Pub Date : 2024-04-04DOI: 10.1038/s41437-024-00682-5
Emanuel M. Fonseca, Nathaniel S. Pope, William E. Peterman, Fernanda P. Werneck, Guarino R. Colli, Bryan C. Carstens
One key research goal of evolutionary biology is to understand the origin and maintenance of genetic variation. In the Cerrado, the South American savanna located primarily in the Central Brazilian Plateau, many hypotheses have been proposed to explain how landscape features (e.g., geographic distance, river barriers, topographic compartmentalization, and historical climatic fluctuations) have promoted genetic structure by mediating gene flow. Here, we asked whether these landscape features have influenced the genetic structure and differentiation in the lizard species Norops brasiliensis (Squamata: Dactyloidae). To achieve our goal, we used a genetic clustering analysis and estimate an effective migration surface to assess genetic structure in the focal species. Optimized isolation-by-resistance models and a simulation-based approach combined with machine learning (convolutional neural network; CNN) were then used to infer current and historical effects on population genetic structure through 12 unique landscape models. We recovered five geographically distributed populations that are separated by regions of lower-than-expected gene flow. The results of the CNN showed that geographic distance is the sole predictor of genetic variation in N. brasiliensis, and that slope, rivers, and historical climate had no discernible influence on gene flow. Our novel CNN approach was accurate (89.5%) in differentiating each landscape model. CNN and other machine learning approaches are still largely unexplored in landscape genetics studies, representing promising avenues for future research with increasingly accessible genomic datasets.
{"title":"Genetic structure and landscape effects on gene flow in the Neotropical lizard Norops brasiliensis (Squamata: Dactyloidae)","authors":"Emanuel M. Fonseca, Nathaniel S. Pope, William E. Peterman, Fernanda P. Werneck, Guarino R. Colli, Bryan C. Carstens","doi":"10.1038/s41437-024-00682-5","DOIUrl":"10.1038/s41437-024-00682-5","url":null,"abstract":"One key research goal of evolutionary biology is to understand the origin and maintenance of genetic variation. In the Cerrado, the South American savanna located primarily in the Central Brazilian Plateau, many hypotheses have been proposed to explain how landscape features (e.g., geographic distance, river barriers, topographic compartmentalization, and historical climatic fluctuations) have promoted genetic structure by mediating gene flow. Here, we asked whether these landscape features have influenced the genetic structure and differentiation in the lizard species Norops brasiliensis (Squamata: Dactyloidae). To achieve our goal, we used a genetic clustering analysis and estimate an effective migration surface to assess genetic structure in the focal species. Optimized isolation-by-resistance models and a simulation-based approach combined with machine learning (convolutional neural network; CNN) were then used to infer current and historical effects on population genetic structure through 12 unique landscape models. We recovered five geographically distributed populations that are separated by regions of lower-than-expected gene flow. The results of the CNN showed that geographic distance is the sole predictor of genetic variation in N. brasiliensis, and that slope, rivers, and historical climate had no discernible influence on gene flow. Our novel CNN approach was accurate (89.5%) in differentiating each landscape model. CNN and other machine learning approaches are still largely unexplored in landscape genetics studies, representing promising avenues for future research with increasingly accessible genomic datasets.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00682-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140590920","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}
Pub Date : 2024-03-27DOI: 10.1038/s41437-024-00680-7
Takumi Yokomizo, Yuma Takahashi
Organisms have diverse biological clocks synchronised with environmental cycles depending on their habitats. Anticipation of tidal changes has driven the evolution of circatidal rhythms in some marine species. In the freshwater snail, Semisulcospira reiniana, individuals in nontidal areas exhibit circadian rhythms, whereas those in tidal areas exhibit both circadian and circatidal rhythms. We investigated whether the circatidal rhythms are genetically determined or induced by environmental cycles. The exposure to a simulated tidal cycle did not change the intensity of circatidal rhythm in individuals in the nontidal population. However, snails in the tidal population showed different activity rhythms depending on the presence or absence of the exposure. Transcriptome analysis revealed that genes with circatidal oscillation increased due to entrainment to the tidal cycle in both populations and dominant rhythmicity was consistent with the environmental cycle. These results suggest plasticity in the endogenous rhythm in the gene expression in both populations. Note that circatidal oscillating genes were more abundant in the tidal population than in the nontidal population, suggesting that a greater number of genes are associated with circatidal clocks in the tidal population compared to the nontidal population. This increase of circatidal clock–controlled genes in the tidal population could be caused by genetic changes in the biological clock or the experience of tidal cycle in the early life stage. Our findings suggest that the plasticity of biological rhythms may have contributed to the adaptation to the tidal environment in S. reiniana.
{"title":"Plasticity of circadian and circatidal rhythms in activity and transcriptomic dynamics in a freshwater snail","authors":"Takumi Yokomizo, Yuma Takahashi","doi":"10.1038/s41437-024-00680-7","DOIUrl":"10.1038/s41437-024-00680-7","url":null,"abstract":"Organisms have diverse biological clocks synchronised with environmental cycles depending on their habitats. Anticipation of tidal changes has driven the evolution of circatidal rhythms in some marine species. In the freshwater snail, Semisulcospira reiniana, individuals in nontidal areas exhibit circadian rhythms, whereas those in tidal areas exhibit both circadian and circatidal rhythms. We investigated whether the circatidal rhythms are genetically determined or induced by environmental cycles. The exposure to a simulated tidal cycle did not change the intensity of circatidal rhythm in individuals in the nontidal population. However, snails in the tidal population showed different activity rhythms depending on the presence or absence of the exposure. Transcriptome analysis revealed that genes with circatidal oscillation increased due to entrainment to the tidal cycle in both populations and dominant rhythmicity was consistent with the environmental cycle. These results suggest plasticity in the endogenous rhythm in the gene expression in both populations. Note that circatidal oscillating genes were more abundant in the tidal population than in the nontidal population, suggesting that a greater number of genes are associated with circatidal clocks in the tidal population compared to the nontidal population. This increase of circatidal clock–controlled genes in the tidal population could be caused by genetic changes in the biological clock or the experience of tidal cycle in the early life stage. Our findings suggest that the plasticity of biological rhythms may have contributed to the adaptation to the tidal environment in S. reiniana.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00680-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140305473","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}
Pub Date : 2024-03-27DOI: 10.1038/s41437-024-00681-6
Erika C. Johnston, Carlo Caruso, Elena Mujica, Nia S. Walker, Crawford Drury
Coral populations must be able to adapt to changing environmental conditions for coral reefs to persist under climate change. The adaptive potential of these organisms is difficult to forecast due to complex interactions between the host animal, dinoflagellate symbionts and the environment. Here we created 26 larval families from six Montipora capitata colonies from a single reef, showing significant, heritable variation in thermal tolerance. Our results indicate that 9.1% of larvae are expected to exhibit four times the thermal tolerance of the general population. Differences in larval thermotolerance were driven mainly by maternal contributions, but we found no evidence that these effects were driven by symbiont identity despite vertical transmission from the dam. We also document no evidence of reproductive incompatibility attributable to symbiont identity. These data demonstrate significant genetic variation within this population which provides the raw material upon which natural selection can act.
{"title":"Complex parental effects impact variation in larval thermal tolerance in a vertically transmitting coral","authors":"Erika C. Johnston, Carlo Caruso, Elena Mujica, Nia S. Walker, Crawford Drury","doi":"10.1038/s41437-024-00681-6","DOIUrl":"10.1038/s41437-024-00681-6","url":null,"abstract":"Coral populations must be able to adapt to changing environmental conditions for coral reefs to persist under climate change. The adaptive potential of these organisms is difficult to forecast due to complex interactions between the host animal, dinoflagellate symbionts and the environment. Here we created 26 larval families from six Montipora capitata colonies from a single reef, showing significant, heritable variation in thermal tolerance. Our results indicate that 9.1% of larvae are expected to exhibit four times the thermal tolerance of the general population. Differences in larval thermotolerance were driven mainly by maternal contributions, but we found no evidence that these effects were driven by symbiont identity despite vertical transmission from the dam. We also document no evidence of reproductive incompatibility attributable to symbiont identity. These data demonstrate significant genetic variation within this population which provides the raw material upon which natural selection can act.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00681-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140305472","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}
Pub Date : 2024-03-20DOI: 10.1038/s41437-024-00679-0
Guan-Yu Chen, Shih-Ying Huang, Ming-Der Lin, Thomas Chouvenc, Yung-Hao Ching, Hou-Feng Li
Hybridization between invasive pest species may lead to significant genetic and economic impacts that require close monitoring. The two most invasive and destructive termite species worldwide, Coptotermes formosanus Shiraki and Coptotermes gestroi (Wasmann), have the potential for hybridization in the field. A three-year field survey conducted during the dispersal flight season of Coptotermes in Taiwan identified alates with atypical morphology, which were confirmed as hybrids of the two Coptotermes species using microsatellite and mitochondrial analyses. Out of 27,601 alates collected over three years, 4.4% were confirmed as hybrid alates, and some advanced hybrids (>F1 generations) were identified. The hybrid alates had a dispersal flight season that overlapped with the two parental species 13 out of 15 times. Most of the hybrid alates were females, implying that mating opportunities beyond F1 may primarily be possible through female hybrids. However, the incipient colony growth results from all potential mating combinations suggest that only backcross colonies with hybrid males could sometimes lead to brood development. The observed asymmetrical viability and fertility of hybrid alates may critically reduce the probability of advanced-hybrid colonies being established in the field.
入侵害虫物种之间的杂交可能会导致重大的遗传和经济影响，需要密切监测。世界上两种最具入侵性和破坏性的白蚁--Coptotermes formosanus Shiraki 和 Coptotermes gestroi (Wasmann)，在野外都有可能发生杂交。在台湾白蚁扩散飞行季节进行的为期三年的野外调查发现了形态不典型的白蚁，并通过微卫星和线粒体分析证实了它们是两个白蚁种的杂交种。在历时三年采集的27601只白头翁中，有4.4%被确认为杂交白头翁，并发现了一些高级杂交种（F1代）。在15次杂交中，有13次杂交鸥的扩散飞行季节与两个亲本重叠。大多数杂交杓鹬都是雌性，这意味着 F1 代以外的交配机会可能主要通过雌性杂交种来实现。然而，所有潜在交配组合的初生蚁群生长结果表明，只有与杂交雄蚁回交的蚁群有时才能育雏。观察到的杂交胭脂鱼不对称的生存力和繁殖力可能会严重降低在野外建立高级杂交群落的可能性。
{"title":"Hybrids of two destructive subterranean termites established in the field, revealing a potential for gene flow between species","authors":"Guan-Yu Chen, Shih-Ying Huang, Ming-Der Lin, Thomas Chouvenc, Yung-Hao Ching, Hou-Feng Li","doi":"10.1038/s41437-024-00679-0","DOIUrl":"10.1038/s41437-024-00679-0","url":null,"abstract":"Hybridization between invasive pest species may lead to significant genetic and economic impacts that require close monitoring. The two most invasive and destructive termite species worldwide, Coptotermes formosanus Shiraki and Coptotermes gestroi (Wasmann), have the potential for hybridization in the field. A three-year field survey conducted during the dispersal flight season of Coptotermes in Taiwan identified alates with atypical morphology, which were confirmed as hybrids of the two Coptotermes species using microsatellite and mitochondrial analyses. Out of 27,601 alates collected over three years, 4.4% were confirmed as hybrid alates, and some advanced hybrids (>F1 generations) were identified. The hybrid alates had a dispersal flight season that overlapped with the two parental species 13 out of 15 times. Most of the hybrid alates were females, implying that mating opportunities beyond F1 may primarily be possible through female hybrids. However, the incipient colony growth results from all potential mating combinations suggest that only backcross colonies with hybrid males could sometimes lead to brood development. The observed asymmetrical viability and fertility of hybrid alates may critically reduce the probability of advanced-hybrid colonies being established in the field.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00679-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140172230","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}
Pub Date : 2024-03-18DOI: 10.1038/s41437-024-00677-2
Luke Ambrose, Scott L. Allen, Charlie Iro’ofa, Charles Butafa, Nigel W. Beebe
Indoor insecticide applications are the primary tool for reducing malaria transmission in the Solomon Archipelago, a region where Anopheles farauti is the only common malaria vector. Due to the evolution of behavioural resistance in some An. farauti populations, these applications have become less effective. New malaria control interventions are therefore needed in this region, and gene-drives provide a promising new technology. In considering developing a population-specific (local) gene-drive in An. farauti, we detail the species’ population genetic structure using microsatellites and whole mitogenomes, finding many spatially confined populations both within and between landmasses. This strong population structure suggests that An. farauti would be a useful system for developing a population-specific, confinable gene-drive for field release, where private alleles can be used as Cas9 targets. Previous work on Anopheles gambiae has used the Cardinal gene for the development of a global population replacement gene-drive. We therefore also analyse the Cardinal gene to assess whether it may be a suitable target to engineer a gene-drive for the modification of local An. farauti populations. Despite the extensive population structure observed in An. farauti for microsatellites, only one remote island population from Vanuatu contained fixed and private alleles at the Cardinal locus. Nonetheless, this study provides an initial framework for further population genomic investigations to discover high-frequency private allele targets in localized An. farauti populations. This would enable the development of gene-drive strains for modifying localised populations with minimal chance of escape and may provide a low-risk route to field trial evaluations.
{"title":"Genetic and geographic population structure in the malaria vector, Anopheles farauti, provides a candidate system for pioneering confinable gene-drive releases","authors":"Luke Ambrose, Scott L. Allen, Charlie Iro’ofa, Charles Butafa, Nigel W. Beebe","doi":"10.1038/s41437-024-00677-2","DOIUrl":"10.1038/s41437-024-00677-2","url":null,"abstract":"Indoor insecticide applications are the primary tool for reducing malaria transmission in the Solomon Archipelago, a region where Anopheles farauti is the only common malaria vector. Due to the evolution of behavioural resistance in some An. farauti populations, these applications have become less effective. New malaria control interventions are therefore needed in this region, and gene-drives provide a promising new technology. In considering developing a population-specific (local) gene-drive in An. farauti, we detail the species’ population genetic structure using microsatellites and whole mitogenomes, finding many spatially confined populations both within and between landmasses. This strong population structure suggests that An. farauti would be a useful system for developing a population-specific, confinable gene-drive for field release, where private alleles can be used as Cas9 targets. Previous work on Anopheles gambiae has used the Cardinal gene for the development of a global population replacement gene-drive. We therefore also analyse the Cardinal gene to assess whether it may be a suitable target to engineer a gene-drive for the modification of local An. farauti populations. Despite the extensive population structure observed in An. farauti for microsatellites, only one remote island population from Vanuatu contained fixed and private alleles at the Cardinal locus. Nonetheless, this study provides an initial framework for further population genomic investigations to discover high-frequency private allele targets in localized An. farauti populations. This would enable the development of gene-drive strains for modifying localised populations with minimal chance of escape and may provide a low-risk route to field trial evaluations.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00677-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140143319","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}
Pub Date : 2024-03-13DOI: 10.1038/s41437-024-00678-1
Laura Garaud, David Nusbaumer, Lucas Marques da Cunha, Christian de Guttry, Laurie Ançay, Audrey Atherton, Emilien Lasne, Claus Wedekind
The ‘good genes’ hypotheses of sexual selection predict that females prefer males with strong ornaments because they are in good health and vigor and can afford the costs of the ornaments. A key assumption of this concept is that male health and vigor are useful predictors of genetic quality and hence offspring performance. We tested this prediction in wild-caught lake char (Salvelinus umbla) whose breeding coloration is known to reveal aspects of male health. We first reanalyzed results from sperm competition trials in which embryos of known parenthood had been raised singly in either a stress- or non-stress environment. Paternal coloration did not correlate with any measures of offspring performance. However, offspring growth was reduced with higher kinship coefficients between the parents. To test the robustness of these first observations, we collected a new sample of wild males and females, used their gametes in a full-factorial in vitro breeding experiment, and singly raised about 3000 embryos in either a stress- or non-stress environment (stress induced by microbes). Again, paternal coloration did not predict offspring performance, while offspring growth was reduced with higher kinship between the parents. We conclude that, in lake char, the genetic benefits of mate choice would be strongest if females could recognize and avoid genetically related males, while male breeding colors may be more relevant in intra-sexual selection.
{"title":"Parental kinship coefficient but not paternal coloration predicts early offspring growth in lake char","authors":"Laura Garaud, David Nusbaumer, Lucas Marques da Cunha, Christian de Guttry, Laurie Ançay, Audrey Atherton, Emilien Lasne, Claus Wedekind","doi":"10.1038/s41437-024-00678-1","DOIUrl":"10.1038/s41437-024-00678-1","url":null,"abstract":"The ‘good genes’ hypotheses of sexual selection predict that females prefer males with strong ornaments because they are in good health and vigor and can afford the costs of the ornaments. A key assumption of this concept is that male health and vigor are useful predictors of genetic quality and hence offspring performance. We tested this prediction in wild-caught lake char (Salvelinus umbla) whose breeding coloration is known to reveal aspects of male health. We first reanalyzed results from sperm competition trials in which embryos of known parenthood had been raised singly in either a stress- or non-stress environment. Paternal coloration did not correlate with any measures of offspring performance. However, offspring growth was reduced with higher kinship coefficients between the parents. To test the robustness of these first observations, we collected a new sample of wild males and females, used their gametes in a full-factorial in vitro breeding experiment, and singly raised about 3000 embryos in either a stress- or non-stress environment (stress induced by microbes). Again, paternal coloration did not predict offspring performance, while offspring growth was reduced with higher kinship between the parents. We conclude that, in lake char, the genetic benefits of mate choice would be strongest if females could recognize and avoid genetically related males, while male breeding colors may be more relevant in intra-sexual selection.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00678-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140119329","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}
Pub Date : 2024-03-12DOI: 10.1038/s41437-024-00676-3
Carolina Pacheco, Helena Rio-Maior, Mónia Nakamura, Francisco Álvares, Raquel Godinho
Inbreeding can reduce offspring fitness and has substantial implications for the genetic diversity and long-term viability of populations. In social cooperative canids, inbreeding is conditioned by the geographic proximity between opposite-sex kin outside natal groups and the presence of related individuals in neighbouring groups. Consequently, challenges in moving into other regions where the species is present can also affect inbreeding rates. These can be particularly problematic in areas of high human density, where movement can be restricted, even for highly vagile species. In this study, we investigate the socio-ecological dynamics of Iberian wolf packs in the human-dominated landscape of Alto Minho, in northwest Portugal, where wolves exhibit a high prevalence of short-distance dispersal and limited gene flow with neighbouring regions. We hypothesise that mating occurs regardless of relatedness, resulting in recurrent inbreeding due to high kin encounter rates. Using data from a 10-year non-invasive genetic monitoring programme and a combination of relatedness estimates and genealogical reconstructions, we describe genetic diversity, mate choice, and dispersal strategies among Alto Minho packs. In contrast with expectations, our findings reveal relatedness-based mate choice, low kin encounter rates, and a reduced number of inbreeding events. We observed a high prevalence of philopatry, particularly among female breeders, with the most common breeding strategy involving the pairing of a philopatric female with an unrelated immigrant male. Overall, wolves were not inbred, and temporal changes in genetic diversity were not significant. Our findings are discussed, considering the demographic trend of wolves in Alto Minho and its human-dominated landscape.
{"title":"Relatedness-based mate choice and female philopatry: inbreeding trends of wolf packs in a human-dominated landscape","authors":"Carolina Pacheco, Helena Rio-Maior, Mónia Nakamura, Francisco Álvares, Raquel Godinho","doi":"10.1038/s41437-024-00676-3","DOIUrl":"10.1038/s41437-024-00676-3","url":null,"abstract":"Inbreeding can reduce offspring fitness and has substantial implications for the genetic diversity and long-term viability of populations. In social cooperative canids, inbreeding is conditioned by the geographic proximity between opposite-sex kin outside natal groups and the presence of related individuals in neighbouring groups. Consequently, challenges in moving into other regions where the species is present can also affect inbreeding rates. These can be particularly problematic in areas of high human density, where movement can be restricted, even for highly vagile species. In this study, we investigate the socio-ecological dynamics of Iberian wolf packs in the human-dominated landscape of Alto Minho, in northwest Portugal, where wolves exhibit a high prevalence of short-distance dispersal and limited gene flow with neighbouring regions. We hypothesise that mating occurs regardless of relatedness, resulting in recurrent inbreeding due to high kin encounter rates. Using data from a 10-year non-invasive genetic monitoring programme and a combination of relatedness estimates and genealogical reconstructions, we describe genetic diversity, mate choice, and dispersal strategies among Alto Minho packs. In contrast with expectations, our findings reveal relatedness-based mate choice, low kin encounter rates, and a reduced number of inbreeding events. We observed a high prevalence of philopatry, particularly among female breeders, with the most common breeding strategy involving the pairing of a philopatric female with an unrelated immigrant male. Overall, wolves were not inbred, and temporal changes in genetic diversity were not significant. Our findings are discussed, considering the demographic trend of wolves in Alto Minho and its human-dominated landscape.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00676-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140109845","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}
Pub Date : 2024-02-29DOI: 10.1038/s41437-024-00675-4
Katherine L. Bell, Anna Noreuil, Erin K. Molloy, Megan L. Fritz
Efficiency of mosquito-borne disease transmission is dependent upon both the preference and fidelity of mosquitoes as they seek the blood of vertebrate hosts. While mosquitoes select their blood hosts through multi-modal integration of sensory cues, host-seeking is primarily an odor-guided behavior. Differences in mosquito responses to hosts and their odors have been demonstrated to have a genetic component, but the underlying genomic architecture of these responses has yet to be fully resolved. Here, we provide the first characterization of the genomic architecture of host preference in the polymorphic mosquito species, Culex pipiens. The species exists as two morphologically identical bioforms, each with distinct avian and mammalian host preferences. Cx. pipiens females with empirically measured host responses were prepared into reduced representation DNA libraries and sequenced to identify genomic regions associated with host preference. Multiple genomic regions associated with host preference were identified on all 3 Culex chromosomes, and these genomic regions contained clusters of chemosensory genes, as expected based on work in Anopheles gambiae complex mosquitoes and in Aedes aegypti. One odorant receptor and one odorant binding protein gene showed one-to-one orthologous relationships to differentially expressed genes in A. gambiae complex members with divergent host preferences. Overall, our work identifies a distinct set of odorant receptors and odorant binding proteins that may enable Cx. pipiens females to distinguish between their vertebrate blood host species, and opens avenues for future functional studies that could measure the unique contributions of each gene to host preference phenotypes.
蚊子传播疾病的效率取决于蚊子在寻找脊椎动物宿主血液时的偏好和忠诚度。蚊子通过对感觉线索的多模式整合来选择血液宿主，而寻找宿主主要是一种气味引导的行为。蚊子对宿主及其气味的反应差异已被证明有遗传因素，但这些反应的潜在基因组结构尚未完全确定。在这里，我们首次描述了多态蚊子库蚊对宿主偏好的基因组结构。该物种有两种形态完全相同的生物形式，每种都有不同的禽类和哺乳动物宿主偏好。根据经验测得的宿主反应，将雌性喙库蚊制备成缩小代表 DNA 文库并进行测序，以确定与宿主偏好相关的基因组区域。在库蚊的所有 3 条染色体上都发现了与宿主偏好相关的多个基因组区域，这些基因组区域包含化学感觉基因簇，这与在冈比亚按蚊复合体和埃及伊蚊中的研究结果是一致的。一个气味受体基因和一个气味结合蛋白基因与具有不同宿主偏好的冈比亚按蚊复合体成员中的不同表达基因显示出一对一的同源关系。总之，我们的研究发现了一组不同的气味受体和气味结合蛋白，它们可能使蝰蛇雌虫能够区分其脊椎动物血液宿主的种类，并为未来的功能研究开辟了途径，可以测量每个基因对宿主偏好表型的独特贡献。
{"title":"Genetic and behavioral differences between above and below ground Culex pipiens bioforms","authors":"Katherine L. Bell, Anna Noreuil, Erin K. Molloy, Megan L. Fritz","doi":"10.1038/s41437-024-00675-4","DOIUrl":"10.1038/s41437-024-00675-4","url":null,"abstract":"Efficiency of mosquito-borne disease transmission is dependent upon both the preference and fidelity of mosquitoes as they seek the blood of vertebrate hosts. While mosquitoes select their blood hosts through multi-modal integration of sensory cues, host-seeking is primarily an odor-guided behavior. Differences in mosquito responses to hosts and their odors have been demonstrated to have a genetic component, but the underlying genomic architecture of these responses has yet to be fully resolved. Here, we provide the first characterization of the genomic architecture of host preference in the polymorphic mosquito species, Culex pipiens. The species exists as two morphologically identical bioforms, each with distinct avian and mammalian host preferences. Cx. pipiens females with empirically measured host responses were prepared into reduced representation DNA libraries and sequenced to identify genomic regions associated with host preference. Multiple genomic regions associated with host preference were identified on all 3 Culex chromosomes, and these genomic regions contained clusters of chemosensory genes, as expected based on work in Anopheles gambiae complex mosquitoes and in Aedes aegypti. One odorant receptor and one odorant binding protein gene showed one-to-one orthologous relationships to differentially expressed genes in A. gambiae complex members with divergent host preferences. Overall, our work identifies a distinct set of odorant receptors and odorant binding proteins that may enable Cx. pipiens females to distinguish between their vertebrate blood host species, and opens avenues for future functional studies that could measure the unique contributions of each gene to host preference phenotypes.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139996119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-10DOI: 10.1038/s41437-024-00673-6
Caelinn James, Josephine M. Pemberton, Pau Navarro, Sara Knott
Estimates of narrow sense heritability derived from genomic data that contain related individuals may be biased due to the within-family effects such as dominance, epistasis and common environmental factors. However, for many wild populations, removal of related individuals from the data would result in small sample sizes. In 2013, Zaitlen et al. proposed a method to estimate heritability in populations that include close relatives by simultaneously fitting an identity-by-state (IBS) genomic relatedness matrix (GRM) and an identity-by-descent (IBD) GRM. The IBD GRM is identical to the IBS GRM, except relatedness estimates below a specified threshold are set to 0. We applied this method to a sample of 8557 wild Soay sheep from St. Kilda, with genotypic information for 419,281 single nucleotide polymorphisms. We aimed to see how this method would partition heritability into population-level (IBS) and family-associated (IBD) variance for a range of genetic architectures, and so we focused on a mixture of polygenic and monogenic traits. We also implemented a variant of the model in which the IBD GRM was replaced by a GRM constructed from SNPs with low minor allele frequency to examine whether any additive genetic variance is captured by rare alleles. Whilst the inclusion of the IBD GRM did not significantly improve the fit of the model for the monogenic traits, it improved the fit for some of the polygenic traits, suggesting that dominance, epistasis and/or common environment not already captured by the non-genetic random effects fitted in our models may influence these traits.
{"title":"Investigating pedigree- and SNP-associated components of heritability in a wild population of Soay sheep","authors":"Caelinn James, Josephine M. Pemberton, Pau Navarro, Sara Knott","doi":"10.1038/s41437-024-00673-6","DOIUrl":"10.1038/s41437-024-00673-6","url":null,"abstract":"Estimates of narrow sense heritability derived from genomic data that contain related individuals may be biased due to the within-family effects such as dominance, epistasis and common environmental factors. However, for many wild populations, removal of related individuals from the data would result in small sample sizes. In 2013, Zaitlen et al. proposed a method to estimate heritability in populations that include close relatives by simultaneously fitting an identity-by-state (IBS) genomic relatedness matrix (GRM) and an identity-by-descent (IBD) GRM. The IBD GRM is identical to the IBS GRM, except relatedness estimates below a specified threshold are set to 0. We applied this method to a sample of 8557 wild Soay sheep from St. Kilda, with genotypic information for 419,281 single nucleotide polymorphisms. We aimed to see how this method would partition heritability into population-level (IBS) and family-associated (IBD) variance for a range of genetic architectures, and so we focused on a mixture of polygenic and monogenic traits. We also implemented a variant of the model in which the IBD GRM was replaced by a GRM constructed from SNPs with low minor allele frequency to examine whether any additive genetic variance is captured by rare alleles. Whilst the inclusion of the IBD GRM did not significantly improve the fit of the model for the monogenic traits, it improved the fit for some of the polygenic traits, suggesting that dominance, epistasis and/or common environment not already captured by the non-genetic random effects fitted in our models may influence these traits.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00673-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716041","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}
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