Rose M H Driscoll, Xiaomi Liu, Julia McDonough, James Schmidt, Jennifer A Brisson
Phenotypic plasticity, the ability of a single genotype to produce a range of phenotypes in response to environmental cues, can exhibit genetic variation like any trait. Discovering the genetic basis of plasticity and plasticity variation is critical to understand how populations will respond to the ongoing environmental challenges brought about by, for example, climate change. Here, we investigate the genetic basis of the pea aphid (Acyrthosiphon pisum) wing plasticity variation. In this species, genetically identical, highly fecund wingless and dispersive winged individuals are produced by pea aphid mothers in uncrowded versus crowded environments, respectively. We focus specifically on the genetic basis of the propensity to produce winged individuals in response to crowding. We crossed a low to a high plasticity line and examined plasticity variation in backcross progeny (F1 x low parent), finding that differences between lines had a strong genetic component and that multiple loci likely to contribute to this variation. Transcriptional profiling revealed a candidate gene, yellow-h, which was found within a genomic locus contributing to plasticity variation. Overall, we provide novel information about the genetic basis of an ecologically-relevant trait and contribute to the growing literature recognizing the importance of understanding the genetic basis of plasticity variation.
{"title":"Pea aphid wing plasticity variation has a multigenic basis.","authors":"Rose M H Driscoll, Xiaomi Liu, Julia McDonough, James Schmidt, Jennifer A Brisson","doi":"10.1093/jhered/esaf006","DOIUrl":"https://doi.org/10.1093/jhered/esaf006","url":null,"abstract":"<p><p>Phenotypic plasticity, the ability of a single genotype to produce a range of phenotypes in response to environmental cues, can exhibit genetic variation like any trait. Discovering the genetic basis of plasticity and plasticity variation is critical to understand how populations will respond to the ongoing environmental challenges brought about by, for example, climate change. Here, we investigate the genetic basis of the pea aphid (Acyrthosiphon pisum) wing plasticity variation. In this species, genetically identical, highly fecund wingless and dispersive winged individuals are produced by pea aphid mothers in uncrowded versus crowded environments, respectively. We focus specifically on the genetic basis of the propensity to produce winged individuals in response to crowding. We crossed a low to a high plasticity line and examined plasticity variation in backcross progeny (F1 x low parent), finding that differences between lines had a strong genetic component and that multiple loci likely to contribute to this variation. Transcriptional profiling revealed a candidate gene, yellow-h, which was found within a genomic locus contributing to plasticity variation. Overall, we provide novel information about the genetic basis of an ecologically-relevant trait and contribute to the growing literature recognizing the importance of understanding the genetic basis of plasticity variation.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143124106","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}
Ingrid E Alvial, Noemi Rojas-Hernández, Nicolas Guerra, David Véliz, Christian R González, Laura M Pérez, Hugo A Benítez
Mosquitoes from the Culex pipiens complex are found worldwide and have been the focus of numerous studies due to their role as vectors of human pathogens. We investigated the population genetic structure of Cx. pipiens s.l. by analyzing SNPs and the COI gene, focusing on the genetic grouping signals of the ecotypes pipiens and molestus. Our analysis revealed no genetic association between the ecotypes and the SNPs, suggesting that the classification is based on ecological traits rather than genetic factors. Using data from 2,641 SNPs and 164 genotypes, our Bayesian clustering analysis categorized the populations into six distinct genetic groups, distinguishing the Rapa Nui island population from those on the American mainland. The estimated effective migration rates (EEMR) showed low levels of migration between island and continental populations, with significant migration occurring only among populations between 29° S and 33° S. Genetic differentiation between Rapa Nui island and the American continent was observed. In contrast, no significant differentiation was noted in other regions. The haplotype network suggests a possible migration pathway from that area of the South Pacific. Additionally, demographic history analysis indicates a relatively recent founder effect of Cx. pipiens s.l. on the island. Geographic isolation and variations in genetic makeup can limit the spread of pathogens regionally and globally. However, these same factors can also promote specialization and enhance adaptation to new ecological niches, thereby improving the ability of pathogens to function as effective vectors in isolated environments.
{"title":"Genetic structure of the northern house mosquito (Diptera: Culicidae) in a WNV-susceptible area.","authors":"Ingrid E Alvial, Noemi Rojas-Hernández, Nicolas Guerra, David Véliz, Christian R González, Laura M Pérez, Hugo A Benítez","doi":"10.1093/jhered/esaf005","DOIUrl":"https://doi.org/10.1093/jhered/esaf005","url":null,"abstract":"<p><p>Mosquitoes from the Culex pipiens complex are found worldwide and have been the focus of numerous studies due to their role as vectors of human pathogens. We investigated the population genetic structure of Cx. pipiens s.l. by analyzing SNPs and the COI gene, focusing on the genetic grouping signals of the ecotypes pipiens and molestus. Our analysis revealed no genetic association between the ecotypes and the SNPs, suggesting that the classification is based on ecological traits rather than genetic factors. Using data from 2,641 SNPs and 164 genotypes, our Bayesian clustering analysis categorized the populations into six distinct genetic groups, distinguishing the Rapa Nui island population from those on the American mainland. The estimated effective migration rates (EEMR) showed low levels of migration between island and continental populations, with significant migration occurring only among populations between 29° S and 33° S. Genetic differentiation between Rapa Nui island and the American continent was observed. In contrast, no significant differentiation was noted in other regions. The haplotype network suggests a possible migration pathway from that area of the South Pacific. Additionally, demographic history analysis indicates a relatively recent founder effect of Cx. pipiens s.l. on the island. Geographic isolation and variations in genetic makeup can limit the spread of pathogens regionally and globally. However, these same factors can also promote specialization and enhance adaptation to new ecological niches, thereby improving the ability of pathogens to function as effective vectors in isolated environments.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069194","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}
Andrey Tomarovsky, Ruqayya Khan, Olga Dudchenko, Azamat Totikov, Natalia A Serdyukova, David Weisz, Nadejda V Vorobieva, Tatiana Bulyonkova, Alexei V Abramov, Wenhui Nie, Jinhuan Wang, Svetlana A Romanenko, Anastasiya A Proskuryakova, Nikolay Cherkasov, Malcolm A Ferguson-Smith, Fengtang Yang, Elena Balanovskaya, M Thomas P Gilbert, Alexander S Graphodatsky, Erez Lieberman Aiden, Roger Powell, Klaus-Peter Koepfli, Polina L Perelman, Sergei Kliver
The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species. Using linked-read and Hi-C sequencing, we generated a chromosome-length genome assembly of a male stone marten (Gansu province, China) from a primary cell line. The stone marten assembly had a length of 2.42 Gbp, scaffold N50 of 144 Mbp, and a 96.2% BUSCO completeness score. We identified 19 chromosomal scaffolds (2n=38) and assigned them chromosome ids based on chromosome painting data. Annotation identified 20,087 protein-coding gene models, of which 18,283 were assigned common names. Comparison of the stone marten assembly with the cat, dog, and human genomes revealed several small syntenic blocks absent on the published painting maps. Finally, we assessed the heterozygosity and its distribution over the chromosomes. The detected low heterozygosity level (0.4 hetSNPs/kbp) and the presence of long RoHs require further research and a new evaluation of the conservation status of the stone marten in China. Combined with available carnivoran genomes in large scale synteny analysis, the stone marten genome will highlight new features and events in carnivoran evolution, hidden from cytogenetic approaches.
{"title":"Chromosome length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics.","authors":"Andrey Tomarovsky, Ruqayya Khan, Olga Dudchenko, Azamat Totikov, Natalia A Serdyukova, David Weisz, Nadejda V Vorobieva, Tatiana Bulyonkova, Alexei V Abramov, Wenhui Nie, Jinhuan Wang, Svetlana A Romanenko, Anastasiya A Proskuryakova, Nikolay Cherkasov, Malcolm A Ferguson-Smith, Fengtang Yang, Elena Balanovskaya, M Thomas P Gilbert, Alexander S Graphodatsky, Erez Lieberman Aiden, Roger Powell, Klaus-Peter Koepfli, Polina L Perelman, Sergei Kliver","doi":"10.1093/jhered/esaf001","DOIUrl":"https://doi.org/10.1093/jhered/esaf001","url":null,"abstract":"<p><p>The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species. Using linked-read and Hi-C sequencing, we generated a chromosome-length genome assembly of a male stone marten (Gansu province, China) from a primary cell line. The stone marten assembly had a length of 2.42 Gbp, scaffold N50 of 144 Mbp, and a 96.2% BUSCO completeness score. We identified 19 chromosomal scaffolds (2n=38) and assigned them chromosome ids based on chromosome painting data. Annotation identified 20,087 protein-coding gene models, of which 18,283 were assigned common names. Comparison of the stone marten assembly with the cat, dog, and human genomes revealed several small syntenic blocks absent on the published painting maps. Finally, we assessed the heterozygosity and its distribution over the chromosomes. The detected low heterozygosity level (0.4 hetSNPs/kbp) and the presence of long RoHs require further research and a new evaluation of the conservation status of the stone marten in China. Combined with available carnivoran genomes in large scale synteny analysis, the stone marten genome will highlight new features and events in carnivoran evolution, hidden from cytogenetic approaches.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069192","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}
Yan Yu, Ziying Li, Yichao Wu, Gang Xie, Yuhuan Guo, Zaijun Yang
Salvia miltiorrhiza Bunge is an ornamental plant known for its diverse flower colors, ranging from white to dark violet. To elucidate the regulatory mechanisms underlying flower color, we conducted QTL mapping and identified candidate genes involved in anthocyanidin accumulation. Total anthocyanidin content and six anthocyanidins in the corollas of S. miltiorrhiza were quantified using the pH differential method and HPLC, respectively. Composite interval mapping was employed to identify QTLs, followed by the identification of candidate genes based on stable QTL intervals across at least two different planting environments. These candidate genes were further validated through gene cloning and expression analysis. Anthocyanidin analysis in the F2 population revealed a positive correlation between total anthocyanidin content and flower color intensity. Notably, three major anthocyanidins of delphinidin (Dp), cyanidin (Cy), and petunidin (Pt) were detected in varying degrees of purple flowers, while no anthocyanidins were found in white flowers. In total, 33 QTLs associated with anthocyanidin content were identified, with two major QTLs located on linkage groups LG4 and LG5. Two candidate genes, CHS1 (a chalcone synthase) and TCP15 (a transcription factor), were identified in the genetic intervals of two major QTL sites, respectively. Preliminary verification experiments suggest that CHS1 may play a positive role in anthocyanidin biosynthesis, whereas TCP15 appears to potentially act as a negative regulator. This study provides a foundation for cloning genes controlling flower color and advances our understanding of the molecular mechanisms regulating flower color in S. miltiorrhiza.
{"title":"QTL mapping and identification of candidate genes for anthocyanidin accumulation in Salvia miltiorrhiza flowers.","authors":"Yan Yu, Ziying Li, Yichao Wu, Gang Xie, Yuhuan Guo, Zaijun Yang","doi":"10.1093/jhered/esaf004","DOIUrl":"https://doi.org/10.1093/jhered/esaf004","url":null,"abstract":"<p><p>Salvia miltiorrhiza Bunge is an ornamental plant known for its diverse flower colors, ranging from white to dark violet. To elucidate the regulatory mechanisms underlying flower color, we conducted QTL mapping and identified candidate genes involved in anthocyanidin accumulation. Total anthocyanidin content and six anthocyanidins in the corollas of S. miltiorrhiza were quantified using the pH differential method and HPLC, respectively. Composite interval mapping was employed to identify QTLs, followed by the identification of candidate genes based on stable QTL intervals across at least two different planting environments. These candidate genes were further validated through gene cloning and expression analysis. Anthocyanidin analysis in the F2 population revealed a positive correlation between total anthocyanidin content and flower color intensity. Notably, three major anthocyanidins of delphinidin (Dp), cyanidin (Cy), and petunidin (Pt) were detected in varying degrees of purple flowers, while no anthocyanidins were found in white flowers. In total, 33 QTLs associated with anthocyanidin content were identified, with two major QTLs located on linkage groups LG4 and LG5. Two candidate genes, CHS1 (a chalcone synthase) and TCP15 (a transcription factor), were identified in the genetic intervals of two major QTL sites, respectively. Preliminary verification experiments suggest that CHS1 may play a positive role in anthocyanidin biosynthesis, whereas TCP15 appears to potentially act as a negative regulator. This study provides a foundation for cloning genes controlling flower color and advances our understanding of the molecular mechanisms regulating flower color in S. miltiorrhiza.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061489","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}
Zhen-Bo Wu, Zheng-Yan Sui, Lan-Hui Peng, Mirna Ghemrawi, George Duncan, Henry Jones, Stephen J O'Brien, Shu-Jin Luo
In the fall of 2003, a two-year-old tiger named Ming, weighing some four hundred pounds, was discovered living in an apartment in Harlem, New York. Ming's rescue by NYPD was witnessed, recalled, and venerated by scores of neighbors. The tiger's history and ancestry stimulated considerable media interest, investigative sleuthing, and forensic genomic analyses. The Harlem tiger's subspecies makeup, his relationship to his putative sibling named Cheeky living in Homestead, Florida, and his genetic distinctiveness from wild tigers was assessed by Whole Genome Sequence (WGS) analyses of trace materials from plucked whiskers. Verified Subspecies Ancestry (VSA) of Ming and Cheeky was determined by comparing their WGS to SNP annotation from WGS of 35 voucher (pure subspecies) tiger specimens from six living subspecies. Genome-wide structure analyses based on 3,422,109 SNPs and a subset of 6,724 Ancestry-Informative Markers (AIMS) showed that Ming has an admixed genetic background from five subspecies: Indochinese tiger (Panthera tigris corbetti 35 ~ 40%), Bengal tiger (P. t. tigris 17 ~ 23%), Sumatran tiger (P. t. sumatrae 12 ~ 14%), Amur tiger (P. t. altaica ~ 10%), and Malayan tiger (P. t. jacksoni 1 ~ 10%). Cheeky is confirmed to be a full sibling to Ming and displayed an admixed genetic background with similar subspecies proportions as Ming's. The forensic assessment of the tigers' subspecies composition, kinship, and recent history of animal transaction provides an analytical pipeline and promises to assist in tiger conservation effort worldwide through standardized genomic analysis of tigers or tiger products with unknown origin.
{"title":"Forensic Assessment of Kinship, Genomic Ancestry, and Natural History of an Iconic Tiger of Harlem-New York City.","authors":"Zhen-Bo Wu, Zheng-Yan Sui, Lan-Hui Peng, Mirna Ghemrawi, George Duncan, Henry Jones, Stephen J O'Brien, Shu-Jin Luo","doi":"10.1093/jhered/esaf003","DOIUrl":"https://doi.org/10.1093/jhered/esaf003","url":null,"abstract":"<p><p>In the fall of 2003, a two-year-old tiger named Ming, weighing some four hundred pounds, was discovered living in an apartment in Harlem, New York. Ming's rescue by NYPD was witnessed, recalled, and venerated by scores of neighbors. The tiger's history and ancestry stimulated considerable media interest, investigative sleuthing, and forensic genomic analyses. The Harlem tiger's subspecies makeup, his relationship to his putative sibling named Cheeky living in Homestead, Florida, and his genetic distinctiveness from wild tigers was assessed by Whole Genome Sequence (WGS) analyses of trace materials from plucked whiskers. Verified Subspecies Ancestry (VSA) of Ming and Cheeky was determined by comparing their WGS to SNP annotation from WGS of 35 voucher (pure subspecies) tiger specimens from six living subspecies. Genome-wide structure analyses based on 3,422,109 SNPs and a subset of 6,724 Ancestry-Informative Markers (AIMS) showed that Ming has an admixed genetic background from five subspecies: Indochinese tiger (Panthera tigris corbetti 35 ~ 40%), Bengal tiger (P. t. tigris 17 ~ 23%), Sumatran tiger (P. t. sumatrae 12 ~ 14%), Amur tiger (P. t. altaica ~ 10%), and Malayan tiger (P. t. jacksoni 1 ~ 10%). Cheeky is confirmed to be a full sibling to Ming and displayed an admixed genetic background with similar subspecies proportions as Ming's. The forensic assessment of the tigers' subspecies composition, kinship, and recent history of animal transaction provides an analytical pipeline and promises to assist in tiger conservation effort worldwide through standardized genomic analysis of tigers or tiger products with unknown origin.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048770","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}
Maximilian Genetti, Merly Escalona, Cade Mirchandani, Jonas Oppenheimer, Eric Beraut, Samuel Sacco, William Seligmann, Colin W Fairbairn, Ruta Sahasrabudhe, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Russell Corbett-Detig
The Pacific banana slug, Ariolimax columbianus, is endemic to the forests of the Pacific Northern West. Found throughout coastal foothills and mountains of California, the hermaphroditic molluscs Ariolimax spp. are niche-constrained, hyper-localized, and phenotypically diverse. The evolutionary history and more recent population history and environmental conditions leading to their phenotypic and genetic variation are not understood. To facilitate such research, we present the first high-quality de novo genome assembly of A. columbianus as part of the California Conservation Genomics Project (CCGP). Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technologies were used to produce a de novo genome assembly, consistent with the standard CCGP genome assembly protocol. This assembly comprises 401 scaffolds spanning 2.29 Gb, represented by a scaffold N50 of 94.9 Mb, a contig N50 of 3.7 Mb, and a benchmarking universal single-copy ortholog (BUSCO) completeness score of 93.9%. Future work will use the A. columbianus genome to study the population structure of Ariolimax spp. across California to understand patterns of population structure, genetic diversity and the broader ecological connections with their habitat. This data will contribute to the CCGP, expanding the knowledge about the partitioning of genomic variation across the different ecoregions of California.
{"title":"Secrets of the Goo: the Genome assembly of the Pacific Banana Slug, Ariolimax columbianus.","authors":"Maximilian Genetti, Merly Escalona, Cade Mirchandani, Jonas Oppenheimer, Eric Beraut, Samuel Sacco, William Seligmann, Colin W Fairbairn, Ruta Sahasrabudhe, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Russell Corbett-Detig","doi":"10.1093/jhered/esaf002","DOIUrl":"https://doi.org/10.1093/jhered/esaf002","url":null,"abstract":"<p><p>The Pacific banana slug, Ariolimax columbianus, is endemic to the forests of the Pacific Northern West. Found throughout coastal foothills and mountains of California, the hermaphroditic molluscs Ariolimax spp. are niche-constrained, hyper-localized, and phenotypically diverse. The evolutionary history and more recent population history and environmental conditions leading to their phenotypic and genetic variation are not understood. To facilitate such research, we present the first high-quality de novo genome assembly of A. columbianus as part of the California Conservation Genomics Project (CCGP). Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technologies were used to produce a de novo genome assembly, consistent with the standard CCGP genome assembly protocol. This assembly comprises 401 scaffolds spanning 2.29 Gb, represented by a scaffold N50 of 94.9 Mb, a contig N50 of 3.7 Mb, and a benchmarking universal single-copy ortholog (BUSCO) completeness score of 93.9%. Future work will use the A. columbianus genome to study the population structure of Ariolimax spp. across California to understand patterns of population structure, genetic diversity and the broader ecological connections with their habitat. This data will contribute to the CCGP, expanding the knowledge about the partitioning of genomic variation across the different ecoregions of California.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143030353","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}
The ability to self-fertilize often varies among closely related hermaphroditic plant species, though, variation can also exist within species. In the North American Arabidopsis lyrata, the shift from self-incompatibility (SI) to selfing established in multiple regions independently, mostly since recent postglacial range expansion. This has made the species an ideal model for the investigation of the genomic basis of the breakdown of SI and its population genetic consequences. By comparing nearby selfing and outcrossing populations across the entire species' geographic distribution, we investigated variation at the self-incompatibility (S-)locus and across the genome. Furthermore, a diallel crossing experiment on one mixed-mating population was performed to gain insight into the inheritance of mating system variation. We confirmed that the breakdown of SI had evolved in several S-locus backgrounds. The diallel suggested the involvement of biparental contributions with dominance relations. Though, the population-level genome-wide association study did not single out clear-cut candidate genes but several regions with one near the S-locus. On the implication side, selfing as compared to outcrossing populations had less than half of the genomic diversity, while the number and length of runs of homozygosity (ROHs) scaled with the degree of inbreeding. Selfing populations with a history of long expansion had the longest ROHs. The results highlight that mating system shift to selfing, its genetic underpinning and the likely negative genomic consequences for evolutionary potential can be strongly interlinked with past range dynamics.
{"title":"Genomic implications of the repeated shift to self-fertilization across a species' geographic distribution.","authors":"Kay Lucek, Jana M Flury, Yvonne Willi","doi":"10.1093/jhered/esae046","DOIUrl":"10.1093/jhered/esae046","url":null,"abstract":"<p><p>The ability to self-fertilize often varies among closely related hermaphroditic plant species, though, variation can also exist within species. In the North American Arabidopsis lyrata, the shift from self-incompatibility (SI) to selfing established in multiple regions independently, mostly since recent postglacial range expansion. This has made the species an ideal model for the investigation of the genomic basis of the breakdown of SI and its population genetic consequences. By comparing nearby selfing and outcrossing populations across the entire species' geographic distribution, we investigated variation at the self-incompatibility (S-)locus and across the genome. Furthermore, a diallel crossing experiment on one mixed-mating population was performed to gain insight into the inheritance of mating system variation. We confirmed that the breakdown of SI had evolved in several S-locus backgrounds. The diallel suggested the involvement of biparental contributions with dominance relations. Though, the population-level genome-wide association study did not single out clear-cut candidate genes but several regions with one near the S-locus. On the implication side, selfing as compared to outcrossing populations had less than half of the genomic diversity, while the number and length of runs of homozygosity (ROHs) scaled with the degree of inbreeding. Selfing populations with a history of long expansion had the longest ROHs. The results highlight that mating system shift to selfing, its genetic underpinning and the likely negative genomic consequences for evolutionary potential can be strongly interlinked with past range dynamics.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"43-53"},"PeriodicalIF":3.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142019604","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}
Riley D Thoen, Andrea Southgate, Gretel Kiefer, Ruth G Shaw, Stuart Wagenius
Anthropogenically fragmented populations may have reduced fitness due to loss of genetic diversity and inbreeding. The extent of such fitness losses due to fragmentation and potential gains from conservation actions are infrequently assessed together empirically. Controlled crosses within and among populations can identify whether populations are at risk of inbreeding depression and whether inter-population crossing alleviates fitness loss. Because fitness depends on the environment and life stage, studies quantifying cumulative fitness over a large portion of the lifecycle in conditions that mimic natural environments are most informative. To assess the fitness consequences of habitat fragmentation, we leveraged controlled within-family, within-population, and between-population crosses to quantify inbreeding depression and heterosis in seven populations of Echinacea angustifolia within a 6,400-ha area. We then assessed cumulative offspring fitness after 14 yr of growth in a natural experimental plot (N = 1,136). The mean fitness of progeny from within-population crosses varied considerably, indicating genetic differentiation among source populations, even though these sites are all less than 9 km apart. The fitness consequences of within-family and between-population crosses varied in magnitude and direction. Only one of the seven populations showed inbreeding depression of high effect, while four populations showed substantial heterosis. Outbreeding depression was rare and slight. Our findings indicate that local crossings between isolated populations yield unpredictable fitness consequences ranging from slight decreases to substantial increases. Interestingly, inbreeding depression and heterosis did not relate closely to population size, suggesting that all fragmented populations could contribute to conservation goals as either pollen recipients or donors.
{"title":"The conservation value of small population remnants: Variability in inbreeding depression and heterosis of a perennial herb, the narrow-leaved purple coneflower (Echinacea angustifolia).","authors":"Riley D Thoen, Andrea Southgate, Gretel Kiefer, Ruth G Shaw, Stuart Wagenius","doi":"10.1093/jhered/esae055","DOIUrl":"10.1093/jhered/esae055","url":null,"abstract":"<p><p>Anthropogenically fragmented populations may have reduced fitness due to loss of genetic diversity and inbreeding. The extent of such fitness losses due to fragmentation and potential gains from conservation actions are infrequently assessed together empirically. Controlled crosses within and among populations can identify whether populations are at risk of inbreeding depression and whether inter-population crossing alleviates fitness loss. Because fitness depends on the environment and life stage, studies quantifying cumulative fitness over a large portion of the lifecycle in conditions that mimic natural environments are most informative. To assess the fitness consequences of habitat fragmentation, we leveraged controlled within-family, within-population, and between-population crosses to quantify inbreeding depression and heterosis in seven populations of Echinacea angustifolia within a 6,400-ha area. We then assessed cumulative offspring fitness after 14 yr of growth in a natural experimental plot (N = 1,136). The mean fitness of progeny from within-population crosses varied considerably, indicating genetic differentiation among source populations, even though these sites are all less than 9 km apart. The fitness consequences of within-family and between-population crosses varied in magnitude and direction. Only one of the seven populations showed inbreeding depression of high effect, while four populations showed substantial heterosis. Outbreeding depression was rare and slight. Our findings indicate that local crossings between isolated populations yield unpredictable fitness consequences ranging from slight decreases to substantial increases. Interestingly, inbreeding depression and heterosis did not relate closely to population size, suggesting that all fragmented populations could contribute to conservation goals as either pollen recipients or donors.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"24-33"},"PeriodicalIF":3.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142382482","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}
Sergei Kliver, Iva Kovacic, Sarah Mak, Mikkel-Holger S Sinding, Julia Stagegaard, Bent Petersen, Joseph Nesme, Marcus Thomas Pius Gilbert
The African hunting dog (Lycaon pictus, 2n = 78) once ranged over most sub-Saharan ecosystems except its deserts and rainforests. However, as a result of (still ongoing) population declines, today they remain only as small fragmented populations. Furthermore, the future of the species remains unclear, due to both anthropogenic pressure and interactions with domestic dogs, thus their preservation is a conservation priority. On the tree of life, the hunting dog is basal to Canis and Cuon and forms a crown group with them, making it a useful species for comparative genomic studies. Here, we present a diploid chromosome-level assembly of an African hunting dog. Assembled according to Vertebrate Genomes Project guidelines from a combination of PacBio HiFi reads and HiC data, it is phased at the level of individual chromosomes. The maternal (pseudo)haplotype (mat) of our assembly has a length of 2.38 Gbp, and 99.36% of the sequence is encompassed by 39 chromosomal scaffolds. The rest is included in only 36 unplaced short scaffolds. At the contig level, the mat consists of only 166 contigs with an N50 of 39 Mbp. BUSCO (Benchmarking Universal Single-Copy Orthologue) analysis showed 95.4% completeness based on Carnivora conservative genes (carnivora_odb10). When compared with other available genomes from subtribe Canina, the quality of the assembly is excellent, typically between the first and third depending on the parameter used, and a significant improvement on previously published genomes for the species. We hope this assembly will play an important role in future conservation efforts and comparative studies of canid genomes.
{"title":"A chromosome phased diploid genome assembly of African hunting dog (Lycaon pictus).","authors":"Sergei Kliver, Iva Kovacic, Sarah Mak, Mikkel-Holger S Sinding, Julia Stagegaard, Bent Petersen, Joseph Nesme, Marcus Thomas Pius Gilbert","doi":"10.1093/jhered/esae052","DOIUrl":"10.1093/jhered/esae052","url":null,"abstract":"<p><p>The African hunting dog (Lycaon pictus, 2n = 78) once ranged over most sub-Saharan ecosystems except its deserts and rainforests. However, as a result of (still ongoing) population declines, today they remain only as small fragmented populations. Furthermore, the future of the species remains unclear, due to both anthropogenic pressure and interactions with domestic dogs, thus their preservation is a conservation priority. On the tree of life, the hunting dog is basal to Canis and Cuon and forms a crown group with them, making it a useful species for comparative genomic studies. Here, we present a diploid chromosome-level assembly of an African hunting dog. Assembled according to Vertebrate Genomes Project guidelines from a combination of PacBio HiFi reads and HiC data, it is phased at the level of individual chromosomes. The maternal (pseudo)haplotype (mat) of our assembly has a length of 2.38 Gbp, and 99.36% of the sequence is encompassed by 39 chromosomal scaffolds. The rest is included in only 36 unplaced short scaffolds. At the contig level, the mat consists of only 166 contigs with an N50 of 39 Mbp. BUSCO (Benchmarking Universal Single-Copy Orthologue) analysis showed 95.4% completeness based on Carnivora conservative genes (carnivora_odb10). When compared with other available genomes from subtribe Canina, the quality of the assembly is excellent, typically between the first and third depending on the parameter used, and a significant improvement on previously published genomes for the species. We hope this assembly will play an important role in future conservation efforts and comparative studies of canid genomes.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"78-87"},"PeriodicalIF":3.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332622","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}
Daniele Battilani, Roberta Gargiulo, Romolo Caniglia, Elena Fabbri, Jazmín Ramos- Madrigal, Claudia Fontsere, Marta Maria Ciucani, Shyam Gopalakrishnan, Matteo Girardi, Ilaria Fracasso, Matteo Mastroiaco, Paolo Ciucci, Cristiano Vernesi
Preserving genetic diversity and adaptive potential while avoiding inbreeding depression is crucial for the long-term conservation of natural populations. Despite demographic increases, traces of past bottleneck events at the genomic level should be carefully considered for population management. From this perspective, the peninsular Italian wolf is a paradigmatic case. After being on the brink of extinction in the late 1960s, peninsular Italian wolves rebounded and recolonized most of the peninsula aided by conservation measures, including habitat and legal protection. Notwithstanding their demographic recovery, a comprehensive understanding of the genomic consequences of the historical bottleneck in Italian wolves is still lacking. To fill this gap, we sequenced whole genomes of 13 individuals sampled in the core historical range of the species in Central Italy to conduct population genomic analyses, including a comparison with wolves from two highly-inbred wolf populations (i.e. Scandinavia and Isle Royale). We found that peninsular Italian wolves, despite their recent recovery, still exhibit relatively low genetic diversity, a small effective population size, signatures of inbreeding, and a non-negligible genetic load. Our findings indicate that the peninsular Italian wolf population is still susceptible to bottleneck legacies, which could lead to local inbreeding depression in case of population reduction or fragmentations. This study emphasizes the importance of considering key genetic parameters to design appropriate long-term conservation management plans.
{"title":"Beyond population size: Whole-genome data reveal bottleneck legacies in the peninsular Italian wolf.","authors":"Daniele Battilani, Roberta Gargiulo, Romolo Caniglia, Elena Fabbri, Jazmín Ramos- Madrigal, Claudia Fontsere, Marta Maria Ciucani, Shyam Gopalakrishnan, Matteo Girardi, Ilaria Fracasso, Matteo Mastroiaco, Paolo Ciucci, Cristiano Vernesi","doi":"10.1093/jhered/esae041","DOIUrl":"10.1093/jhered/esae041","url":null,"abstract":"<p><p>Preserving genetic diversity and adaptive potential while avoiding inbreeding depression is crucial for the long-term conservation of natural populations. Despite demographic increases, traces of past bottleneck events at the genomic level should be carefully considered for population management. From this perspective, the peninsular Italian wolf is a paradigmatic case. After being on the brink of extinction in the late 1960s, peninsular Italian wolves rebounded and recolonized most of the peninsula aided by conservation measures, including habitat and legal protection. Notwithstanding their demographic recovery, a comprehensive understanding of the genomic consequences of the historical bottleneck in Italian wolves is still lacking. To fill this gap, we sequenced whole genomes of 13 individuals sampled in the core historical range of the species in Central Italy to conduct population genomic analyses, including a comparison with wolves from two highly-inbred wolf populations (i.e. Scandinavia and Isle Royale). We found that peninsular Italian wolves, despite their recent recovery, still exhibit relatively low genetic diversity, a small effective population size, signatures of inbreeding, and a non-negligible genetic load. Our findings indicate that the peninsular Italian wolf population is still susceptible to bottleneck legacies, which could lead to local inbreeding depression in case of population reduction or fragmentations. This study emphasizes the importance of considering key genetic parameters to design appropriate long-term conservation management plans.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"10-23"},"PeriodicalIF":3.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074569","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}