis (PCoA), Neighbour-Net Network and Structure clustering, we reveal not just distinct genetic groups but also hybridisation across all species, suggesting the potential for triple hybrids. Genetic admixture is further supported by environmental background and niche overlap analyses that reveal substantial overlap among species, particularly in line with their vertical distribution. Climate envelope plots indicate a likely reduction in available habitat for mountainous species due to climate change, leading to an increase in competition and an intensification of hybridisation. Anthropogenic influences are further intensifying these hybridisation trends. Among the studied species, L. gaudinii is most at risk of overwhelming hybridisation, whereas L. ircutianum may experience habitat expansion. By providing a comprehensive genetic and ecological overview, our research highlights the significance of hybridisation in biodiversity conservation and the challenges posed by environmental changes and anthropogenic activities in mountain environments. This study not only contributes to the understanding of genetic diversity in the Carpathians but also underscores the broader implications for molecular ecology and conservation strategies in mountain ecosystems.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581562","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}
Shingo Fujimoto, Bayu K A Sumarto, Iki Murase, Daniel F Mokodongan, Taijun Myosho, Mitsuharu Yagi, Satoshi Ansai, Jun Kitano, Satoshi Takeda, Kazunori Yamahira
In most fishes, the number of offspring increases with maternal body size. Although this size-fecundity relationship often varies among species as a result of the coevolution of life-history traits, the genetic basis of such size-fecundity relationships remains unclear. We explored the genetic basis underlying this size-fecundity relationship in two small medaka species, Oryzias latipes and O. sakaizumii. Our findings showed that O. sakaizumii has a higher fecundity than O. latipes, and quantitative trait locus analysis using interspecific F2 hybrids showed that chromosome 23 is linked to the size-fecundity relationship. In particular, the genes igf1 and lep-b in this region are known to be associated with life-history traits, including somatic growth, gonad maturation, and progeny numbers in various taxa. Because O. sakaizumii is distributed at higher latitudes and has a shorter spawning season than O. latipes in the wild, we propose that the relatively high fecundity observed in O. sakaizumii is an adaptation to high latitudes. We also discuss the potential ecological ramifications associated with the evolution of increased fecundity in this species.
{"title":"Evolution of Size-Fecundity Relationship in Medaka Fish From Different Latitudes.","authors":"Shingo Fujimoto, Bayu K A Sumarto, Iki Murase, Daniel F Mokodongan, Taijun Myosho, Mitsuharu Yagi, Satoshi Ansai, Jun Kitano, Satoshi Takeda, Kazunori Yamahira","doi":"10.1111/mec.17578","DOIUrl":"https://doi.org/10.1111/mec.17578","url":null,"abstract":"<p><p>In most fishes, the number of offspring increases with maternal body size. Although this size-fecundity relationship often varies among species as a result of the coevolution of life-history traits, the genetic basis of such size-fecundity relationships remains unclear. We explored the genetic basis underlying this size-fecundity relationship in two small medaka species, Oryzias latipes and O. sakaizumii. Our findings showed that O. sakaizumii has a higher fecundity than O. latipes, and quantitative trait locus analysis using interspecific F<sub>2</sub> hybrids showed that chromosome 23 is linked to the size-fecundity relationship. In particular, the genes igf1 and lep-b in this region are known to be associated with life-history traits, including somatic growth, gonad maturation, and progeny numbers in various taxa. Because O. sakaizumii is distributed at higher latitudes and has a shorter spawning season than O. latipes in the wild, we propose that the relatively high fecundity observed in O. sakaizumii is an adaptation to high latitudes. We also discuss the potential ecological ramifications associated with the evolution of increased fecundity in this species.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581550","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}
Peter A Moran, Thomas J Colgan, Karl P Phillips, Jamie Coughlan, Philip McGinnity, Thomas E Reed
Migration in animals and associated adaptations to contrasting environments are underpinned by complex genetic architecture. Here, we explore the genomic basis of facultative anadromy in brown trout (Salmo trutta), wherein some individuals migrate to sea while others remain resident in natal rivers, to better understand how alternative migratory tactics (AMTs) are maintained evolutionarily. To identify genomic variants associated with AMTs, we sequenced whole genomes for 194 individual trout from five anadromous-resident population pairs, situated above and below waterfalls, in five different Irish rivers. These waterfalls act as natural barriers to upstream migration and hence we predicted that loci underpinning AMTs should be under similar divergent selection across these replicate pairs. A sliding windows based analysis revealed a highly polygenic adaptive divergence between anadromous and resident populations, encompassing 329 differentiated genomic regions. These regions were associated with 292 genes involved in various processes crucial for AMTs, including energy homeostasis, reproduction, osmoregulation, immunity, circadian rhythm and neural function. Furthermore, examining patterns of diversity we were able to link specific genes and biological processes to putative AMT trait classes: migratory-propensity, migratory-lifestyle and residency. Importantly, AMT outlier regions possessed higher genetic diversity than the background genome, particularly in the anadromous group, suggesting balancing selection may play a role in maintaining genetic variation. Overall, the results from this study provide important insights into the genetic architecture of migration and the evolutionary mechanisms shaping genomic diversity within and across populations.
动物的洄游以及对不同环境的相关适应性是由复杂的遗传结构支撑的。在这里,我们探索了褐鳟(Salmo trutta)的溯河洄游基因组学基础,即一些个体洄游到海洋,而另一些个体则留在出生地的河流中,从而更好地了解替代性洄游策略(AMTs)是如何在进化过程中得以维持的。为了确定与AMTs相关的基因组变异,我们对来自爱尔兰五条不同河流中瀑布上方和下方的五个溯河而居种群对的194条鳟鱼个体进行了全基因组测序。这些瀑布是鳟鱼向上游迁徙的天然屏障,因此我们预测,在这些重复的鳟鱼种群对中,支撑AMT的基因位点应该受到类似的分化选择。基于滑动窗口的分析表明,溯河洄游种群和常住种群之间存在高度多基因适应性差异,包括 329 个差异基因组区域。这些区域与 292 个基因有关,这些基因参与了对溯河生态系统至关重要的各种过程,包括能量平衡、繁殖、渗透调节、免疫、昼夜节律和神经功能。此外,通过研究多样性模式,我们能够将特定基因和生物过程与推定的 AMT 特征类别联系起来:迁徙倾向、迁徙生活方式和居住地。重要的是,AMT离群区域的遗传多样性高于背景基因组,尤其是在溯河群中,这表明平衡选择可能在维持遗传变异方面发挥了作用。总之,这项研究的结果为我们了解迁徙的遗传结构以及形成种群内和种群间基因组多样性的进化机制提供了重要的启示。
{"title":"Whole-Genome Resequencing Reveals Polygenic Signatures of Directional and Balancing Selection on Alternative Migratory Life Histories.","authors":"Peter A Moran, Thomas J Colgan, Karl P Phillips, Jamie Coughlan, Philip McGinnity, Thomas E Reed","doi":"10.1111/mec.17538","DOIUrl":"https://doi.org/10.1111/mec.17538","url":null,"abstract":"<p><p>Migration in animals and associated adaptations to contrasting environments are underpinned by complex genetic architecture. Here, we explore the genomic basis of facultative anadromy in brown trout (Salmo trutta), wherein some individuals migrate to sea while others remain resident in natal rivers, to better understand how alternative migratory tactics (AMTs) are maintained evolutionarily. To identify genomic variants associated with AMTs, we sequenced whole genomes for 194 individual trout from five anadromous-resident population pairs, situated above and below waterfalls, in five different Irish rivers. These waterfalls act as natural barriers to upstream migration and hence we predicted that loci underpinning AMTs should be under similar divergent selection across these replicate pairs. A sliding windows based analysis revealed a highly polygenic adaptive divergence between anadromous and resident populations, encompassing 329 differentiated genomic regions. These regions were associated with 292 genes involved in various processes crucial for AMTs, including energy homeostasis, reproduction, osmoregulation, immunity, circadian rhythm and neural function. Furthermore, examining patterns of diversity we were able to link specific genes and biological processes to putative AMT trait classes: migratory-propensity, migratory-lifestyle and residency. Importantly, AMT outlier regions possessed higher genetic diversity than the background genome, particularly in the anadromous group, suggesting balancing selection may play a role in maintaining genetic variation. Overall, the results from this study provide important insights into the genetic architecture of migration and the evolutionary mechanisms shaping genomic diversity within and across populations.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575208","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}
Emily J Booth, Chris J Brauer, Jonathan Sandoval-Castillo, Katherine Harrisson, Meaghan L Rourke, Catherine R M Attard, Dean M Gilligan, Zeb Tonkin, Jason D Thiem, Peter J Unmack, Brenton Zampatti, Luciano B Beheregaray
Genomic vulnerability is a measure of how much evolutionary change is required for a population to maintain optimal genotype-environment associations under projected climates. Aquatic species, and in particular migratory ectotherms, are largely underrepresented in studies of genomic vulnerability. Such species might be well equipped for tracking suitable habitat and spreading diversity that could promote adaptation to future climates. We characterised range-wide genomic diversity and genomic vulnerability in the migratory and fisheries-important golden perch (Macquaria ambigua) from Australia's expansive Murray-Darling Basin (MDB). The MDB has a steep hydroclimatic gradient and is one of the world's most variable regions in terms of climate and streamflow. Golden perch are threatened by fragmentation and obstruction of waterways, alteration of flow regimes, and a progressively hotter and drying climate. We gathered a genomic dataset of 1049 individuals from 186 MDB localities. Despite high range-wide gene flow, golden perch in the warmer, northern catchments had higher predicted vulnerability than those in the cooler, southern catchments. A new cross-validation approach showed that these predictions were insensitive to the exclusion of individual catchments. The results raise concern for populations at warm range edges, which may already be close to their thermal limits. However, a population with functional variants beneficial for climate adaptation found in the most arid and hydrologically variable catchment was predicted to be less vulnerable. Native fish management plans, such as captive breeding and stocking, should consider spatial variation in genomic vulnerability to improve conservation outcomes under climate change, even for dispersive species with high connectivity.
{"title":"Genomic Vulnerability to Climate Change of an Australian Migratory Freshwater Fish, the Golden Perch (Macquaria ambigua).","authors":"Emily J Booth, Chris J Brauer, Jonathan Sandoval-Castillo, Katherine Harrisson, Meaghan L Rourke, Catherine R M Attard, Dean M Gilligan, Zeb Tonkin, Jason D Thiem, Peter J Unmack, Brenton Zampatti, Luciano B Beheregaray","doi":"10.1111/mec.17570","DOIUrl":"https://doi.org/10.1111/mec.17570","url":null,"abstract":"<p><p>Genomic vulnerability is a measure of how much evolutionary change is required for a population to maintain optimal genotype-environment associations under projected climates. Aquatic species, and in particular migratory ectotherms, are largely underrepresented in studies of genomic vulnerability. Such species might be well equipped for tracking suitable habitat and spreading diversity that could promote adaptation to future climates. We characterised range-wide genomic diversity and genomic vulnerability in the migratory and fisheries-important golden perch (Macquaria ambigua) from Australia's expansive Murray-Darling Basin (MDB). The MDB has a steep hydroclimatic gradient and is one of the world's most variable regions in terms of climate and streamflow. Golden perch are threatened by fragmentation and obstruction of waterways, alteration of flow regimes, and a progressively hotter and drying climate. We gathered a genomic dataset of 1049 individuals from 186 MDB localities. Despite high range-wide gene flow, golden perch in the warmer, northern catchments had higher predicted vulnerability than those in the cooler, southern catchments. A new cross-validation approach showed that these predictions were insensitive to the exclusion of individual catchments. The results raise concern for populations at warm range edges, which may already be close to their thermal limits. However, a population with functional variants beneficial for climate adaptation found in the most arid and hydrologically variable catchment was predicted to be less vulnerable. Native fish management plans, such as captive breeding and stocking, should consider spatial variation in genomic vulnerability to improve conservation outcomes under climate change, even for dispersive species with high connectivity.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567133","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}
Alison McAfee, Baptiste Martinet, Kimberly Przybyla, Félicien Degueldre, Shelley E Hoover, Serge Aron, Leonard J Foster
Hymenopteran queens are collectively highly fecund, often long-lived individuals that undergo dramatic physiological changes after they mate and establish a nest. However, the degree to which these changes are conserved among species with different life histories is not well-defined. We conducted a comparative proteomic study investigating differences between reproductive stages (virgin, mated and established queens) of Apis mellifera, Bombus impatiens, B. terrestris and Lasius niger. We analysed haemolymph for all species except L. niger, for which a whole-body analysis was performed due to the small size of these queens. We identified conserved upregulation of proteins involved in anatomical and system development as queens transition to establishing a nest in all species except B. terrestris. We also identified conserved patterns of vitellogenin, vitellogenin receptor and immune-responsive protein (IRP)30, all of which are proteins typically associated with oviposition. However, expression patterns of other immune proteins, heat-shock proteins (HSPs), detoxification enzymes and antioxidant enzymes were more dissimilar, with some species exhibiting similar trends and co-occurrence through reproductive stages, while others exhibited variable or opposite patterns. These conserved and unique profiles likely in part reflect similarities and differences in selective pressure on reproductive stages of each species and may indicate differing abilities to respond to emergent pathogens or environmental change.
{"title":"Conserved and Unique Protein Expression Patterns Across Reproductive Stage Transitions in Social Hymenopteran Queens.","authors":"Alison McAfee, Baptiste Martinet, Kimberly Przybyla, Félicien Degueldre, Shelley E Hoover, Serge Aron, Leonard J Foster","doi":"10.1111/mec.17568","DOIUrl":"https://doi.org/10.1111/mec.17568","url":null,"abstract":"<p><p>Hymenopteran queens are collectively highly fecund, often long-lived individuals that undergo dramatic physiological changes after they mate and establish a nest. However, the degree to which these changes are conserved among species with different life histories is not well-defined. We conducted a comparative proteomic study investigating differences between reproductive stages (virgin, mated and established queens) of Apis mellifera, Bombus impatiens, B. terrestris and Lasius niger. We analysed haemolymph for all species except L. niger, for which a whole-body analysis was performed due to the small size of these queens. We identified conserved upregulation of proteins involved in anatomical and system development as queens transition to establishing a nest in all species except B. terrestris. We also identified conserved patterns of vitellogenin, vitellogenin receptor and immune-responsive protein (IRP)30, all of which are proteins typically associated with oviposition. However, expression patterns of other immune proteins, heat-shock proteins (HSPs), detoxification enzymes and antioxidant enzymes were more dissimilar, with some species exhibiting similar trends and co-occurrence through reproductive stages, while others exhibited variable or opposite patterns. These conserved and unique profiles likely in part reflect similarities and differences in selective pressure on reproductive stages of each species and may indicate differing abilities to respond to emergent pathogens or environmental change.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567132","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}
Peter T Euclide, Heiner Kuhl, Chris C Wilson, Kim T Scribner, Loren M Miller, Wendylee Stott, Wesley A Larson
Artificial propagation and wild release may influence the genetic integrity of wild populations. This practice has been prevalent in fisheries for centuries and is often termed 'stocking'. In the Laurentian Great Lakes (Great Lakes here-on), walleye populations faced declines from the 1950s to the 1970s, prompting extensive stocking efforts for restoration. By the mid-2010s, walleye populations showed signs of recovery, but the genetic legacy of stocking on population structure at the genomic level remains unclear. Using a dataset of 45,600 genome-aligned SNP loci genotyped in 1075 walleye individuals, we investigated the genetic impacts of over 50 years of stocking across the Great Lakes. Population structure was associated with both natural geographic barriers and stocking from non-native sources. Admixture between Lake Erie walleye and walleye from the re-populated Tittabawassee River indicate that stocking may have re-distributed putatively adaptive alleles around the Great Lakes. Genome scans identified FST outliers and evidence of selective sweeps, indicating local adaptation of spawning populations is likely. Notably, one genomic region showed strong differentiation between Muskegon River and walleye from the Tittabawassee River, which was re-populated by Muskegon strain walleye, suggesting admixture and selection both impact the observed genetic diversity. Overall, our study underscores how artificial propagation and translocations can significantly alter the evolutionary trajectory of populations. The findings highlight the complex interplay between stocking practices and population genetic diversity, emphasising the need for careful management strategies to preserve the genetic integrity of wild populations amidst conservation efforts.
{"title":"Human Impacts on Great Lakes Walleye Sander vitreus Structure, Diversity and Local Adaptation.","authors":"Peter T Euclide, Heiner Kuhl, Chris C Wilson, Kim T Scribner, Loren M Miller, Wendylee Stott, Wesley A Larson","doi":"10.1111/mec.17558","DOIUrl":"https://doi.org/10.1111/mec.17558","url":null,"abstract":"<p><p>Artificial propagation and wild release may influence the genetic integrity of wild populations. This practice has been prevalent in fisheries for centuries and is often termed 'stocking'. In the Laurentian Great Lakes (Great Lakes here-on), walleye populations faced declines from the 1950s to the 1970s, prompting extensive stocking efforts for restoration. By the mid-2010s, walleye populations showed signs of recovery, but the genetic legacy of stocking on population structure at the genomic level remains unclear. Using a dataset of 45,600 genome-aligned SNP loci genotyped in 1075 walleye individuals, we investigated the genetic impacts of over 50 years of stocking across the Great Lakes. Population structure was associated with both natural geographic barriers and stocking from non-native sources. Admixture between Lake Erie walleye and walleye from the re-populated Tittabawassee River indicate that stocking may have re-distributed putatively adaptive alleles around the Great Lakes. Genome scans identified F<sub>ST</sub> outliers and evidence of selective sweeps, indicating local adaptation of spawning populations is likely. Notably, one genomic region showed strong differentiation between Muskegon River and walleye from the Tittabawassee River, which was re-populated by Muskegon strain walleye, suggesting admixture and selection both impact the observed genetic diversity. Overall, our study underscores how artificial propagation and translocations can significantly alter the evolutionary trajectory of populations. The findings highlight the complex interplay between stocking practices and population genetic diversity, emphasising the need for careful management strategies to preserve the genetic integrity of wild populations amidst conservation efforts.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142563405","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}
Suvratha Jayaprasad, Valentina Peona, Simon J Ellerstrand, Roberto Rossini, Ignas Bunikis, Olga V Pettersson, Remi-André Olsen, Carl-Johan Rubin, Elisabet Einarsdottir, Franziska Bonath, Tessa M Bradford, Steven J B Cooper, Bengt Hansson, Alexander Suh, Takeshi Kawakami, Holger Schielzeth, Octavio M Palacios-Gimenez
The early evolution of sex chromosomes has remained obscure for more than a century. The Vandiemenella viatica species group of morabine grasshoppers is highly suited for studying the early stages of sex chromosome divergence and degeneration of the Y chromosome. This stems from the fact that neo-XY sex chromosomes have independently evolved multiple times by X-autosome fusions with different autosomes. Here, we generated new chromosome-level assemblies for two chromosomal races representing karyotypes with and without neo-sex chromosomes (P24XY and P24X0), and sequence data of a third chromosomal race with a different neo-XY chromosome system (P25XY). Interestingly, these two neo-XY chromosomal races are formed by different X-autosome fusions (involving chr1 and chrB, respectively), and we found that both neo-Y chromosomes have partly ceased to recombine with their neo-X counterpart. We show that the neo-XY chromosomes have diverged through accumulation of SNPs and structural mutations, and that many neo-Y-linked genes have degenerated since recombination ceased. However, the non-recombining regions of neo-Y chromosomes host non-degenerated genes crucial for sex determination, such as sex-lethal and transformer, alongside genes associated with spermatogenesis, fertility, and reproduction, illustrating their integrative role as a masculinizing supergene. Contrary to expectations, the neo-Y chromosomes showed (slightly) lower density of transposable elements (TEs) compared to other genomic regions. The study reveals the unique dynamics of young sex chromosomes, with evolution of recombination suppression and pronounced decay of (some) neo-sex chromosome genes, and provides a compelling case illustrating how chromosomal fusions and post-fusion mutational processes contribute to the evolution of supergenes.
一个多世纪以来,性染色体的早期进化一直模糊不清。摩拉宾蚱蜢的 Vandiemenella viatica 物种群非常适合研究性染色体分化和 Y 染色体退化的早期阶段。这是因为新XY性染色体是通过X-常染色体与不同的常染色体融合而独立进化多次的。在这里,我们生成了代表具有和不具有新性染色体核型的两个染色体种族(P24XY 和 P24X0)的新染色体组,以及具有不同新 XY 染色体系统的第三个染色体种族(P25XY)的序列数据。有趣的是,这两个新 XY 染色体种族是由不同的 X 自体融合(分别涉及 chr1 和 chrB)形成的,而且我们发现这两个新 Y 染色体都部分停止了与新 X 染色体的重组。我们发现,新 XY 染色体通过 SNPs 和结构突变的积累而发生了分化,许多新 Y 连锁基因在重组停止后发生了退化。然而,新-Y 染色体的非重组区域除了与精子发生、生育和繁殖相关的基因外,还含有对性别决定至关重要的未退化基因,如性致死基因和转化基因,这说明了它们作为男性化超级基因的整合作用。与预期相反,与其他基因组区域相比,新Y染色体上转座元件(TE)的密度(略低)。这项研究揭示了年轻性染色体的独特动态,即重组抑制的进化和(某些)新性染色体基因的明显衰变,并提供了一个令人信服的案例,说明染色体融合和融合后突变过程如何促进超级基因的进化。
{"title":"Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes.","authors":"Suvratha Jayaprasad, Valentina Peona, Simon J Ellerstrand, Roberto Rossini, Ignas Bunikis, Olga V Pettersson, Remi-André Olsen, Carl-Johan Rubin, Elisabet Einarsdottir, Franziska Bonath, Tessa M Bradford, Steven J B Cooper, Bengt Hansson, Alexander Suh, Takeshi Kawakami, Holger Schielzeth, Octavio M Palacios-Gimenez","doi":"10.1111/mec.17567","DOIUrl":"https://doi.org/10.1111/mec.17567","url":null,"abstract":"<p><p>The early evolution of sex chromosomes has remained obscure for more than a century. The Vandiemenella viatica species group of morabine grasshoppers is highly suited for studying the early stages of sex chromosome divergence and degeneration of the Y chromosome. This stems from the fact that neo-XY sex chromosomes have independently evolved multiple times by X-autosome fusions with different autosomes. Here, we generated new chromosome-level assemblies for two chromosomal races representing karyotypes with and without neo-sex chromosomes (P24XY and P24X0), and sequence data of a third chromosomal race with a different neo-XY chromosome system (P25XY). Interestingly, these two neo-XY chromosomal races are formed by different X-autosome fusions (involving chr1 and chrB, respectively), and we found that both neo-Y chromosomes have partly ceased to recombine with their neo-X counterpart. We show that the neo-XY chromosomes have diverged through accumulation of SNPs and structural mutations, and that many neo-Y-linked genes have degenerated since recombination ceased. However, the non-recombining regions of neo-Y chromosomes host non-degenerated genes crucial for sex determination, such as sex-lethal and transformer, alongside genes associated with spermatogenesis, fertility, and reproduction, illustrating their integrative role as a masculinizing supergene. Contrary to expectations, the neo-Y chromosomes showed (slightly) lower density of transposable elements (TEs) compared to other genomic regions. The study reveals the unique dynamics of young sex chromosomes, with evolution of recombination suppression and pronounced decay of (some) neo-sex chromosome genes, and provides a compelling case illustrating how chromosomal fusions and post-fusion mutational processes contribute to the evolution of supergenes.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542397","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}
Xin Sun, Emily Louisa Cavill, Ashot Margaryan, Jianqing Lin, Søren Thingaard, Tamrini A Said, Shyam Gopalakrishnan, M Thomas P Gilbert
The recently extirpated Zanzibar leopard was the only known African leopard (Panthera pardus spp.) population restricted exclusively to a major island habitat. Although its demise was driven through habitat change and conflict with humans, given its role as a keystone species for the Zanzibar Archipelago, its successful potential reintroduction might offer a means for helping preserve the natural biodiversity of its former habitat. Whether this is feasible, however, would be contingent on both whether closely related source populations can be identified on mainland Africa, and whether the Zanzibar form exhibited any special adaptations that might need to be considered when choosing such a source. In light of these questions, we genomically profiled two of the six known historic specimens, to explore whether they represent a realistic candidate for de-extirpation through reintroduction. Our analyses indicate that despite its geographical separation, the Zanzibar leopard shared a close genetic relationship with mainland East African individuals. Furthermore, although its uniqueness as an island population was emphasised by genomic signatures of high inbreeding and increased mutation load, the latter similar to the level of the critically endangered Amur leopard (P. p. orientalis), we find no evidence of functionally significant genetic diversity unique to Zanzibar. We therefore conclude that should attempts to restore leopards to Zanzibar be considered, then mainland East African leopards would provide a suitable gene pool.
最近灭绝的桑给巴尔豹是已知的非洲豹(Panthera pardus spp.)种群中唯一仅局限于一个主要岛屿栖息地的物种。虽然它的灭绝是由于栖息地的改变和与人类的冲突,但鉴于它是桑给巴尔群岛的关键物种,成功地重新引入它可能为帮助保护其前栖息地的自然生物多样性提供了一种手段。然而,这是否可行,将取决于能否在非洲大陆找到密切相关的来源种群,以及桑给巴尔种是否表现出任何特殊的适应性,在选择来源地时可能需要考虑这些因素。鉴于这些问题,我们对已知的六个历史标本中的两个进行了基因组分析,以探讨它们是否是通过重新引入来实现去外来化的现实候选物种。我们的分析表明,尽管桑给巴尔豹与东非大陆的个体在地理上相隔遥远,但它们之间却有着密切的遗传关系。此外,尽管近亲繁殖和变异负荷增加的基因组特征(后者与极度濒危的阿穆尔豹(P. p. orientalis)的水平相似)强调了桑给巴尔豹作为一个岛屿种群的独特性,但我们并没有发现桑给巴尔豹独有的具有重要功能的遗传多样性的证据。因此,我们得出结论,如果考虑在桑给巴尔恢复豹,那么东非大陆的豹将提供一个合适的基因库。
{"title":"A Genomic Exploration of the Possible De-Extirpation of the Zanzibar Leopard.","authors":"Xin Sun, Emily Louisa Cavill, Ashot Margaryan, Jianqing Lin, Søren Thingaard, Tamrini A Said, Shyam Gopalakrishnan, M Thomas P Gilbert","doi":"10.1111/mec.17566","DOIUrl":"https://doi.org/10.1111/mec.17566","url":null,"abstract":"<p><p>The recently extirpated Zanzibar leopard was the only known African leopard (Panthera pardus spp.) population restricted exclusively to a major island habitat. Although its demise was driven through habitat change and conflict with humans, given its role as a keystone species for the Zanzibar Archipelago, its successful potential reintroduction might offer a means for helping preserve the natural biodiversity of its former habitat. Whether this is feasible, however, would be contingent on both whether closely related source populations can be identified on mainland Africa, and whether the Zanzibar form exhibited any special adaptations that might need to be considered when choosing such a source. In light of these questions, we genomically profiled two of the six known historic specimens, to explore whether they represent a realistic candidate for de-extirpation through reintroduction. Our analyses indicate that despite its geographical separation, the Zanzibar leopard shared a close genetic relationship with mainland East African individuals. Furthermore, although its uniqueness as an island population was emphasised by genomic signatures of high inbreeding and increased mutation load, the latter similar to the level of the critically endangered Amur leopard (P. p. orientalis), we find no evidence of functionally significant genetic diversity unique to Zanzibar. We therefore conclude that should attempts to restore leopards to Zanzibar be considered, then mainland East African leopards would provide a suitable gene pool.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542396","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}