Pub Date : 2024-07-05DOI: 10.1038/s41437-024-00704-2
Joseph J. Dubie, Vaishali Katju, Ulfar Bergthorsson
Mitochondrial genomes exist in a nested hierarchy of populations where mitochondrial variants are subject to genetic drift and selection at each level of organization, sometimes engendering conflict between different levels of selection, and between the nuclear and mitochondrial genomes. Deletion mutants in the Caenorhabditis elegans mitochondrial genome can reach high intracellular frequencies despite strongly detrimental effects on fitness. During a mutation accumulation (MA) experiment in C. elegans, a 499 bp deletion in ctb-1 rose to 90% frequency within cells while significantly reducing fitness. During the experiment, the deletion-bearing mtDNA acquired three additional mutations in nd5, namely two single insertion frameshift mutations in a homopolymeric run, and a base substitution. Despite an additional fitness cost of these secondary mutations, all deletion-bearing molecules contained the nd5 mutations at the termination of the MA experiment. The presence of mutant mtDNA was associated with increased mtDNA copy-number. Variation in mtDNA copy-number was greater in the MA lines than in a wildtype nuclear background, including a severe reduction in copy-number at one generational timepoint. Evolutionary replay experiments using different generations of the MA experiment as starting points suggests that two of the secondary mutations contribute to the proliferation of the original ctb-1 deletion by unknown mechanisms.
线粒体基因组存在于嵌套的种群层次结构中，线粒体变体在每个组织层次上都会受到遗传漂移和选择的影响，有时会导致不同层次的选择之间以及核基因组和线粒体基因组之间发生冲突。秀丽隐杆线粒体基因组中的缺失突变体可以达到很高的细胞内频率，尽管这对适应性有很大的不利影响。在对秀丽隐杆线粒体进行突变积累（MA）实验期间，ctb-1中499 bp的缺失突变在细胞内的频率上升到90%，同时显著降低了适存度。在实验过程中，带有缺失的 mtDNA 在 nd5 中获得了三个额外的突变，即同源多聚运行中的两个单插入移帧突变和一个碱基置换。尽管这些次级突变会带来额外的适应性代价，但在 MA 实验结束时，所有携带缺失的分子都含有 nd5 突变。突变mtDNA的存在与mtDNA拷贝数的增加有关。与野生型核背景相比，MA品系中mtDNA拷贝数的变化更大，包括在一个世代时间点上拷贝数的严重减少。以不同世代的 MA 实验为起点进行的进化重放实验表明，其中两个次级突变通过未知机制促进了原始 ctb-1 缺失的扩散。
{"title":"Dissecting the sequential evolution of a selfish mitochondrial genome in Caenorhabditis elegans","authors":"Joseph J. Dubie, Vaishali Katju, Ulfar Bergthorsson","doi":"10.1038/s41437-024-00704-2","DOIUrl":"10.1038/s41437-024-00704-2","url":null,"abstract":"Mitochondrial genomes exist in a nested hierarchy of populations where mitochondrial variants are subject to genetic drift and selection at each level of organization, sometimes engendering conflict between different levels of selection, and between the nuclear and mitochondrial genomes. Deletion mutants in the Caenorhabditis elegans mitochondrial genome can reach high intracellular frequencies despite strongly detrimental effects on fitness. During a mutation accumulation (MA) experiment in C. elegans, a 499 bp deletion in ctb-1 rose to 90% frequency within cells while significantly reducing fitness. During the experiment, the deletion-bearing mtDNA acquired three additional mutations in nd5, namely two single insertion frameshift mutations in a homopolymeric run, and a base substitution. Despite an additional fitness cost of these secondary mutations, all deletion-bearing molecules contained the nd5 mutations at the termination of the MA experiment. The presence of mutant mtDNA was associated with increased mtDNA copy-number. Variation in mtDNA copy-number was greater in the MA lines than in a wildtype nuclear background, including a severe reduction in copy-number at one generational timepoint. Evolutionary replay experiments using different generations of the MA experiment as starting points suggests that two of the secondary mutations contribute to the proliferation of the original ctb-1 deletion by unknown mechanisms.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00704-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141537841","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 : 2024-07-03DOI: 10.1038/s41437-024-00695-0
Xi Wang, Kerry Reid, Ying Chen, David Dudgeon, Juha Merilä
Many endangered species live in fragmented and isolated populations with low genetic variability, signs of inbreeding, and small effective population sizes - all features elevating their extinction risk. The flat-headed loach (Oreonectes platycephalus), a small noemacheilid fish, is widely across southern China, but only in the headwaters of hillstreams; as a result, they are spatially isolated from conspecific populations. We surveyed single nucleotide polymorphisms in 16 Hong Kong populations of O. platycephalus to determine whether loach populations from different streams were genetically isolated from each other, showed low levels of genetic diversity, signs of inbreeding, and had small contemporary effective population sizes. Estimates of average observed heterozygosity (HO = 0.0473), average weighted nucleotide diversity (πw = 0.0546) and contemporary effective population sizes (Ne = 10.2 ~ 129.8) were very low, and several populations showed clear signs of inbreeding as judged from relatedness estimates. The degree of genetic differentiation among populations was very high (average FST = 0.668), even over short geographic distances (<1.5 km), with clear patterns of isolation by distance. These results suggest that Hong Kong populations of O. platycephalus have experienced strong genetic drift and loss of genetic variability because sea-level rise after the last glaciation reduced connectedness among paleodrainages, isolating populations in headwaters. All this, together with the fact that the levels of genetic diversity and contemporary effective population sizes within O. platycephalus populations are lower than most other freshwater fishes, suggests that they face high local extinction risk and have limited capacity for future adaptation.
{"title":"Ecological genetics of isolated loach populations indicate compromised adaptive potential","authors":"Xi Wang, Kerry Reid, Ying Chen, David Dudgeon, Juha Merilä","doi":"10.1038/s41437-024-00695-0","DOIUrl":"10.1038/s41437-024-00695-0","url":null,"abstract":"Many endangered species live in fragmented and isolated populations with low genetic variability, signs of inbreeding, and small effective population sizes - all features elevating their extinction risk. The flat-headed loach (Oreonectes platycephalus), a small noemacheilid fish, is widely across southern China, but only in the headwaters of hillstreams; as a result, they are spatially isolated from conspecific populations. We surveyed single nucleotide polymorphisms in 16 Hong Kong populations of O. platycephalus to determine whether loach populations from different streams were genetically isolated from each other, showed low levels of genetic diversity, signs of inbreeding, and had small contemporary effective population sizes. Estimates of average observed heterozygosity (HO = 0.0473), average weighted nucleotide diversity (πw = 0.0546) and contemporary effective population sizes (Ne = 10.2 ~ 129.8) were very low, and several populations showed clear signs of inbreeding as judged from relatedness estimates. The degree of genetic differentiation among populations was very high (average FST = 0.668), even over short geographic distances (<1.5 km), with clear patterns of isolation by distance. These results suggest that Hong Kong populations of O. platycephalus have experienced strong genetic drift and loss of genetic variability because sea-level rise after the last glaciation reduced connectedness among paleodrainages, isolating populations in headwaters. All this, together with the fact that the levels of genetic diversity and contemporary effective population sizes within O. platycephalus populations are lower than most other freshwater fishes, suggests that they face high local extinction risk and have limited capacity for future adaptation.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11286901/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141497902","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 : 2024-07-02DOI: 10.1038/s41437-024-00697-y
Pouya Ahadi, Balabhaskar Balasundaram, Juan S. Borrero, Charles Chen
In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic characteristics are selected to cross in order to maximize the likelihood of the inheritance of desirable genetic materials to the progeny. Unlike approaches that use phenotypic values for parental selection and evaluate individuals separately, we use a criterion that relies on the genetic architecture of traits and evaluates combinations of genomic information of the pairs of individuals. We introduce the expected cross value (ECV) criterion that measures the expected number of desirable alleles for gametes produced by pairs of individuals sampled from a population of potential parents. We use the ECV criterion to develop an integer linear programming formulation for the parental selection problem. The formulation is capable of controlling the inbreeding level between selected mates. We evaluate the approach or two applications: (i) improving multiple target traits simultaneously, and (ii) finding a multi-parental solution to design crossing blocks. We evaluate the performance of the ECV criterion using a simulation study. Finally, we discuss how the ECV criterion and the proposed integer linear programming techniques can be applied to improve breeding efficiency while maintaining genetic diversity in a breeding program.
{"title":"Development and optimization of expected cross value for mate selection problems","authors":"Pouya Ahadi, Balabhaskar Balasundaram, Juan S. Borrero, Charles Chen","doi":"10.1038/s41437-024-00697-y","DOIUrl":"10.1038/s41437-024-00697-y","url":null,"abstract":"In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic characteristics are selected to cross in order to maximize the likelihood of the inheritance of desirable genetic materials to the progeny. Unlike approaches that use phenotypic values for parental selection and evaluate individuals separately, we use a criterion that relies on the genetic architecture of traits and evaluates combinations of genomic information of the pairs of individuals. We introduce the expected cross value (ECV) criterion that measures the expected number of desirable alleles for gametes produced by pairs of individuals sampled from a population of potential parents. We use the ECV criterion to develop an integer linear programming formulation for the parental selection problem. The formulation is capable of controlling the inbreeding level between selected mates. We evaluate the approach or two applications: (i) improving multiple target traits simultaneously, and (ii) finding a multi-parental solution to design crossing blocks. We evaluate the performance of the ECV criterion using a simulation study. Finally, we discuss how the ECV criterion and the proposed integer linear programming techniques can be applied to improve breeding efficiency while maintaining genetic diversity in a breeding program.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11286873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141491650","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 : 2024-06-28DOI: 10.1038/s41437-024-00702-4
Victor Papin, Alexandre Bosc, Leopoldo Sanchez, Laurent Bouffier
Global warming threatens the productivity of forest plantations. We propose here the integration of environmental information into a genomic evaluation scheme using individual reaction norms, to enable the quantification of resilience in forest tree improvement and conservation strategies in the coming decades. Random regression models were used to fit wood ring series, reflecting the longitudinal phenotypic plasticity of tree growth, according to various environmental gradients. The predictive ability of the models was considered to select the most relevant environmental gradient, namely a gradient derived from an ecophysiological model and combining trunk water potential and temperature. Even if the individual ranking was preserved over most of the environmental gradient, strong genotype x environment interactions were detected in the extreme unfavorable part of the gradient, which includes environmental conditions that are very likely to be more frequent in the future. Combining genomic information and longitudinal data allowed to predict the growth of individuals in environments where they have not been observed. Phenotyping of 50% of the individuals in all the environments studied allowed to predict the growth of the remaining 50% of individuals in all these environments with a predictive ability of 0.25. Without changing the total number of observations, adding observations in a reduced number of environments for the individuals to be predicted, while decreasing the number of individuals phenotyped in all environments, increased the predictive ability to 0.59, highlighting the importance of phenotypic data allocation. We found that genomic reaction norms are useful for the characterization and prediction of the function of genetic parameters and facilitate breeding in a climate change context.
{"title":"Integrating environmental gradients into breeding: application of genomic reactions norms in a perennial species","authors":"Victor Papin, Alexandre Bosc, Leopoldo Sanchez, Laurent Bouffier","doi":"10.1038/s41437-024-00702-4","DOIUrl":"10.1038/s41437-024-00702-4","url":null,"abstract":"Global warming threatens the productivity of forest plantations. We propose here the integration of environmental information into a genomic evaluation scheme using individual reaction norms, to enable the quantification of resilience in forest tree improvement and conservation strategies in the coming decades. Random regression models were used to fit wood ring series, reflecting the longitudinal phenotypic plasticity of tree growth, according to various environmental gradients. The predictive ability of the models was considered to select the most relevant environmental gradient, namely a gradient derived from an ecophysiological model and combining trunk water potential and temperature. Even if the individual ranking was preserved over most of the environmental gradient, strong genotype x environment interactions were detected in the extreme unfavorable part of the gradient, which includes environmental conditions that are very likely to be more frequent in the future. Combining genomic information and longitudinal data allowed to predict the growth of individuals in environments where they have not been observed. Phenotyping of 50% of the individuals in all the environments studied allowed to predict the growth of the remaining 50% of individuals in all these environments with a predictive ability of 0.25. Without changing the total number of observations, adding observations in a reduced number of environments for the individuals to be predicted, while decreasing the number of individuals phenotyped in all environments, increased the predictive ability to 0.59, highlighting the importance of phenotypic data allocation. We found that genomic reaction norms are useful for the characterization and prediction of the function of genetic parameters and facilitate breeding in a climate change context.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141467604","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 : 2024-06-27DOI: 10.1038/s41437-024-00698-x
Ryan J. Eckert, Alexis B. Sturm, Ashley M. Carreiro, Allison M. Klein, Joshua D. Voss
Population genetic analyses can provide useful data on species’ regional connectivity and diversity which can inform conservation and restoration efforts. In this study, we quantified the genetic connectivity and diversity of Stephanocoenia intersepta corals from shallow (<30 m) to mesophotic (30–45 m) depths across Florida Keys National Marine Sanctuary. We generated single nucleotide polymorphism (SNP) markers to identify genetic structuring of shallow and mesophotic S. intersepta corals. We uncovered four distinct, cryptic genetic lineages with varying levels of depth-specificity. Shallow-specific lineages exhibited lower heterozygosity and higher inbreeding relative to depth-generalist lineages found across both shallow and mesophotic reefs. Estimation of recent genetic migration rates demonstrated that mesophotic sites are more prolific sources than shallow sites, particularly in the Lower Keys and Upper Keys. Additionally, we compared endosymbiotic Symbiodiniaceae among sampled S. intersepta using the ITS2 region and SymPortal analysis framework, identifying symbionts from the genera Symbiodinium, Breviolum, and Cladocopium. Symbiodiniaceae varied significantly across depth and location and exhibited significant, but weak correlation with host lineage and genotype. Together, these data demonstrate that despite population genetic structuring across depth, some mesophotic populations may provide refuge for shallow populations moving forward and remain important contributors to the overall genetic diversity of this species throughout the region. This study highlights the importance of including mesophotic as well as shallow corals in population genetic assessments and informs future science-based management, conservation, and restoration efforts within Florida Keys National Marine Sanctuary.
{"title":"Cryptic diversity of shallow and mesophotic Stephanocoenia intersepta corals across Florida Keys National Marine Sanctuary","authors":"Ryan J. Eckert, Alexis B. Sturm, Ashley M. Carreiro, Allison M. Klein, Joshua D. Voss","doi":"10.1038/s41437-024-00698-x","DOIUrl":"10.1038/s41437-024-00698-x","url":null,"abstract":"Population genetic analyses can provide useful data on species’ regional connectivity and diversity which can inform conservation and restoration efforts. In this study, we quantified the genetic connectivity and diversity of Stephanocoenia intersepta corals from shallow (<30 m) to mesophotic (30–45 m) depths across Florida Keys National Marine Sanctuary. We generated single nucleotide polymorphism (SNP) markers to identify genetic structuring of shallow and mesophotic S. intersepta corals. We uncovered four distinct, cryptic genetic lineages with varying levels of depth-specificity. Shallow-specific lineages exhibited lower heterozygosity and higher inbreeding relative to depth-generalist lineages found across both shallow and mesophotic reefs. Estimation of recent genetic migration rates demonstrated that mesophotic sites are more prolific sources than shallow sites, particularly in the Lower Keys and Upper Keys. Additionally, we compared endosymbiotic Symbiodiniaceae among sampled S. intersepta using the ITS2 region and SymPortal analysis framework, identifying symbionts from the genera Symbiodinium, Breviolum, and Cladocopium. Symbiodiniaceae varied significantly across depth and location and exhibited significant, but weak correlation with host lineage and genotype. Together, these data demonstrate that despite population genetic structuring across depth, some mesophotic populations may provide refuge for shallow populations moving forward and remain important contributors to the overall genetic diversity of this species throughout the region. This study highlights the importance of including mesophotic as well as shallow corals in population genetic assessments and informs future science-based management, conservation, and restoration efforts within Florida Keys National Marine Sanctuary.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141467603","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 : 2024-06-25DOI: 10.1038/s41437-024-00700-6
Sean James Buckley, Chris J. Brauer, Peter J. Unmack, Michael P. Hammer, Mark Adams, Stephen J. Beatty, David L. Morgan, Luciano B. Beheregaray
Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic to the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, we explored the phylogeographic history of western (Nannoperca vittata) and little (Nannoperca pygmaea) pygmy perches, assessing population divergence and phylogenetic relationships, delimiting species and estimating changes in species distributions from the Pliocene to 2100. We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability but with significant range contractions likely under future climate change. Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region.
{"title":"Long-term climatic stability drives accumulation and maintenance of divergent freshwater fish lineages in a temperate biodiversity hotspot","authors":"Sean James Buckley, Chris J. Brauer, Peter J. Unmack, Michael P. Hammer, Mark Adams, Stephen J. Beatty, David L. Morgan, Luciano B. Beheregaray","doi":"10.1038/s41437-024-00700-6","DOIUrl":"10.1038/s41437-024-00700-6","url":null,"abstract":"Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic to the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, we explored the phylogeographic history of western (Nannoperca vittata) and little (Nannoperca pygmaea) pygmy perches, assessing population divergence and phylogenetic relationships, delimiting species and estimating changes in species distributions from the Pliocene to 2100. We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability but with significant range contractions likely under future climate change. Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00700-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450367","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 : 2024-06-25DOI: 10.1038/s41437-024-00701-5
Sarah E. Orr, Nicole A. Hedrick, Kayla A. Murray, Abhinav K. Pasupuleti, Jennifer L. Kovacs, Michael A. D. Goodisman
Many species exhibit distinct phenotypic classes, such as sexes in dioecious species or castes in social species. The evolution of these classes is affected by the genetic architecture governing traits shared between phenotypes. However, estimates of the genetic and environmental factors contributing to phenotypic variation in distinct classes have rarely been examined. We studied the genetic architecture underlying morphological traits in phenotypic classes in the social wasp Vespula maculifrons. Our data revealed patriline effects on a few traits, indicating weak genetic influences on caste phenotypic variation. Interestingly, traits exhibited higher heritability in queens than workers. This result suggests that genetic variation has a stronger influence on trait variation in the queen caste than the worker caste, which is unexpected because queens typically experience direct selection. Moreover, estimates of heritability for traits were correlated between the castes, indicating that variability in trait size was governed by similar genetic architecture in the two castes. However, we failed to find evidence for a significant relationship between caste dimorphism and caste correlation, as would be expected if trait evolution was constrained by intralocus genetic conflict. Our analyses also uncovered variation in the allometric relationships for traits. These analyses suggested that worker traits were proportionally smaller than queen traits for most traits examined. Overall, our data provide evidence for a strong environmental and moderate genetic basis of trait variation among castes. Moreover, our results suggest that selection previously operated on caste phenotype in this species, and phenotypic variation is now governed primarily by environmental differences.
{"title":"Genetic and environmental effects on morphological traits of social phenotypes in wasps","authors":"Sarah E. Orr, Nicole A. Hedrick, Kayla A. Murray, Abhinav K. Pasupuleti, Jennifer L. Kovacs, Michael A. D. Goodisman","doi":"10.1038/s41437-024-00701-5","DOIUrl":"10.1038/s41437-024-00701-5","url":null,"abstract":"Many species exhibit distinct phenotypic classes, such as sexes in dioecious species or castes in social species. The evolution of these classes is affected by the genetic architecture governing traits shared between phenotypes. However, estimates of the genetic and environmental factors contributing to phenotypic variation in distinct classes have rarely been examined. We studied the genetic architecture underlying morphological traits in phenotypic classes in the social wasp Vespula maculifrons. Our data revealed patriline effects on a few traits, indicating weak genetic influences on caste phenotypic variation. Interestingly, traits exhibited higher heritability in queens than workers. This result suggests that genetic variation has a stronger influence on trait variation in the queen caste than the worker caste, which is unexpected because queens typically experience direct selection. Moreover, estimates of heritability for traits were correlated between the castes, indicating that variability in trait size was governed by similar genetic architecture in the two castes. However, we failed to find evidence for a significant relationship between caste dimorphism and caste correlation, as would be expected if trait evolution was constrained by intralocus genetic conflict. Our analyses also uncovered variation in the allometric relationships for traits. These analyses suggested that worker traits were proportionally smaller than queen traits for most traits examined. Overall, our data provide evidence for a strong environmental and moderate genetic basis of trait variation among castes. Moreover, our results suggest that selection previously operated on caste phenotype in this species, and phenotypic variation is now governed primarily by environmental differences.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11286790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450366","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 : 2024-06-18DOI: 10.1038/s41437-024-00696-z
Andrea Modica, Hadrien Lalagüe, Sylvie Muratorio, Ivan Scotti
Forest tree populations harbour high genetic diversity thanks to large effective population sizes and strong gene flow, allowing them to diversify through adaptation to local environmental pressures within dispersal distance. Many tree populations also experienced historical demographic fluctuations, including spatial population contraction or expansions at various temporal scales, which may constrain their ability to adapt to environmental variations. Our aim is to investigate how recent contraction and expansion events interfere with local adaptation, by studying patterns of adaptive divergence between closely related stands undergoing environmentally contrasted conditions, and having or not recently expanded. To investigate genome-wide signatures of local adaptation while accounting for demography, we analysed divergence in a European beech population by testing pairwise differentiation among four tree stands at ~35k Single Nucleotide Polymorphisms from ~9k genomic regions. We applied three divergence outlier search methods resting on different assumptions and targeting either single SNPs or contiguous genomic regions, while accounting for the effect of population size variations on genetic divergence. We found 27 signals of selective signatures in 19 target regions. Putatively adaptive divergence involved all stand pairs. We retrieved signals both when comparing old-growth stands and recently colonised areas and when comparing stands within the old-growth area. Therefore, adaptive divergence processes have taken place both over short time spans, under strong environmental contrasts, and over short ecological gradients, in populations that have been stable in the long term. This suggests that standing genetic variation supports local, microgeographic divergence processes, which can maintain genetic diversity at the landscape level.
由于有效种群规模大、基因流动强，森林树木种群具有很高的遗传多样性，使其能够在扩散距离内通过适应当地环境压力而实现多样化。许多树木种群也经历过历史上的人口波动，包括不同时间尺度上的空间种群收缩或扩张，这可能会限制它们适应环境变化的能力。我们的目的是通过研究环境条件反差较大、近期是否扩张的近缘树种之间的适应性差异模式，研究近期的收缩和扩张事件如何干扰当地的适应性。为了在考虑人口因素的同时研究局部适应的全基因组特征，我们分析了一个欧洲山毛榉种群的分化情况，方法是测试四个林分之间来自约9千个基因组区域的约3.5万个单核苷酸多态性的配对分化。我们采用了三种基于不同假设的差异离群点搜索方法，分别针对单个 SNP 或连续基因组区域，同时考虑了种群规模变化对遗传差异的影响。我们在 19 个目标区域发现了 27 个选择性特征信号。假定的适应性分化涉及所有站对。我们在比较老林区和新殖民地时，以及在比较老林区内的林区时，都发现了信号。因此，适应性分化过程既发生在环境对比强烈的短时间内，也发生在长期稳定的种群的短生态梯度上。这表明，长期存在的遗传变异支持局部、微观地理的分化过程，这可以在景观层面维持遗传多样性。
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Pub Date : 2024-06-10DOI: 10.1038/s41437-024-00694-1
Leeban H. Yusuf, Yolitzi Saldívar Lemus, Peter Thorpe, Constantino Macías Garcia, Michael G. Ritchie
Understanding the phylogeographic history of a group and identifying the factors contributing to speciation is an important challenge in evolutionary biology. The Goodeinae are a group of live-bearing fishes endemic to Mexico. Here, we develop genomic resources for species within the Goodeinae and use phylogenomic approaches to characterise their evolutionary history. We sequenced, assembled and annotated the genomes of four Goodeinae species, including Ataeniobius toweri, the only matrotrophic live-bearing fish without a trophotaenia in the group. We estimated timings of species divergence and examined the extent and timing of introgression between the species to assess if this may have occurred during an early radiation, or in more recent episodes of secondary contact. We used branch-site models to detect genome-wide positive selection across Goodeinae, and we specifically asked whether this differs in A. toweri, where loss of placental viviparity has recently occurred. We found evidence of gene flow between geographically isolated species, suggesting vicariant speciation was supplemented by limited post-speciation gene flow, and gene flow may explain previous uncertainties about Goodeid phylogeny. Genes under positive selection in the group are likely to be associated with the switch to live-bearing. Overall, our studies suggest that both volcanism-driven vicariance and changes in reproductive mode influenced radiation in the Goodeinae.
了解一个族群的系统地理历史并确定导致物种变异的因素是进化生物学中的一项重要挑战。古德伊纳科是墨西哥特有的活体鱼类。在这里，我们开发了古德伊纳科物种的基因组资源，并使用系统发生学方法来描述它们的进化历史。我们对四个古德氏鱼科物种的基因组进行了测序、组装和注释，其中包括Ataeniobius toweri。我们估算了物种分化的时间，并考察了物种间的引种范围和时间，以评估这是否可能发生在早期辐射期间，或发生在较近的二次接触中。我们使用了分支位点模型来检测古德伊纳亚科的全基因组正选择，并特别询问了最近发生胎盘胎生性丧失的 A. toweri 的正选择是否有所不同。我们发现了地理上孤立的物种之间基因流动的证据，这表明沧桑物种的分化得到了有限的分化后基因流动的补充，基因流动可能解释了以前古德伊亚科系统发育的不确定性。该类群中受到正选择的基因很可能与活体繁殖的转变有关。总之，我们的研究表明，火山作用驱动的沧海桑田和繁殖模式的变化都影响了古德伊纳科的辐射。
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Pub Date : 2024-06-04DOI: 10.1038/s41437-024-00693-2
J. Skytte af Sätra, L. Garkava-Gustavsson, P. K. Ingvarsson
Good understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into ‘hardy’ and ‘not hardy’ cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 MbHFTH1 of chromosome 1 among apple cultivars in the ‘hardy’ group. Using phased genotypic data from the 20 K apple Infinium® SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.
要想高效培育适应当地气候的苹果栽培品种，就必须充分了解苹果适应北方气候的基因组区域。适当的表型鉴定和评估基础设施对于鉴定适应性性状和分析其遗传组成至关重要。然而，这种基础设施成本高昂，目前在瑞典北部北方地区还不具备。因此，我们利用有关 59 个苹果栽培品种气候适应性的历史果树学数据和全基因组测序技术，在瑞典北部推荐种植的苹果栽培品种中确定了经过历史选择的基因组区域。我们发现苹果栽培品种由两个祖先群体组成，这两个群体与根据果树学文献划分的 "耐寒 "和 "不耐寒 "栽培品种群体基本一致。通过对选择信号的全基因组扫描，我们在 "耐寒 "组苹果栽培品种的 1 号染色体 29 MbHFTH1 附近的基因组区域获得了正选择的有力证据。利用来自 20 K 苹果 Infinium® SNP 阵列的分阶段基因型数据，我们确定了与两个栽培品种组相关的单倍型，并追踪了这些单倍型在一些苹果栽培品种血统中的传播情况。这表明，可以通过群体基因组学方法分析来自果树学文献的历史数据，从而揭示园艺利基市场关键特性的基因组控制。我们需要这些知识来促进高效的育种策略，以便在未来开发出适应当地的苹果栽培品种。当前的研究说明了气候因素对林木作物施加的强大选择压力的反应，也说明了在当前气候变化的背景下，对这一主题进行基因研究的重要性和育种工作的可行性。
{"title":"Why we thrive beneath a northern sky – genomic signals of selection in apple for adaptation to northern Sweden","authors":"J. Skytte af Sätra, L. Garkava-Gustavsson, P. K. Ingvarsson","doi":"10.1038/s41437-024-00693-2","DOIUrl":"10.1038/s41437-024-00693-2","url":null,"abstract":"Good understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into ‘hardy’ and ‘not hardy’ cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 MbHFTH1 of chromosome 1 among apple cultivars in the ‘hardy’ group. Using phased genotypic data from the 20 K apple Infinium® SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11286948/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141247246","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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