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Correction: Population genomics of the white-beaked dolphin (Lagenorhynchus albirostris): implications for conservation amid climate-driven range shifts 更正:白喙海豚(Lagenorhynchus albirostris)的种群基因组学:在气候驱动的范围变化中对保护的影响。
IF 3.1 2区 生物学
Heredity Pub Date : 2024-07-29 DOI: 10.1038/s41437-024-00699-w
Marc-Alexander Gose, Emily Humble, Andrew Brownlow, Dave Wall, Emer Rogan, Guðjón Már Sigurðsson, Jeremy J. Kiszka, Charlotte Bie Thøstesen, Lonneke L. IJsseldijk, Mariel ten Doeschate, Nicholas J. Davison, Nils Øien, Rob Deaville, Ursula Siebert, Rob Ogden
{"title":"Correction: Population genomics of the white-beaked dolphin (Lagenorhynchus albirostris): implications for conservation amid climate-driven range shifts","authors":"Marc-Alexander Gose, Emily Humble, Andrew Brownlow, Dave Wall, Emer Rogan, Guðjón Már Sigurðsson, Jeremy J. Kiszka, Charlotte Bie Thøstesen, Lonneke L. IJsseldijk, Mariel ten Doeschate, Nicholas J. Davison, Nils Øien, Rob Deaville, Ursula Siebert, Rob Ogden","doi":"10.1038/s41437-024-00699-w","DOIUrl":"10.1038/s41437-024-00699-w","url":null,"abstract":"","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 3","pages":"206-206"},"PeriodicalIF":3.1,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00699-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141792333","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}
引用次数: 0
The genetic basis of divergent melanic pigmentation in benthic and limnetic threespine stickleback 底栖三刺鱼和湖泊三刺鱼黑色素差异的遗传基础。
IF 3.1 2区 生物学
Heredity Pub Date : 2024-07-24 DOI: 10.1038/s41437-024-00706-0
Elizabeth Tapanes, Diana J. Rennison
{"title":"The genetic basis of divergent melanic pigmentation in benthic and limnetic threespine stickleback","authors":"Elizabeth Tapanes, Diana J. Rennison","doi":"10.1038/s41437-024-00706-0","DOIUrl":"10.1038/s41437-024-00706-0","url":null,"abstract":"Pigmentation is an excellent trait to examine patterns of evolutionary change because it is often under natural selection. Benthic and limnetic threespine stickleback (Gasterosteus aculeatus) exhibit distinct pigmentation phenotypes, likely an adaptation to occupation of divergent niches. The genetic architecture of pigmentation in vertebrates appears to be complex. Prior QTL mapping of threespine stickleback pigmentation phenotypes has identified several candidate loci. However—relative to other morphological phenotypes (e.g., spines or lateral plates)—the genetic architecture of threespine stickleback pigmentation remains understudied. Here, we performed QTL mapping for two melanic pigmentation traits (melanophore density and lateral barring) using benthic-limnetic F2 crosses. The two traits mapped to different chromosomes, suggesting a distinct genetic basis. The resulting QTLs were additive, but explained a relatively small fraction of the total variance (~6%). QTLs maps differed by F1 family, suggesting variation in genetic architecture or ability to detect loci of small effect. Functional analysis identified enriched pathways for candidate loci. Several of the resulting candidate loci for pigmentation, including three loci in enriched pathways (bco1, sulf1, and tyms) have been previously indicated to affect pigmentation in other vertebrates. These findings add to a growing body of evidence suggesting pigmentation is often polygenic.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 4","pages":"207-215"},"PeriodicalIF":3.1,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00706-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758404","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}
引用次数: 0
Multiple karyotype differences between populations of the Hoplias malabaricus (Teleostei; Characiformes), a species complex in the gray area of the speciation process 处于物种演化灰色地带的马拉巴里鱼(Hoplias malabaricus)种群之间存在多种核型差异。
IF 3.1 2区 生物学
Heredity Pub Date : 2024-07-22 DOI: 10.1038/s41437-024-00707-z
Fernando H. S. Souza, Manolo F. Perez, Pedro H. N. Ferreira, Luiz A. C. Bertollo, Tariq Ezaz, Deborah Charlesworth, Marcelo B. Cioffi
{"title":"Multiple karyotype differences between populations of the Hoplias malabaricus (Teleostei; Characiformes), a species complex in the gray area of the speciation process","authors":"Fernando H. S. Souza, Manolo F. Perez, Pedro H. N. Ferreira, Luiz A. C. Bertollo, Tariq Ezaz, Deborah Charlesworth, Marcelo B. Cioffi","doi":"10.1038/s41437-024-00707-z","DOIUrl":"10.1038/s41437-024-00707-z","url":null,"abstract":"Neotropical fishes exhibit remarkable karyotype diversity, whose evolution is poorly understood. Here, we studied genetic differences in 60 individuals, from 11 localities of one species, the wolf fish Hoplias malabaricus, from populations that include six different “karyomorphs”. These differ in Y-X chromosome differentiation, and, in several cases, by fusions with autosomes that have resulted in multiple sex chromosomes. Other differences are also observed in diploid chromosome numbers and morphologies. In an attempt to start understanding how this diversity was generated, we analyzed within- and between-population differences in a genome-wide sequence data set. We detect clear genotype differences between karyomorphs. Even in sympatry, samples with different karyomorphs differ more in sequence than samples from allopatric populations of the same karyomorph, suggesting that they represent populations that are to some degree reproductively isolated. However, sequence divergence between populations with different karyomorphs is remarkably low, suggesting that chromosome rearrangements may have evolved during a brief evolutionary time. We suggest that the karyotypic differences probably evolved in allopatry, in small populations that would have allowed rapid fixation of rearrangements, and that they became sympatric after their differentiation. Further studies are needed to test whether the karyotype differences contribute to reproductive isolation detected between some H. malabaricus karyomorphs.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 4","pages":"216-226"},"PeriodicalIF":3.1,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141748029","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}
引用次数: 0
Genomic predictions of genetic variances and correlations among traits for breeding crosses in soybean 从基因组学角度预测大豆育种杂交的遗传变异和性状间的相关性。
IF 3.1 2区 生物学
Heredity Pub Date : 2024-07-12 DOI: 10.1038/s41437-024-00703-3
Cleiton A. Wartha, Aaron J. Lorenz
{"title":"Genomic predictions of genetic variances and correlations among traits for breeding crosses in soybean","authors":"Cleiton A. Wartha, Aaron J. Lorenz","doi":"10.1038/s41437-024-00703-3","DOIUrl":"10.1038/s41437-024-00703-3","url":null,"abstract":"Parental selection is perhaps the most critical decision a breeder makes, establishing the foundation of the entire program for years to come. Cross selection based on predicted mean and genetic variance can be further expanded to multiple-trait improvement by predicting the genetic correlation ( $${r}_{G}$$ ) between pairs of traits. Our objective was to empirically assess the ability to predict the family mean, genetic variance, superior progeny mean and genetic correlation through genomic prediction in a soybean population. Data made available through the Soybean Nested Association Mapping project included phenotypic data on seven traits (days to maturity, lodging, oil, plant height, protein, seed size, and seed yield) for 39 families. Training population composition followed a leave-one-family-out cross-validation scheme, with the validation family genetic parameters predicted using the remaining families as the training set. The predictive abilities for family mean and superior progeny mean were significant for all traits while predictive ability of genetic variance was significant for four traits. We were able to validate significant predictive abilities of $${r}_{G}$$ for 18 out of 21 (86%) pairwise trait combinations (P < 0.05). The findings from this study support the use of genome-wide marker effects for predicting $${r}_{G}$$ in soybean biparental crosses. If successfully implemented in breeding programs, this methodology could help to increase the rate of genetic gain for multiple correlated traits.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 3","pages":"173-185"},"PeriodicalIF":3.1,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00703-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141599259","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}
引用次数: 0
A complete chromosome substitution mapping panel reveals genome-wide epistasis in Arabidopsis 一个完整的染色体替换图谱面板揭示了拟南芥全基因组的表观性。
IF 3.1 2区 生物学
Heredity Pub Date : 2024-07-09 DOI: 10.1038/s41437-024-00705-1
Cris L. Wijnen, Ramon Botet, José van de Belt, Laurens Deurhof, Hans de Jong, C. Bastiaan de Snoo, Rob Dirks, Martin P. Boer, Fred A. van Eeuwijk, Erik Wijnker, Joost J. B. Keurentjes
{"title":"A complete chromosome substitution mapping panel reveals genome-wide epistasis in Arabidopsis","authors":"Cris L. Wijnen, Ramon Botet, José van de Belt, Laurens Deurhof, Hans de Jong, C. Bastiaan de Snoo, Rob Dirks, Martin P. Boer, Fred A. van Eeuwijk, Erik Wijnker, Joost J. B. Keurentjes","doi":"10.1038/s41437-024-00705-1","DOIUrl":"10.1038/s41437-024-00705-1","url":null,"abstract":"Chromosome substitution lines (CSLs) are tentatively supreme resources to investigate non-allelic genetic interactions. However, the difficulty of generating such lines in most species largely yielded imperfect CSL panels, prohibiting a systematic dissection of epistasis. Here, we present the development and use of a unique and complete panel of CSLs in Arabidopsis thaliana, allowing the full factorial analysis of epistatic interactions. A first comparison of reciprocal single chromosome substitutions revealed a dependency of QTL detection on different genetic backgrounds. The subsequent analysis of the complete panel of CSLs enabled the mapping of the genetic interactors and identified multiple two- and three-way interactions for different traits. Some of the detected epistatic effects were as large as any observed main effect, illustrating the impact of epistasis on quantitative trait variation. We, therefore, have demonstrated the high power of detection and mapping of genome-wide epistasis, confirming the assumed supremacy of comprehensive CSL sets. Development of a complete panel of chromosome substitution lines enables high power mapping of epistatic interactions in Arabidopsis thaliana.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"133 3","pages":"198-205"},"PeriodicalIF":3.1,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-024-00705-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141563298","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}
引用次数: 0
Dissecting the sequential evolution of a selfish mitochondrial genome in Caenorhabditis elegans 剖析线虫自私线粒体基因组的连续进化。
IF 3.1 2区 生物学
Heredity Pub Date : 2024-07-05 DOI: 10.1038/s41437-024-00704-2
Joseph J. Dubie, Vaishali Katju, Ulfar Bergthorsson
{"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":"133 3","pages":"186-197"},"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}
引用次数: 0
Ecological genetics of isolated loach populations indicate compromised adaptive potential 与世隔绝的泥鳅种群的生态遗传学表明其适应潜力受到损害。
IF 3.1 2区 生物学
Heredity Pub Date : 2024-07-03 DOI: 10.1038/s41437-024-00695-0
Xi Wang, Kerry Reid, Ying Chen, David Dudgeon, Juha Merilä
{"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":"133 2","pages":"88-98"},"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}
引用次数: 0
Development and optimization of expected cross value for mate selection problems 开发和优化择偶问题的预期交叉值。
IF 3.1 2区 生物学
Heredity Pub Date : 2024-07-02 DOI: 10.1038/s41437-024-00697-y
Pouya Ahadi, Balabhaskar Balasundaram, Juan S. Borrero, Charles Chen
{"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":"133 2","pages":"113-125"},"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}
引用次数: 0
Integrating environmental gradients into breeding: application of genomic reactions norms in a perennial species 将环境梯度纳入育种:基因组反应规范在多年生物种中的应用。
IF 3.1 2区 生物学
Heredity Pub Date : 2024-06-28 DOI: 10.1038/s41437-024-00702-4
Victor Papin, Alexandre Bosc, Leopoldo Sanchez, Laurent Bouffier
{"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":"133 3","pages":"160-172"},"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}
引用次数: 0
Cryptic diversity of shallow and mesophotic Stephanocoenia intersepta corals across Florida Keys National Marine Sanctuary 佛罗里达礁岛群国家海洋保护区浅海和中海 Stephanocoenia intersepta 珊瑚的隐秘多样性。
IF 3.1 2区 生物学
Heredity Pub Date : 2024-06-27 DOI: 10.1038/s41437-024-00698-x
Ryan J. Eckert, Alexis B. Sturm, Ashley M. Carreiro, Allison M. Klein, Joshua D. Voss
{"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":"133 3","pages":"137-148"},"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}
引用次数: 0
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