Journal of Heredity最新文献_第3页

A genome assembly for the Chryxus Arctic (Oeneis chryxus), the highest butterfly in North America 北美洲最高蝶类北极蝶（Oeneis chryxus）的基因组组装

IF 3.1 2区生物学

Journal of Heredity Pub Date : 2024-09-13 DOI: 10.1093/jhered/esae051

Zachary G MacDonald, Sean Schoville, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Erin Toffelmier, Thomas Gillespie, H Bradley Shaffer

{"title":"A genome assembly for the Chryxus Arctic (Oeneis chryxus), the highest butterfly in North America","authors":"Zachary G MacDonald, Sean Schoville, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Erin Toffelmier, Thomas Gillespie, H Bradley Shaffer","doi":"10.1093/jhered/esae051","DOIUrl":"https://doi.org/10.1093/jhered/esae051","url":null,"abstract":"We describe a highly contiguous and complete diploid genome assembly for the Chryxus Arctic, Oeneis chryxus (E. Doubleday, [1849]), a butterfly species complex spanning much of northern and western North America. One subspecies, the Ivallda Arctic (O. c. ivallda), is endemic to California’s Sierra Nevada and of particular biogeographic interest and conservation concern. Extreme alpine habitats occupied by this subspecies include the summit of Mt. Whitney, California, representing the highest elevation butterfly population in North America. The assembly presented here consists of two haplotypes, 738.92 and 770.85 Mb in length, with contig N50 values of 10.49 and 10.13 Mb, scaffold N50 values of 25.35 and 25.69 Mb, scaffold L50 values of 13 and 14, and BUSCO completeness scores of 96.5 and 98.3%, respectively. More than 97% of the assembly is organized into 29 scaffolds, which likely represent whole chromosomes. This assembly is the first major genomic resource for Oeneis, providing a foundational reference for future genomic studies on the taxonomy, evolutionary history, and conservation of the genus. As part of the California Conservation Genomics Project, we will use this assembly in conjunction with short-read resequencing to resolve patterns of evolutionary differentiation, adaptive genomic variation, and gene flow among remaining O. c. ivallda populations. These data can and will be used to inform the subspecies’ conservation as warming climatic conditions continue to lead to the loss and fragmentation of alpine habitats. We also provide genome assemblies for the O. chryxus mitochondrion and a Wolbachia endosymbiont.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247352","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

"The Reference Genome Of The Kidnapper Ant, Polyergus Mexicanus". "绑架蚁 Polyergus Mexicanus 的参考基因组"。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-09-09 DOI: 10.1093/jhered/esae047

Elizabeth I Cash, Merly Escalona, Philip S Ward, Ruta Sahasrabudhe, Courtney Miller, Erin Toffelmier, Colin Fairbairn, William Seligmann, H Bradley Shaffer, Neil D Tsutsui

{"title":"\"The Reference Genome Of The Kidnapper Ant, Polyergus Mexicanus\".","authors":"Elizabeth I Cash, Merly Escalona, Philip S Ward, Ruta Sahasrabudhe, Courtney Miller, Erin Toffelmier, Colin Fairbairn, William Seligmann, H Bradley Shaffer, Neil D Tsutsui","doi":"10.1093/jhered/esae047","DOIUrl":"https://doi.org/10.1093/jhered/esae047","url":null,"abstract":"Polyergus kidnapper ants are widely distributed, but relatively uncommon, throughout the Holarctic, spanning an elevational range from sea level to over 3000 m. These species are well known for their obligate social parasitism with various Formica ant species, which they kidnap in dramatic, highly coordinated raids. Kidnapped Formica larvae and pupae become integrated into the Polyergus colony where they develop into adults and perform nearly all of the necessary colony tasks for the benefit of their captors. In California, Polyergus mexicanus is the most widely distributed Polyergus, but recent evidence has identified substantial genetic polymorphism within this species, including genetically divergent lineages associated with the use of different Formica host species. Given its unique behavior and genetic diversity, Polyergus mexicanus plays a critical role in maintaining ecosystem balance by influencing the population dynamics and genetic diversity of its host ant species, Formica, highlighting its conservation value and importance in the context of biodiversity preservation. Here, we present a high-quality genome assembly of P. mexicanus from a sample collected in Plumas County, CA, USA, in the foothills of the central Sierra Nevada. This genome assembly consists of 364 scaffolds spanning 252.31 Mb, with contig N50 of 481,250 kb, scaffold N50 of 10.36 Mb, and BUSCO completeness of 95.4%. We also assembled the genome of the Wolbachia endosymbiont of P. mexicanus - a single, circular contig spanning 1.23 Mb. These genome sequences provide essential resources for future studies of conservation genetics, population genetics, speciation, and behavioral ecology in this charismatic social insect.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142156745","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

A chromosome-level genome assembly of the common eider, Somateria mollissima (Linnaeus, 1758). 普通凫（Somateria mollissima (Linnaeus, 1758)）染色体级基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-09-04 DOI: 10.1093/jhered/esae042

Ole K Tørresen, Oliver Kersten, Benedicte Garmann-Aarhus, Morten Helberg, Ave Tooming-Klunderud, Morten Skage, Sanne Boessenkool, Kjetill S Jakobsen

引用次数: 0

Functional and evolutionary insights into chemosensation and specialized herbivory from the genome of the red milkweed beetle, Tetraopes tetrophthalmus (Cerambycidae: Lamiinae). 从红色乳草甲虫 Tetraopes tetrophthalmus（Cerambycidae: Lamiinae）的基因组洞察化学感应和专门化食草的功能与进化。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-30 DOI: 10.1093/jhered/esae049

Richard Adams, Terrence Sylvester, Robert F Mitchell, Mathew A Price, Rongrong Shen, Duane D McKenna

{"title":"Functional and evolutionary insights into chemosensation and specialized herbivory from the genome of the red milkweed beetle, Tetraopes tetrophthalmus (Cerambycidae: Lamiinae).","authors":"Richard Adams, Terrence Sylvester, Robert F Mitchell, Mathew A Price, Rongrong Shen, Duane D McKenna","doi":"10.1093/jhered/esae049","DOIUrl":"https://doi.org/10.1093/jhered/esae049","url":null,"abstract":"Tetraopes are aposematic longhorn beetles (Cerambycidae) that feed primarily on toxic plants in the genus Asclepias (milkweeds). Studies of Tetraopes and their host plants have revealed compelling evidence for insect-plant coevolution and cospeciation. We sequenced, assembled and annotated the genome of the common red milkweed beetle, Tetraopes tetrophthalmus, and explored gene content and evolution, focusing on annotated genes putatively involved in chemosensation, allelochemical detoxification, and phytophagy. Comparisons were made to the Asian longhorned beetle (Anoplophora glabripennis) genome. The genome assembly comprised 779 Mb distributed across 1057 contigs, with an N50 of 2.21 Mb and 13,089 putative genes, including 97.3% of expected single-copy orthologs. Manual curation identified 122 putative odorant receptors (OR) and 162 gustatory receptors (GR), the former number similar to A. glabripennis but the latter only 69% of the A. glabripennis suite. We also documented a greater percentage of pseudogenic GRs and ORs compared to A. glabripennis, suggesting an ongoing reduction in chemosensory function, perhaps related to host specialization. We found lower diversity within certain well-studied gene families predicted to encode putative plant cell wall degrading enzymes in the T. tetrophthalmus genome, perhaps also due to host specialization. Exploring genes relevant to stress and allelochemical detoxification revealed evidence of an abundance of ABC-family genes in the T. tetrophthalmus genome, which may be related to sequestering toxic cardiac glycosides. Our studies further illuminate the genomic basis and evolution of chemosensation in longhorn beetles and provide a new vantage point from which to explore the ecology and evolution of specialized plant-feeding in Tetraopes and other phytophagous beetles.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114896","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

Beyond population size: whole-genome data reveal bottleneck legacies in the peninsular Italian wolf. 超越种群规模：全基因组数据揭示了意大利半岛狼的瓶颈遗留问题。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-27 DOI: 10.1093/jhered/esae041

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

{"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":"https://doi.org/10.1093/jhered/esae041","url":null,"abstract":"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 thirteen 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.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-27","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}

引用次数: 0

De novo genome assembly of a Geomyid rodent, Botta's pocket gopher (Thomomys bottae bottae). 一种地啮类动物--博塔袋鼠（Thomomys bottae bottae）的全新基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-27 DOI: 10.1093/jhered/esae045

Erin R Voss, Merly Escalona, Krzysztof M Kozak, William Seligmann, Colin W Fairbairn, Oanh Nguyen, Mohan P A Marimuthu, Christopher J Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman

{"title":"De novo genome assembly of a Geomyid rodent, Botta's pocket gopher (Thomomys bottae bottae).","authors":"Erin R Voss, Merly Escalona, Krzysztof M Kozak, William Seligmann, Colin W Fairbairn, Oanh Nguyen, Mohan P A Marimuthu, Christopher J Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman","doi":"10.1093/jhered/esae045","DOIUrl":"https://doi.org/10.1093/jhered/esae045","url":null,"abstract":"Botta's pocket gopher (Thomomys bottae) is a common and widespread subterranean rodent of the North American west. The species has been of long interest to evolutionary biologists due to the phenotypic diversity across its range and unusual levels of variation in chromosome number and composition. Here, we present a high-quality reference genome from a male T. b. bottae individual captured in the San Francisco Bay Area. The assembly is comprised of 2,792 scaffolds, with a scaffold N50 value of 23.6 Mb and a BUSCO score of 91.0%. This genome helps fill a significant taxonomic sampling gap in rodent genome resources. With this reference genome, we envision new opportunities to investigate questions regarding the genomics of adaptation to the belowground niche. Further, we can begin to explore the impact of associated life history traits, such as limited dispersal and low population connectivity, on intraspecific genetic and phenotypic variation, genome evolution, speciation, and phylogenetic relationships across the Geomyoidea.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074570","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 implications of the repeated shift to self-fertilization across a species' geographic distribution. 在一个物种的地理分布范围内反复转向自交的基因组影响。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-22 DOI: 10.1093/jhered/esae046

Kay Lucek, Jana M Flury, Yvonne Willi

{"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":"https://doi.org/10.1093/jhered/esae046","url":null,"abstract":"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 underpinnings 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 in the genetics of mating system variation. We confirmed that the breakdown of SI had evolved in several S-locus backgrounds. The diallel suggested the involvement of binuclearly expressed parental genes 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 of runs of homozygosity and their length scaled with the degree of inbreeding. The results highlight that mating system shifts to selfing, its genetic underpinning and the likely negative genomic consequences for evolutionary potential can be strongly interlinked with past range dynamics.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-22","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}

引用次数: 0

An unusually large genome from an unusually large stonefly: a chromosome-length genome assembly for the giant salmonfly, Pteronarcys californica (Plecoptera: Pteronarcyidae). 来自异常大的石蝇的异常大的基因组：巨型鲑蝇 Pteronarcys californica（鳞翅目：Pteronarcyidae）的染色体长基因组组装。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-22 DOI: 10.1093/jhered/esae044

Anna Eichert, John Sproul, Ethan R Tolman, Jackson Birrell, Jared Meek, Jacqueline Heckenhauer, C Riley Nelson, Olga Dudchenko, Jiyun Jeong, David Weisz, Erez Lieberman Aiden, Scott Hotaling, Jessica L Ware, Paul B Frandsen

{"title":"An unusually large genome from an unusually large stonefly: a chromosome-length genome assembly for the giant salmonfly, Pteronarcys californica (Plecoptera: Pteronarcyidae).","authors":"Anna Eichert, John Sproul, Ethan R Tolman, Jackson Birrell, Jared Meek, Jacqueline Heckenhauer, C Riley Nelson, Olga Dudchenko, Jiyun Jeong, David Weisz, Erez Lieberman Aiden, Scott Hotaling, Jessica L Ware, Paul B Frandsen","doi":"10.1093/jhered/esae044","DOIUrl":"https://doi.org/10.1093/jhered/esae044","url":null,"abstract":"Pteronarcys californica (Newport 1848) is commonly referred to as the giant salmonfly and is the largest species of stonefly (Insecta: Plecoptera) in the western United States. Historically, it was widespread and abundant in western rivers, but populations have experienced a substantial decline in the past few decades, becoming locally extirpated in numerous rivers in Utah, Colorado, and Montana. Although previous research has explored the ecological variables conducive to the survivability of populations of the giant salmonfly, a lack of genomic resources hampers exploration of how genetic variation is spread across extant populations. To accelerate research on this imperiled species, we present a de novo chromosomal-length genome assembly of P. californica generated from PacBio HiFi sequencing and Hi-C chromosome conformation capture. Our assembly includes 14 predicted pseudo chromosomes and 98.8% of Insecta universal core orthologs. At 2.40 gigabases, the P. californica assembly is the largest of available stonefly assemblies, highlighting at least 9.5-fold variation in assembly size across the order. Repetitive elements (REs) account for much of the genome size increase in P. californica relative to other stonefly species, with the content of Class I retroelements alone exceeding the entire assembly size of all but two other species studied. We also observed preliminary suborder-specific trends in genome size that merit testing with more robust taxon sampling.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142019572","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

Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics. 十八个蛇科（Serpentes: Caenophidia）的全蛇基因组及其在系统学中的应用。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae026

Jackson R Roberts, Justin M Bernstein, Christopher C Austin, Taylor Hains, Joshua Mata, Michael Kieras, Stacy Pirro, Sara Ruane

{"title":"Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics.","authors":"Jackson R Roberts, Justin M Bernstein, Christopher C Austin, Taylor Hains, Joshua Mata, Michael Kieras, Stacy Pirro, Sara Ruane","doi":"10.1093/jhered/esae026","DOIUrl":"10.1093/jhered/esae026","url":null,"abstract":"We present genome assemblies for 18 snake species representing 18 families (Serpentes: Caenophidia): Acrochordus granulatus, Aparallactus werneri, Boaedon fuliginosus, Calamaria suluensis, Cerberus rynchops, Grayia smithii, Imantodes cenchoa, Mimophis mahfalensis, Oxyrhabdium leporinum, Pareas carinatus, Psammodynastes pulverulentus, Pseudoxenodon macrops, Pseudoxyrhopus heterurus, Sibynophis collaris, Stegonotus admiraltiensis, Toxicocalamus goodenoughensis, Trimeresurus albolabris, and Tropidonophis doriae. From these new genome assemblies, we extracted thousands of loci commonly used in systematic and phylogenomic studies on snakes, including target-capture datasets composed of ultraconserved elements (UCEs) and anchored hybrid enriched loci (AHEs), as well as traditional Sanger loci. Phylogenies inferred from the two target-capture loci datasets were identical with each other and strongly congruent with previously published snake phylogenies. To show the additional utility of these non-model genomes for investigative evolutionary research, we mined the genome assemblies of two New Guinea island endemics in our dataset (S. admiraltiensis and T. doriae) for the ATP1a3 gene, a thoroughly researched indicator of resistance to toad toxin ingestion by squamates. We find that both these snakes possess the genotype for toad toxin resistance despite their endemism to New Guinea, a region absent of any toads until the human-mediated introduction of Cane Toads in the 1930s. These species possess identical substitutions that suggest the same bufotoxin resistance as their Australian congenerics (Stegonotus australis and Tropidonophis mairii) which forage on invasive Cane Toads. Herein, we show the utility of short-read high-coverage genomes, as well as improving the deficit of available squamate genomes with associated voucher specimens.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140900365","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

Plastomes of Nothofagus reflect a shared biogeographic history in Patagonia. Nothofagus的质粒反映了巴塔哥尼亚地区共同的生物地理历史。

IF 3 2区生物学

Journal of Heredity Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae032

Gabriela Juri, Ramiro R Ripa, Andrea C Premoli

{"title":"Plastomes of Nothofagus reflect a shared biogeographic history in Patagonia.","authors":"Gabriela Juri, Ramiro R Ripa, Andrea C Premoli","doi":"10.1093/jhered/esae032","DOIUrl":"10.1093/jhered/esae032","url":null,"abstract":"Plastomes are used in phylogenetic reconstructions because of their relatively conserved nature. Nonetheless, some limitations arise, particularly at lower taxonomic levels due to reduced interspecific polymorphisms and frequent hybridization events that result in unsolved phylogenies including polytomies and reticulate evolutionary patterns. Next-generation sequencing technologies allow access to genomic data and strongly supported phylogenies, yet biased topologies may be obtained due to insufficient taxon sampling. We analyze the hypothesis that intraspecific plastome diversity reflects biogeographic history and hybridization cycles among taxa. We generated 12 new plastome sequences covering distinct latitudinal locations of all species of subgenus Nothofagus from North Patagonia. Chloroplast genomes were assembled, annotated, and searched for simple sequence repeats (SSRs). Phylogenetic reconstructions included species and sampled locations. The six Nothofagus species analyzed were of similar size and structure; only Nothofagus obliqua of subgenus Lophozonia, used as an outgroup, presented slight differences in size. We detected a variable number of SSRs in distinct species and locations. Phylogenetic analyses of plastomes confirmed that subgenus Nothofagus organizes into two monophyletic clades each consisting of individuals of different species. We detected a geographic structure within subgenus Nothofagus and found evidence of local chloroplast sharing due to past hybridization, followed by adaptive introgression and ecological divergence. These contributions enrich the comprehension of transversal evolutionary mechanisms such as chloroplast capture and its implications for phylogenetic and phylogenomic analyses.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141319039","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