Nathan Alexander, Alida de Flamingh, Bradley J Cosentino, Robert L Schooley
Range contraction and expansion from glaciation have led to genetic divergence that may be particularly pronounced in fossorial species with low dispersal. The plains pocket gopher (Geomys bursarius) is a fossorial species that ranges widely across North America but has a poorly understood phylogeny. We used mitogenomes (14,996 base pairs) from 56 individuals across seven subspecies, plus two outgroup species, to assess genetic divergence from minimum spanning trees, measure genetic distances, and infer phylogenetic trees using BEAST. We found G. b. wisconsinensis was monophyletic with recent divergence. Further assessment is needed for G. b. major because it was paraphyletic and exhibited inconsistent groupings with other clades. Importantly, we identified G. b. illinoensis as being genetically distinct and monophyletic likely due to a unique colonization event eastward across the Mississippi River. Because G. b. illinoensis faces continued pressures from niche reduction and habitat loss, we recommend that G. b. illinoensis be considered an evolutionary significant unit warranting conservation actions to promote connectivity and restore suitable habitat. Such conservation efforts should benefit other grassland species including those originating from clades west of the Mississippi River that may also be evolutionary significant units.
冰川作用造成的范围收缩和扩张导致了基因分化,这在低散播性的化石物种中可能尤为明显。平原袋地鼠(Geomys bursarius)是一种广泛分布于北美的化石物种,但其系统发育却鲜为人知。我们利用来自 7 个亚种和 2 个外群物种的 56 个个体的有丝分裂基因组(14,996 碱基对),评估了最小跨度树的遗传差异,测量了遗传距离,并利用 BEAST 推断了系统发生树。我们发现 G. b. wisconsinensis 是单系物种,最近才出现分化。b.major需要进一步评估,因为它属于旁系,而且与其他支系的分组不一致。重要的是,我们发现 G. b. illinoensis 在遗传学上是独特的、单系的,这可能是由于它跨越密西西比河向东殖民的独特事件。由于伊利诺斯鹅膏菌(G. b. illinoensis)面临着生态位减少和栖息地丧失的持续压力,我们建议将伊利诺斯鹅膏菌(G. b. illinoensis)视为一个重要的进化单元,采取保护行动,促进连通性并恢复合适的栖息地。这种保护工作应惠及其他草原物种,包括那些来自密西西比河以西支系的物种,它们也可能是重要的进化单元。
{"title":"Phylogenetic assessment within a species complex of a subterranean rodent (Geomys bursarius) with conservation implications for isolated subspecies.","authors":"Nathan Alexander, Alida de Flamingh, Bradley J Cosentino, Robert L Schooley","doi":"10.1093/jhered/esae035","DOIUrl":"10.1093/jhered/esae035","url":null,"abstract":"<p><p>Range contraction and expansion from glaciation have led to genetic divergence that may be particularly pronounced in fossorial species with low dispersal. The plains pocket gopher (Geomys bursarius) is a fossorial species that ranges widely across North America but has a poorly understood phylogeny. We used mitogenomes (14,996 base pairs) from 56 individuals across seven subspecies, plus two outgroup species, to assess genetic divergence from minimum spanning trees, measure genetic distances, and infer phylogenetic trees using BEAST. We found G. b. wisconsinensis was monophyletic with recent divergence. Further assessment is needed for G. b. major because it was paraphyletic and exhibited inconsistent groupings with other clades. Importantly, we identified G. b. illinoensis as being genetically distinct and monophyletic likely due to a unique colonization event eastward across the Mississippi River. Because G. b. illinoensis faces continued pressures from niche reduction and habitat loss, we recommend that G. b. illinoensis be considered an evolutionary significant unit warranting conservation actions to promote connectivity and restore suitable habitat. Such conservation efforts should benefit other grassland species including those originating from clades west of the Mississippi River that may also be evolutionary significant units.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"565-574"},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565044","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}
Megan A Supple, Merly Escalona, Jillian Adkins, Michael R Buchalski, Nicolas Alexandre, Ruta M Sahasrabudhe, Oanh Nguyen, Samuel Sacco, Colin Fairbairn, Eric Beraut, William Seligmann, Richard E Green, Erin Meredith, Beth Shapiro
The American black bear, Ursus americanus, is a widespread and ecologically important species in North America. In California, the black bear plays an important role in a variety of ecosystems and serves as an important species for recreational hunting. While research suggests that the populations in California are currently healthy, continued monitoring is critical, with genomic analyses providing an important surveillance tool. Here we report a high-quality, near chromosome-level genome assembly from a U. americanus sample from California. The primary assembly has a total length of 2.5 Gb contained in 316 scaffolds, a contig N50 of 58.9 Mb, a scaffold N50 of 67.6 Mb, and a BUSCO completeness score of 96%. This U. americanus genome assembly will provide an important resource for the targeted management of black bear populations in California, with the goal of achieving an appropriate balance between the recreational value of black bears and the maintenance of viable populations. The high quality of this genome assembly will also make it a valuable resource for comparative genomic analyses among black bear populations and among bear species.
{"title":"A genome assembly of the American black bear, Ursus americanus, from California.","authors":"Megan A Supple, Merly Escalona, Jillian Adkins, Michael R Buchalski, Nicolas Alexandre, Ruta M Sahasrabudhe, Oanh Nguyen, Samuel Sacco, Colin Fairbairn, Eric Beraut, William Seligmann, Richard E Green, Erin Meredith, Beth Shapiro","doi":"10.1093/jhered/esae037","DOIUrl":"10.1093/jhered/esae037","url":null,"abstract":"<p><p>The American black bear, Ursus americanus, is a widespread and ecologically important species in North America. In California, the black bear plays an important role in a variety of ecosystems and serves as an important species for recreational hunting. While research suggests that the populations in California are currently healthy, continued monitoring is critical, with genomic analyses providing an important surveillance tool. Here we report a high-quality, near chromosome-level genome assembly from a U. americanus sample from California. The primary assembly has a total length of 2.5 Gb contained in 316 scaffolds, a contig N50 of 58.9 Mb, a scaffold N50 of 67.6 Mb, and a BUSCO completeness score of 96%. This U. americanus genome assembly will provide an important resource for the targeted management of black bear populations in California, with the goal of achieving an appropriate balance between the recreational value of black bears and the maintenance of viable populations. The high quality of this genome assembly will also make it a valuable resource for comparative genomic analyses among black bear populations and among bear species.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"498-506"},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334205/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617668","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}
Terrence Sylvester, Richard Adams, Robert F Mitchell, Ann M Ray, Rongrong Shen, Na Ra Shin, Duane D McKenna
Rosalia funebris (RFUNE; Cerambycidae), the banded alder borer, is a longhorn beetle whose larvae feed on the wood of various economically and ecologically significant trees in western North America. Adults are short-lived and not known to consume plant material substantially. We sequenced, assembled, and annotated the RFUNE genome using HiFi and RNASeq data. We documented genome architecture and gene content, focusing on genes putatively involved in plant feeding (phytophagy). Comparisons were made to the well-studied genome of the Asian longhorned beetle (AGLAB; Anoplophora glabripennis) and other Cerambycidae. The 814 Mb RFUNE genome assembly was distributed across 42 contigs, with an N50 of 30.18 Mb. Repetitive sequences comprised 60.27% of the genome, and 99.0% of expected single-copy orthologous genes were fully assembled. We identified 12,657 genes, fewer than in the four other species studied, and 46.4% fewer than for Aromia moschata (same subfamily as RFUNE). Of the 7,258 orthogroups shared between RFUNE and AGLAB, 1,461 had more copies in AGLAB and 1,023 had more copies in RFUNE. We identified 240 genes in RFUNE that putatively arose via horizontal transfer events. The RFUNE genome encoded substantially fewer putative plant cell wall degrading enzymes than AGLAB, which may relate to the longer-lived plant-feeding adults of the latter species. The RFUNE genome provides new insights into cerambycid genome architecture and gene content and provides a new vantage point from which to study the evolution and genomic basis of phytophagy in beetles.
{"title":"Comparative analyses of the banded alder borer (Rosalia funebris) and Asian longhorned beetle (Anoplophora glabripennis) genomes reveal significant differences in genome architecture and gene content among these and other Cerambycidae.","authors":"Terrence Sylvester, Richard Adams, Robert F Mitchell, Ann M Ray, Rongrong Shen, Na Ra Shin, Duane D McKenna","doi":"10.1093/jhered/esae021","DOIUrl":"10.1093/jhered/esae021","url":null,"abstract":"<p><p>Rosalia funebris (RFUNE; Cerambycidae), the banded alder borer, is a longhorn beetle whose larvae feed on the wood of various economically and ecologically significant trees in western North America. Adults are short-lived and not known to consume plant material substantially. We sequenced, assembled, and annotated the RFUNE genome using HiFi and RNASeq data. We documented genome architecture and gene content, focusing on genes putatively involved in plant feeding (phytophagy). Comparisons were made to the well-studied genome of the Asian longhorned beetle (AGLAB; Anoplophora glabripennis) and other Cerambycidae. The 814 Mb RFUNE genome assembly was distributed across 42 contigs, with an N50 of 30.18 Mb. Repetitive sequences comprised 60.27% of the genome, and 99.0% of expected single-copy orthologous genes were fully assembled. We identified 12,657 genes, fewer than in the four other species studied, and 46.4% fewer than for Aromia moschata (same subfamily as RFUNE). Of the 7,258 orthogroups shared between RFUNE and AGLAB, 1,461 had more copies in AGLAB and 1,023 had more copies in RFUNE. We identified 240 genes in RFUNE that putatively arose via horizontal transfer events. The RFUNE genome encoded substantially fewer putative plant cell wall degrading enzymes than AGLAB, which may relate to the longer-lived plant-feeding adults of the latter species. The RFUNE genome provides new insights into cerambycid genome architecture and gene content and provides a new vantage point from which to study the evolution and genomic basis of phytophagy in beetles.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"516-523"},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140319882","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}
Ross Crates, Brenton von Takach, Catherine M Young, Dejan Stojanovic, Linda E Neaves, Liam Murphy, Daniel Gautschi, Carolyn J Hogg, Robert Heinsohn, Phil Bell, Katherine A Farquharson
Small, fragmented, or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of <100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analyzed independently of the Tasmanian scrubtit. Pairwise FST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity, and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct.
由于近亲繁殖和遗传漂变带来的适应成本,小规模、支离破碎或孤立的种群面临种群数量下降的风险。国王岛恙虫(Acanthornis magna greeniana)是塔斯马尼亚恙虫(A. m. magna)的一个极度濒危亚种,估计种群数量小于 100 只,仅存于三片沼泽森林中。塔斯马尼亚恙螨广泛分布于塔斯马尼亚大陆的潮湿森林中。我们使用 PacBio HiFi 对恙虫的基因组进行了测序,并使用包含 5,239 个 SNP 位点的双检测限制性位点相关 DNA(ddRAD)数据集对国王岛和塔斯马尼亚恙虫进行了种群基因组研究。基因组长 1.48 Gb,由 1,518 个等位基因组成,N50 为 7.715 Mb。国王岛恙虫形成了四个总体基因群之一,但在与塔斯马尼亚恙虫独立分析时,又分成了三个不同的亚群。与大多数塔斯马尼亚恙虫亚群相比,国王岛恙虫亚群的配对 FST 值更大。除一个塔斯马尼亚沼泽狸亚种群外,国王岛沼泽狸的遗传多样性较低,近交系数较高。我们在8/15只国王岛亚灌木鸟中观察到秃冠现象,但在0/55只塔斯马尼亚亚灌木鸟中观察到秃冠现象。有六个基因位点与秃顶有明显的相关性,其中包括一个与早期羽毛发育有关的 DOCK11 基因位点。国王岛黄雀亚种群之间不太可能发生基因流动,需要进一步的实地监测,以量化其种群规模小、遗传多样性低和近亲繁殖率高所造成的健康后果。然后,就可以在该分类群灭绝之前采取基于证据的保护行动。
{"title":"Genomic insights into the critically endangered King Island scrubtit.","authors":"Ross Crates, Brenton von Takach, Catherine M Young, Dejan Stojanovic, Linda E Neaves, Liam Murphy, Daniel Gautschi, Carolyn J Hogg, Robert Heinsohn, Phil Bell, Katherine A Farquharson","doi":"10.1093/jhered/esae029","DOIUrl":"10.1093/jhered/esae029","url":null,"abstract":"<p><p>Small, fragmented, or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of <100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analyzed independently of the Tasmanian scrubtit. Pairwise FST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity, and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"552-564"},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141181523","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}
{"title":"Correction to: Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes: Leuciscidae).","authors":"","doi":"10.1093/jhered/esae038","DOIUrl":"10.1093/jhered/esae038","url":null,"abstract":"","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"600"},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141789931","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}
Rena M Schweizer, Colleen G Meidt, Ligia R Benavides, Joseph S Wilson, Terry L Griswold, Sheina B Sim, Scott M Geib, Michael G Branstetter
The Mojave poppy bee, Perdita meconis Griswold (Hymenoptera: Anthophila: Andrenidae), is a species of conservation concern that is restricted to the eastern Mojave Desert of North America. It is a specialist pollinator of two poppy genera, Arctomecon and Argemone (Papaveraceae), and is being considered for listing under the US Endangered Species Act along with one of its pollinator hosts, the Las Vegas bearpoppy (Arctomecon californica). Here, we present a near chromosome-level genome of the Mojave poppy bee to provide a genomic resource that will aid conservation efforts and future research. We isolated DNA from a single, small (<7 mm), male specimen collected using non-ideal preservation methods and then performed whole-genome sequencing using PacBio HiFi technology. After quality and contaminant filtering, the final draft genome assembly is 327 Mb, with an N50 length of 17.5 Mb. Annotated repetitive elements compose 37.3% of the genome, although a large proportion (24.87%) of those are unclassified repeats. Additionally, we annotated 18,245 protein-coding genes and 19,433 transcripts. This genome represents one of only a few genomes from the large bee family Andrenidae and one of only a few genomes for pollinator specialists. We highlight both the potential of this genome as a resource for future research, and how high-quality genomes generated from small, non-ideal (in terms of preservation) specimens could facilitate biodiversity genomics.
{"title":"Reference genome for the Mojave poppy bee (Perdita meconis), a specialist pollinator of conservation concern.","authors":"Rena M Schweizer, Colleen G Meidt, Ligia R Benavides, Joseph S Wilson, Terry L Griswold, Sheina B Sim, Scott M Geib, Michael G Branstetter","doi":"10.1093/jhered/esad076","DOIUrl":"10.1093/jhered/esad076","url":null,"abstract":"<p><p>The Mojave poppy bee, Perdita meconis Griswold (Hymenoptera: Anthophila: Andrenidae), is a species of conservation concern that is restricted to the eastern Mojave Desert of North America. It is a specialist pollinator of two poppy genera, Arctomecon and Argemone (Papaveraceae), and is being considered for listing under the US Endangered Species Act along with one of its pollinator hosts, the Las Vegas bearpoppy (Arctomecon californica). Here, we present a near chromosome-level genome of the Mojave poppy bee to provide a genomic resource that will aid conservation efforts and future research. We isolated DNA from a single, small (<7 mm), male specimen collected using non-ideal preservation methods and then performed whole-genome sequencing using PacBio HiFi technology. After quality and contaminant filtering, the final draft genome assembly is 327 Mb, with an N50 length of 17.5 Mb. Annotated repetitive elements compose 37.3% of the genome, although a large proportion (24.87%) of those are unclassified repeats. Additionally, we annotated 18,245 protein-coding genes and 19,433 transcripts. This genome represents one of only a few genomes from the large bee family Andrenidae and one of only a few genomes for pollinator specialists. We highlight both the potential of this genome as a resource for future research, and how high-quality genomes generated from small, non-ideal (in terms of preservation) specimens could facilitate biodiversity genomics.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"470-479"},"PeriodicalIF":3.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11235129/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138813205","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}
Joanna W Elmore, Taylor M Wilcox, Alex E Dutcher, Yuki Reiss, Michael K Schwartz
Predation is an important species interaction to monitor when assessing an invasive species' impact on a particular ecosystem, but it can be difficult to observe and thus, fully understand. On Kaua'i island, invasive Barn Owls (Tyto alba) predate native seabirds, but difficult terrain in this region and the cryptic nature of owl predation make traditional monitoring of predation quite challenging. Using Barn Owls collected as part of removal efforts on Kaua'i and Lehua islands, we conducted DNA metabarcoding of owl digestive tracts to detect and determine seabird species they predate. We used a seabird-targeted 12s marker to sequence 112 swabs from 55 owls and detected 6 seabird taxa, including 2 ESA-listed seabirds-Hawaiian Petrel (Pterodroma sandwichensis) and Newell's Shearwater (Puffinus newelli), in 12 swabs from 11 owls (20% of sampled owls). Corresponding morphological assessment of owl stomach contents detected seabird species as prey items in only 2% (1/55) of sampled owls, highlighting the utility of molecular approaches for detecting diet items, especially degraded or visually absent items. Additionally, this approach has proven very useful in revealing cryptic trophic interactions in inaccessible seabird populations. For the most comprehensive analysis of diet, the use of both esophageal and cloacal swabs for metabarcoding is recommended. Supplementing metabarcoding with other methods that can provide complementary prey information, such as stable isotope analysis, would help to characterize trophic interactions more fully. The method described here has proven to be a reliable tool for investigating diet in invasive owls and may be used to investigate cryptic predation in living birds as a minimally invasive technique, as well.
{"title":"An inside \"beak\": Molecular analysis of swab samples reveals the seabird diet of invasive Barn Owls in Hawai'i.","authors":"Joanna W Elmore, Taylor M Wilcox, Alex E Dutcher, Yuki Reiss, Michael K Schwartz","doi":"10.1093/jhered/esad068","DOIUrl":"10.1093/jhered/esad068","url":null,"abstract":"<p><p>Predation is an important species interaction to monitor when assessing an invasive species' impact on a particular ecosystem, but it can be difficult to observe and thus, fully understand. On Kaua'i island, invasive Barn Owls (Tyto alba) predate native seabirds, but difficult terrain in this region and the cryptic nature of owl predation make traditional monitoring of predation quite challenging. Using Barn Owls collected as part of removal efforts on Kaua'i and Lehua islands, we conducted DNA metabarcoding of owl digestive tracts to detect and determine seabird species they predate. We used a seabird-targeted 12s marker to sequence 112 swabs from 55 owls and detected 6 seabird taxa, including 2 ESA-listed seabirds-Hawaiian Petrel (Pterodroma sandwichensis) and Newell's Shearwater (Puffinus newelli), in 12 swabs from 11 owls (20% of sampled owls). Corresponding morphological assessment of owl stomach contents detected seabird species as prey items in only 2% (1/55) of sampled owls, highlighting the utility of molecular approaches for detecting diet items, especially degraded or visually absent items. Additionally, this approach has proven very useful in revealing cryptic trophic interactions in inaccessible seabird populations. For the most comprehensive analysis of diet, the use of both esophageal and cloacal swabs for metabarcoding is recommended. Supplementing metabarcoding with other methods that can provide complementary prey information, such as stable isotope analysis, would help to characterize trophic interactions more fully. The method described here has proven to be a reliable tool for investigating diet in invasive owls and may be used to investigate cryptic predation in living birds as a minimally invasive technique, as well.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"432-443"},"PeriodicalIF":3.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72016200","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}
Lauren M Hennelly, Ghulam Sarwar, Hira Fatima, Geraldine Werhahn, Fakhar I Abbas, Abdul M Khan, Tariq Mahmood, Shannon Kachel, Zairbek Kubanychbekov, Muhammad T Waseem, Rubab Zahra Naqvi, Abdul Hamid, Yasir Abbas, Hamera Aisha, Muhammad Waseem, Muhammad Farooq, Benjamin N Sacks
Among the three main divergent lineages of gray wolf (Canis lupus), the Holarctic lineage is the most widespread and best studied, particularly in North America and Europe. Less is known about Tibetan (also called Himalayan) and Indian wolf lineages in southern Asia, especially in areas surrounding Pakistan where all three lineages are thought to meet. Given the endangered status of the Indian wolf in neighboring India and unclear southwestern boundary of the Tibetan wolf range, we conducted mitochondrial and genome-wide sequencing of wolves from Pakistan and Kyrgyzstan. Sequences of the mitochondrial D-loop region of 81 wolves from Pakistan indicated contact zones between Holarctic and Indian lineages across the northern and western mountains of Pakistan. Reduced-representation genome sequencing of eight wolves indicated an east-to-west cline of Indian to Holarctic ancestry, consistent with a contact zone between these two lineages in Pakistan. The western boundary of the Tibetan lineage corresponded to the Ladakh region of India's Himalayas with a narrow zone of admixture spanning this boundary from the Karakoram Mountains of northern Pakistan into Ladakh, India. Our results highlight the conservation significance of Pakistan's wolf populations, especially the remaining populations in Sindh and Southern Punjab that represent the highly endangered Indian lineage.
{"title":"Genomic analysis of wolves from Pakistan clarifies boundaries among three divergent wolf lineages.","authors":"Lauren M Hennelly, Ghulam Sarwar, Hira Fatima, Geraldine Werhahn, Fakhar I Abbas, Abdul M Khan, Tariq Mahmood, Shannon Kachel, Zairbek Kubanychbekov, Muhammad T Waseem, Rubab Zahra Naqvi, Abdul Hamid, Yasir Abbas, Hamera Aisha, Muhammad Waseem, Muhammad Farooq, Benjamin N Sacks","doi":"10.1093/jhered/esad066","DOIUrl":"10.1093/jhered/esad066","url":null,"abstract":"<p><p>Among the three main divergent lineages of gray wolf (Canis lupus), the Holarctic lineage is the most widespread and best studied, particularly in North America and Europe. Less is known about Tibetan (also called Himalayan) and Indian wolf lineages in southern Asia, especially in areas surrounding Pakistan where all three lineages are thought to meet. Given the endangered status of the Indian wolf in neighboring India and unclear southwestern boundary of the Tibetan wolf range, we conducted mitochondrial and genome-wide sequencing of wolves from Pakistan and Kyrgyzstan. Sequences of the mitochondrial D-loop region of 81 wolves from Pakistan indicated contact zones between Holarctic and Indian lineages across the northern and western mountains of Pakistan. Reduced-representation genome sequencing of eight wolves indicated an east-to-west cline of Indian to Holarctic ancestry, consistent with a contact zone between these two lineages in Pakistan. The western boundary of the Tibetan lineage corresponded to the Ladakh region of India's Himalayas with a narrow zone of admixture spanning this boundary from the Karakoram Mountains of northern Pakistan into Ladakh, India. Our results highlight the conservation significance of Pakistan's wolf populations, especially the remaining populations in Sindh and Southern Punjab that represent the highly endangered Indian lineage.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"339-348"},"PeriodicalIF":3.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61566168","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}
Alexandra L DeCandia, Laura Adeduro, Piper Thacher, Adrienne Crosier, Paul Marinari, Robyn Bortner, Della Garelle, Travis Livieri, Rachel Santymire, Pierre Comizzoli, Michael Maslanka, Jesús E Maldonado, Klaus-Peter Koepfli, Carly Muletz-Wolz, Sally L Bornbusch
The gut microbiome of mammals engages in a dynamic relationship with the body and contributes to numerous physiological processes integral to overall health. Understanding the factors shaping animal-associated bacterial communities is therefore paramount to the maintenance and management in ex situ wildlife populations. Here, we characterized the gut microbiome of 48 endangered black-footed ferrets (Mustela nigripes) housed at Smithsonian's National Zoo and Conservation Biology Institute (Front Royal, Virginia, USA). We collected longitudinal fecal samples from males and females across two distinct reproductive seasons to consider the role of host sex and reproductive physiology in shaping bacterial communities, as measured using 16S rRNA amplicon sequencing. Within each sex, gut microbial composition differed between breeding and non-breeding seasons, with five bacterial taxa emerging as differentially abundant. Between sexes, female and male microbiomes were similar during non-breeding season but significantly different during breeding season, which may result from sex-specific physiological changes associated with breeding. Finally, we found low overall diversity consistent with other mammalian carnivores alongside high relative abundances of potentially pathogenic microbes such as Clostridium, Escherichia, Paeniclostridium, and (to a lesser degree) Enterococcus-all of which have been associated with gastrointestinal or reproductive distress in mammalian hosts, including black-footed ferrets. We recommend further study of these microbes and possible therapeutic interventions to promote more balanced microbial communities. These results have important implications for ex situ management practices that can improve the gut microbial health and long-term viability of black-footed ferrets.
{"title":"Gut bacterial composition shows sex-specific shifts during breeding season in ex situ managed black-footed ferrets.","authors":"Alexandra L DeCandia, Laura Adeduro, Piper Thacher, Adrienne Crosier, Paul Marinari, Robyn Bortner, Della Garelle, Travis Livieri, Rachel Santymire, Pierre Comizzoli, Michael Maslanka, Jesús E Maldonado, Klaus-Peter Koepfli, Carly Muletz-Wolz, Sally L Bornbusch","doi":"10.1093/jhered/esad065","DOIUrl":"10.1093/jhered/esad065","url":null,"abstract":"<p><p>The gut microbiome of mammals engages in a dynamic relationship with the body and contributes to numerous physiological processes integral to overall health. Understanding the factors shaping animal-associated bacterial communities is therefore paramount to the maintenance and management in ex situ wildlife populations. Here, we characterized the gut microbiome of 48 endangered black-footed ferrets (Mustela nigripes) housed at Smithsonian's National Zoo and Conservation Biology Institute (Front Royal, Virginia, USA). We collected longitudinal fecal samples from males and females across two distinct reproductive seasons to consider the role of host sex and reproductive physiology in shaping bacterial communities, as measured using 16S rRNA amplicon sequencing. Within each sex, gut microbial composition differed between breeding and non-breeding seasons, with five bacterial taxa emerging as differentially abundant. Between sexes, female and male microbiomes were similar during non-breeding season but significantly different during breeding season, which may result from sex-specific physiological changes associated with breeding. Finally, we found low overall diversity consistent with other mammalian carnivores alongside high relative abundances of potentially pathogenic microbes such as Clostridium, Escherichia, Paeniclostridium, and (to a lesser degree) Enterococcus-all of which have been associated with gastrointestinal or reproductive distress in mammalian hosts, including black-footed ferrets. We recommend further study of these microbes and possible therapeutic interventions to promote more balanced microbial communities. These results have important implications for ex situ management practices that can improve the gut microbial health and long-term viability of black-footed ferrets.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"385-398"},"PeriodicalIF":3.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54232358","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}
Megha Srigyan, Blaine W Schubert, Matthew Bushell, Sarah H D Santos, Henrique Vieira Figueiró, Samuel Sacco, Eduardo Eizirik, Beth Shapiro
The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses that jaguars from this continent represent a now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). Here, we used a hybridization capture approach to recover an ancient mitochondrial genome from a large, late Pleistocene jaguar from Kingston Saltpeter Cave, Georgia, United States, which we sequenced to 26-fold coverage. We then estimated the evolutionary relationship between the ancient jaguar mitogenome and those from other extinct and living large felids, including multiple jaguars sampled across the species' current range. The ancient mitogenome falls within the diversity of living jaguars. All sampled jaguar mitogenomes share a common mitochondrial ancestor ~400 thousand years ago, indicating that the lineage represented by the ancient specimen dispersed into North America from the south at least once during the late Pleistocene. While genomic data from additional and older specimens will continue to improve understanding of Pleistocene jaguar diversity in the Americas, our results suggest that this specimen falls within the variation of extant jaguars despite the relatively larger size and geographic location and does not represent a distinct taxon.
{"title":"Mitogenomic analysis of a late Pleistocene jaguar from North America.","authors":"Megha Srigyan, Blaine W Schubert, Matthew Bushell, Sarah H D Santos, Henrique Vieira Figueiró, Samuel Sacco, Eduardo Eizirik, Beth Shapiro","doi":"10.1093/jhered/esad082","DOIUrl":"10.1093/jhered/esad082","url":null,"abstract":"<p><p>The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses that jaguars from this continent represent a now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). Here, we used a hybridization capture approach to recover an ancient mitochondrial genome from a large, late Pleistocene jaguar from Kingston Saltpeter Cave, Georgia, United States, which we sequenced to 26-fold coverage. We then estimated the evolutionary relationship between the ancient jaguar mitogenome and those from other extinct and living large felids, including multiple jaguars sampled across the species' current range. The ancient mitogenome falls within the diversity of living jaguars. All sampled jaguar mitogenomes share a common mitochondrial ancestor ~400 thousand years ago, indicating that the lineage represented by the ancient specimen dispersed into North America from the south at least once during the late Pleistocene. While genomic data from additional and older specimens will continue to improve understanding of Pleistocene jaguar diversity in the Americas, our results suggest that this specimen falls within the variation of extant jaguars despite the relatively larger size and geographic location and does not represent a distinct taxon.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":" ","pages":"424-431"},"PeriodicalIF":3.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11235123/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139049804","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}