Paolo Moccetti, Jamie R. Dodd, Domino A. Joyce, Andy D. Nunn, Ben Gillespie, Jonathan D. Bolland
Fragmentation of watercourses poses a significant threat to biodiversity, particularly for migratory fish species. Mitigation measures such as fishways, have been increasingly implemented to restore river connectivity and support fish migration. The effects of such restoration efforts are typically tested using telemetry and fisheries methods, which do not fully capture the broader population movements that may have important consequences for population viability. We performed a before-and-after control-impact (BACI) study using genetic tools (SNPs) to investigate the effect of a newly implemented fishway, aiming to enhance upstream spawning migration of brown trout (Salmo trutta Linnaeus) in a reservoir with two headwater tributaries fragmented by man-made weirs. Another reservoir with two barrier-free tributaries was also analysed as a control. Our results showed that the isolated brown trout population was spawning in the reservoir before the installation of the fishway, and we found genetic structuring and differentiation between fragmented headwater tributaries before the fishway construction, but not in the control reservoir. Unexpectedly, after the fishway construction we observed signals consistent with increased genetic differentiation between populations of newly recruited juvenile fish in the reservoir tributary and fish in the reservoir. We propose this was caused by newly enabled philopatric behaviour of brown trout to their natal spawning tributary. In contrast, we did not find any genetic changes in the tributary without a fishway or in the barrier-free reservoir system. Given the scarcity of similar studies, we advocate for an increased use of genetic analyses in BACI studies to monitor and evaluate the effect of efforts to restore habitat connectivity and inform future management strategies.
{"title":"Genetic consequences of improved river connectivity in brown trout (Salmo trutta L.)","authors":"Paolo Moccetti, Jamie R. Dodd, Domino A. Joyce, Andy D. Nunn, Ben Gillespie, Jonathan D. Bolland","doi":"10.1111/eva.13660","DOIUrl":"https://doi.org/10.1111/eva.13660","url":null,"abstract":"<p>Fragmentation of watercourses poses a significant threat to biodiversity, particularly for migratory fish species. Mitigation measures such as fishways, have been increasingly implemented to restore river connectivity and support fish migration. The effects of such restoration efforts are typically tested using telemetry and fisheries methods, which do not fully capture the broader population movements that may have important consequences for population viability. We performed a before-and-after control-impact (BACI) study using genetic tools (SNPs) to investigate the effect of a newly implemented fishway, aiming to enhance upstream spawning migration of brown trout (<i>Salmo trutta</i> Linnaeus) in a reservoir with two headwater tributaries fragmented by man-made weirs. Another reservoir with two barrier-free tributaries was also analysed as a control. Our results showed that the isolated brown trout population was spawning in the reservoir before the installation of the fishway, and we found genetic structuring and differentiation between fragmented headwater tributaries before the fishway construction, but not in the control reservoir. Unexpectedly, after the fishway construction we observed signals consistent with increased genetic differentiation between populations of newly recruited juvenile fish in the reservoir tributary and fish in the reservoir. We propose this was caused by newly enabled philopatric behaviour of brown trout to their natal spawning tributary. In contrast, we did not find any genetic changes in the tributary without a fishway or in the barrier-free reservoir system. Given the scarcity of similar studies, we advocate for an increased use of genetic analyses in BACI studies to monitor and evaluate the effect of efforts to restore habitat connectivity and inform future management strategies.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13660","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140546698","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}
Amanda Kyle Gibson, Fabiane M. Mundim, Abbey L. Ramirez, Patricia Timper
Parasite local adaptation has been a major focus of (co)evolutionary research on host–parasite interactions. Studies of wild host–parasite systems frequently find that parasites paired with local, sympatric host genotypes perform better than parasites paired with allopatric host genotypes. In contrast, there are few such tests in biological control systems to establish whether biological control parasites commonly perform better on sympatric pest genotypes. This knowledge gap prevents the optimal design of biological control programs: strong local adaptation could argue for the use of sympatric parasites to achieve consistent pest control. To address this gap, we tested for local adaptation of the biological control bacterium Pasteuria penetrans to the root-knot nematode Meloidogyne arenaria, a global threat to a wide range of crops. We measured the probability and intensity of P. penetrans infection on sympatric and allopatric M. arenaria over the course of 4 years. Our design accounted for variation in adaptation across scales by conducting tests within and across fields, and we isolated the signature of parasite adaptation by comparing parasites collected over the course of the growing season. Our results are largely inconsistent with local adaptation of P. penetrans to M. arenaria: in 3 of 4 years, parasites performed similarly well in sympatric and allopatric combinations. In 1 year, however, infection probability was 28% higher for parasites paired with hosts from their sympatric plot, relative to parasites paired with hosts from other plots within the same field. These mixed results argue for population genetic data to characterize the scale of gene flow and genetic divergence in this system. Overall, our findings do not provide strong support for using P. penetrans from local fields to enhance biological control of Meloidogyne.
寄生虫的本地适应性一直是寄主-寄生虫相互作用(共)进化研究的一个重点。对野生寄主-寄生虫系统的研究经常发现,与本地同域寄主基因型配对的寄生虫比与异域寄主基因型配对的寄生虫表现更好。相比之下,在生物防治系统中很少有这样的测试来确定生物防治寄生虫是否通常在同域害虫基因型上表现更好。这一知识空白阻碍了生物防治计划的优化设计:强烈的地方适应性可能会主张使用同域寄生虫来实现一致的害虫控制。为了填补这一空白,我们测试了生物防治细菌巴斯德氏菌对根结线虫(Meloidogyne arenaria)的本地适应性,根结线虫是对多种作物的全球性威胁。我们测量了穿心莲巴斯德菌在4年时间里对同域和异域根结线虫的感染概率和强度。我们的设计通过在田块内和田块间进行测试,考虑了不同尺度的适应性差异,并通过比较生长季节中收集的寄生虫,分离出寄生虫适应性的特征。我们的结果在很大程度上与 P. penetrans 对 M. arenaria 的本地适应性不一致:在 4 年中的 3 年,寄生虫在同域和异域组合中的表现类似。但有一年,寄生虫与同域地块宿主配对的感染概率比与同一地块其他地块宿主配对的感染概率高出 28%。这些喜忧参半的结果表明,需要群体遗传数据来描述该系统中基因流动和遗传分化的规模。总之,我们的研究结果并不能有力地支持利用当地田间的穿心莲寄生虫来加强对褐飞虱的生物防治。
{"title":"Do biological control agents adapt to local pest genotypes? A multiyear test across geographic scales","authors":"Amanda Kyle Gibson, Fabiane M. Mundim, Abbey L. Ramirez, Patricia Timper","doi":"10.1111/eva.13682","DOIUrl":"https://doi.org/10.1111/eva.13682","url":null,"abstract":"<p>Parasite local adaptation has been a major focus of (co)evolutionary research on host–parasite interactions. Studies of wild host–parasite systems frequently find that parasites paired with local, sympatric host genotypes perform better than parasites paired with allopatric host genotypes. In contrast, there are few such tests in biological control systems to establish whether biological control parasites commonly perform better on sympatric pest genotypes. This knowledge gap prevents the optimal design of biological control programs: strong local adaptation could argue for the use of sympatric parasites to achieve consistent pest control. To address this gap, we tested for local adaptation of the biological control bacterium <i>Pasteuria penetrans</i> to the root-knot nematode <i>Meloidogyne arenaria</i>, a global threat to a wide range of crops. We measured the probability and intensity of <i>P. penetrans</i> infection on sympatric and allopatric <i>M. arenaria</i> over the course of 4 years. Our design accounted for variation in adaptation across scales by conducting tests within and across fields, and we isolated the signature of parasite adaptation by comparing parasites collected over the course of the growing season. Our results are largely inconsistent with local adaptation of <i>P. penetrans</i> to <i>M. arenaria</i>: in 3 of 4 years, parasites performed similarly well in sympatric and allopatric combinations. In 1 year, however, infection probability was 28% higher for parasites paired with hosts from their sympatric plot, relative to parasites paired with hosts from other plots within the same field. These mixed results argue for population genetic data to characterize the scale of gene flow and genetic divergence in this system. Overall, our findings do not provide strong support for using <i>P. penetrans</i> from local fields to enhance biological control of <i>Meloidogyne</i>.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13682","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140546701","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}
Aryn P. Wilder, Cynthia C. Steiner, Sarah Hendricks, Benjamin C. Haller, Chang Kim, Marisa L. Korody, Oliver A. Ryder
As biodiversity loss outpaces recovery, conservationists are increasingly turning to novel tools for preventing extinction, including cloning and in vitro gametogenesis of biobanked cells. However, restoration of populations can be hindered by low genetic diversity and deleterious genetic load. The persistence of the northern white rhino (Ceratotherium simum cottoni) now depends on the cryopreserved cells of 12 individuals. These banked genomes have higher genetic diversity than southern white rhinos (C. s. simum), a sister subspecies that successfully recovered from a severe bottleneck, but the potential impact of genetic load is unknown. We estimated how demographic history has shaped genome-wide genetic load in nine northern and 13 southern white rhinos. The bottleneck left southern white rhinos with more fixed and homozygous deleterious alleles and longer runs of homozygosity, whereas northern white rhinos retained more deleterious alleles masked in heterozygosity. To gauge the impact of genetic load on the fitness of a northern white rhino population restored from biobanked cells, we simulated recovery using fitness of southern white rhinos as a benchmark for a viable population. Unlike traditional restoration, cell-derived founders can be reintroduced in subsequent generations to boost lost genetic diversity and relieve inbreeding. In simulations with repeated reintroduction of founders into a restored population, the fitness cost of genetic load remained lower than that borne by southern white rhinos. Without reintroductions, rapid growth of the restored population (>20–30% per generation) would be needed to maintain comparable fitness. Our results suggest that inbreeding depression from genetic load is not necessarily a barrier to recovery of the northern white rhino and demonstrate how restoration from biobanked cells relieves some constraints of conventional restoration from a limited founder pool. Established conservation methods that protect healthy populations will remain paramount, but emerging technologies hold promise to bolster these tools to combat the extinction crisis.
由于生物多样性丧失的速度超过了恢复的速度,保护主义者越来越多地采用新工具来防止生物灭绝,包括克隆和生物库细胞的体外配子发生。然而,遗传多样性低和有害遗传负荷会阻碍种群的恢复。目前,北方白犀牛(Ceratotherium simum cottoni)的生存依赖于 12 个个体的低温保存细胞。与成功摆脱严重瓶颈的姐妹亚种南方白犀牛(C. s. simum)相比,这些储存的基因组具有更高的遗传多样性,但遗传负荷的潜在影响尚不清楚。我们估算了九头北方白犀牛和十三头南方白犀牛的人口历史如何影响了整个基因组的遗传负荷。瓶颈使南方白犀牛具有更多固定的同源有害等位基因和更长的同源性,而北方白犀牛则保留了更多被杂合度掩盖的有害等位基因。为了衡量遗传负荷对从生物库细胞中恢复的北方白犀牛种群的适应性的影响,我们以南方白犀牛的适应性作为可行种群的基准来模拟恢复。与传统的恢复不同,细胞来源的始祖犀牛可以在后代中重新引入,以提高丧失的遗传多样性并缓解近亲繁殖。在反复将创始者重新引入恢复种群的模拟中,遗传负荷的适应成本仍然低于南方白犀牛所承担的成本。如果没有重新引入,恢复后的种群需要快速增长(每代20%-30%)才能维持可比的适应性。我们的研究结果表明,遗传负荷造成的近亲繁殖抑制并不一定会阻碍北方白犀牛的恢复,同时也证明了从生物库细胞中恢复种群可以缓解传统的从有限的始祖种群中恢复种群的某些限制。保护健康种群的既定保护方法仍将是最重要的,但新兴技术有望加强这些工具,以应对灭绝危机。
{"title":"Genetic load and viability of a future restored northern white rhino population","authors":"Aryn P. Wilder, Cynthia C. Steiner, Sarah Hendricks, Benjamin C. Haller, Chang Kim, Marisa L. Korody, Oliver A. Ryder","doi":"10.1111/eva.13683","DOIUrl":"https://doi.org/10.1111/eva.13683","url":null,"abstract":"<p>As biodiversity loss outpaces recovery, conservationists are increasingly turning to novel tools for preventing extinction, including cloning and in vitro gametogenesis of biobanked cells. However, restoration of populations can be hindered by low genetic diversity and deleterious genetic load. The persistence of the northern white rhino (<i>Ceratotherium simum cottoni</i>) now depends on the cryopreserved cells of 12 individuals. These banked genomes have higher genetic diversity than southern white rhinos (<i>C. s. simum</i>), a sister subspecies that successfully recovered from a severe bottleneck, but the potential impact of genetic load is unknown. We estimated how demographic history has shaped genome-wide genetic load in nine northern and 13 southern white rhinos. The bottleneck left southern white rhinos with more fixed and homozygous deleterious alleles and longer runs of homozygosity, whereas northern white rhinos retained more deleterious alleles masked in heterozygosity. To gauge the impact of genetic load on the fitness of a northern white rhino population restored from biobanked cells, we simulated recovery using fitness of southern white rhinos as a benchmark for a viable population. Unlike traditional restoration, cell-derived founders can be reintroduced in subsequent generations to boost lost genetic diversity and relieve inbreeding. In simulations with repeated reintroduction of founders into a restored population, the fitness cost of genetic load remained lower than that borne by southern white rhinos. Without reintroductions, rapid growth of the restored population (>20–30% per generation) would be needed to maintain comparable fitness. Our results suggest that inbreeding depression from genetic load is not necessarily a barrier to recovery of the northern white rhino and demonstrate how restoration from biobanked cells relieves some constraints of conventional restoration from a limited founder pool. Established conservation methods that protect healthy populations will remain paramount, but emerging technologies hold promise to bolster these tools to combat the extinction crisis.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13683","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140546607","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}
Alexandra Pavlova, Nadja M. Schneller, Mark Lintermans, Matt Beitzel, Diana A. Robledo-Ruiz, Paul Sunnucks
Augmenting depleted genetic diversity can improve the fitness and evolutionary potential of wildlife populations, but developing effective management approaches requires genetically monitored test cases. One such case is the small, isolated and inbred Cotter River population of an endangered Australian freshwater fish, the Macquarie perch Macquaria australasica, which over 3 years (2017–2019) received 71 translocated migrants from a closely related, genetically more diverse population. We used genetic monitoring to test whether immigrants bred, interbred with local fish and augmented population genetic diversity. We also investigated whether levels of river flow affected recruitment, inbreeding depression and juvenile dispersal. Fish length was used to estimate the age, birth year cohort and growth of 524 individuals born between 2016 and 2020 under variable flow conditions. DArT genome-wide genotypes were used to assess individual ancestry, heterozygosity, short-term effective population size and identify parent-offspring and full-sibling families. Of 442 individuals born after translocations commenced, only two (0.45%) were of mixed ancestry; these were half-sibs with one translocated parent in common. Numbers of breeders and genetic diversity for five birth year cohorts of the Cotter River fish were low, especially in low-flow years. Additionally, individuals born in the year of lowest flow evidently suffered from inbreeding depression for juvenile growth. The year of highest flow was associated with the largest number of breeders, lowest inbreeding in the offspring and greatest juvenile dispersal distances. Genetic diversity decreased in the upstream direction, flagging restricted access of breeders to the most upstream breeding sites, exacerbated by low river flow. Our results suggest that the effectiveness of translocations could be increased by focussing on upstream sites and moving more individuals per year; using riverine sources should be considered. Our results indicate that river flow sufficient to facilitate fish movement through the system would increase the number of breeders, promote individuals' growth, reduce inbreeding depression and promote genetic rescue.
{"title":"Planning and implementing genetic rescue of an endangered freshwater fish population in a regulated river, where low flow reduces breeding opportunities and may trigger inbreeding depression","authors":"Alexandra Pavlova, Nadja M. Schneller, Mark Lintermans, Matt Beitzel, Diana A. Robledo-Ruiz, Paul Sunnucks","doi":"10.1111/eva.13679","DOIUrl":"https://doi.org/10.1111/eva.13679","url":null,"abstract":"<p>Augmenting depleted genetic diversity can improve the fitness and evolutionary potential of wildlife populations, but developing effective management approaches requires genetically monitored test cases. One such case is the small, isolated and inbred Cotter River population of an endangered Australian freshwater fish, the Macquarie perch <i>Macquaria australasica</i>, which over 3 years (2017–2019) received 71 translocated migrants from a closely related, genetically more diverse population. We used genetic monitoring to test whether immigrants bred, interbred with local fish and augmented population genetic diversity. We also investigated whether levels of river flow affected recruitment, inbreeding depression and juvenile dispersal. Fish length was used to estimate the age, birth year cohort and growth of 524 individuals born between 2016 and 2020 under variable flow conditions. DArT genome-wide genotypes were used to assess individual ancestry, heterozygosity, short-term effective population size and identify parent-offspring and full-sibling families. Of 442 individuals born after translocations commenced, only two (0.45%) were of mixed ancestry; these were half-sibs with one translocated parent in common. Numbers of breeders and genetic diversity for five birth year cohorts of the Cotter River fish were low, especially in low-flow years. Additionally, individuals born in the year of lowest flow evidently suffered from inbreeding depression for juvenile growth. The year of highest flow was associated with the largest number of breeders, lowest inbreeding in the offspring and greatest juvenile dispersal distances. Genetic diversity decreased in the upstream direction, flagging restricted access of breeders to the most upstream breeding sites, exacerbated by low river flow. Our results suggest that the effectiveness of translocations could be increased by focussing on upstream sites and moving more individuals per year; using riverine sources should be considered. Our results indicate that river flow sufficient to facilitate fish movement through the system would increase the number of breeders, promote individuals' growth, reduce inbreeding depression and promote genetic rescue.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13679","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140546700","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}
Austin C. Koontz, Emily K. Schumacher, Emma S. Spence, Sean M. Hoban
Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For Quercus acerifolia, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for Q. boyntonii. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.
植物园和树木园收藏的植物是异地保护的重要组成部分。保持这些收藏的遗传多样性,可使它们成为补充野生种群的资源。然而,大多数为实现足够的异地遗传多样性而推荐的最小样本量都是基于微卫星标记,而这些样本量在最近开发的下一代测序(NGS)方法中是否仍然有效仍是未知数。为了填补这一知识空白,我们研究了两种濒危橡树物种的园林样本和野生样本中的微卫星和单核苷酸多态性(SNPs)得出的原生境保护状况和采样建议有何不同。与微卫星相比,SNPs 对野生等位基因多样性的原位代表性较低,最小样本量估计值也略低,而对 Q. boyntonii 而言,每种标记的结果基本相似。应用缺失数据过滤器往往会提高原位代表性,而不同 SNP 调用方法的影响则取决于所分析的物种。不同标记物对物种内种群分化的测量结果大致相似,但更多的 SNP 位点可提高种群结构的分辨率,并更清晰地将异地个体分配到野生源种群中。我们的研究结果为今后利用 SNP 数据进行异地保护评估提供了指导,例如缺失数据过滤器的应用和参考基因组的使用,并说明微卫星和 SNP 仍是植物园和树木园确保其收藏品遗传多样性的可行选择。
{"title":"Ex situ conservation of two rare oak species using microsatellite and SNP markers","authors":"Austin C. Koontz, Emily K. Schumacher, Emma S. Spence, Sean M. Hoban","doi":"10.1111/eva.13650","DOIUrl":"https://doi.org/10.1111/eva.13650","url":null,"abstract":"<p>Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For <i>Quercus acerifolia</i>, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for <i>Q. boyntonii</i>. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13650","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140192117","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}
Mary A. Rogalski, Elizabeth S. Baker, Clara M. Benadon, Christoph Tatgenhorst, Brady R. Nichols
The increasing application of road deicing agents (e.g., NaCl) has caused widespread salinization of freshwater environments. Chronic exposure to toxic NaCl levels can impact freshwater biota at genome to ecosystem scales, yet the degree of harm caused by road salt pollution is likely to vary among habitats and populations. The background ion chemistry of freshwater environments may strongly impact NaCl toxicity, with greater harm occurring in ion-poor, soft water conditions. In addition, populations exposed to salinization may evolve increased NaCl tolerance. Notably, if organisms are adapted to the water chemistry of their natal environment, toxicity responses may also vary among populations in a given test medium. We examined the potential for this evolutionary and environmental context to interact in shaping NaCl toxicity with a pair of laboratory reciprocal transplant toxicity experiments, using natural populations of the water flea Daphnia ambigua collected from three lakes that vary in ion availability and composition. We observed a strong effect of the lake water environment on NaCl toxicity in both trials. NaCl caused a much greater decline in reproduction and r in lake water from a low-ion/calcium-poor environment (20 μS/cm specific conductance; 1.7 mg/L Ca2+) compared with water from both a Ca2+-rich lake (55 μS/cm; 7.2 mg/L Ca2+) and an ion-rich coastal lake (420 μS/cm; 3.4 mg/L Ca2+). Daphnia from this coastal lake were most robust to the effects of NaCl on reproduction and r. A significant interaction between the population and lake water environment shaped survival in both trials, suggesting that local adaptation to the test waters used may have contributed to toxicity responses. Our findings that the lake water environment, adaptation to that environment, and adaptation to a contaminant of interest may shape toxicity demonstrate the importance of considering environmental and biological complexity in mitigating pollution impacts.
{"title":"Lake water chemistry and local adaptation shape NaCl toxicity in Daphnia ambigua","authors":"Mary A. Rogalski, Elizabeth S. Baker, Clara M. Benadon, Christoph Tatgenhorst, Brady R. Nichols","doi":"10.1111/eva.13668","DOIUrl":"https://doi.org/10.1111/eva.13668","url":null,"abstract":"<p>The increasing application of road deicing agents (e.g., NaCl) has caused widespread salinization of freshwater environments. Chronic exposure to toxic NaCl levels can impact freshwater biota at genome to ecosystem scales, yet the degree of harm caused by road salt pollution is likely to vary among habitats and populations. The background ion chemistry of freshwater environments may strongly impact NaCl toxicity, with greater harm occurring in ion-poor, soft water conditions. In addition, populations exposed to salinization may evolve increased NaCl tolerance. Notably, if organisms are adapted to the water chemistry of their natal environment, toxicity responses may also vary among populations in a given test medium. We examined the potential for this evolutionary and environmental context to interact in shaping NaCl toxicity with a pair of laboratory reciprocal transplant toxicity experiments, using natural populations of the water flea <i>Daphnia ambigua</i> collected from three lakes that vary in ion availability and composition. We observed a strong effect of the lake water environment on NaCl toxicity in both trials. NaCl caused a much greater decline in reproduction and <i>r</i> in lake water from a low-ion/calcium-poor environment (20 μS/cm specific conductance; 1.7 mg/L Ca<sup>2+</sup>) compared with water from both a Ca<sup>2+</sup>-rich lake (55 μS/cm; 7.2 mg/L Ca<sup>2+</sup>) and an ion-rich coastal lake (420 μS/cm; 3.4 mg/L Ca<sup>2+</sup>). <i>Daphnia</i> from this coastal lake were most robust to the effects of NaCl on reproduction and <i>r</i>. A significant interaction between the population and lake water environment shaped survival in both trials, suggesting that local adaptation to the test waters used may have contributed to toxicity responses. Our findings that the lake water environment, adaptation to that environment, and adaptation to a contaminant of interest may shape toxicity demonstrate the importance of considering environmental and biological complexity in mitigating pollution impacts.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13668","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140192114","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}
Laura C. Goetz, Hayley Nuetzel, David L. J. Vendrami, Anne K. Beulke, Eric C. Anderson, John Carlos Garza, Devon E. Pearse
Populations composed of individuals descended from multiple distinct genetic lineages often feature significant differences in phenotypic frequencies. We considered hatchery production of steelhead, the migratory anadromous form of the salmonid species Oncorhynchus mykiss, and investigated how differences among genetic lineages and environmental variation impacted life history traits. We genotyped 23,670 steelhead returning to the four California Central Valley hatcheries over 9 years from 2011 to 2019, confidently assigning parentage to 13,576 individuals to determine age and date of spawning and rates of iteroparity and repeat spawning within each year. We found steelhead from different genetic lineages showed significant differences in adult life history traits despite inhabiting similar environments. Differences between coastal and Central Valley steelhead lineages contributed to significant differences in age at return, timing of spawning, and rates of iteroparity among programs. In addition, adaptive genomic variation associated with life history development in this species varied among hatchery programs and was associated with the age of steelhead spawners only in the coastal lineage population. Environmental variation likely contributed to variations in phenotypic patterns observed over time, as our study period spanned both a marine heatwave and a serious drought in California. Our results highlight evidence of a strong genetic component underlying known phenotypic differences in life history traits between two steelhead lineages.
{"title":"Genetic parentage reveals the (un)natural history of Central Valley hatchery steelhead","authors":"Laura C. Goetz, Hayley Nuetzel, David L. J. Vendrami, Anne K. Beulke, Eric C. Anderson, John Carlos Garza, Devon E. Pearse","doi":"10.1111/eva.13681","DOIUrl":"10.1111/eva.13681","url":null,"abstract":"<p>Populations composed of individuals descended from multiple distinct genetic lineages often feature significant differences in phenotypic frequencies. We considered hatchery production of steelhead, the migratory anadromous form of the salmonid species <i>Oncorhynchus mykiss,</i> and investigated how differences among genetic lineages and environmental variation impacted life history traits. We genotyped 23,670 steelhead returning to the four California Central Valley hatcheries over 9 years from 2011 to 2019, confidently assigning parentage to 13,576 individuals to determine age and date of spawning and rates of iteroparity and repeat spawning within each year. We found steelhead from different genetic lineages showed significant differences in adult life history traits despite inhabiting similar environments. Differences between coastal and Central Valley steelhead lineages contributed to significant differences in age at return, timing of spawning, and rates of iteroparity among programs. In addition, adaptive genomic variation associated with life history development in this species varied among hatchery programs and was associated with the age of steelhead spawners only in the coastal lineage population. Environmental variation likely contributed to variations in phenotypic patterns observed over time, as our study period spanned both a marine heatwave and a serious drought in California. Our results highlight evidence of a strong genetic component underlying known phenotypic differences in life history traits between two steelhead lineages.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10956469/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140183292","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}
Zachary L. Robinson, Jeff Stephenson, Kim Vertacnik, Stuart Willis, Rebekah Horn, Jesse McCane, D. Katharine Coykendall, Shawn R. Narum
Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage-based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species-specific Genotyping-in-Thousands by sequencing (GT-seq) panels. For laboratories involved in large-scale genotyping efforts, diagnosing non-target species and reassigning them to the appropriate monitoring program can be costly and time-consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross-species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species-specific GT-seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species-informative amplicons (16) were newly identified from the four existing GT-seq panels, thus demonstrating a low-cost approach to species identification when using targeted sequencing methods. A species-calling script was developed that is tailored for routine GT-seq genotyping pipelines and automates the identification of non-target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low-frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost-effective approach to species identification for genetic monitoring programs.
{"title":"Efficient species identification for Pacific salmon genetic monitoring programs","authors":"Zachary L. Robinson, Jeff Stephenson, Kim Vertacnik, Stuart Willis, Rebekah Horn, Jesse McCane, D. Katharine Coykendall, Shawn R. Narum","doi":"10.1111/eva.13680","DOIUrl":"https://doi.org/10.1111/eva.13680","url":null,"abstract":"<p>Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage-based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species-specific Genotyping-in-Thousands by sequencing (GT-seq) panels. For laboratories involved in large-scale genotyping efforts, diagnosing non-target species and reassigning them to the appropriate monitoring program can be costly and time-consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross-species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species-specific GT-seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species-informative amplicons (16) were newly identified from the four existing GT-seq panels, thus demonstrating a low-cost approach to species identification when using targeted sequencing methods. A species-calling script was developed that is tailored for routine GT-seq genotyping pipelines and automates the identification of non-target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low-frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost-effective approach to species identification for genetic monitoring programs.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13680","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140164433","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}
Mumbi Chege, Bobbie Sewalt, Francis Lesilau, Geert de Snoo, Bruce D. Patterson, Linus Kariuki, Moses Otiende, Patrick Omondi, Hans de Iongh, K. Vrieling, Laura D. Bertola
The decline of lions (Panthera leo) in Kenya has raised conservation concerns about their overall population health and long-term survival. This study aimed to assess the genetic structure, differentiation and diversity of lion populations in the country, while considering the influence of past management practices. Using a lion-specific Single Nucleotide Polymorphism (SNP) panel, we genotyped 171 individuals from 12 populations representative of areas with permanent lion presence. Our results revealed a distinct genetic pattern with pronounced population structure, confirmed a north-south split and found no indication of inbreeding in any of the tested populations. Differentiation seems to be primarily driven by geographical barriers, human presence and climatic factors, but management practices may have also affected the observed patterns. Notably, the Tsavo population displayed evidence of admixture, perhaps attributable to its geographic location as a suture zone, vast size or past translocations, while the fenced populations of Lake Nakuru National Park and Solio Ranch exhibited reduced genetic diversity due to restricted natural dispersal. The Amboseli population had a high number of monomorphic loci likely reflecting a historical population decline. This illustrates that patterns of genetic diversity should be seen in the context of population histories and that future management decisions should take these insights into account. To address the conservation implications of our findings, we recommend prioritizing the maintenance of suitable habitats to facilitate population connectivity. Initiation of genetic restoration efforts and separately managing populations with unique evolutionary histories is crucial for preserving genetic diversity and promoting long-term population viability.
{"title":"Genetic diversity of lion populations in Kenya: Evaluating past management practices and recommendations for future conservation actions","authors":"Mumbi Chege, Bobbie Sewalt, Francis Lesilau, Geert de Snoo, Bruce D. Patterson, Linus Kariuki, Moses Otiende, Patrick Omondi, Hans de Iongh, K. Vrieling, Laura D. Bertola","doi":"10.1111/eva.13676","DOIUrl":"https://doi.org/10.1111/eva.13676","url":null,"abstract":"<p>The decline of lions (<i>Panthera leo</i>) in Kenya has raised conservation concerns about their overall population health and long-term survival. This study aimed to assess the genetic structure, differentiation and diversity of lion populations in the country, while considering the influence of past management practices. Using a lion-specific Single Nucleotide Polymorphism (SNP) panel, we genotyped 171 individuals from 12 populations representative of areas with permanent lion presence. Our results revealed a distinct genetic pattern with pronounced population structure, confirmed a north-south split and found no indication of inbreeding in any of the tested populations. Differentiation seems to be primarily driven by geographical barriers, human presence and climatic factors, but management practices may have also affected the observed patterns. Notably, the Tsavo population displayed evidence of admixture, perhaps attributable to its geographic location as a suture zone, vast size or past translocations, while the fenced populations of Lake Nakuru National Park and Solio Ranch exhibited reduced genetic diversity due to restricted natural dispersal. The Amboseli population had a high number of monomorphic loci likely reflecting a historical population decline. This illustrates that patterns of genetic diversity should be seen in the context of population histories and that future management decisions should take these insights into account. To address the conservation implications of our findings, we recommend prioritizing the maintenance of suitable habitats to facilitate population connectivity. Initiation of genetic restoration efforts and separately managing populations with unique evolutionary histories is crucial for preserving genetic diversity and promoting long-term population viability.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13676","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140164434","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}
Laurie Lecomte, Mariann Árnyasi, Anne-Laure Ferchaud, Matthew Kent, Sigbjørn Lien, Kristina Stenløkk, Florent Sylvestre, Louis Bernatchez, Claire Mérot
Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short-read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine-scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (<50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short- (16X) and long-read sequencing (20X) for variant discovery with graph-based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns of FST and density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore demonstrates the feasibility of large-scale SV characterization and highlights its relevance for salmonid population genomics.
{"title":"Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations","authors":"Laurie Lecomte, Mariann Árnyasi, Anne-Laure Ferchaud, Matthew Kent, Sigbjørn Lien, Kristina Stenløkk, Florent Sylvestre, Louis Bernatchez, Claire Mérot","doi":"10.1111/eva.13653","DOIUrl":"https://doi.org/10.1111/eva.13653","url":null,"abstract":"<p>Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short-read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (<i>Salmo salar</i>), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine-scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (<50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short- (16X) and long-read sequencing (20X) for variant discovery with graph-based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns of <i>F</i><sub>ST</sub> and density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore demonstrates the feasibility of large-scale SV characterization and highlights its relevance for salmonid population genomics.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13653","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140135308","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}