{"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":"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":"134 7","pages":"408-416"},"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}
HeredityPub Date : 2025-05-23DOI: 10.1038/s41437-025-00771-z
Trenton C. Agrelius, Jeffry L. Dudycha
{"title":"Correction: Maternal effects in the model system Daphnia: the ecological past meets the epigenetic future","authors":"Trenton C. Agrelius, Jeffry L. Dudycha","doi":"10.1038/s41437-025-00771-z","DOIUrl":"10.1038/s41437-025-00771-z","url":null,"abstract":"","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 7","pages":"450-450"},"PeriodicalIF":3.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00771-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132331","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}
HeredityPub Date : 2025-05-23DOI: 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}
HeredityPub Date : 2025-05-22DOI: 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":"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":"134 7","pages":"396-407"},"PeriodicalIF":3.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00768-8.pdf","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
HeredityPub Date : 2025-05-18DOI: 10.1038/s41437-025-00769-7
Rachel Webster, Maria Quintana, Bin Yu, Stacey Fluke, Ran Kafri, W Brent Derry
{"title":"CDK-4 regulates nucleolar size and metabolism at the cost of late-life fitness in C. elegans.","authors":"Rachel Webster, Maria Quintana, Bin Yu, Stacey Fluke, Ran Kafri, W Brent Derry","doi":"10.1038/s41437-025-00769-7","DOIUrl":"https://doi.org/10.1038/s41437-025-00769-7","url":null,"abstract":"<p><p>Studies on aging have centered on two molecular pathways: CDK4/6 and insulin/mTORC1. These pathways are thought to influence aging through distinct mechanisms: mTORC1 by reprogramming systemic metabolism, and CDK4 through p16-mediated senescence and inflammatory signaling (SASP). Here, we investigate the connection between aging and CDK4 in Caenorhabditis elegans, an organism lacking both p16 and SASP. Using a conditional degradation system, we demonstrate that CDK-4 inhibition in C. elegans phenocopies its aging-related functions observed in mammals. Worms with depleted CDK-4 exhibited accelerated aging phenotypes, including reduced lifespan, decreased motility, increased yolk accumulation, and earlier onset of senescence. At the physiological level, CDK4-inhibited worms show substantial metabolic shifts; including enhanced protein synthesis, elevated ATP production, and increased fat accumulation. These metabo-aging phenotypes occur independently of mTORC1, instead operating through the canonical CDK-4 effectors LIN-35 (Rb) and EFL-1 (E2F).</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092961","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}
HeredityPub Date : 2025-05-16DOI: 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}
HeredityPub Date : 2025-05-09DOI: 10.1038/s41437-025-00759-9
Annalaura Jokiniemi, Tanja Turunen, Mikko Kohonen, Martina Magris, Jarmo Ritari, Liisa Kuusipalo, Jukka Partanen, Jukka Kekäläinen
{"title":"Female-mediated selective sperm activation may remodel major histocompatibility complex-based mate choice decisions in humans","authors":"Annalaura Jokiniemi, Tanja Turunen, Mikko Kohonen, Martina Magris, Jarmo Ritari, Liisa Kuusipalo, Jukka Partanen, Jukka Kekäläinen","doi":"10.1038/s41437-025-00759-9","DOIUrl":"10.1038/s41437-025-00759-9","url":null,"abstract":"Major histocompatibility complex (MHC) genes are known to mediate mate choice both at the individual and gamete level. However, it has remained unclear how different episodes of MHC-associated mate choice interact and contribute to the total selection on MHC genes. Here, we clarified this interaction in humans by performing a full-factorial experiment where 10 females first ranked the attractiveness and intensity of the body odours of 11 males. Then we studied whether female odour preferences in these same 110 male-female combinations predicted sperm performance in the presence of follicular fluid (sperm-stimulating female reproductive fluid). When analyzing the total MHC similarity (including classical and non-classical MHC genes) of the male-female combinations, we found that females preferred the body odours of MHC-similar males, but that sperm motility was positively affected by the MHC dissimilarity of the male-female combinations. No associations were found for classical MHC genes only. Furthermore, odour preferences were negatively associated with sperm motility at the end of the follicular fluid treatment. Together, our results indicate that individual and gamete-level mate choice processes may act in opposing directions and that the most attractive males are not necessarily the most optimal partners at the post-copulatory level. Finally, our findings suggest that gamete-mediated mate choice may have a definitive role in disfavouring genetically incompatible partners from fertilizing oocytes.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 6","pages":"321-330"},"PeriodicalIF":3.1,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41437-025-00759-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144003476","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}
HeredityPub Date : 2025-05-05DOI: 10.1038/s41437-025-00765-x
André Yves, Josué A. R. Azevedo, Renata M. Pirani, Fernanda P. Werneck
{"title":"Local adaptation has a role in reducing vulnerability to climate change in a widespread Amazonian forest lizard","authors":"André Yves, Josué A. R. Azevedo, Renata M. Pirani, Fernanda P. Werneck","doi":"10.1038/s41437-025-00765-x","DOIUrl":"10.1038/s41437-025-00765-x","url":null,"abstract":"The extant genetic variation within and among taxa reflects a long history of diversification and adaptive mechanisms in response to climate change and landscape alterations. However, the velocity of current anthropogenic changes poses an imminent threat to global biodiversity. Understanding how species and populations might respond to global climate change provides valuable information for conservation in the face of these impacts. Here, we use genomic data to observe candidate loci under climate selection and test for genetic vulnerability to climate change in a widespread Amazonian ombrophilous lizard population. We found nine populations across Amazonia with a considerable amount of admixture among them. Distinct approaches of genome-environment association analyses revealed 56 candidate single-nucleotide polymorphisms (SNPs) under climatic selection, showing an east–west gradient in the adaptive landscape and a signal of local climate adaptation across the species range. According to our results, signals of local adaptation indicate that the species may not respond equally throughout its range, with some populations facing higher extinction risks. Genomic offset analysis predicts the southern and central portions of Amazonia to have a higher vulnerability to future climate change. Our findings highlight the importance of considering spatially explicit contexts with a large sampling coverage to evaluate how local adaptation and climatic vulnerability affect Amazonian forest ectothermic fauna.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 6","pages":"1-10"},"PeriodicalIF":3.1,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143965163","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}
HeredityPub Date : 2025-04-30DOI: 10.1038/s41437-025-00763-z
Renata M. Pirani, Carlos F. Arias, John David Curlis, Daniel J. Nicholson, Jessica Stapley, W. Owen McMillan, Christian L. Cox, Michael L. Logan
{"title":"The genetic basis of a colorful signal: the polymorphic dewlap of the slender anole (Anolis apletophallus)","authors":"Renata M. Pirani, Carlos F. Arias, John David Curlis, Daniel J. Nicholson, Jessica Stapley, W. Owen McMillan, Christian L. Cox, Michael L. Logan","doi":"10.1038/s41437-025-00763-z","DOIUrl":"10.1038/s41437-025-00763-z","url":null,"abstract":"Organisms often use colorful morphological traits to communicate with members of their own or other species. While “colorful signaling” systems exemplify well-known examples of the evolution of phenotypic diversity, the genetic basis of most of these traits remains unknown. Male lizards of the genus Anolis possess a colorful throat fan, or “dewlap”, that is flashed during social displays. These displays have been extensively studied in the context of their role in the adaptive radiation of the genus. In contrast, the genetic basis of the Anolis dewlap has received relatively little attention. Here, we studied the dewlap of the slender anole (Anolis apletophallus) which exhibits a dewlap polymorphism: males have either an entirely orange dewlap (“solid” morph) or a white dewlap with a basal orange spot (“bicolor” morph). To understand the inheritance of this polymorphism, we conducted 99 crosses between individuals from populations that were fixed for one morph (single/fixed/monomorphic) or contained both morphs (mixed/polymorphic). Next, we investigated the genetic architecture of this trait using a pooled population sequencing (Pool-seq) experiment. Our findings indicate that the slender anole dewlap polymorphism is best explained as an autosomal, single-locus, Mendelian trait with the solid morph allele dominant to the bicolor morph allele. Our outlier analysis of the Pool-seq data identified a region strongly associated with this trait and within this region we identified a promising candidate locus—the transcription factor single-minded 1 (SIM1)—that may underly the dewlap polymorphism.","PeriodicalId":12991,"journal":{"name":"Heredity","volume":"134 6","pages":"343-351"},"PeriodicalIF":3.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143968147","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}
HeredityPub Date : 2025-04-25DOI: 10.1038/s41437-025-00764-y
Patrice S Albert, Hua Yang, Zhi Gao, Cassidy DeVore, James A Birchler
{"title":"Aneuploidy and ploidy variation conditioned by the B chromosome of maize.","authors":"Patrice S Albert, Hua Yang, Zhi Gao, Cassidy DeVore, James A Birchler","doi":"10.1038/s41437-025-00764-y","DOIUrl":"https://doi.org/10.1038/s41437-025-00764-y","url":null,"abstract":"<p><p>The supernumerary B chromosome of maize has a drive mechanism to maintain itself in a population despite being dispensible. This involves nondisjunction of the B centromere at the second pollen mitosis that produces the two sperm followed by preferential fertilization of the egg by the B containing sperm during double fertilization. During an introgression of the supernumerary B chromosome into the inbred line B73, an unusually high frequency of trisomies for A chromosomes was observed. Due to parallels to the High Loss phenomenon in which three or more B chromosomes in a specific genetic background cause chromosomal breakage at heterochromatic knob sites during the second pollen mitosis as well as ploidy changes, this phenomenon was revisited. Examination of pollen of the High Loss line revealed a high frequency of single sperm in the presence of the B chromosomes, which was previously not realized. Crosses to tetraploid females confirmed that the single sperm were diploid and functional but also revealed the presence of diploids with their A chromosomes derived solely from the tetraploid parent indicating a \"diploid induction\". Collectively, the results reveal two backgrounds in which the B drive mechanism is not confined to this chromosome causing detrimental effects by adherence of heterochromatic knobs and apparently A centromeres at the mitosis preceding sperm development. In most genetic backgrounds this process is restricted to the B chromosome but in B73 and the High Loss line, there is spillover to the normal chromosomes in distinct ways.</p>","PeriodicalId":12991,"journal":{"name":"Heredity","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143995285","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}