IF 3.1 2区生物学

Heredity Pub Date : 2025-06-13 DOI: 10.1038/s41437-025-00775-9

Léo Dejeux, Nathanaëlle Saclier, Juliette Tariel-Adam, Maxime Hoareau, Tristan Lefébure, Lara Konecny, Sandrine Plénet, Emilien Luquet

{"title":"Transcriptomic basis of within- and trans-generational predator-induced plasticity in the freshwater snail Physa acuta.","authors":"Léo Dejeux, Nathanaëlle Saclier, Juliette Tariel-Adam, Maxime Hoareau, Tristan Lefébure, Lara Konecny, Sandrine Plénet, Emilien Luquet","doi":"10.1038/s41437-025-00775-9","DOIUrl":"https://doi.org/10.1038/s41437-025-00775-9","url":null,"abstract":"Inducible defences in response to predation risk are a well-known example of adaptive phenotypic plasticity. Although inducible defences have been studied mainly within a generation (within-generational plasticity), there is now clear evidence that ancestral exposure to predation risk can influence the defences expressed by offspring, even if they have not been exposed themselves (transgenerational plasticity). The molecular mechanisms allowing the transmission of environmental information across generations are not well understood. In this study, we combined measures of antipredator responses (behavioural and morphological) with transcriptomic investigations across two generations in the freshwater snail Physa acuta. We hypothesised that both within- and transgenerational plasticity would induce phenotypic changes associated with differential gene expression. Our results confirmed within- and transgenerational plasticity: F1 snails respond to predator-cue exposure by increasing escape behaviour, reducing shell length, and developing thicker and slenderer shells, whereas F2 snails from exposed parents have longer and thicker shells with narrower apertures. Within- and transgenerational plasticity were accompanied by the differential expression of 112 genes (101 up- and 11 downregulated) and 23 differentially expressed genes (17 up- and 6 downregulated), respectively. Within- and transgenerational plasticity did not share common differentially expressed genes, but the associated molecular functions, involving metabolism and transcription regulation, were similar. These results suggest that predator-induced within-generational plasticity and transgenerational plasticity may result from different genomic pathways and may evolve independently.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293665","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

Rate of de novo mutations in the three-spined stickleback. 三棘棘鱼的新生突变率。

IF 3.1 2区生物学

Heredity Pub Date : 2025-06-12 DOI: 10.1038/s41437-025-00767-9

Chaowei Zhang, Kerry Reid, Mikkel Heide Schierup, Hongbo Wang, Ulrika Candolin, Juha Merilä

引用次数: 0

Assessing simulation-based supervised machine learning for demographic parameter inference from genomic data. 评估基于模拟的监督机器学习对基因组数据的人口统计参数推断。

IF 3.1 2区生物学

Heredity Pub Date : 2025-06-06 DOI: 10.1038/s41437-025-00773-x

Arnaud Quelin, Frédéric Austerlitz, Flora Jay

{"title":"Assessing simulation-based supervised machine learning for demographic parameter inference from genomic data.","authors":"Arnaud Quelin, Frédéric Austerlitz, Flora Jay","doi":"10.1038/s41437-025-00773-x","DOIUrl":"https://doi.org/10.1038/s41437-025-00773-x","url":null,"abstract":"The ever-increasing availability of high-throughput DNA sequences and the development of numerous computational methods have led to considerable advances in our understanding of the evolutionary and demographic history of populations. Several demographic inference methods have been developed to take advantage of these massive genomic data. Simulation-based approaches, such as approximate Bayesian computation (ABC), have proved particularly efficient for complex demographic models. However, taking full advantage of the comprehensive information contained in massive genomic data remains a challenge for demographic inference methods, which generally rely on partial information from these data. Using advanced computational methods, such as machine learning, is valuable for efficiently integrating more comprehensive information. Here, we showed how simulation-based supervised machine learning methods applied to an extensive range of summary statistics are effective in inferring demographic parameters for connected populations. We compared three machine learning (ML) methods: a neural network, the multilayer perceptron (MLP), and two ensemble methods, random forest (RF) and the gradient boosting system XGBoost (XGB), to infer demographic parameters from genomic data under a standard isolation with migration model and a secondary contact model with varying population sizes. We showed that MLP outperformed the other two methods and that, on the basis of permutation feature importance, its predictions involved a larger combination of summary statistics. Moreover, they outperformed all three tested ABC algorithms. Finally, we demonstrated how a method called SHAP, from the field of explainable artificial intelligence, can be used to shed light on the contribution of summary statistics within the ML models.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144233970","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

Genetic diversity and structure lag the effects of contemporary environmental changes in a platypus meta-population. 鸭嘴兽元种群的遗传多样性和结构滞后于当代环境变化的影响。

IF 3.1 2区生物学

Heredity Pub Date : 2025-06-06 DOI: 10.1038/s41437-025-00774-w

Collin W Ahrens, Josh Griffiths, Al Danger, Rhys Coleman, Anthony van Rooyen, Elise Furlan, Andrew R Weeks

{"title":"Genetic diversity and structure lag the effects of contemporary environmental changes in a platypus meta-population.","authors":"Collin W Ahrens, Josh Griffiths, Al Danger, Rhys Coleman, Anthony van Rooyen, Elise Furlan, Andrew R Weeks","doi":"10.1038/s41437-025-00774-w","DOIUrl":"https://doi.org/10.1038/s41437-025-00774-w","url":null,"abstract":"The platypus is an evolutionary unique mammal on the east coast of mainland Australia and throughout Tasmania. The species is dependent on freshwater ecosystems, is declining throughout its range, and is listed as Vulnerable in the state of Victoria, and Near Threatened on the IUCN Red List. This relatively long-lived species is cryptic and nocturnal making it difficult to study in natural populations. Relatively little is known about its demographic history or the forces that shape genetic variation. We use a unique genomic dataset comprising 2715 single-nucleotide polymorphisms from 545 individual platypuses sampled from five catchments across Melbourne, Victoria. This dataset enabled us to describe the genetic variation across the catchments and test hypotheses relating to migration, effective population size, and potential negative effects of anthropogenic barriers. We found relatively consistent levels of genetic diversity in platypuses across Melbourne's catchments, moderate levels of within-catchment migration, and genetic differentiation both between and within catchments. This genetic structure is explained by several factors, including isolation-by-river-distance, isolation-by-environment and within-catchment sex biased dispersal at short distances. These patterns are likely explained by a temporal lag between indirect and direct anthropogenic changes to the environmental and genetic variation, and these contemporary analyses likely reflect historical demographic patterns. In addition, we find that anthropogenic barriers such as dams have not measurably affected migration in these catchments. Our study highlights future evolutionary challenges that exist for platypuses in Melbourne's catchments, which could be representative of their entire range along the east coast of Australia.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247648","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

Mitogenomic resolution of phylogenetic conflicts and adaptive signatures in feliform carnivorans. 类人猿系统发育冲突和适应特征的丝分裂基因组分析。

IF 3.1 2区生物学

Heredity Pub Date : 2025-05-28 DOI: 10.1038/s41437-025-00772-y

Xiaoyang Wu, Yamin Xing, Xibao Wang, Yongquan Shang, Yao Chen, Liangkai Wang, Mingke Han, Weilai Sha, Honghai Zhang

{"title":"Mitogenomic resolution of phylogenetic conflicts and adaptive signatures in feliform carnivorans.","authors":"Xiaoyang Wu, Yamin Xing, Xibao Wang, Yongquan Shang, Yao Chen, Liangkai Wang, Mingke Han, Weilai Sha, Honghai Zhang","doi":"10.1038/s41437-025-00772-y","DOIUrl":"https://doi.org/10.1038/s41437-025-00772-y","url":null,"abstract":"Feliform carnivores face dual threats from habitat fragmentation and climate change, but unresolved phylogenetic relationships and unclear adaptive mechanisms hinder the development of conservation strategies. This study integrates mitochondrial genome data from 75 extant species (including three newly obtained taxa: Helogale parvula, Suricata suricatta, and Neofelis diardi) to resolve taxonomic controversies and reveal adaptive evolutionary mechanisms. Bayesian phylogenetic reconstruction strongly supports a sister-group relationship between Felidae and Prionodontidae (posterior probability PP = 1.0), overturning traditional morphological classifications. Divergence time estimation indicates that the crown group of Feliformia originated in the Middle Eocene (46 Ma), with key radiation events synchronized with Oligocene-Miocene climatic upheavals and continental collisions. Adaptive evolution analyses show that mitochondrial protein-coding genes (PCGs) are predominantly under purifying selection. However, significant positive selection signals were detected in the ND4 gene of Nandinia binotata and the COX2 gene of Pantherinae, potentially linked to arid adaptation and predatory energy demands, respectively. The frequent use of GTG start codons in the COX1 gene of Neofelis diardi suggests metabolic fine-tuning for island ecosystems. Conservation genomics identifies Prionodon pardicolor and Neofelis nebulosa as Evolutionarily Significant Units (ESUs) with heightened vulnerability to habitat fragmentation. By integrating mitogenomic architecture, deep-time biogeography, and contemporary selection pressures, this study establishes a unified framework bridging molecular systematics and conservation strategies, providing scientific guidance for protecting rapidly evolving lineages.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173718","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

Correction: Maternal effects in the model system Daphnia: the ecological past meets the epigenetic future. 修正：模型系统中的母系效应水蚤：生态的过去与表观遗传的未来相遇。

IF 3.1 2区生物学

Heredity Pub Date : 2025-05-23 DOI: 10.1038/s41437-025-00771-z

Trenton C Agrelius, Jeffry L Dudycha

引用次数: 0

Evaluating regional heritability mapping methods for identifying QTLs in a wild population of Soay sheep 评价Soay羊野生群体qtl的区域遗传力定位方法。

IF 3.1 2区生物学

Heredity Pub Date : 2025-05-23 DOI: 10.1038/s41437-025-00770-0

Caelinn James, Josephine M. Pemberton, Pau Navarro, Sara Knott

{"title":"Evaluating regional heritability mapping methods for identifying QTLs in a wild population of Soay sheep","authors":"Caelinn James, Josephine M. Pemberton, Pau Navarro, Sara Knott","doi":"10.1038/s41437-025-00770-0","DOIUrl":"10.1038/s41437-025-00770-0","url":null,"abstract":"The study of complex traits and their genetic underpinnings is crucial for understanding the evolutionary processes and mechanisms that shape natural populations. Regional heritability mapping (RHM) is a method for estimating the heritability of genomic segments that may contain both common and rare variants affecting a complex trait. This research is important because it advances our ability to detect genetic loci that contribute to phenotypic variation, even those that might be missed by traditional methods such as genome-wide association studies (GWAS). Here, we compare three RHM methods: SNP-RHM, which uses genomic relationship matrices (GRMs) based on SNP genotypes; Hap-RHM, which utilizes GRMs based on haplotypes; and SNHap-RHM, which integrates both SNP-based and haplotype-based GRMs jointly. These methods were applied to data from a wild population of sheep, focusing on the analysis of eleven polygenic traits. The results were compared with findings from previous GWAS to assess how RHM performed at identifying both known and novel associated loci. We found that while the inclusion of the regional matrix did not account for significant variation in all regions associated with trait variation as identified by GWAS, it did uncover several regions that were not previously linked to trait variation. This suggests that RHM methods can provide additional insights into the genetic architecture of complex traits, highlighting regions of the genome that may be overlooked by GWAS alone. This study underscores the importance of using complementary approaches to fully understand the genetic basis of complex traits in natural populations.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 6","pages":"374-386"},"PeriodicalIF":3.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00770-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132334","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

How partial phenotyping to reduce generation intervals can help to increase annual genetic gain in selected honeybee populations. 减少世代间隔的部分表型如何有助于增加选定蜜蜂种群的年遗传增益。

IF 3.1 2区生物学

Heredity Pub Date : 2025-05-22 DOI: 10.1038/s41437-025-00768-8

Tristan Kistler, Evert W Brascamp, Benjamin Basso, Florence Phocas, Piter Bijma

{"title":"How partial phenotyping to reduce generation intervals can help to increase annual genetic gain in selected honeybee populations.","authors":"Tristan Kistler, Evert W Brascamp, Benjamin Basso, Florence Phocas, Piter Bijma","doi":"10.1038/s41437-025-00768-8","DOIUrl":"https://doi.org/10.1038/s41437-025-00768-8","url":null,"abstract":"Honeybee breeding is organized around annual cycles, following seasonal change. Generation intervals are thus commonly multiples of whole years. Most queens are generally raised during spring or early summer in temperate climates. A generation interval of 1 year limits phenotyping to early recordable traits, before the spring following queens' births. Some traits, however, can only be recorded later, as is typically the case for total honey yield. Their recording on selection candidates thus increases the generation interval to at least 2 years, a common interval on the dam path. Using stochastic simulation, we investigated the impact of halving the dam generation interval and therefore recording only early traits on candidate dams. The generation interval on the sire path remained at 2 years with complete phenotyping. Breeding goals with varying weights on early and late traits were considered, as well as negative to positive genetic correlations between traits. The acceleration of the breeding scheme generally increased genetic gain for two-trait breeding goals, from 0% up to +47% after 20 years of selection. Although inbreeding rates per generation were slightly lower in the accelerated breeding scheme, inbreeding rates per year were significantly higher. This was due to the faster generation turnover (+33%) leading to 20-30% higher inbreeding coefficients (+0.04 to +0.07) after 20 years of selection. To avoid too high inbreeding, shortening the generation interval should be accompanied by strategies to limit inbreeding while still retaining most of the genetic gain, such as increasing the breeding nucleus size by relaxing selection intensity.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127503","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

CDK-4 regulates nucleolar size and metabolism at the cost of late-life fitness in C. elegans. CDK-4调节秀丽隐杆线虫的核仁大小和代谢，以牺牲其晚年的适应性为代价。

IF 3.1 2区生物学

Heredity Pub Date : 2025-05-18 DOI: 10.1038/s41437-025-00769-7

Rachel Webster, Maria Quintana, Bin Yu, Stacey Fluke, Ran Kafri, W Brent Derry

引用次数: 0

Multiple source locations and long-distance dispersal explain the rapid spread of a recent amphibian invasion 多种来源和远距离传播解释了最近两栖动物入侵的快速传播。

IF 3.1 2区生物学

Heredity Pub Date : 2025-05-16 DOI: 10.1038/s41437-025-00766-w

Teun Everts, Io Deflem, Charlotte Van Driessche, Sabrina Neyrinck, Tom Ruttink, Hans Jacquemyn, Rein Brys

{"title":"Multiple source locations and long-distance dispersal explain the rapid spread of a recent amphibian invasion","authors":"Teun Everts, Io Deflem, Charlotte Van Driessche, Sabrina Neyrinck, Tom Ruttink, Hans Jacquemyn, Rein Brys","doi":"10.1038/s41437-025-00766-w","DOIUrl":"10.1038/s41437-025-00766-w","url":null,"abstract":"Rapid range expansions are characteristic for non-native invasive species when introduced outside their native range. Understanding the dynamics and mechanisms of expanding non-native invasive species is key for regional management. While population genetics and long-term occurrence records are often used in this context, each provides only partial insights, highlighting the need for a combined approach. We demonstrate this synergy using the American bullfrog (Lithobates catesbeianus) invasion in the Grote Nete river valley (Belgium) as a case study. It is commonly believed that this invasion constitutes a single metapopulation established by one primary introduction followed by downstream dispersal. However, recent evidence suggests a more complex scenario, involving introduction at multiple locations and bidirectional dispersal. To differentiate between both scenarios, we analysed nearly three decades of occurrence records and 8592 single nucleotide polymorphisms across 372 individuals from 31 localities, and determined the number of source locations, the range expansion rate, the population genetic structure, and the magnitude and direction of gene flow. We found that invasive spread originated from up to six source locations followed by bidirectional dispersal and downstream long-distance dispersal (LDD) events. Our results suggest that at least two source locations were founded by primary introductions, two from LDD events, while the remaining resulted from secondary introductions. A canal crossing the river was identified as a dispersal barrier, leading to different invasion dynamics on both sides. Our study shows how asynchronous introductions at multiple locations, dispersal barriers, and environmental heterogeneity can lead to distinct spread dynamics within a seemingly continuous and interconnected metapopulation.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 6","pages":"362-373"},"PeriodicalIF":3.1,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00766-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144086176","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

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