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Genomic SNPs resolve the phylogeny of an ancient amphibian island radiation from the Seychelles 基因组 SNP 解决了塞舌尔群岛古老两栖动物岛屿辐射的系统发育问题
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-16 DOI: 10.1016/j.ympev.2024.108130
Miranda B. Sherlock , Jeffrey W. Streicher , David J. Gower , Simon T. Maddock , Ronald A. Nussbaum , Oommen V. Oommen , Ana Serra Silva , Julia J. Day , Mark Wilkinson

Unusually for oceanic islands, the granitic Seychelles host multiple lineages of endemic amphibians. This includes an ancient (likely ca. 60 million years) radiation of eight caecilian species, most of which occur on multiple islands. These caecilians have a complicated taxonomic history and their phylogenetic inter-species relationships have been difficult to resolve. Double-digest RAD sequencing (ddRADseq) has been applied extensively to phylogeography and increasingly to phylogenetics but its utility for resolving ancient divergences is less well established. To address this, we applied ddRADseq to generate a genome-wide SNP panel for phylogenomic analyses of the Seychelles caecilians, whose phylogeny has so far not been satisfactorily resolved with traditional DNA markers. Based on 129,154 SNPs, we resolved deep and shallow splits, with strong support. Our findings demonstrate the capability of genome-wide SNPs for evolutionary inference at multiple taxonomic levels and support the recently proposed synonymy of Grandisonia Taylor, 1968 with Hypogeophis Peters, 1879. We revealed three clades of Hypogeophis (large-, medium- and short-bodied) and identify a single origin of the diminutive, stocky-bodied and pointy-snouted phenotype.

对于海洋岛屿来说,塞舌尔群岛的花岗岩质地非常罕见,这里有多个特有的两栖动物品系。其中包括一个古老的(可能约 6000 万年前)八种凯西拉类,它们中的大多数出现在多个岛屿上。这些无尾类有着复杂的分类历史,其物种间的系统发育关系一直难以解决。双位 RAD 测序(ddRADseq)已被广泛应用于系统地理学,并越来越多地应用于系统发育学,但其在解决远古分化方面的实用性还不太成熟。为了解决这个问题,我们应用 ddRADseq 生成了一个全基因组 SNP 面板,用于塞舌尔群岛无尾类的系统发生学分析。基于 129,154 个 SNPs,我们解决了深层和浅层分裂问题,并获得了强有力的支持。我们的研究结果证明了全基因组 SNP 在多个分类水平上的进化推断能力,并支持最近提出的 Grandisonia Taylor, 1968 与 Hypogeophis Peters, 1879 的同义。我们揭示了 Hypogeophis 的三个支系(大体型、中体型和短体型),并确定了体型矮小、体格粗壮和尖嘴表型的单一起源。
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引用次数: 0
Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia) 测试双壳类动物(软体动物门:双壳类)中用于系统发育推断的超保守元素(UCE)。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-06-13 DOI: 10.1016/j.ympev.2024.108129
Sara González-Delgado , Paula C. Rodríguez-Flores , Gonzalo Giribet

Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.

双壳类动物是重要的渔业资源和文物。利用形态学和分子特征进行双壳类动物系统发育的传统由来已久,许多具有重要商业价值的物种都有基因组资源。然而,双壳类家族之间的关系一直不稳定,有丝分裂基因组学与基于桑格扩增子测序或系统转录组学的结果之间存在重大冲突。在这里,我们设计并测试了双壳纲的超保守元素探针集,目的是使用数百个位点,而无需对昂贵且复杂的全基因组或转录组进行测序分析,并将双壳纲系统发生学应用于博物馆标本。我们的探针集成功捕获了 1,513 个 UCE,总长度为 263,800 bp,每个 UCE 的平均长度为 174.59 ± 3.44(从 28 到 842 bp 不等)。利用不同的数据矩阵和系统发育推断方法,在双壳纲和多纳科内对该 UCE 探针集进行了系统发育测试,结果表明在多个分类水平上都取得了良好的效果。此外,我们的探针集还能捕捉到 1900 年前采集的博物馆标本中的大量 UCE。总之,这是双壳类系统发生学的一个新颖而有用的资源。
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引用次数: 0
Artificial intelligence enables unified analysis of historical and landscape influences on genetic diversity 人工智能可对遗传多样性的历史和景观影响进行统一分析。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-06-12 DOI: 10.1016/j.ympev.2024.108116
Emanuel M. Fonseca , Bryan C. Carstens

While genetic variation in any species is potentially shaped by a range of processes, phylogeography and landscape genetics are largely concerned with inferring how environmental conditions and landscape features impact neutral intraspecific diversity. However, even as both disciplines have come to utilize SNP data over the last decades, analytical approaches have remained for the most part focused on either broad-scale inferences of historical processes (phylogeography) or on more localized inferences about environmental and/or landscape features (landscape genetics). Here we demonstrate that an artificial intelligence model-based analytical framework can consider both deeper historical factors and landscape-level processes in an integrated analysis. We implement this framework using data collected from two Brazilian anurans, the Brazilian sibilator frog (Leptodactylus troglodytes) and granular toad (Rhinella granulosa). Our results indicate that historical demographic processes shape most the genetic variation in the sibulator frog, while landscape processes primarily influence variation in the granular toad. The machine learning framework used here allows both historical and landscape processes to be considered equally, rather than requiring researchers to make an a priori decision about which factors are important.

虽然任何物种的遗传变异都可能受到一系列过程的影响,但系统地理学和景观遗传学主要关注的是推断环境条件和景观特征如何影响中性的种内多样性。然而,即使这两个学科在过去几十年中都开始利用 SNP 数据,分析方法在很大程度上仍然集中在对历史进程的大范围推断(系统地理学)或对环境和/或景观特征的局部推断(景观遗传学)上。在这里,我们证明了基于人工智能模型的分析框架可以在综合分析中同时考虑更深层次的历史因素和景观层面的过程。我们利用从两种巴西无尾类动物--巴西咝蛙(Leptodactylus troglodytes)和颗粒蟾蜍(Rhinella granulosa)--收集到的数据实施了这一框架。我们的研究结果表明,历史人口统计过程决定了箭蛙的大部分遗传变异,而景观过程则主要影响颗粒蟾蜍的变异。这里使用的机器学习框架允许同时考虑历史和景观过程,而不是要求研究人员先验地决定哪些因素是重要的。
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引用次数: 0
Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages 以被忽视的品系为重点的赭藻(葡萄孢藻)系统发生组分析
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-06-07 DOI: 10.1016/j.ympev.2024.108120
Anna Cho, Gordon Lax, Patrick J. Keeling

Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable groupings with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenetic relationships, and discrete gene properties affect lineages of stramenopiles differently. This is something which may be explored to further our understanding of the molecular evolution of stramenopiles.

裸子植物是一种光合作用植物,在真核生物超群之一--石蒜科植物的系统发育树中居于首位。由于其作为主要初级生产者对生态环境的影响,与其他石龙子类相比,对水华藻的研究相对较多,但对其进化关系的了解仍然很少。这部分是由于在大规模多基因分析中缺失了一些世系,以及明显的快速辐射导致树上的赭藻亚群之间出现了许多短节间。这些短节间也出现在系统发育信号有限的石莲花类深枝系中,使得许多关系在整体上存在争议。最近,我们通过其他深枝葡萄科植物解决了这一问题,现在我们要研究的是,是否可以通过在最新的赭藻系统发生组数据集中填补缺失的世系,同时探索各种基因筛选标准来确定最具系统发生信息的基因,从而解决赭藻内部有争议的关系问题。我们从各种培养物和环境样本的单细胞分离中生成了十个新的转录组,将这些转录组添加到现有的系统发生组数据集中,并研究了选择具有高系统发生信号或低系统发生噪声的基因的效果。对于一些以前有争议的关系,我们发现各种分析和基因筛选标准都能以强有力的统计支持将以前不稳定的分组统一起来。例如,我们恢复了红叶石龙子科(Eustigmatophyceae)与石龙子科(Raphidophyceae)-白叶石龙子科(Phaeophyceae)-黄叶石龙子科(Xanthophyceae)的稳健分组关系,而橄榄叶石龙子科(Olisthodiscophyceae)则与红叶石龙子科(Pinguiophyceae)形成姊妹系。选择具有高系统发育信号或数据质量的基因可以恢复更稳定的拓扑结构。总之,我们发现,在不同种系中增加代表性不足的类群对于解决系统发生关系仍然至关重要,而且离散基因的特性对葡萄孢植物的种系有着不同的影响。为了进一步了解石龙子的分子进化,我们可以对这一点进行探索。
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引用次数: 0
Speciation in savanna birds in South America: The case of the Least Nighthawk Chordeiles pusillus (Aves: Caprimulgidae) in and out of the Amazon 南美洲热带草原鸟类的物种变异:亚马逊河内外的最小夜鹰 Chordeiles pusillus(鸟类:Caprimulgidae)的案例。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-06-07 DOI: 10.1016/j.ympev.2024.108117
Alexandre M. Fernandes , Mario Cohn-Haft , Luís Fábio Silveira , Alexandre Aleixo , Nathália Nascimento , Urban Olsson

The Least Nighthawk Chordeiles pusillus is widespread wherever there are savannas in the South American tropics, often in isolated patches, such as white-sands savannas in the Amazon rainforest realm. Here, we investigate genetic relationships between populations of the Least Nighthawk to understand historical processes leading to its diversification and to determine dispersal routes between northern and southern savannas by way of three hypothesized dispersal corridors by comparing samples from white-sand savannas to samples from other savannas outside of the Amazon rainforest region. We use 32 mtDNA samples from the range of C. pusillus to infer a dated phylogeny. In a subset of 17 samples, we use shotgun sequences to infer a distance-based phylogeny and to estimate individual admixture proportions. We calculate gene flow and shared alleles between white-sand and non-Amazonian populations using the ABBA-BABA test (D statistics), and Principal Component Analysis (PCA) to examine genetic structure within and between lineages. Finally, we use species distribution modelling (SDM) of conditions during the Last Glacial Maximum (LGM), currently, and in the future (2050–2080) to predict potential species occurrence under a climate change scenario. Two main clades (estimated to have diverged around 1.07 million years ago) were recovered with mtDNA sequences and Single Nucleotide Polymorphism (SNPs) and were supported by NGSadmix and PCA: one in the Amazon basin white-sand savannas, the other in the non-Amazonian savannas. Possible allele sharing between these clades was indicated by the D-statistics between northern non-Amazonian populations and the white-sand savanna population, but this was not corroborated by the admixture analyses. Dispersal among northern non-Amazonian populations may have occurred in a dry corridor between the Guianan and the Brazilian Shield, which has since moved eastward. Our data suggest that the lineages separated well before the Last Glacial Maximum, consequently dispersal could have happened at any earlier time during similar climatic conditions. Subsequently, non-Amazonian lineages became more divergent among themselves, possibly connecting and dispersing across the mouth of the Amazon River across Marajó island during favourable climatic conditions in the Pleistocene.

在南美洲热带地区,只要有热带稀树草原的地方,就有夜鹰(Least Nighthawk Chordeiles pusillus)的踪迹,它们通常分布在亚马逊热带雨林地区的白沙稀树草原等孤立区域。在这里,我们通过比较来自白沙稀树草原的样本和来自亚马逊热带雨林地区以外的其他稀树草原的样本,研究最矮夜鹰种群之间的遗传关系,以了解导致其多样化的历史进程,并通过三条假定的扩散走廊来确定南北稀树草原之间的扩散路线。我们利用来自 C. pusillus 分布区的 32 个 mtDNA 样本推断出了一个有年代的系统发育。在 17 个样本的子集中,我们使用猎枪序列来推断基于距离的系统发育,并估计个体的混杂比例。我们使用 ABBA-BABA 检验(D 统计量)和主成分分析(PCA)计算白沙种群和非亚马逊种群之间的基因流和共享等位基因,以考察种系内部和种系之间的遗传结构。最后,我们利用物种分布模型(SDM)对末次冰川极盛时期(LGM)、当前和未来(2050-2080 年)的条件进行模拟,以预测气候变化情景下可能出现的物种。利用 mtDNA 序列和单核苷酸多态性(SNPs)发现了两个主要支系(估计在距今约 107 万年前分化),并得到了 NGSadmix 和 PCA 的支持:一个支系位于亚马逊盆地的白沙稀树草原,另一个支系位于非亚马逊稀树草原。北部非亚马孙种群与白沙稀树草原种群之间的 D 统计表明,这些支系之间可能存在等位基因共享,但掺杂分析并未证实这一点。北部非亚马孙种群之间的扩散可能发生在圭亚那和巴西地盾之间的干旱走廊,该走廊后来向东移动。我们的数据表明,这些种群早在末次冰川极盛期之前就已分离,因此扩散可能发生在气候条件相似的任何更早的时期。随后,非亚马孙河流域的世系之间变得更加分化,可能在更新世有利的气候条件下连接并扩散到马拉霍岛对面的亚马孙河口。
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引用次数: 0
Integrative taxonomy, phylogenetics and historical biogeography of subgenus Aeschyntelus Stål, 1872 (Hemiptera: Heteroptera: Rhopalidae) 亚属 Aeschyntelus Stål, 1872(半翅目:异型昆虫纲:Rhopalidae)的综合分类学、系统发生学和历史生物地理学。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-06 DOI: 10.1016/j.ympev.2024.108121
Juhong Chen , Kun Jiang , Tianyi Qi , Yanfei Li , Huaxi Liu , Huaijun Xue , Zhen Ye , Shujing Wang , Wenjun Bu

The subgenus Aeschyntelus includes six species that show variations in body color and shape, thus making it difficult to identify them based on morphological identification alone. To date, no genetic study has evaluated species within this genus. Herein, we collected 171 individuals from 90 localities of Rhopalus and employed an integrative taxonomic approach that incorporated morphological data, mitochondrial genomic data (COI, whole mitochondrial data) and nuclear genomic data (18S + 28S rRNAs, nuclear genome-wide SNPs) to delineate species boundaries. Our analyses confirmed the status of nine described species of Rhopalus and proposed the recognition of one new species known as Rhopalus qinlinganus sp. nov., which is classified within the subgenus Aeschyntelus. Discrepancies arising from nuclear and mitochondrial data suggest the presence of mito-nuclear discordance. Specifically, mitochondrial data indicated admixture within Clade A, comprising R. kerzhneri and R. latus, whereas genome-wide SNPs unambiguously identified two separate species, aligning with morphological classification. Conversely, mitochondrial data clearly distinguished Clade B- consisting of R. sapporensis into two lineages, whereas genome-wide SNPs unequivocally identified a single species. Our study also provides insights into the evolutionary history of Aeschyntelus, thus indicating that it likely originated in East Asia during the middle Miocene. The development of Aeschyntelus biodiversity in the southwestern mountains of China occurred via an uplift-driven diversification process. Our findings highlight the necessity of integrating both morphological and multiple molecular datasets for precise species identification, particularly when delineating closely related species. Additionally, it reveals the important role of mountain orogenesis on speciation within the southwestern mountains of China.

Aeschyntelus 亚属包括六个物种,这些物种的体色和体形各不相同,因此很难仅凭形态鉴定来识别它们。迄今为止,还没有基因研究对该属的物种进行评估。在本文中,我们从 Rhopalus 的 90 个地点收集了 171 个个体,并采用了综合分类方法,结合形态学数据、线粒体基因组数据(COI、全线粒体数据)和核基因组数据(18S + 28S rRNAs、核全基因组 SNPs)来划分物种边界。我们的分析确认了 9 个已描述的 Rhopalus 物种的地位,并提议确认一个新物种,即 Rhopalus qinlinganus sp.nov.,将其归入 Aeschyntelus 亚属。核与线粒体数据的不一致表明存在有丝分裂与核分裂不一致的现象。具体来说,线粒体数据表明,在由 R. kerzhneri 和 R. latus 组成的支系 A 中存在混杂现象,而全基因组 SNP 则明确指出了两个独立的物种,与形态学分类一致。相反,线粒体数据清楚地将由 R. sapporensis 组成的支系 B 区分为两个世系,而全基因组 SNP 则明确地确定了一个物种。我们的研究还揭示了Aeschyntelus的进化历史,从而表明它很可能起源于中新世中期的东亚。Aeschyntelus生物多样性在中国西南山区的发展经历了一个隆升驱动的多样化过程。我们的研究结果突显了整合形态学和多种分子数据集进行精确物种鉴定的必要性,尤其是在划分近缘物种时。此外,它还揭示了山地造山运动对中国西南山区物种分化的重要作用。
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引用次数: 0
Corrigendum to “Systematics of deep-sea starfish order Brisingida (Echinodermata: Asteroidea), with a revised classification and assessments of morphological characters” [Mol. Phylogenetics Evol. 191 (2024) 107993] Corrigendum to "Systematics of deep-sea starfish order Brisingida (Echinodermata: Asteroidea), with a revised classification and assessments of morphological characters" [Mol. Phylogenetics Evol. 191 (2024) 107993].
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-06-05 DOI: 10.1016/j.ympev.2024.108096
Ruiyan Zhang , Marine Fau , Christopher Mah , Marc Eléaume , Dongsheng Zhang , Yadong Zhou , Bo Lu , Chunsheng Wang
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引用次数: 0
Molecular phylogeny of Hesperiidae (Lepidoptera) with an emphasis on Asian and African genera 以亚洲和非洲属种为重点的鳞翅目分子系统发育。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-06-05 DOI: 10.1016/j.ympev.2024.108119
Zhenfu Huang , Hideyuki Chiba , Yanqing Hu , Xiaohua Deng , Wen Fei , Szabolcs Sáfián , Liwei Wu , Min Wang , Xiaoling Fan

Despite considerable research efforts in recent years, the deeper phylogenetic relationships among skipper butterflies (Hesperiidae) remain unresolved. This is primarily because of limited sampling, especially within Asian and African lineages. In this study, we consolidated previous data and extensively sampled Asian and African taxa to elucidate the phylogenetic relationships within Hesperiidae. The molecular dataset comprised sequences from two mitochondrial and two nuclear gene regions from 563 species that represented 353 genera. Our analyses revealed seven subfamilies within Hesperiidae: Coeliadinae, Euschemoninae, Eudaminae, Pyrginae, Heteropterinae, Trapezitinae, and Hesperiinae. The systematics of most tribes and genera aligned with those of prior studies. However, notable differences were observed in several tribes and genera. Overall, the position of taxa assigned to incertae sedis in Hesperiinae is largely clarified in this study. Our results strongly support the monophyly of the tribe Tagiadini (Pyrginae), and the systematics of some genera are clarified with comprehensive discussion. We recognize 15 tribes within the subfamily Hesperiinae. Of these, nine tribes are discussed in detail: Aeromachini, Astictopterini, Erionotini, Unkanini (new status), Ancistroidini, Ismini (confirmed status), Plastingini (new status), Gretnini (confirmed status), and Eetionini (confirmed status). We propose four subtribes within Astictopterini: Hypoleucina subtrib.n., Aclerosina, Cupithina, and Astictopterina. Furthermore, we describe a new genus (Hyarotoides gen.n.) and reinstate two genera (Zea reinst.stat. and Sepa reinst.stat.) as valid. Additionally, we propose several new combinations: Zea mytheca comb.n., Sepa bononia comb.n. & reinst.stat., and Sepa umbrosa comb.n. This study, with extensive sampling of Asian and African taxa, greatly enhances the understanding of the knowledge of the skipper tree of life.

尽管近年来开展了大量研究工作,但蹼蝶(Hesperiidae)之间更深层次的系统发育关系仍未得到解决。这主要是因为取样有限,尤其是在亚洲和非洲品系中。在本研究中,我们整合了之前的数据,并对亚洲和非洲的分类群进行了广泛采样,以阐明蝶科(Hesperiidae)内部的系统发育关系。分子数据集包括代表 353 个属的 563 个物种的两个线粒体和两个核基因区的序列。我们的分析揭示了 Hesperiidae 中的七个亚科:Coeliadinae、Euschemoninae、Eudaminae、Pyrginae、Heteropterinae、Trapezitinae 和 Hesperiinae。大多数科和属的系统学与之前的研究一致。然而,在几个科和属中也发现了明显的差异。总体而言,本研究在很大程度上澄清了被归入 Hesperiinae 的分类群的位置。我们的研究结果有力地支持了 Tagiadini 支(Pyrginae)的单系性,并对一些属的系统学进行了全面的讨论。我们确认了 Hesperiinae 亚科中的 15 个部落。我们对其中的 9 个支系进行了详细讨论:Aeromachini、Astictopterini、Erionotini、Unkanini(新地位)、Ancistroidini、Ismini(已确认地位)、Plastingini(新地位)、Gretnini(已确认地位)和 Eetionini(已确认地位)。我们在 Astictopterini 中提出了四个亚属:Hypoleucina subtrib.n.、Aclerosina、Cupithina 和 Astictopterina。此外,我们描述了一个新属(Hyarotoidesgen.n.),并恢复了两个属(Zeareinst.stat. 和 Separeinst.stat.)的有效地位。此外,我们还提出了几个新的组合:这项研究对亚洲和非洲分类群进行了广泛取样,极大地增强了对虹彩蝶生命树知识的了解。
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引用次数: 0
Sea anemone (Anthozoa, Actiniaria) diversity in Mo’orea (French Polynesia) 莫奥里亚(法属波利尼西亚)的海葵(Anthozoa, Actiniaria)多样性。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-06-05 DOI: 10.1016/j.ympev.2024.108118
Charlotte Benedict , Alonso Delgado , Isabel Pen , Claudia Vaga , Marymegan Daly , Andrea M. Quattrini

Sea anemones (Order Actiniaria) are a diverse group of marine invertebrates ubiquitous across marine ecosystems. Despite their wide distribution and success, a knowledge gap persists in our understanding of their diversity within tropical systems, owed to sampling bias of larger and more charismatic species overshadowing cryptic lineages. This study aims to delineate the sea anemone diversity in Mo’orea (French Polynesia) with the use of a dataset from the Mo’orea Biocode’s “BioBlitz” initiative, which prioritized the sampling of more cryptic and understudied taxa. Implementing a target enrichment approach, we integrate 71 newly sequenced samples into an expansive phylogenetic framework and contextualize Mo’orea’s diversity within global distribution patterns of sea anemones. Our analysis corroborates the presence of several previously documented sea anemones in French Polynesia and identifies for the first time the occurrence of members of genera Andvakia and Aiptasiomorpha. This research unveils the diverse sea anemone ecosystem in Mo’orea, spotlighting the area’s ecological significance and emphasizing the need for continued exploration. Our methodology, encompassing a broad BLAST search coupled with phylogenetic analysis, proved to be a practical and effective approach for overcoming the limitations posed by the lack of comprehensive sequence data for sea anemones. We discuss the merits and limitations of current molecular methodologies and stress the importance of further research into lesser-studied marine organisms like sea anemones. Our work sets a precedent for future phylogenetic studies stemming from BioBlitz endeavors.

海葵(Actiniaria 目)是一类种类繁多的海洋无脊椎动物,在海洋生态系统中无处不在。尽管海葵分布广泛并取得了巨大成功,但我们对其在热带系统中多样性的了解仍存在知识空白,原因是取样偏向于大型和更具魅力的物种,而忽略了隐蔽的品系。本研究旨在利用莫奥里亚生物代码 "BioBlitz "计划的数据集来描述莫奥里亚(法属波利尼西亚)海葵的多样性。通过目标富集方法,我们将 71 个新测序样本整合到一个广阔的系统发生学框架中,并将莫奥里亚的多样性与海葵的全球分布模式结合起来。我们的分析证实了法属波利尼西亚存在几种以前有记载的海葵,并首次发现了 Andvakia 属和 Aiptasiomorpha 属的成员。这项研究揭示了莫奥里亚海葵生态系统的多样性,突出了该地区的生态意义,并强调了继续探索的必要性。我们的研究方法包括广泛的 BLAST 搜索和系统进化分析,这被证明是一种实用而有效的方法,可以克服海葵缺乏全面序列数据所带来的局限性。我们讨论了当前分子方法的优点和局限性,并强调了进一步研究海葵等研究较少的海洋生物的重要性。我们的工作为未来由 BioBlitz 活动引发的系统发育研究开创了先例。
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引用次数: 0
The distinct spatiotemporal evolutionary landscape of HBV and HDV largely determines the unique epidemic features of HDV globally HBV 和 HDV 不同的时空进化景观在很大程度上决定了 HDV 在全球范围内的独特流行特征。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-05-31 DOI: 10.1016/j.ympev.2024.108114
Yibo Ding , Hongbo Guo , Xinfang Hong , Qiudi Li , Zhijiang Miao , Qiuwei Pan , Kuiyang Zheng , Wenshi Wang

Chronic infection of hepatitis B virus (HBV) and hepatitis D virus (HDV) causes the most severe form of viral hepatitis. Due to the dependence on HBV, HDV was deemed to co-evolve and co-migrate with HBV. However, we previously found that the naturally occurred HDV/HBV combinations do not always reflect the most efficient virological adaptation (Wang et al., 2021). Moreover, regions with heavy HBV burden do not always correlate with high HDV prevalence (e.g., East Asia), and vice versa (e.g., Central Asia). Herein, we systematically elucidated the spatiotemporal evolutionary landscape of HDV to understand the unique epidemic features of HDV. We found that the MRCA of HDV was from South America around the late 13th century, was globally dispersed mainly via Central Asia, and evolved into eight genotypes from the 19th to 20th century. In contrast, the MRCA of HBV was from Europe ∼23.7 thousand years ago (Kya), globally dispersed mainly via Africa and East Asia, and evolved into eight genotypes ∼1100 years ago. When HDV stepped in, all present-day HBV genotypes had already formed and its global genotypic distribution had stayed stable geographically. Nevertheless, regionalized HDV adapted to local HBV genotypes and human lineages, contributing to the global geographical separation of HDV genotypes. Additionally, a sharp increase in HDV infections was observed after the 20th century. In conclusion, HDV exhibited a distinct spatiotemporal distribution path compared with HBV. This unique evolutionary relationship largely fostered the unique epidemic features we observe nowadays. Moreover, HDV infections may continue to ramp up globally, thus more efforts are urgently needed to combat this disease.

乙型肝炎病毒(HBV)和丁型肝炎病毒(HDV)的慢性感染会导致最严重的病毒性肝炎。由于对 HBV 的依赖,HDV 被认为是与 HBV 共同进化和共同迁移的。然而,我们之前发现,自然发生的 HDV/HBV 组合并不总是反映最有效的病毒适应(Wang 等人,2021 年)。此外,HBV 负担沉重的地区并不总是与 HDV 的高流行率相关(如东亚),反之亦然(如中亚)。在此,我们系统地阐明了 HDV 的时空进化景观,以了解 HDV 独特的流行特征。我们发现,HDV 的 MRCA 大约在 13 世纪晚期来自南美洲,主要通过中亚向全球扩散,并在 19 世纪至 20 世纪演化成 8 个基因型。相比之下,HBV 的 MRCA 来自 2.37 万年前的欧洲,主要通过非洲和东亚向全球扩散,在 1100 年前演化成 8 个基因型。当 HDV 出现时,现今所有的 HBV 基因型都已形成,其全球基因型分布在地理上保持稳定。然而,区域化的 HDV 适应了当地的 HBV 基因型和人类血统,促成了 HDV 基因型的全球地理分离。此外,20 世纪后,HDV 感染急剧增加。总之,与 HBV 相比,HDV 表现出独特的时空分布路径。这种独特的进化关系在很大程度上促成了我们今天所观察到的独特流行特征。此外,HDV 感染可能会在全球范围内持续上升,因此迫切需要更多的努力来防治这种疾病。
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Molecular Phylogenetics and Evolution
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