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Differentiated sex chromosomes, karyotype evolution, and spontaneous triploidy in carphodactylid geckos. 腕足动物的性染色体分化、核型进化和自发三倍体。
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-05-09 DOI: 10.1093/jhered/esae010
Eleonora Pensabene, Barbora Augstenová, Lukáš Kratochvíl, Michail Rovatsos

Geckos exhibit derived karyotypes without a clear distinction between macrochromosomes and microchromosomes and intriguing diversity in sex determination mechanisms. We conducted cytogenetic analyses in six species from the genera Nephrurus, Phyllurus, and Saltuarius of the gecko family Carphodactylidae. We confirmed the presence of a female heterogametic system with markedly differentiated and heteromorphic sex chromosomes in all examined species, typically with the W chromosome notably larger than the Z chromosome. One species, Nephrurus cinctus, possesses unusual multiple Z1Z1Z2Z2/Z1Z2W sex chromosomes. The morphology of the sex chromosomes, along with repetitive DNA content, suggests that the differentiation or emergence of sex chromosomes occurred independently in the genus Phyllurus. Furthermore, our study unveils a case of spontaneous triploidy in a fully grown individual of Saltuarius cornutus (3n = 57) and explores its implications for reproduction in carphodactylid geckos. We revealed that most carphodactylids retain the putative ancestral gekkotan karyotype of 2n = 38, characterized by predominantly acrocentric chromosomes that gradually decrease in size. If present, biarmed chromosomes emerge through pericentric inversions, maintaining the chromosome (and centromere) numbers. However, Phyllurus platurus is a notable exception, with a karyotype of 2n = 22 chromosomes. Its eight pairs of biarmed chromosomes were probably formed by Robertsonian fusions of acrocentric chromosomes. The family underscores a remarkable instance of evolutionary stability in chromosome numbers, followed by a profound transformation through parallel interchromosomal rearrangements. Our study highlights the need to continue generating cytogenetic data in order to test long-standing ideas about reproductive biology and the evolution of genome and sex determination.

壁虎表现出衍生核型,大染色体和微染色体之间没有明显的区别,而且性别决定机制具有令人好奇的多样性。我们对壁虎科Nephrurus属、Phyllurus属和Saltuarius属的6个物种进行了细胞遗传学分析。我们证实了雌性异配系统的存在,在所有被研究的物种中,性染色体都有明显的分化和异形,典型的情况是W染色体明显大于Z染色体。其中一个物种(Nephrurus cinctus)具有不寻常的多条 Z1Z1Z2Z2/Z1Z2W 性染色体。性染色体的形态以及重复的 DNA 含量表明,性染色体的分化或出现是在 Phyllurus 属中独立发生的。此外,我们的研究还揭示了在一只完全生长的 Saltuarius cornutus(3n = 57)个体中出现的自发三倍体现象,并探讨了其对腕足动物繁殖的影响。我们发现,大多数角足类壁虎保留了 2n = 38 的推定祖先革科坦核型,其特点是主要为尖头染色体,且大小逐渐减小。如果存在,双臂染色体会通过会心倒位出现,从而保持染色体(和中心粒)的数目。然而,Phyllurus platurus 是一个明显的例外,其核型为 2n = 22 条染色体。它的 8 对双臂染色体可能是由非中心染色体的罗伯逊融合形成的。该家族强调了染色体数目在进化过程中的稳定性,以及随后通过染色体间平行重排发生的深刻转变。我们的研究突出表明,有必要继续生成细胞遗传学数据,以检验有关生殖生物学、基因组进化和性别决定的长期观点。
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引用次数: 0
Phylogeography of the freshwater crab Potamon persicum (Decapoda: Potamidae): an ancestral ring species? 淡水蟹Potamon persicum(十足目:Potamidae)的系统地理学:一个祖先环物种?
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-05-09 DOI: 10.1093/jhered/esae016
Yaser Amir Afzali, Reza Naderloo, Alireza Keikhosravi, Sebastian Klaus

The Zagros Mountains, characterized by complex topography and three large drainage systems, harbor the endemic freshwater crab Potamon persicum in Iran. Our study delves into the evolutionary history of P. persicum, utilizing two mitochondrial and one nuclear marker. We collected 214 specimens from 24 localities, identifying 21 haplotypes grouped into two major evolutionary lineages. Substantial differentiation exists between drainage systems and lineages. Historical demographic analysis revealed a significant decrease in population size during the late Holocene, accompanied by a recent population bottleneck. Species distribution modeling has revealed eastward shifts in suitable habitats between the last glacial maximum and the present day. Following the last glacial maximum, habitat fragmentation occurred, resulting in the establishment of small populations. These smaller populations are more vulnerable to climatic and geological events, thereby limiting gene flow and accelerating genetic differentiation within species. Historical biogeographic analysis traced the origin of P. persicum to the western Zagros Mountains, with major genetic divergence occurring during the Pleistocene. Our genetic analyses suggest that P. persicum may have shown a genetic pattern similar to a classical ring species before the Pleistocene. The Namak Lake sub-basin could have served as a contact zone where populations did not interbreed but were connected through gene flow in a geographic ring. Currently, genetic separation is evident between basins, indicating that P. persicum in the Zagros Mountains is not a contemporary ring species. Also, our biogeographical analysis estimated that range evolution may have been driven initially by dispersal, and only during the late Pleistocene by vicariance.

扎格罗斯山脉地形复杂,有三个大型排水系统,是伊朗特有淡水蟹 Potamon persicum 的栖息地。我们的研究利用两个线粒体标记和一个核标记深入研究了P. persicum的进化史。我们从 24 个地方采集了 214 个标本,鉴定出 21 个单倍型,分为两大进化系。排水系统和进化系之间存在很大差异。历史人口分析表明,在全新世晚期,种群数量显著减少,同时出现了近期的种群瓶颈。物种分布模型显示,从上一个冰川极盛期到现在,适宜的栖息地发生了东移。在上一个冰川最大值之后,栖息地发生了破碎化,导致小种群的建立。这些较小的种群更容易受到气候和地质事件的影响,从而限制了基因流动,加速了物种内部的基因分化。历史生物地理分析表明,P. persicum 的起源地在扎格罗斯山脉西部,主要的遗传分化发生在更新世。我们的遗传分析表明,在更新世之前,P. persicum 可能已经表现出类似于经典环斑物种的遗传模式。纳玛克湖子流域可能曾是一个接触区,那里的种群并没有杂交,而是通过基因流动连接成一个地理环。目前,盆地之间的基因分离非常明显,这表明扎格罗斯山脉的 P. persicum 并非当代的环状物种。此外,根据我们的生物地理学分析估计,其分布范围的演变最初可能是由散布驱动的,在更新世晚期才是由邻近物种驱动的。
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引用次数: 0
Patterns of genetic divergence in the Rio Grande cooter (Pseudemys gorzugi), a riverine turtle inhabiting an arid and anthropogenically modified system. 格兰德河乌龟(Pseudemys gorzugi)的遗传分化模式,这是一种栖息在干旱和人为改造系统中的河龟。
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-05-09 DOI: 10.1093/jhered/esae011
Michael W Vandewege, Javier Gutierrez, Drew R Davis, Michael R J Forstner, Ivana Mali

The lower Rio Grande and Pecos River of the southwest United States have been heavily modified by human activities, profoundly impacting the integrity of their aquatic wildlife. In this context, we focused our study on the population genomics of the Rio Grande Cooter (Pseudemys gorzugi), a freshwater turtle of increasing conservation concern, residing in these two rivers and their tributaries. The genetic data revealed two distinct populations: one in the Pecos and Black Rivers of New Mexico and another in the Rio Grande and Devils River of Texas, with admixed individuals identified at the confluence of the Rio Grande and Pecos River. In addition to having a smaller geographic range, we found lower observed heterozygosity, reduced nucleotide diversity, and a smaller effective population size (Ne) in New Mexico population. Our results depict a significant isolation-by-distance pattern across their distribution, with migration being notably infrequent at river confluences. These findings are pivotal for future conservation and restoration strategies, emphasizing the need to recognize the unique needs of each population.

美国西南部的格兰德河下游和佩科斯河受到人类活动的严重破坏,对其水生野生动物的完整性产生了深远影响。在这种情况下,我们重点研究了这两条河流及其支流中日益受到保护关注的淡水龟--格兰德河鳕(Pseudemys gorzugi)的种群基因组学。遗传数据揭示了两个不同的种群:一个在新墨西哥州的佩科斯河和布莱克河,另一个在得克萨斯州的格兰德河和魔鬼河,在格兰德河和佩科斯河的交汇处发现了混居个体。除了地理范围较小之外,我们还发现新墨西哥种群的杂合度较低,核苷酸多样性减少,有效种群规模(Ne)较小。我们的研究结果表明,新墨西哥种群在其分布范围内存在明显的距离隔离模式,在河流交汇处迁移的频率明显较低。这些发现对未来的保护和恢复策略至关重要,强调了认识每个种群独特需求的必要性。
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引用次数: 0
Genomic Diversity and Demographic History of the Endangered Sichuan hill-partridge (Arborophila rufipectus) 濒危四川山鹧鸪的基因组多样性和种群历史
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-04-18 DOI: 10.1093/jhered/esae020
Yi Liu, Weimin Kuang, Bisong Yue, Chuang Zhou
Species conservation can be improved by knowledge of genetic diversity and demographic history. The Sichuan hill-partridge (Arborophila rufipectus, SP) is an endangered species endemic to the mountains in southwestern China. However, little is known about this species’ genomic variation and demographic history. Here, we present a comprehensive whole-genome analysis of six SP individuals from the Laojunshan National Nature Reserve in Sichuan Province, China. We observe a relatively high genetic diversity and low level of recent inbreeding in the studied SP individuals. This suggests that the current population carries genetic variability that may benefit the long-term survival of this species, and that the present population may be larger than currently recognized. Analyses of demographic history showed that fluctuations in the effective population size of SP are inconsistent with changes of the historical climate. Strikingly, evidence from demographic modeling suggests SPs population decreased dramatically 15,100 years ago after the Last Glacial Maximum (LGM), possibly due to refugial isolation and later human interference. These results provide the first detailed and comprehensive genomic insights into genetic diversity, genomic inbreeding levels, and demographic history of the Sichuan hill-partridge, which are crucial for the conservation and management of this endangered species.
物种保护可以通过了解遗传多样性和种群历史得到改善。四川山鹧鸪(Arborophila rufipectus,SP)是中国西南部山区特有的濒危物种。然而,人们对该物种的基因组变异和种群历史知之甚少。在此,我们对来自中国四川省老君山国家级自然保护区的6个SP个体进行了全面的全基因组分析。我们观察到所研究的SP个体具有相对较高的遗传多样性和较低的近亲繁殖水平。这表明目前的种群具有遗传变异性,这可能有利于该物种的长期生存,而且目前的种群可能比目前公认的要大。对人口历史的分析表明,SP有效种群数量的波动与历史气候的变化不一致。令人震惊的是,人口模型的证据表明,在1.51万年前的末次冰川极盛期(LGM)之后,SP的种群数量急剧下降,这可能是由于避难隔离和后来的人为干扰造成的。这些结果首次从基因组学角度详细而全面地揭示了四川山鹧鸪的遗传多样性、基因组近交水平和人口历史,这对这一濒危物种的保护和管理至关重要。
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引用次数: 0
Missing History of a Modern Domesticate: Historical Demographics and Genetic Diversity in Farm-bred Red Fox Populations 现代驯养动物的缺失历史:农场饲养的赤狐种群的历史人口统计和遗传多样性
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-04-16 DOI: 10.1093/jhered/esae022
Halie Rando, Emmarie P Alexander, Sophie Preckler-Quisquater, Cate B Quinn, Jeremy T Stutchman, Jennifer L Johnson, Estelle R Bastounes, Beata Horecka, Kristina L Black, Michael P Robson, Darya V Shepeleva, Yury E Herbeck, Anastasiya V Kharlamova, Lyudmila N Trut, Jonathan N Pauli, Benjamin N Sacks, Anna V Kukekova
The first record of captive bred red foxes (Vulpes vulpes) dates to 1896, when a breeding enterprise emerged in the provinces of Atlantic Canada. Because its domestication happened during recent history, the red fox offers a unique opportunity to examine the genetic diversity of an emerging domesticated species in the context of documented historical and economic influences. In particular, the historical record suggests that North American and Eurasian farm-bred populations likely experienced different demographic trajectories. Here, we focus on the likely impacts of founder effects and genetic drift given historical trends in fox farming on North American and Eurasian farms. A total of 15 mitochondrial haplotypes were identified in 369 foxes from 10 farm populations that we genotyped (n=161) or that were previously published. All haplotypes are endemic to North America. Although most haplotypes were consistent with eastern Canadian ancestry, a small number of foxes carried haplotypes typically found in Alaska and other regions of western North America. The presence of these haplotypes supports historical reports of wild foxes outside of Atlantic Canada being introduced into the breeding stock. These putative Alaskan and Western haplotypes were more frequently identified in Eurasian farms compared to North American farms, consistent with historical documentation suggesting that Eurasian economic and breeding practices were likely to maintain low-frequency haplotypes more effectively than in North America. Contextualizing inter- versus intra-farm genetic diversity alongside the historical record is critical to understanding of the origins of this emerging domesticate and the relationships between wild and farm-bred fox populations.
人工饲养赤狐(Vulpes vulpes)的首次记录可追溯到 1896 年,当时加拿大大西洋省份出现了一家饲养企业。由于赤狐的驯化发生在近代史上,因此赤狐为我们提供了一个独特的机会,在有据可查的历史和经济影响的背景下,研究一个新兴驯化物种的遗传多样性。特别是,历史记录表明,北美和欧亚农场饲养的种群可能经历了不同的人口轨迹。鉴于北美和欧亚农场养狐业的历史趋势,我们在此重点探讨始祖鸟效应和遗传漂变可能产生的影响。我们对来自 10 个农场种群的 369 只狐狸进行了基因分型(n=161),或在之前发表的文章中发现了共 15 种线粒体单倍型。所有单倍型均为北美特有。虽然大多数单倍型与加拿大东部的祖先一致,但也有少量狐狸携带了通常在阿拉斯加和北美西部其他地区发现的单倍型。这些单倍型的出现证实了加拿大大西洋以外的野生狐狸被引入种群的历史报道。与北美的养殖场相比,这些推定的阿拉斯加和西部单倍型在欧亚养殖场中被发现的频率更高,这与历史文献中的说法一致,即欧亚的经济和养殖方式可能比北美更有效地维持低频单倍型。将农场间与农场内的遗传多样性与历史记录结合起来,对于了解这种新兴驯化动物的起源以及野生狐狸种群与农场饲养狐狸种群之间的关系至关重要。
{"title":"Missing History of a Modern Domesticate: Historical Demographics and Genetic Diversity in Farm-bred Red Fox Populations","authors":"Halie Rando, Emmarie P Alexander, Sophie Preckler-Quisquater, Cate B Quinn, Jeremy T Stutchman, Jennifer L Johnson, Estelle R Bastounes, Beata Horecka, Kristina L Black, Michael P Robson, Darya V Shepeleva, Yury E Herbeck, Anastasiya V Kharlamova, Lyudmila N Trut, Jonathan N Pauli, Benjamin N Sacks, Anna V Kukekova","doi":"10.1093/jhered/esae022","DOIUrl":"https://doi.org/10.1093/jhered/esae022","url":null,"abstract":"The first record of captive bred red foxes (Vulpes vulpes) dates to 1896, when a breeding enterprise emerged in the provinces of Atlantic Canada. Because its domestication happened during recent history, the red fox offers a unique opportunity to examine the genetic diversity of an emerging domesticated species in the context of documented historical and economic influences. In particular, the historical record suggests that North American and Eurasian farm-bred populations likely experienced different demographic trajectories. Here, we focus on the likely impacts of founder effects and genetic drift given historical trends in fox farming on North American and Eurasian farms. A total of 15 mitochondrial haplotypes were identified in 369 foxes from 10 farm populations that we genotyped (n=161) or that were previously published. All haplotypes are endemic to North America. Although most haplotypes were consistent with eastern Canadian ancestry, a small number of foxes carried haplotypes typically found in Alaska and other regions of western North America. The presence of these haplotypes supports historical reports of wild foxes outside of Atlantic Canada being introduced into the breeding stock. These putative Alaskan and Western haplotypes were more frequently identified in Eurasian farms compared to North American farms, consistent with historical documentation suggesting that Eurasian economic and breeding practices were likely to maintain low-frequency haplotypes more effectively than in North America. Contextualizing inter- versus intra-farm genetic diversity alongside the historical record is critical to understanding of the origins of this emerging domesticate and the relationships between wild and farm-bred fox populations.","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":"126 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140608838","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 draft reference genome assembly of California Pipevine, Aristolochia californica Torr 加利福尼亚琵琶藤(Aristolochia californica Torr)参考基因组组装草案
IF 3.1 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2024-04-15 DOI: 10.1093/jhered/esae023
Samridhi Chaturvedi, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Courtney Miller, H Bradley Shaffer, Noah K Whiteman
The California Pipevine, Aristolochia californica Torr., is the only endemic California species within the cosmopolitan birthwort family Aristolochiaceae. It occurs as an understory vine in riparian and chaparral areas and in forest edges and windrows. The geographic range of this plant species almost entirely overlaps with that of its major specialized herbivore, the California Pipevine Swallowtail Butterfly Battus philenor hirsuta. While this species pair is a useful, ecologically well-understood system to study co-evolution, until recently, genomic resources for both have been lacking. Here, we report a new, chromosome-level assembly of A. californica as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 531 scaffolds spanning 661 megabase (Mb) pairs, with a contig N50 of 6.53 Mb, a scaffold N50 of 42.2 Mb, and BUSCO complete score of 98%. In combination with the recently published B. philenor hirsuta reference genome assembly, the A. californica reference genome assembly will be a powerful tool for studying co-evolution in a rapidly changing California landscape.
加利福尼亚管藤(Aristolochia californica Torr.)是马兜铃科(Aristolochiaceae)世界性胎生植物中唯一的加利福尼亚特有物种。它作为林下藤本植物出现在河岸和灌丛地区以及森林边缘和风口处。该植物物种的地理分布范围几乎完全与其主要的专门食草动物加利福尼亚琵琶藤燕尾蝶 Battus philenor hirsuta 重叠。虽然这对物种是研究共同进化的一个有用的、生态学上很好理解的系统,但直到最近,两者的基因组资源一直缺乏。在此,我们报告了作为加利福尼亚保护基因组学项目(CCGP)一部分的新的加利福尼亚蝶染色体组组装结果。按照 CCGP 的测序和组装策略,我们使用太平洋生物科学公司的 HiFi 长读数和 Hi-C 染色质近似测序技术,重新组装了基因组。我们的基因组组装是该属任何物种的首次组装,包含 531 个支架,跨度为 661 兆位元组(Mb)对,等位基因 N50 为 6.53 Mb,支架 N50 为 42.2 Mb,BUSCO 完整得分率为 98%。结合最近发表的 B. philenor hirsuta 参考基因组组装,A. californica 参考基因组组装将成为研究快速变化的加利福尼亚景观中共同进化的有力工具。
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引用次数: 0
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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Journal of Heredity
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