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Phylogenetic assessment within a species complex of a subterranean rodent (Geomys bursarius) with conservation implications for isolated subspecies. 地下啮齿动物(Geomys bursarius)物种群内部的系统发育评估,以及对孤立亚种的保护意义。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae035
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。
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引用次数: 0
A genome assembly of the American black bear, Ursus americanus, from California. 加利福尼亚州美洲黑熊的基因组组装。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae037
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.

美洲黑熊(Ursus americanus)是北美洲分布广泛且具有重要生态意义的物种。在加利福尼亚,黑熊在各种生态系统中发挥着重要作用,也是休闲狩猎的重要物种。虽然研究表明加州的黑熊种群目前是健康的,但持续的监测对于维持健康的种群至关重要,而基因组分析则是重要的监测工具。在此,我们报告了一个来自加利福尼亚州的美洲狮样本的高质量、近染色体水平的基因组组装结果。该主装配的总长度为 2.5 Gb,包含在 317 个支架中,等位基因 N50 为 58.9 Mb,支架 N50 为 67.6 Mb,BUSCO 完整性得分为 96%。这个来自加利福尼亚样本的美洲黑熊基因组组装将为加利福尼亚黑熊种群的目标管理提供重要资源,其目标是在黑熊的娱乐价值和维持种群活力之间实现适当的平衡。该基因组的高质量也将使其成为黑熊种群间和黑熊物种间进行基因组比较分析的宝贵资源。
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引用次数: 0
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. 对带状桤木螟(Rosalia funebris)和亚洲长角甲虫(Anoplophora glabripennis)基因组的比较分析表明,这些甲虫和其他角虫的基因组结构和基因含量存在显著差异。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae021
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.

带状桤木螟(Rosalia funebris,RFUNE;Cerambycidae)是一种长角甲虫,其幼虫以北美西部各种具有重要经济和生态意义的树木的木材为食。成虫寿命短,不会大量消耗植物材料。我们利用 HiFi 和 RNASeq 数据对 RFUNE 基因组进行了测序、组装和注释。我们记录了基因组结构和基因内容,重点关注可能参与植物摄食(植食)的基因。我们将其与亚洲长角金龟子(AGLAB;Anoplophora glabripennis)和其他角金龟子科动物的基因组进行了比较。814 Mb的RFUNE基因组集合分布在42个等位基因上,N50为30.18 Mb。重复序列占基因组的 60.27%,99.0% 的预期单拷贝同源基因被完全组装。我们发现了 12657 个基因,少于所研究的其他四个物种,比 Aromia moschata(与 RFUNE 属同一亚科)少 46.4%。在 RFUNE 和 AGLAB 共享的 7258 个正交组中,1461 个拷贝在 AGLAB 中较多,1023 个拷贝在 RFUNE 中较多。我们发现 RFUNE 中有 240 个基因可能是通过水平转移事件产生的。与 AGLAB 相比,RFUNE 基因组编码的假定植物细胞壁降解酶数量要少得多,这可能与后者以植物为食的成虫寿命较长有关。RFUNE 基因组为了解甲虫基因组结构和基因内容提供了新的视角,也为研究甲虫植食性的进化和基因组基础提供了新的视点。
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引用次数: 0
Genomic insights into the critically endangered King Island scrubtit. 从基因组学角度了解极度濒危的国王岛恙虫病。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae029
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。
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引用次数: 0
Correction to: Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes: Leuciscidae). 更正:鲤形目:鯈鱼X和Y染色体广泛遗传分化的有限证据。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-08-20 DOI: 10.1093/jhered/esae038
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引用次数: 0
Reference genome for the Mojave poppy bee (Perdita meconis), a specialist pollinator of conservation concern. 莫哈韦罂粟蜂(Perdita meconis)的参考基因组,这是一种受保护的专业授粉动物。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-07-10 DOI: 10.1093/jhered/esad076
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.

莫哈韦罂粟蜂(Perdita meconis Griswold)(膜翅目:嗜蚁蜂科:Andrenidae)是一种受保护的物种,仅限于北美莫哈韦沙漠东部。它是两个罂粟属(木罂粟属)Arctomecon 和 Argemone 的专性授粉动物,目前正考虑将其与授粉宿主之一拉斯维加斯罂粟(Arctomecon californica)一起列入美国《濒危物种法》。在这里,我们展示了莫哈韦罂粟蜂的近染色体级基因组,以提供有助于保护工作和未来研究的基因组资源。我们从一只小(
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引用次数: 0
An inside "beak": Molecular analysis of swab samples reveals the seabird diet of invasive Barn Owls in Hawai'i. 内部“喙”:对拭子样本的分子分析揭示了夏威夷入侵仓猫头鹰的海鸟饮食。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-07-10 DOI: 10.1093/jhered/esad068
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.

在评估入侵物种对特定生态系统的影响时,捕食是一种需要监测的重要物种相互作用,但很难观察到,因此也很难完全理解。在考艾岛上,入侵的仓鸮(Tyto alba)捕食本地海鸟,但该地区地形困难,猫头鹰捕食的隐蔽性使传统的捕食监测变得非常具有挑战性。利用在考艾岛和乐华岛上作为清除工作的一部分收集的仓鸮,我们对猫头鹰消化道进行了DNA代谢编码,以检测和确定它们捕食的海鸟物种。我们使用海鸟靶向12s标记对55只猫头鹰的112个拭子进行了测序,并在11只猫头鹰(20%的采样猫头鹰)的12个拭子中检测到了6种海鸟,包括两种欧空局列出的海鸟——夏威夷海燕(Pterodroma sandwichensis)和纽厄尔剪水(Puffinus newelli)。猫头鹰胃内容物的相应形态学评估仅在2%(1/55)的猫头鹰样本中检测到海鸟物种作为猎物,这突出了分子方法在检测饮食项目,特别是退化或视觉缺失项目方面的实用性。此外,这种方法已被证明在揭示无法接近的海鸟种群中的隐性营养相互作用方面非常有用。为了对饮食进行最全面的分析,建议同时使用食道和泄殖腔拭子进行代谢编码。用其他可以提供互补猎物信息的方法补充代谢编码,如稳定同位素分析,将有助于更全面地表征营养相互作用。本文描述的方法已被证明是研究入侵猫头鹰饮食的可靠工具,也可作为一种微创技术用于研究活禽的隐性捕食。
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引用次数: 0
Genomic analysis of wolves from Pakistan clarifies boundaries among three divergent wolf lineages. 对巴基斯坦狼的基因组分析阐明了三种不同狼系之间的界限。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-07-10 DOI: 10.1093/jhered/esad066
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.

在灰狼(Canis lupus)的三个主要分支谱系中,全北极谱系是最广泛和研究最好的,尤其是在北美和欧洲。对于南亚的西藏狼(也称为喜马拉雅狼)和印度狼的谱系,人们知之甚少,尤其是在巴基斯坦周围的地区,这三个谱系被认为是相遇的。考虑到印度狼在邻国印度的濒危状态以及西藏狼群西南边界的不明确,我们对巴基斯坦和吉尔吉斯斯坦的狼进行了线粒体和全基因组测序。来自巴基斯坦的81只狼的线粒体D环区序列表明,巴基斯坦北部和西部山区的全北极和印度谱系之间存在接触区。对8只狼的代表性降低的基因组测序表明,这是一个从东到西的印度到全北极血统的谱系,与巴基斯坦这两个谱系之间的接触区一致。西藏血统的西部边界与印度喜马拉雅山脉的拉达克地区相对应,从巴基斯坦北部的喀喇昆仑山脉到印度的拉达克,有一条狭窄的混合带。我们的研究结果强调了巴基斯坦狼种群的保护意义,特别是信德省和旁遮普邦南部的剩余种群,它们代表着高度濒危的印度血统。
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引用次数: 0
Gut bacterial composition shows sex-specific shifts during breeding season in ex situ managed black-footed ferrets. 在迁地管理的黑足雪貂的繁殖季节,肠道细菌组成显示出性别特异性的变化。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-07-10 DOI: 10.1093/jhered/esad065
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.

哺乳动物的肠道微生物组与身体有着动态的关系,并参与了许多对整体健康不可或缺的生理过程。因此,了解形成动物相关细菌群落的因素对于迁地野生动物种群的维护和管理至关重要。在这里,我们对史密森尼国家动物园和保护生物学研究所(美国弗吉尼亚州Front Royal)饲养的48只濒危黑足雪貂的肠道微生物组进行了表征。我们在两个不同的繁殖季节收集了雄性和雌性的纵向粪便样本,以考虑宿主性别和繁殖生理在形成细菌群落中的作用,如使用16S rRNA扩增子测序所测量的。在每个性别中,繁殖季节和非繁殖季节的肠道微生物组成不同,有五种细菌类群的数量不同。在性别之间,雌性和雄性微生物组在非繁殖季节相似,但在繁殖季节显著不同,这可能是由于与繁殖相关的性别特异性生理变化所致。最后,我们发现,与其他哺乳动物食肉动物一致的总体多样性较低,同时潜在致病微生物的相对丰度较高,如梭菌、埃希氏菌、Paeniclostridium和(在较小程度上)肠球菌,所有这些都与哺乳动物宿主(包括黑足雪貂)的胃肠道或生殖困难有关。我们建议对这些微生物进行进一步研究,并采取可能的治疗干预措施,以促进微生物群落的平衡。这些结果对异地管理实践具有重要意义,可以改善黑足雪貂的肠道微生物健康和长期生存能力。
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引用次数: 0
Mitogenomic analysis of a late Pleistocene jaguar from North America. 北美更新世晚期美洲虎的微基因组分析。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-07-10 DOI: 10.1093/jhered/esad082
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.

美洲虎(Panthera onca)是美洲原生的最大猫科动物,也是少数几种存活到全新世的美洲大型食肉动物之一。然而,美洲虎多样性在更新世末期灭绝事件中的衰退程度仍不清楚。例如,北美的更新世美洲虎化石明显比现存美洲虎的平均体型大,因此有人提出假设,认为北美大陆的美洲虎代表了一个现已灭绝的亚种(Panthera onca augusta)或种(Panthera augusta)。在这里,我们使用杂交捕获方法从美国佐治亚州金斯敦盐密洞的一只大型晚更新世美洲虎身上恢复了一个古老的线粒体基因组,并对其进行了26倍覆盖率的测序。然后,我们估算了古美洲虎有丝分裂基因组与其他已灭绝和存活的大型猫科动物(包括在该物种目前分布区采样的多只美洲虎)有丝分裂基因组之间的进化关系。古美洲虎有丝分裂基因组属于现生美洲虎的多样性范围。所有取样的美洲虎有丝分裂基因组都有一个共同的线粒体祖先(距今约 40 万年),这表明该古老标本所代表的血统至少在更新世晚期从南方扩散到北美一次。虽然来自更多和更古老标本的基因组数据将继续增进人们对美洲更新世美洲豹多样性的了解,但我们的研究结果表明,尽管该标本体型相对较大,地理位置相对较远,但它属于现生美洲豹的变异范围,并不代表一个独特的类群。
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Journal of Heredity
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