R. Andrew King, Charlie D. Ellis, Dorte Bekkevold, Dennis Ensing, Thomas Lecointre, Daniel R. Osmond, Adam Piper, Dylan E. Roberts, Sophie Launey, Jamie R. Stevens
Populations of anadromous brown trout, also known as sea trout, have suffered recent marked declines in abundance due to multiple factors, including climate change and human activities. While much is known about their freshwater phase, less is known about the species' marine feeding migrations. This situation is hindering the effective management and conservation of anadromous trout in the marine environment. Using a panel of 95 single nucleotide polymorphism markers we developed a genetic baseline, which demonstrated strong regional structuring of genetic diversity in trout populations around the English Channel and adjacent waters. Extensive baseline testing showed this structuring allowed high-confidence assignment of known-origin individuals to region of origin. This study presents new data on the movements of anadromous trout in the English Channel and southern North Sea. Assignment of anadromous trout sampled from 12 marine and estuarine localities highlighted contrasting results for these areas. The majority of these fisheries are composed predominately of stocks local to the sampling location. However, there were multiple cases of long-distance movements of anadromous trout, with several individuals originating from rivers in northeast England being caught in the English Channel and southern North Sea, in some cases more than 1000 km from their natal region. These results have implications for the management of sea trout in inshore waters around the English Channel and southern North Sea.
{"title":"Leveraging the genetic diversity of trout in the rivers of the British Isles and northern France to understand the movements of sea trout (Salmo trutta L.) around the English Channel","authors":"R. Andrew King, Charlie D. Ellis, Dorte Bekkevold, Dennis Ensing, Thomas Lecointre, Daniel R. Osmond, Adam Piper, Dylan E. Roberts, Sophie Launey, Jamie R. Stevens","doi":"10.1111/eva.13759","DOIUrl":"10.1111/eva.13759","url":null,"abstract":"<p>Populations of anadromous brown trout, also known as sea trout, have suffered recent marked declines in abundance due to multiple factors, including climate change and human activities. While much is known about their freshwater phase, less is known about the species' marine feeding migrations. This situation is hindering the effective management and conservation of anadromous trout in the marine environment. Using a panel of 95 single nucleotide polymorphism markers we developed a genetic baseline, which demonstrated strong regional structuring of genetic diversity in trout populations around the English Channel and adjacent waters. Extensive baseline testing showed this structuring allowed high-confidence assignment of known-origin individuals to region of origin. This study presents new data on the movements of anadromous trout in the English Channel and southern North Sea. Assignment of anadromous trout sampled from 12 marine and estuarine localities highlighted contrasting results for these areas. The majority of these fisheries are composed predominately of stocks local to the sampling location. However, there were multiple cases of long-distance movements of anadromous trout, with several individuals originating from rivers in northeast England being caught in the English Channel and southern North Sea, in some cases more than 1000 km from their natal region. These results have implications for the management of sea trout in inshore waters around the English Channel and southern North Sea.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747033","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}
Xuezhen Ge, Jonathan A. Newman, Cortland K. Griswold
Species distribution models (SDMs) are often built upon the “niche conservatism” assumption, such that they ignore the possibility of “evolutionary rescue” and may underestimate species' future range limits under climate change. We select aphids and ladybirds as model species and develop an eco-evolutionary model to explore evolutionary rescue in a predator–prey system under climate change. We model the adaptive change of species' thermal performances, accounting for biotic interactions. Our study suggests that, without considering evolutionary adaptation, the warming climate will result in a reduction in aphid populations and the extinction of ladybirds in large parts of the United States. However, when incorporating evolutionary adaptation into the model, aphids can adapt to climate change, whereas ladybirds demonstrate geographic variation in their evolutionary rescue potential. Specifically, ladybirds in southern regions are more likely to be rescued than those in the north. In certain northern regions, ladybirds do not avoid extinction due to severe warming trends and seasonality of the climate. While higher warming trends do prompt stronger evolutionary changes in phenotype, they also lead to reduced aphid population abundance such that ecology constrains ladybird population growth. Higher seasonality induces an ecological effect by limiting the length of reproductive season, thereby reducing the capacity for evolutionary rescue. Together, these findings reveal the complex interplay between ecological and evolutionary dynamics in the context of evolutionary adaptation to climate change.
{"title":"Geographic variation in evolutionary rescue under climate change in a crop pest–predator system","authors":"Xuezhen Ge, Jonathan A. Newman, Cortland K. Griswold","doi":"10.1111/eva.13750","DOIUrl":"10.1111/eva.13750","url":null,"abstract":"<p>Species distribution models (SDMs) are often built upon the “niche conservatism” assumption, such that they ignore the possibility of “evolutionary rescue” and may underestimate species' future range limits under climate change. We select aphids and ladybirds as model species and develop an eco-evolutionary model to explore evolutionary rescue in a predator–prey system under climate change. We model the adaptive change of species' thermal performances, accounting for biotic interactions. Our study suggests that, without considering evolutionary adaptation, the warming climate will result in a reduction in aphid populations and the extinction of ladybirds in large parts of the United States. However, when incorporating evolutionary adaptation into the model, aphids can adapt to climate change, whereas ladybirds demonstrate geographic variation in their evolutionary rescue potential. Specifically, ladybirds in southern regions are more likely to be rescued than those in the north. In certain northern regions, ladybirds do not avoid extinction due to severe warming trends and seasonality of the climate. While higher warming trends do prompt stronger evolutionary changes in phenotype, they also lead to reduced aphid population abundance such that ecology constrains ladybird population growth. Higher seasonality induces an ecological effect by limiting the length of reproductive season, thereby reducing the capacity for evolutionary rescue. Together, these findings reveal the complex interplay between ecological and evolutionary dynamics in the context of evolutionary adaptation to climate change.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261214/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747016","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}
Andrea Bertram, Justin Bell, Chris Brauer, David Fairclough, Paul Hamer, Jonathan Sandoval-Castillo, Maren Wellenreuther, Luciano B. Beheregaray
Obtaining reliable estimates of the effective number of breeders (Nb) and generational effective population size (Ne) for fishery-important species is challenging because they are often iteroparous and highly abundant, which can lead to bias and imprecision. However, recent advances in understanding of these parameters, as well as the development of bias correction methods, have improved the capacity to generate reliable estimates. We utilized samples of both single-cohort young of the year and mixed-age adults from two geographically and genetically isolated stocks of the Australasian snapper (Chrysophrys auratus) to investigate the feasibility of generating reliable Nb and Ne estimates for a fishery species. Snapper is an abundant, iteroparous broadcast spawning teleost that is heavily exploited by recreational and commercial fisheries. Employing neutral genome-wide SNPs and the linkage-disequilibrium method, we determined that the most reliable Nb and Ne estimates could be derived by genotyping at least 200 individuals from a single cohort. Although our estimates made from the mixed-age adult samples were generally lower and less precise than those based on a single cohort, they still proved useful for understanding relative differences in genetic effective size between stocks. The correction formulas applied to adjust for biases due to physical linkage of loci and age structure resulted in substantial upward modifications of our estimates, demonstrating the importance of applying these bias corrections. Our findings provide important guidelines for estimating Nb and Ne for iteroparous species with large populations. This work also highlights the utility of samples originally collected for stock structure and stock assessment work for investigating genetic effective size in fishery-important species.
获得重要渔业物种有效繁殖数量(N b)和世代有效种群数量(N e)的可靠估算值具有挑战性,因为这些物种通常是迭代繁殖且数量丰富,这可能导致偏差和不精确。然而,最近对这些参数的理解以及偏差校正方法的发展提高了产生可靠估计值的能力。我们利用澳大利亚鲷鱼(Chrysophrys auratus)两个地理和遗传隔离种群的单群幼鱼和混龄成鱼样本,研究为渔业物种生成可靠的 N b 和 N e 估计值的可行性。鲷鱼是一种丰富的迭代广播产卵远洋鱼类,被休闲渔业和商业渔业大量捕捞。利用中性全基因组 SNPs 和连锁失衡法,我们确定最可靠的 N b 和 N e 估计值可通过对来自一个群组的至少 200 个个体进行基因分型得出。尽管我们从混龄成鱼样本中得出的估计值通常比基于单一群组的估计值低且不精确,但它们仍然有助于了解种群间遗传有效大小的相对差异。应用校正公式来调整由于位点的物理连接和年龄结构造成的偏差,导致我们的估计值大幅上调,这表明了应用这些偏差校正的重要性。我们的研究结果为估算具有大量种群的迭代物种的 N b 和 N e 提供了重要指导。这项工作还强调了最初为种群结构和种群评估工作采集的样本在调查重要渔业物种遗传有效大小方面的实用性。
{"title":"Estimation of effective number of breeders and effective population size in an abundant and heavily exploited marine teleost","authors":"Andrea Bertram, Justin Bell, Chris Brauer, David Fairclough, Paul Hamer, Jonathan Sandoval-Castillo, Maren Wellenreuther, Luciano B. Beheregaray","doi":"10.1111/eva.13758","DOIUrl":"10.1111/eva.13758","url":null,"abstract":"<p>Obtaining reliable estimates of the effective number of breeders (<i>N</i><sub>b</sub>) and generational effective population size (<i>N</i><sub>e</sub>) for fishery-important species is challenging because they are often iteroparous and highly abundant, which can lead to bias and imprecision. However, recent advances in understanding of these parameters, as well as the development of bias correction methods, have improved the capacity to generate reliable estimates. We utilized samples of both single-cohort young of the year and mixed-age adults from two geographically and genetically isolated stocks of the Australasian snapper (<i>Chrysophrys auratus</i>) to investigate the feasibility of generating reliable <i>N</i><sub>b</sub> and <i>N</i><sub>e</sub> estimates for a fishery species. Snapper is an abundant, iteroparous broadcast spawning teleost that is heavily exploited by recreational and commercial fisheries. Employing neutral genome-wide SNPs and the linkage-disequilibrium method, we determined that the most reliable <i>N</i><sub>b</sub> and <i>N</i><sub>e</sub> estimates could be derived by genotyping at least 200 individuals from a single cohort. Although our estimates made from the mixed-age adult samples were generally lower and less precise than those based on a single cohort, they still proved useful for understanding relative differences in genetic effective size between stocks. The correction formulas applied to adjust for biases due to physical linkage of loci and age structure resulted in substantial upward modifications of our estimates, demonstrating the importance of applying these bias corrections. Our findings provide important guidelines for estimating <i>N</i><sub>b</sub> and <i>N</i><sub>e</sub> for iteroparous species with large populations. This work also highlights the utility of samples originally collected for stock structure and stock assessment work for investigating genetic effective size in fishery-important species.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261160/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747015","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}
Anita Wray, Eleni Petrou, Krista M. Nichols, Robert Pacunski, Larry LeClair, Kelly S. Andrews, Marty Kardos, Lorenz Hauser
Hybridization can provide evolutionary benefits (e.g., population resilience to climate change) through the introduction of adaptive alleles and increase of genetic diversity. Nevertheless, management strategies may be designed based only on the parental species within a hybrid zone, without considering the hybrids. This can lead to ineffective spatial management of species, which can directly harm population diversity and negatively impact food webs. Three species of rockfish (Brown Rockfish (Sebastes caurinus), Copper Rockfish (S. auriculatus), and Quillback Rockfish (S. maliger)) are known to hybridize within Puget Sound, Washington, but genetic data from these species are used to infer population structure in the entire genus, including in species that do not hybridize. The goal of this project was to estimate the hybridization rates within the region and determine the effect of hybridization on geographic patterns of genetic structure. We sequenced 290 Brown, Copper, and Quillback rockfish using restriction-site associated DNA sequencing (RADseq) from four regions within and outside Puget Sound, Washington. We show that (i) hybridization within Puget Sound was asymmetrical, not recent, widespread among individuals, and relatively low level within the genome, (ii) hybridization affected population structure in Copper and Brown rockfish, but not in Quillback Rockfish and (iii) after taking hybridization into account we found limited directional dispersal in Brown and Copper rockfish, and evidence for two isolated populations in Quillback Rockfish. Our results suggest that rockfish population structure is species-specific, dependent on the extent of hybridization, and cannot be inferred from one species to another despite similar life history.
{"title":"Contrasting effect of hybridization on genetic differentiation in three rockfish species with similar life history","authors":"Anita Wray, Eleni Petrou, Krista M. Nichols, Robert Pacunski, Larry LeClair, Kelly S. Andrews, Marty Kardos, Lorenz Hauser","doi":"10.1111/eva.13749","DOIUrl":"https://doi.org/10.1111/eva.13749","url":null,"abstract":"<p>Hybridization can provide evolutionary benefits (e.g., population resilience to climate change) through the introduction of adaptive alleles and increase of genetic diversity. Nevertheless, management strategies may be designed based only on the parental species within a hybrid zone, without considering the hybrids. This can lead to ineffective spatial management of species, which can directly harm population diversity and negatively impact food webs. Three species of rockfish (Brown Rockfish (<i>Sebastes caurinus</i>), Copper Rockfish (<i>S. auriculatus</i>), and Quillback Rockfish (<i>S. maliger</i>)) are known to hybridize within Puget Sound, Washington, but genetic data from these species are used to infer population structure in the entire genus, including in species that do not hybridize. The goal of this project was to estimate the hybridization rates within the region and determine the effect of hybridization on geographic patterns of genetic structure. We sequenced 290 Brown, Copper, and Quillback rockfish using restriction-site associated DNA sequencing (RADseq) from four regions within and outside Puget Sound, Washington. We show that (i) hybridization within Puget Sound was asymmetrical, not recent, widespread among individuals, and relatively low level within the genome, (ii) hybridization affected population structure in Copper and Brown rockfish, but not in Quillback Rockfish and (iii) after taking hybridization into account we found limited directional dispersal in Brown and Copper rockfish, and evidence for two isolated populations in Quillback Rockfish. Our results suggest that rockfish population structure is species-specific, dependent on the extent of hybridization, and cannot be inferred from one species to another despite similar life history.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13749","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141732575","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}
Freya Adele Pappert, Daniel Kolbe, Arseny Dubin, Olivia Roth
Parental age impacts offspring quantity and quality. Most prior research focused on maternal age. Since in most organisms the mother produces the costly eggs plus provides all or most parental care, it is difficult to distinguish maternal effects mediated via the egg from later maternal care. Here, we addressed the effects of parental age on offspring in Syngnathus typhle, a pipefish with male pregnancy. The divide between one parent producing the eggs and the second parent being the exclusive provider of parental care facilitates a distinction between the effects of parental age on egg quality versus parental age on early development. We fully reciprocally crossed young and old mothers and young and old fathers and assessed impact of parental age combination on offspring number, offspring size, and offspring gene expression patterns. Neither parental combination significantly influenced offspring size or male gestation duration; however, they influenced the number of offspring. Paternal, but not maternal, age strongly affected the offspring gene expression. Offspring from old fathers exhibited substantial changes in the expression of genes related to cell cycle regulation, protein synthesis, DNA repair, and neurogenesis. Our findings thus highlight the importance of gestation, as opposed to gamete production, in shaping the parental contribution to offspring development.
{"title":"The effect of parental age on the quantity and quality of offspring in Syngnathus typhle, a species with male pregnancy","authors":"Freya Adele Pappert, Daniel Kolbe, Arseny Dubin, Olivia Roth","doi":"10.1111/eva.13755","DOIUrl":"https://doi.org/10.1111/eva.13755","url":null,"abstract":"<p>Parental age impacts offspring quantity and quality. Most prior research focused on maternal age. Since in most organisms the mother produces the costly eggs plus provides all or most parental care, it is difficult to distinguish maternal effects mediated via the egg from later maternal care. Here, we addressed the effects of parental age on offspring in <i>Syngnathus typhle</i>, a pipefish with male pregnancy. The divide between one parent producing the eggs and the second parent being the exclusive provider of parental care facilitates a distinction between the effects of parental age on egg quality versus parental age on early development. We fully reciprocally crossed young and old mothers and young and old fathers and assessed impact of parental age combination on offspring number, offspring size, and offspring gene expression patterns. Neither parental combination significantly influenced offspring size or male gestation duration; however, they influenced the number of offspring. Paternal, but not maternal, age strongly affected the offspring gene expression. Offspring from old fathers exhibited substantial changes in the expression of genes related to cell cycle regulation, protein synthesis, DNA repair, and neurogenesis. Our findings thus highlight the importance of gestation, as opposed to gamete production, in shaping the parental contribution to offspring development.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13755","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141639453","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}
Phenotypic plasticity can buffer organisms against short-term environmental fluctuations. For example, previous exposure to increased temperatures can increase thermal tolerance in many species. Prior studies have found that acclimation to higher temperature can influence the magnitude of transcriptional response to subsequent acute thermal stress (hereafter, “transcriptional response modulation”). However, mechanisms mediating this gene expression response and, ultimately, phenotypic plasticity remain largely unknown. Epigenetic modifications are good candidates for modulating transcriptional response, as they broadly correlate with gene expression. Here, we investigate changes in DNA methylation as a possible mechanism controlling shifts in gene expression plasticity and thermal acclimation in the reef-building coral Acropora nana. We find that gene expression response to acute stress is altered in corals acclimated to different temperatures, with many genes exhibiting a dampened response to heat stress in corals pre-conditioned to higher temperatures. At the same time, we observe shifts in methylation during both acclimation (11 days) and acute heat stress (24 h). We observed that the acute heat stress results in shifts in gene-level methylation and elicits an acute transcriptional response in distinct gene sets. Further, acclimation-induced shifts in gene expression plasticity and differential methylation also largely occur in separate sets of genes. Counter to our initial hypothesis no overall correlation between the magnitude of differential methylation and the change in gene expression plasticity. We do find a small but statistically significant overlap in genes exhibiting both dampened expression response and shifts in methylation (14 genes), which could be candidates for further inquiry. Overall, our results suggest transcriptional response modulation occurs independently from methylation changes induced by thermal acclimation.
表型可塑性可以使生物体在短期环境波动中得到缓冲。例如,在许多物种中,先前暴露于升高的温度可提高热耐受性。先前的研究发现,对较高温度的适应可以影响对随后急性热应力的转录反应(以下简称 "转录反应调制")。然而,介导这种基因表达反应以及最终导致表型可塑性的机制在很大程度上仍不为人所知。表观遗传修饰是调节转录反应的良好候选机制,因为它们与基因表达广泛相关。在这里,我们研究了 DNA 甲基化的变化作为控制造礁珊瑚 Acropora nana 基因表达可塑性和热适应性变化的一种可能机制。我们发现,在适应不同温度的珊瑚中,基因表达对急性应激的反应发生了改变,在预适应较高温度的珊瑚中,许多基因对热应激的反应减弱。同时,我们观察到甲基化在适应期(11 天)和急性热应激期(24 小时)的变化。我们观察到,急性热胁迫导致基因水平甲基化的变化,并引起不同基因集的急性转录反应。此外,驯化诱导的基因表达可塑性变化和不同的甲基化也主要发生在不同的基因组中。与我们最初的假设相反,差异甲基化的程度与基因表达可塑性的变化之间没有整体相关性。我们确实发现有少量基因(14 个基因)同时表现出表达反应减弱和甲基化变化,但在统计学上有显著的重叠,这可能是进一步研究的候选基因。总之,我们的研究结果表明,转录反应调节的发生与热适应所诱导的甲基化变化无关。
{"title":"Patterns of methylation and transcriptional plasticity during thermal acclimation in a reef-building coral","authors":"Leslie Guerrero, Rachael Bay","doi":"10.1111/eva.13757","DOIUrl":"https://doi.org/10.1111/eva.13757","url":null,"abstract":"<p>Phenotypic plasticity can buffer organisms against short-term environmental fluctuations. For example, previous exposure to increased temperatures can increase thermal tolerance in many species. Prior studies have found that acclimation to higher temperature can influence the magnitude of transcriptional response to subsequent acute thermal stress (hereafter, “transcriptional response modulation”). However, mechanisms mediating this gene expression response and, ultimately, phenotypic plasticity remain largely unknown. Epigenetic modifications are good candidates for modulating transcriptional response, as they broadly correlate with gene expression. Here, we investigate changes in DNA methylation as a possible mechanism controlling shifts in gene expression plasticity and thermal acclimation in the reef-building coral <i>Acropora nana</i>. We find that gene expression response to acute stress is altered in corals acclimated to different temperatures, with many genes exhibiting a dampened response to heat stress in corals pre-conditioned to higher temperatures. At the same time, we observe shifts in methylation during both acclimation (11 days) and acute heat stress (24 h). We observed that the acute heat stress results in shifts in gene-level methylation and elicits an acute transcriptional response in distinct gene sets. Further, acclimation-induced shifts in gene expression plasticity and differential methylation also largely occur in separate sets of genes. Counter to our initial hypothesis no overall correlation between the magnitude of differential methylation and the change in gene expression plasticity. We do find a small but statistically significant overlap in genes exhibiting both dampened expression response and shifts in methylation (14 genes), which could be candidates for further inquiry. Overall, our results suggest transcriptional response modulation occurs independently from methylation changes induced by thermal acclimation.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13757","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141639536","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}
Biological control of weeds involves deliberate introduction of host-specific natural enemies into invaded range to reduce the negative impacts of invasive species. Assessing the specificity is a crucial step, as introduction of generalist natural enemies into a new territory may pose risks to the recipient communities. A mechanistic understanding of host use can provide valuable insights for the selection of specialist natural enemies, bolster confidence in non-target risk assessment and potentially accelerate the host specificity testing process in biological control. We conducted a comprehensive analysis of studies on the genomics of host specialization with a view to examine if genomic signatures can help predict host specificity in insects. Focusing on phytophagous Lepidoptera, Coleoptera and Diptera, we compared chemosensory receptors and enzymes between “specialist” (insects with narrow host range) and “generalist” (insects with wide host range) insects. The availability of genomic data for biological control agents (natural enemies of weeds) is limited thus our analyses utilized data from pest insects and model organisms for which genomic data are available. Our findings revealed that specialists generally exhibit a lower number of chemosensory receptors and enzymes compared with their generalist counterparts. This pattern was more prominent in Coleoptera and Diptera relative to Lepidoptera. This information can be used to reject agents with large gene repertoires to potentially accelerate the risk assessment process. Similarly, confirming smaller gene repertoires in specialists could further strengthen the risk evaluation. Despite the distinctive signatures between specialists and generalists, challenges such as finite genomic data for biological control agents, ad hoc comparisons, and fewer comparative studies among congeners limit our ability to use genomic signatures to predict host specificity. A few studies have empirically compared phylogenetically closely related species, enhancing the resolution and the predictive power of genomics signatures thus suggesting the need for more targeted studies comparing congeneric specialists and generalists.
{"title":"Can genomic signatures guide the selection of host-specific agents for weed biological control?","authors":"Nagalingam Kumaran, S. Raghu","doi":"10.1111/eva.13760","DOIUrl":"https://doi.org/10.1111/eva.13760","url":null,"abstract":"<p>Biological control of weeds involves deliberate introduction of host-specific natural enemies into invaded range to reduce the negative impacts of invasive species. Assessing the specificity is a crucial step, as introduction of generalist natural enemies into a new territory may pose risks to the recipient communities. A mechanistic understanding of host use can provide valuable insights for the selection of specialist natural enemies, bolster confidence in non-target risk assessment and potentially accelerate the host specificity testing process in biological control. We conducted a comprehensive analysis of studies on the genomics of host specialization with a view to examine if genomic signatures can help predict host specificity in insects. Focusing on phytophagous Lepidoptera, Coleoptera and Diptera, we compared chemosensory receptors and enzymes between “specialist” (insects with narrow host range) and “generalist” (insects with wide host range) insects. The availability of genomic data for biological control agents (natural enemies of weeds) is limited thus our analyses utilized data from pest insects and model organisms for which genomic data are available. Our findings revealed that specialists generally exhibit a lower number of chemosensory receptors and enzymes compared with their generalist counterparts. This pattern was more prominent in Coleoptera and Diptera relative to Lepidoptera. This information can be used to reject agents with large gene repertoires to potentially accelerate the risk assessment process. Similarly, confirming smaller gene repertoires in specialists could further strengthen the risk evaluation. Despite the distinctive signatures between specialists and generalists, challenges such as finite genomic data for biological control agents, ad hoc comparisons, and fewer comparative studies among congeners limit our ability to use genomic signatures to predict host specificity. A few studies have empirically compared phylogenetically closely related species, enhancing the resolution and the predictive power of genomics signatures thus suggesting the need for more targeted studies comparing congeneric specialists and generalists.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13760","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141639452","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}
Frédéric J. J. Chain, Britta S. Meyer, Melanie J. Heckwolf, Sören Franzenburg, Christophe Eizaguirre, Thorsten B. H. Reusch
Duplicated genes provide the opportunity for evolutionary novelty and adaptive divergence. In many cases, having more gene copies increases gene expression, which might facilitate adaptation to stressful or novel environments. Conversely, overexpression or misexpression of duplicated genes can be detrimental and subject to negative selection. In this scenario, newly duplicate genes may evade purifying selection if they are epigenetically silenced, at least temporarily, leading them to persist in populations as copy number variations (CNVs). In animals and plants, younger gene duplicates tend to have higher levels of DNA methylation and lower levels of gene expression, suggesting epigenetic regulation could promote the retention of gene duplications via expression repression or silencing. Here, we test the hypothesis that DNA methylation variation coincides with young duplicate genes that are segregating as CNVs in six populations of the three-spined stickleback that span a salinity gradient from 4 to 30 PSU. Using reduced-representation bisulfite sequencing, we found DNA methylation and CNV differentiation outliers rarely overlapped. Whereas lineage-specific genes and young duplicates were found to be highly methylated, just two gene CNVs showed a significant association between promoter methylation level and copy number, suggesting that DNA methylation might not interact with CNVs in our dataset. If most new duplications are regulated for dosage by epigenetic mechanisms, our results do not support a strong contribution from DNA methylation soon after duplication. Instead, our results are consistent with a preference to duplicate genes that are already highly methylated.
重复的基因为进化的新颖性和适应性分化提供了机会。在许多情况下,拥有更多的基因拷贝可以增加基因表达,从而促进对压力或新环境的适应。反之,重复基因的过度表达或表达不当也可能是有害的,会受到负面选择的影响。在这种情况下,新复制的基因如果在表观遗传学上被沉默(至少是暂时沉默),就可能逃避纯化选择,从而以拷贝数变异(CNV)的形式在种群中持续存在。在动物和植物中,较年轻的重复基因往往具有较高的DNA甲基化水平和较低的基因表达水平,这表明表观遗传调控可通过表达抑制或沉默促进重复基因的保留。在此,我们在盐度梯度为 4 至 30 PSU 的六个三刺鱼种群中检验了 DNA 甲基化变异与作为 CNVs 分离的年轻重复基因相吻合的假设。通过减少代表性的亚硫酸氢盐测序,我们发现 DNA 甲基化和 CNV 分化异常值很少重叠。我们发现特定品系的基因和年轻的重复基因甲基化程度很高,而只有两个基因的CNV在启动子甲基化水平和拷贝数之间存在显著关联,这表明在我们的数据集中,DNA甲基化可能与CNV之间没有相互作用。如果大多数新的重复是通过表观遗传机制来调节剂量的,那么我们的结果并不支持 DNA 甲基化在重复后不久就会产生强大的贡献。相反,我们的结果符合人们对已经高度甲基化基因的复制偏好。
{"title":"Epigenetic diversity of genes with copy number variations among natural populations of the three-spined stickleback","authors":"Frédéric J. J. Chain, Britta S. Meyer, Melanie J. Heckwolf, Sören Franzenburg, Christophe Eizaguirre, Thorsten B. H. Reusch","doi":"10.1111/eva.13753","DOIUrl":"10.1111/eva.13753","url":null,"abstract":"<p>Duplicated genes provide the opportunity for evolutionary novelty and adaptive divergence. In many cases, having more gene copies increases gene expression, which might facilitate adaptation to stressful or novel environments. Conversely, overexpression or misexpression of duplicated genes can be detrimental and subject to negative selection. In this scenario, newly duplicate genes may evade purifying selection if they are epigenetically silenced, at least temporarily, leading them to persist in populations as copy number variations (CNVs). In animals and plants, younger gene duplicates tend to have higher levels of DNA methylation and lower levels of gene expression, suggesting epigenetic regulation could promote the retention of gene duplications via expression repression or silencing. Here, we test the hypothesis that DNA methylation variation coincides with young duplicate genes that are segregating as CNVs in six populations of the three-spined stickleback that span a salinity gradient from 4 to 30 PSU. Using reduced-representation bisulfite sequencing, we found DNA methylation and CNV differentiation outliers rarely overlapped. Whereas lineage-specific genes and young duplicates were found to be highly methylated, just two gene CNVs showed a significant association between promoter methylation level and copy number, suggesting that DNA methylation might not interact with CNVs in our dataset. If most new duplications are regulated for dosage by epigenetic mechanisms, our results do not support a strong contribution from DNA methylation soon after duplication. Instead, our results are consistent with a preference to duplicate genes that are already highly methylated.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11246597/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141615407","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}
Jacob G. Holland, Kimberley F. Prior, Aidan J. O'Donnell, Sarah E. Reece
Undertaking certain activities at the time of day that maximises fitness is assumed to explain the evolution of circadian clocks. Organisms often use daily environmental cues such as light and food availability to set the timing of their clocks. These cues may be the environmental rhythms that ultimately determine fitness, act as proxies for the timing of less tractable ultimate drivers, or are used simply to maintain internal synchrony. While many pathogens/parasites undertake rhythmic activities, both the proximate and ultimate drivers of their rhythms are poorly understood. Explaining the roles of rhythms in infections offers avenues for novel interventions to interfere with parasite fitness and reduce the severity and spread of disease. Here, we perturb several rhythms in the hosts of malaria parasites to investigate why parasites align their rhythmic replication to the host's feeding-fasting rhythm. We manipulated host rhythms governed by light, food or both, and assessed the fitness implications for parasites, and the consequences for hosts, to test which host rhythms represent ultimate drivers of the parasite's rhythm. We found that alignment with the host's light-driven rhythms did not affect parasite fitness metrics. In contrast, aligning with the timing of feeding-fasting rhythms may be beneficial for the parasite, but only when the host possess a functional canonical circadian clock. Because parasites in clock-disrupted hosts align with the host's feeding-fasting rhythms and yet derive no apparent benefit, our results suggest cue(s) from host food act as a proxy rather than being a key selective driver of the parasite's rhythm. Alternatively, parasite rhythmicity may only be beneficial because it promotes synchrony between parasite cells and/or allows parasites to align to the biting rhythms of vectors. Our results also suggest that interventions can disrupt parasite rhythms by targeting the proxies or the selective factors driving them without impacting host health.
{"title":"Testing the evolutionary drivers of malaria parasite rhythms and their consequences for host–parasite interactions","authors":"Jacob G. Holland, Kimberley F. Prior, Aidan J. O'Donnell, Sarah E. Reece","doi":"10.1111/eva.13752","DOIUrl":"10.1111/eva.13752","url":null,"abstract":"<p>Undertaking certain activities at the time of day that maximises fitness is assumed to explain the evolution of circadian clocks. Organisms often use daily environmental cues such as light and food availability to set the timing of their clocks. These cues may be the environmental rhythms that ultimately determine fitness, act as proxies for the timing of less tractable ultimate drivers, or are used simply to maintain internal synchrony. While many pathogens/parasites undertake rhythmic activities, both the proximate and ultimate drivers of their rhythms are poorly understood. Explaining the roles of rhythms in infections offers avenues for novel interventions to interfere with parasite fitness and reduce the severity and spread of disease. Here, we perturb several rhythms in the hosts of malaria parasites to investigate why parasites align their rhythmic replication to the host's feeding-fasting rhythm. We manipulated host rhythms governed by light, food or both, and assessed the fitness implications for parasites, and the consequences for hosts, to test which host rhythms represent ultimate drivers of the parasite's rhythm. We found that alignment with the host's light-driven rhythms did not affect parasite fitness metrics. In contrast, aligning with the timing of feeding-fasting rhythms may be beneficial for the parasite, but only when the host possess a functional canonical circadian clock. Because parasites in clock-disrupted hosts align with the host's feeding-fasting rhythms and yet derive no apparent benefit, our results suggest cue(s) from host food act as a proxy rather than being a key selective driver of the parasite's rhythm. Alternatively, parasite rhythmicity may only be beneficial because it promotes synchrony between parasite cells and/or allows parasites to align to the biting rhythms of vectors. Our results also suggest that interventions can disrupt parasite rhythms by targeting the proxies or the selective factors driving them without impacting host health.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11246599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141615409","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}
Meaghan I. Clark, Sarah W. Fitzpatrick, Gideon S. Bradburd
Detecting recent demographic changes is a crucial component of species conservation and management, as many natural populations face declines due to anthropogenic habitat alteration and climate change. Genetic methods allow researchers to detect changes in effective population size (Ne) from sampling at a single timepoint. However, in species with long lifespans, there is a lag between the start of a decline in a population and the resulting decrease in genetic diversity. This lag slows the rate at which diversity is lost, and therefore makes it difficult to detect recent declines using genetic data. However, the genomes of old individuals can provide a window into the past, and can be compared to those of younger individuals, a contrast that may help reveal recent demographic declines. To test whether comparing the genomes of young and old individuals can help infer recent demographic bottlenecks, we use forward-time, individual-based simulations with varying mean individual lifespans and extents of generational overlap. We find that age information can be used to aid in the detection of demographic declines when the decline has been severe. When average lifespan is long, comparing young and old individuals from a single timepoint has greater power to detect a recent (within the last 50 years) bottleneck event than comparing individuals sampled at different points in time. Our results demonstrate how longevity and generational overlap can be both a hindrance and a boon to detecting recent demographic declines from population genomic data.
{"title":"Pitfalls and windfalls of detecting demographic declines using population genetics in long-lived species","authors":"Meaghan I. Clark, Sarah W. Fitzpatrick, Gideon S. Bradburd","doi":"10.1111/eva.13754","DOIUrl":"10.1111/eva.13754","url":null,"abstract":"<p>Detecting recent demographic changes is a crucial component of species conservation and management, as many natural populations face declines due to anthropogenic habitat alteration and climate change. Genetic methods allow researchers to detect changes in effective population size (N<sub>e</sub>) from sampling at a single timepoint. However, in species with long lifespans, there is a lag between the start of a decline in a population and the resulting decrease in genetic diversity. This lag slows the rate at which diversity is lost, and therefore makes it difficult to detect recent declines using genetic data. However, the genomes of old individuals can provide a window into the past, and can be compared to those of younger individuals, a contrast that may help reveal recent demographic declines. To test whether comparing the genomes of young and old individuals can help infer recent demographic bottlenecks, we use forward-time, individual-based simulations with varying mean individual lifespans and extents of generational overlap. We find that age information can be used to aid in the detection of demographic declines when the decline has been severe. When average lifespan is long, comparing young and old individuals from a single timepoint has greater power to detect a recent (within the last 50 years) bottleneck event than comparing individuals sampled at different points in time. Our results demonstrate how longevity and generational overlap can be both a hindrance and a boon to detecting recent demographic declines from population genomic data.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11246600/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141615408","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}