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Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider 通过西部黑寡妇蜘蛛染色体级基因组组装深入了解蛛形纲动物全基因组复制的适应性作用
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-04-03 DOI: 10.1093/jhered/esae018
Lindsay S Miles, Hannah Waterman, Nadia A Ayoub, Jessica E Garb, Robert A Haney, Michael S Rosenberg, Trevor J Krabbenhoft, Brian C Verrelli
Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)—a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs—or retained ancestrally duplicated genes—from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.
虽然蜘蛛是节肢动物中最多样化的类群之一,但它们进化适应的遗传结构在很大程度上却不为人知。具体来说,在距今约 450 万年的蛛形纲动物进化过程中发生的古老的全基因组复制导致了庞大的基因家族的集合,然而选择在多大程度上塑造了这种变异还没有得到充分的研究。为了帮助进行基因组序列比较分析,我们提供了西部黑寡妇蜘蛛(Latrodectus hesperus)的染色体级基因组--由于其蛛丝特性、毒液应用以及作为城市适应的模型,该基因组成为研究的重点。我们利用长线程和 Hi-C 测序数据,结合转录组,在 1.46 Gb 的基因组中组装了 14 条染色体,注释了 38,393 个基因,BUSCO 得分为 95.3%。我们的分析发现了高重复基因含量和杂合度,这与其他蜘蛛基因组一致,这导致了基因组特征描述方面的挑战。我们对 Araneoidea 类(球织蜘蛛及其后代)中八个物种的基因组进行了比较进化分析,发现了 1,827 个单拷贝同源物。其中,155 个基因组表现出显著的正向选择,主要与发育基因以及与感官知觉相关的性状有关。这些结果支持这样的假设,即蜘蛛的一些独特性状是由ohnologs--或保留的祖先复制基因--从古老的全基因组复制中适应性进化而来的。这些蜘蛛基因组比较分析可以作为一个模型,用于了解在今天不同分类群内部和之间,正向选择是如何不断塑造祖先的重复基因以产生新的性状的。
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引用次数: 0
NewickTreeModifier: A simple web tool to prune and modify Newick trees. NewickTreeModifier: 用于修剪和修改 Newick 树的简单网页。
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-03-13 DOI: 10.1093/jhered/esae005
Lynn Ogoniak, Raphael Steffen, Norbert Grundmann, Ben Stöver, Kai Müller, Jürgen Schmitz

Large-scale selection analyses of protein-coding sequences and phylogenetic tree reconstructions require suitable trees in Newick format. We developed the NewickTreeModifier (NTM), a simple web-based tool to trim and modify Newick trees for such analyses. The users can choose provided master trees or upload a tree to prune it to selected species available in FASTA, NEXUS, or PHYLIP sequence format with an internal converter, a simple species list, or directly determined from a checklist interface of the master trees. Plant, insect, and vertebrate master trees comprise the maximum number of species in an up-to-date phylogenetic order directly transferable to the pruned Newick outfile. NTM is available at https://retrogenomics.uni-muenster.de/tools/ntm.

蛋白质编码序列的大规模选择分析和系统发生树的重建需要合适的 Newick 格式树。我们开发了 NewickTreeModifier,这是一种基于网络的简单工具,用于修剪和修改 Newick 树以进行此类分析。用户可以选择提供的主树,也可以上传一棵树,通过内部转换器、简单的物种列表或从主树的核对表界面直接确定,将其修剪为以 FASTA、NEXUS 或 PHYLIP 序列格式提供的选定物种。植物、昆虫和脊椎动物的主树包括可直接转移到经过修剪的 Newick outfile 的最新系统发生顺序中的最大物种数量。NTM 可在 https ://retrogenomics.uni-muenster.de/tools/ntm.
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引用次数: 0
The genome assembly of Island Oak (Quercus tomentella), a relictual island tree species. 孤岛橡树(Quercus tomentella)--一种孑遗的岛屿树种--的基因组组装。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-03-13 DOI: 10.1093/jhered/esae002
Alayna Mead, Sorel T Fitz-Gibbon, Merly Escalona, Eric Beraut, Samuel Sacco, Mohan P A Marimuthu, Oanh Nguyen, Victoria L Sork

Island oak (Quercus tomentella) is a rare relictual island tree species that exists only on six islands off the coast of California and Mexico, but was once widespread throughout mainland California. Currently, this species is endangered by threats such as non-native plants, grazing animals, and human removal. Efforts for conservation and restoration of island oak currently underway could benefit from information about its range-wide genetic structure and evolutionary history. Here we present a high-quality genome assembly for Q. tomentella, assembled using PacBio HiFi and Omni-C sequencing, developed as part of the California Conservation Genomics Project (CCGP). The resulting assembly has a length of 781 Mb, with a contig N50 of 22.0 Mb and a scaffold N50 of 63.4 Mb. This genome assembly will provide a resource for genomics-informed conservation of this rare oak species. Additionally, this reference genome will be the first one available for a species in Quercus section Protobalanus, a unique oak clade present only in western North America.

岛栎(Quercus tomentella)是一种罕见的孑遗岛屿树种,仅存于加利福尼亚和墨西哥海岸附近的六个岛屿上,但曾广泛分布于加利福尼亚大陆。目前,由于受到非本地植物、放牧动物和人类迁移等威胁,该物种濒临灭绝。目前正在进行的岛屿橡树保护和恢复工作可以从有关其整个分布区遗传结构和进化历史的信息中获益。在此,我们展示了作为加利福尼亚保护基因组学项目的一部分,使用 PacBio HiFi 和 Omni-C 测序技术为 Q. tomentella 组装的高质量基因组。该基因组的长度为 781 Mb,等位基因 N50 为 22.0 Mb,支架 N50 为 63.4 Mb。该基因组组装将为这种稀有橡树物种的基因组学保护提供资源。此外,该参考基因组还将是栎属 Protobalanus 支系中第一个可用的物种基因组,该支系是仅存在于北美西部的一个独特的栎属支系。
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引用次数: 0
Lion Localizer: A software tool for inferring the provenance of lions (Panthera leo) using mitochondrial DNA. Lion Localizer:一个软件工具,用于推断狮子(Panthera leo)的来源,使用线粒体DNA。
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-03-13 DOI: 10.1093/jhered/esad072
Wesley C Au, Simon G Dures, Yasuko Ishida, Cory E Green, Kai Zhao, Rob Ogden, Alfred L Roca

The illegal poaching of lions for their body parts poses a severe threat to lion populations across Africa. Poaching accounts for 35% of all human-caused lion deaths, with 51% attributed to retaliatory killings following livestock predation. In nearly half of the retaliatory killings, lion body parts are removed, suggesting that high demand for lion body parts may fuel killings attributed to human-lion conflict. Trafficked items are often confiscated in transit or destination countries far from their country of origin. DNA from lion parts may in some cases be the only available means for examining their geographic origins. In this paper, we present the Lion Localizer, a full-stack software tool that houses a comprehensive database of lion mitochondrial DNA (mtDNA) sequences sourced from previously published studies. The database covers 146 localities from across the African continent and India, providing information on the potential provenance of seized lion body parts. Lion mtDNA sequences of 350 or 1,140 bp corresponding to the cytochrome b region can be generated from lion products and queried against the Lion Localizer database. Using the query sequence, the Lion Localizer generates a listing of exact or partial matches, which are displayed on an interactive map of Africa. This allows for the rapid identification of potential regions and localities where lions have been or are presently being targeted by poachers. By examining the potential provenance of lion samples, the Lion Localizer serves as a valuable resource in the fight against lion poaching. The software is available at https://lionlocalizer.org.

非法盗猎狮子以获取其身体部位,对整个非洲的狮子种群构成了严重威胁。偷猎占狮子人为死亡总数的35%,其中51%归因于牲畜捕食后的报复性杀戮。在近一半的报复性杀戮中,狮子的身体部位被切除,这表明对狮子身体部位的高需求可能助长了人狮冲突造成的杀戮。被贩运的物品往往在远离原产国的过境国或目的地国被没收。在某些情况下,来自狮子身体部位的DNA可能是检验其地理起源的唯一可用手段。在本文中,我们介绍了Lion Localizer,这是一个全栈软件工具,它包含了一个来自先前发表的研究的狮子线粒体DNA (mtDNA)序列的综合数据库。该数据库涵盖了非洲大陆和印度的146个地区,提供了有关被查获的狮子身体部位可能来源的信息。可以从狮子产品中生成细胞色素b区对应的350 bp或1140 bp的狮子mtDNA序列,并在Lion Localizer数据库中查询。使用查询序列,Lion Localizer生成一个完全匹配或部分匹配的列表,显示在非洲的交互式地图上。这样就可以快速确定狮子曾经或正在成为偷猎者目标的潜在地区和地点。通过检查狮子样本的潜在来源,狮子定位器是打击狮子偷猎的宝贵资源。该软件可在https: //lionlocalizer.org获得。
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引用次数: 0
Chromosome-level genome of the wood stork (Mycteria americana) provides insight into avian chromosome evolution. 木鹳(Mycteria americana)的染色体级基因组为鸟类染色体进化提供了启示。
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-03-13 DOI: 10.1093/jhered/esad077
Richard Flamio, Kristina M Ramstad

Despite being quite specious (~10,000 extant species), birds have a fairly uniform genome size and karyotype (including the common occurrence of microchromosomes) relative to other vertebrate lineages. Storks (Family Ciconiidae) are a charismatic and distinct group of large wading birds with nearly worldwide distribution but few genomic resources. Here we present an annotated chromosome-level reference genome and chromosome orthology analysis for the wood stork (Mycteria americana), a species that has been federally protected under the Endangered Species Act since 1984. The annotated chromosome-level reference assembly was produced using the blood of a wild female wood stork chick, has a length of 1.35 Gb, a contig N50 of 37 Mb, a scaffold N50 of 80 Mb, and a BUSCO score of 98.8%. We identified 31 autosomal pairs and two sex chromosomes in the wood stork genome, but failed to identify four additional autosomal microchromosomes previously found via karyotyping. Orthology analyses confirmed reported synapomorphies unique to storks and identified the chromosomes participating in these fusions. This study highlights the difficulty and potential problems associated with delineating microchromosomes in reference genome assemblies. It also provides a foundation for studying karyotype evolution in the core water bird clade that includes penguins, albatrosses, storks, cormorants, herons, and ibises. Finally, our reference genome will allow for numerous genomic studies, such as genome-wide association studies of local adaptation, that will aid in wood stork conservation.

尽管鸟类种类繁多(约有 10,000 个现存物种),但与其他脊椎动物相比,鸟类的基因组大小和核型(包括常见的微染色体)相当一致。鹳(鹳科)是一个具有独特魅力的大型涉禽类群,几乎分布于世界各地,但基因组资源却很少。在这里,我们介绍了木鹳(Mycteria americana)的染色体组水平参考基因组注释和染色体正交分析,该物种自 1984 年以来一直受到联邦《濒危物种法》的保护。注释的染色体级参考文献是利用野生雌性木鹳雏鸟的血液制作的,长度为 1.35 Gb,等位基因 N50 为 37 Mb,支架 N50 为 80 Mb,BUSCO 得分为 98.8%。我们在木鹳基因组中鉴定出了 31 对常染色体和 2 条性染色体,但未能鉴定出以前通过核型鉴定发现的另外 4 条常染色体微染色体。正交分析证实了所报道的鹳特有的同源染色体,并确定了参与这些融合的染色体。这项研究强调了在参考基因组组装中划分微染色体的难度和潜在问题。它还为研究包括企鹅、信天翁、鹳、鸬鹚、苍鹭和朱鹭在内的核心水鸟支系的核型进化奠定了基础。最后,我们的参考基因组将允许进行大量的基因组研究,如对当地适应性的全基因组关联研究,这将有助于鹳鸟的保护。
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引用次数: 0
Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction. 基因组分析表明,开普狮子种群在殖民地灭绝前具有连通性。
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-03-13 DOI: 10.1093/jhered/esad081
Alida de Flamingh, Thomas P Gnoske, Angel G Rivera-Colón, Velizar A Simeonovski, Julian C Kerbis Peterhans, Nobuyuki Yamaguchi, Kelsey E Witt, Julian Catchen, Alfred L Roca, Ripan Singh Malhi

Cape lions (Panthera leo melanochaitus) formerly ranged throughout the grassland plains of the "Cape Flats" in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as "black-maned lions" and claimed that they were phenotypically distinct. However, other depictions and historical descriptions of lions from the Cape report mixed or light coloration and without black or extensively developed manes. These findings suggest that, rather than forming a distinct population, Cape lions may have had phenotypic and genotypic variation similar to other African lions. Here we investigate Cape lion genome characteristics, population dynamics, and genetic distinctiveness prior to their extinction. We generated genomic data from 2 historic Cape lions to compare to 118 existing high-coverage mitogenomes, and low-coverage nuclear genomes of 53 lions from 13 African countries. We show that, before their eradication, lions from the Cape Flats had diverse mitogenomes and nuclear genomes that clustered with lions from both southern and eastern Africa. Cape lions had high genome-wide heterozygosity and low inbreeding coefficients, indicating that populations in the Cape Flats went extinct so rapidly that genomic effects associated with long-term small population size and isolation were not detectable. Our findings do not support the characterization of Cape lions as phylogeographically distinct, as originally put forth by some European naturalists, and illustrates how alternative knowledge systems, for example, Indigenous perspectives, could potentially further inform interpretations of species histories.

开普狮子(Panthera leo melanochaitus)以前遍布 "开普平原 "的草原平原,即今天的南非西开普省。欧洲殖民统治后,由于过度捕猎和栖息地丧失,开普狮很可能已经绝迹。欧洲博物学家最初将开普狮子描述为 "黑鬃狮",并声称它们在表型上与众不同。然而,其他关于开普省狮子的描述和历史描述却显示,狮子的体色为混合色或浅色,没有黑色或发达的鬃毛。这些发现表明,开普省的狮子并没有形成一个独特的种群,它们的表型和基因型变异可能与其他非洲狮子类似。在此,我们研究了开普狮灭绝前的基因组特征、种群动态和遗传独特性。我们从两只历史上的开普狮子那里获得了基因组数据,并与现有的 118 个高覆盖率有丝分裂基因组和来自 13 个非洲国家的 53 只狮子的低覆盖率核基因组进行了比较。我们的研究表明,开普平原的狮子在被消灭之前,其有丝分裂基因组和核基因组具有多样性,并与非洲南部和东部的狮子聚集在一起。开普省的狮子具有较高的全基因组杂合度和较低的近亲繁殖系数,这表明开普省的狮子种群灭绝得太快,以至于无法检测到与长期小种群规模和隔离有关的基因组效应。我们的研究结果并不支持最初由一些欧洲博物学家提出的将开普狮描述为在系统地理学上与众不同的物种的观点,并说明了替代知识系统(如土著观点)如何有可能进一步解释物种的生活史。
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引用次数: 0
Drift drives the evolution of chromosome number I: The impact of trait transitions on genome evolution in Coleoptera. 漂移驱动染色体数目的进化 I:性状转变对鞘翅目昆虫基因组进化的影响。
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-03-13 DOI: 10.1093/jhered/esae001
Heath Blackmon, Michelle M Jonika, James M Alfieri, Leen Fardoun, Jeffery P Demuth

Chromosomal mutations such as fusions and fissions are often thought to be deleterious, especially in heterozygotes (underdominant), and consequently are unlikely to become fixed. Yet, many models of chromosomal speciation ascribe an important role to chromosomal mutations. When the effective population size (Ne) is small, the efficacy of selection is weakened, and the likelihood of fixing underdominant mutations by genetic drift is greater. Thus, it is possible that ecological and phenotypic transitions that modulate Ne facilitate the fixation of chromosome changes, increasing the rate of karyotype evolution. We synthesize all available chromosome number data in Coleoptera and estimate the impact of traits expected to change Ne on the rate of karyotype evolution in the family Carabidae and 12 disparate clades from across Coleoptera. Our analysis indicates that in Carabidae, wingless clades have faster rates of chromosome number increase. Additionally, our analysis indicates clades exhibiting multiple traits expected to reduce Ne, including strict inbreeding, oligophagy, winglessness, and island endemism, have high rates of karyotype evolution. Our results suggest that chromosome number changes are likely fixed by genetic drift despite an initial fitness cost and that chromosomal speciation models may be important to consider in clades with very small Ne.

染色体突变(如融合和裂解)通常被认为是有害的,尤其是在杂合子中(显性不足),因此不太可能固定下来。然而,许多染色体物种形成模型都认为染色体突变起着重要作用。当有效种群规模(Ne)较小时,选择的效力就会减弱,遗传漂变固定下显性突变的可能性就会增大。因此,调节 Ne 的生态和表型转变可能会促进染色体变化的固定,从而提高核型进化的速度。我们综合了鞘翅目所有可用的染色体数目数据,并估计了预计会改变 Ne 的性状对腕足动物科和鞘翅目 12 个不同支系的核型进化速度的影响。我们的分析表明,在鞘翅目中,无翅支系的染色体数目增长速度较快。此外,我们的分析表明,表现出多种预期会降低Ne的特征(包括严格近亲繁殖、寡食、无翅和岛屿特有性)的支系具有较高的核型进化率。我们的研究结果表明,染色体数目的变化很可能是通过遗传漂变固定下来的,尽管最初需要付出一定的适应代价,而且染色体物种模式可能是Ne非常小的支系需要考虑的重要因素。
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引用次数: 0
Repeated patterns of reptile diversification in Western North America supported by the Northern Alligator Lizard (Elgaria coerulea). 北美西部爬行动物多样化的重复模式得到了北方鳄蜥(Elgaria coerulea)的支持。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-02-03 DOI: 10.1093/jhered/esad073
Adam D Leaché, Hayden R Davis, Chris R Feldman, Matthew K Fujita, Sonal Singhal

Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard (Elgaria coerulea), which is widely distributed in Western North America across diverse ecoregions (California Floristic Province and Pacific Northwest) and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We collected single-nucleotide polymorphism data from 120 samples of E. coerulea. Biogeographic analyses of squamate reptiles with similar distributions have identified several shared diversification patterns that provide testable predictions for E. coerulea, including deep genetic divisions in the Sierra Nevada, demographic stability of southern populations, and recent post-Pleistocene expansion into the Pacific Northwest. We use genomic data to test these predictions by estimating the structure, connectivity, and phylogenetic history of populations. At least 10 distinct populations are supported, with mixed-ancestry individuals situated at most population boundaries. A species tree analysis provides strong support for the early divergence of populations in the Sierra Nevada Mountains and recent diversification into the Pacific Northwest. Admixture and migration analyses detect gene flow among populations in the Lower Cascades and Northern California, and a spatial analysis of gene flow identified significant barriers to gene flow across both the Sierra Nevada and Coast Ranges. The distribution of genetic diversity in E. coerulea is uneven, patchy, and interconnected at population boundaries. The biogeographic patterns seen in E. coerulea are consistent with predictions from co-distributed species.

了解通过促进或阻止种群分化形成遗传多样性的过程,有助于确定促进或限制基因流动的地理区域。此外,广泛分布的物种使我们能够理解生物地理和生态地理转变如何影响基因流动。我们利用北方短吻鳄蜥蜴(Elgaria coerulea)的基因组数据研究了这些过程,这种蜥蜴广泛分布在北美西部不同的生态区域(加利福尼亚植物区和太平洋西北地区)和山脉(内华达山脉、沿海山脉和喀斯喀特山脉)。本研究收集了120份蓝棘豆样本的单核苷酸多态性(SNP)数据。对分布相似的有鳞爬行动物的生物地理分析已经确定了几种共同的多样化模式,这些模式为蓝棘龙提供了可测试的预测,包括内华达山脉的深层遗传分化,南部种群的人口稳定性,以及最近更新世后向太平洋西北地区的扩张。我们使用基因组数据通过估计种群的结构、连通性和系统发育历史来测试这些预测。至少有10个不同的种群被支持,混合血统的个体位于大多数种群边界。物种树分析为内华达山脉种群的早期分化和最近向太平洋西北地区的多样化提供了强有力的支持。混合和迁移分析发现了下喀斯喀特和北加州种群之间的基因流动,基因流动的空间分析发现了内华达山脉和海岸山脉之间基因流动的重大障碍。蓝棘遗传多样性在种群边界上的分布是不均匀的、斑驳的和相互联系的。蓝棘的生物地理格局与共分布物种的预测一致。
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引用次数: 0
Genomic insights into isolation of the threatened Florida crested caracara (Caracara plancus). 对受威胁的佛罗里达冠卡拉(caracara plancus)分离的基因组见解。
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-02-03 DOI: 10.1093/jhered/esad057
Natalie Payne, John A Erwin, Joan L Morrison, James F Dwyer, Melanie Culver

We conducted a population genomic study of the crested caracara (Caracara plancus) using samples (n = 290) collected from individuals in Florida, Texas, and Arizona, United States. Crested caracaras are non-migratory raptors ranging from the southern tip of South America to the southern United States, including a federally protected relict population in Florida long thought to have been isolated since the last ice age. Our objectives were to evaluate genetic diversity and population structure of Florida's apparently isolated population and to evaluate taxonomic relationships of crested caracaras at the northern edge of their range. Using DNA purified from blood samples, we conducted double-digest restriction site associated DNA sequencing and sequenced the mitochondrial ND2 gene. Analyses of population structure using over 9,000 SNPs suggest that two major clusters are best supported, one cluster including only Florida individuals and the other cluster including Arizona and Texas individuals. Both SNPs and mitochondrial haplotypes reveal the Florida population to be highly differentiated genetically from Arizona and Texas populations, whereas, Arizona and Texas populations are moderately differentiated from each other. The Florida population's mitochondrial haplotypes form a separate monophyletic group, while Arizona and Texas populations share mitochondrial haplotypes. Results of this study provide substantial genetic evidence that Florida's crested caracaras have experienced long-term isolation from caracaras in Arizona and Texas and thus, represent a distinct evolutionary lineage possibly warranting distinction as an Evolutionarily Significant Unit (ESU) or subspecies. This study will inform conservation strategies focused on long-term survival of Florida's distinct, panmictic population.

我们使用从美国佛罗里达州、得克萨斯州和亚利桑那州采集的样本(n=290),对带冠卡拉(caracara plancus)进行了种群基因组研究。凤头甲是从南美洲南端到美国南部的非迁徙猛禽,包括佛罗里达州的一个受联邦保护的残余种群,长期以来被认为自上一个冰河时代以来一直处于孤立状态。我们的目标是评估佛罗里达州明显孤立的种群的遗传多样性和种群结构,并评估其分布范围北部边缘的冠卡拉的分类关系。使用从血液样本中纯化的DNA,我们进行了双消化限制性位点相关DNA测序,并对线粒体ND2基因进行了测序。使用9000多个SNPs对种群结构的分析表明,两个主要集群得到了最好的支持,一个集群只包括佛罗里达州的个体,另一个集群包括亚利桑那州和得克萨斯州的个体。SNPs和线粒体单倍型都表明,佛罗里达州种群在基因上与亚利桑那州和得克萨斯州种群高度分化,而亚利桑那州和德克萨斯州种群彼此中度分化。佛罗里达州种群的线粒体单倍型形成了一个单独的单系群,而亚利桑那州和得克萨斯州种群共享线粒体单倍型。这项研究的结果提供了大量的遗传证据,证明佛罗里达州的冠背甲与亚利桑那州和得克萨斯州的背甲经历了长期的隔离,因此代表了一个独特的进化谱系,可能有必要作为进化重要单位(ESU)或亚种进行区分。这项研究将为佛罗里达州独特的泛米种群的长期生存提供保护策略。
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引用次数: 0
A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides. 向日葵海星的生态修复参考基因组。
IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-02-03 DOI: 10.1093/jhered/esad054
Lauren M Schiebelhut, Melissa B DeBiasse, Lars Gabriel, Katharina J Hoff, Michael N Dawson

Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star, Pycnopodia helianthoides, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric and oceanographic conditions, and there is not yet a consensus on the cause(s). Genomic data may reveal underlying molecular signatures that implicate a subset of factors and, thus, clarify past events while also setting the scene for effective restoration efforts. To advance this goal, we used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly that was then annotated using RNA-seq-informed gene prediction. The genome assembly is 484 Mb long, with contig N50 of 1.9 Mb, scaffold N50 of 21.8 Mb, BUSCO completeness score of 96.1%, and 22 major scaffolds consistent with prior evidence that sea star genomes comprise 22 autosomes. These statistics generally fall between those of other recently assembled chromosome-scale assemblies for two species in the distantly related asteroid genus Pisaster. These novel genomic resources for P. helianthoides will underwrite population genomic, comparative genomic, and phylogenomic analyses-as well as their integration across scales-of SSW and environmental stressors.

野生动物疾病,如2010年代中期爆发的海星消瘦(SSW)流行病,似乎与急性和/或慢性非生物环境变化有关;分离不同驱动因素的影响可能很困难。向日葵海星赫利珊瑚是SSW爆发期间受影响最严重的物种,该爆发与异常大气和海洋条件时期重叠,目前尚未就原因达成共识。基因组数据可能揭示涉及一个子集因素的潜在分子特征,从而澄清过去的事件,同时为有效的修复工作奠定基础。为了推进这一目标,我们使用Pacific Biosciences HiFi长测序读数和Dovetail Omni-C接近读数来生成高度连续的基因组组装,然后使用RNA-seq信息基因预测对其进行注释。基因组组装长度为484 Mb,重叠群N50为1.9 Mb,支架N50为21.8 Mb,BUSCO完整性得分为96.1%,22个主要支架与先前的证据一致,即海星基因组包含22个常染色体。这些统计数据通常介于亲缘关系较远的小行星Pister属中两个物种最近组装的其他染色体规模的组装数据之间。这些新的直升机花腐藻基因组资源将支持SSW和环境压力源的群体基因组、比较基因组和系统发育组学分析,以及它们在尺度上的整合。
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Journal of Heredity
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