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A comprehensive molecular phylogeny of the genus Sylvirana (Anura: Ranidae) highlights unrecognized diversity, revised classification and historical biogeography. Sylvirana 属(Anura: Ranidae)的综合分子系统发育突显了尚未认识到的多样性、修订的分类和历史生物地理学。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-29 DOI: 10.1016/j.ympev.2024.108223
Yun-He Wu, Man-Hao Xu, Chatmongkon Suwannapoom, Sang Ngoc Nguyen, Robert W Murphy, Theodore J Papenfuss, Amy Lathrop, Felista Kasyoka Kilunda, Wei Gao, Zhi-Yong Yuan, Jin-Min Chen, Liang Zhang, Hai-Peng Zhao, Li-Jun Wang, Md Mizanur Rahman, Lotanna Micah Nneji, Gui-Gang Zhao, Yun-Yu Wang, Jie-Qiong Jin, Peng Zhang, Jing Che

The genus Sylvirana includes 12 species widely distributed in South China and Southeast Asia. The phylogenetic relationships and species diversity for Sylvirana and allied genera remain unresolved and controversial due to insufficient data and incomplete taxon sampling. Using a combined dataset of mitochondrial genes (16S and COI) and 101 nuclear genes obtained through the amplicon sequence capture approach, we generated the most comprehensive phylogenetic analysis for the genus Sylvirana to date, inferring diversity, phylogenetic relationships, and historical biogeography with unprecedented levels of taxon and geographic sampling. Our results conservatively reveal six undescribed species, mostly distributed in peninsular Indochina. Phylogenetic analyses strongly support the non-monophyly of Sylvirana with respect to Pterorana. Additionally, phylogenetic results place Sylvirana guentheri and Pelophylax lateralis into genus Humerana, supporting the inclusion of Hylarana latouchii, Papurana milleti, and Hylarana attigua within Pterorana + Sylvirana. The long-disputed species of Hylarana bannanica (previously Sylvirana) cluster with genus Papurana. Because the results of multiple non-monophyletic genera create taxonomic confusion, we suggest relegating all genera to subgenus rank of Hylarana. Sylvirana is a junior synonym of the Pterorana. Biogeographically, we trace the origin of Pterorana to Southeast Asia during the early Miocene, with subsequent dispersal thereafter. Our study shows that climatic changes may have profoundly influenced the diversification of Pterorana during the Miocene.

Sylvirana 属包括 12 个种,广泛分布于华南和东南亚地区。由于数据不足和类群取样不完整,Sylvirana 属及其同属的系统发育关系和物种多样性仍未得到解决并存在争议。我们利用线粒体基因(16S 和 COI)和通过扩增子序列捕获方法获得的 101 个核基因的组合数据集,对 Sylvirana 属进行了迄今为止最全面的系统发育分析,以前所未有的分类群和地理取样水平推断了其多样性、系统发育关系和历史生物地理学。我们的结果保守地揭示了六个未描述的物种,它们大多分布在印度支那半岛。系统发育分析有力地支持了 Sylvirana 与 Pterorana 的非单系关系。此外,系统发育结果将 Sylvirana guentheri 和 Pelophylax lateralis 归入 Humerana 属,支持将 Hylarana latouchii、Papurana milleti 和 Hylarana attigua 纳入 Pterorana + Sylvirana 属。争议已久的 Hylarana bannanica(以前为 Sylvirana)与 Papurana 属聚类。由于多个非单系属的结果造成了分类学上的混乱,我们建议将所有属归入 Hylarana 亚属。Sylvirana 是 Pterorana 的初级异名。在生物地理学上,我们追溯到 Pterorana 在中新世早期起源于东南亚,随后扩散到世界各地。我们的研究表明,气候的变化可能对中新世期间翼手目的多样化产生了深远的影响。
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引用次数: 0
Whole genome data confirm pervasive gene discordance in the evolutionary history of Coenonympha (Nymphalidae) butterflies 全基因组数据证实了蛱蝶科(Coenonympha)蝴蝶进化史中普遍存在的基因不一致现象。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-28 DOI: 10.1016/j.ympev.2024.108222
Phylogenetic inference is challenged by genealogical heterogeneity amongst molecular markers. Such discordance is driven predominantly by incomplete lineage sorting (ILS) and interspecific gene flow, and bears attendant consequences for the accurate resolution of species relationships. Understanding the distribution of gene conflict in organismal genomes is, therefore, a key aspect of phylogenetic analysis. In this study, three large phylogenomic datasets (i.e., whole mitogenomes, conserved nuclear protein-coding loci, and genomic windows) are used to probe the extent to which discordance pervades the unresolved phylogeny of Coenonympha (Nymphalidae) butterflies. Gene tree discordance is found to be elevated at multiple historically recalcitrant phylogenetic positions. In particular, species relationships near the crown of Coenonympha and within a rapidly diversifying subclade (the hero group) remain difficult to resolve, suggesting that ILS and gene flow have obscured the evolution of this genus. These findings have implications for the taxonomy of this butterfly group and the study of its diversification history. In addition, this work lends support to a growing body of evidence that gene conflict driven by biological processes stands to confound phylogeny, even when extensive data are used.
系统发育推断受到分子标记间系谱异质性的挑战。这种不一致性主要是由不完全世系分选(ILS)和种间基因流动造成的,并对物种关系的准确解析产生相应的影响。因此,了解生物基因组中基因冲突的分布是系统发育分析的一个关键方面。本研究利用三个大型系统发生组数据集(即全有丝分裂基因组、保守的核蛋白编码位点和基因组窗口)来探究蛱蝶科(Coenonympha)蝴蝶未解决的系统发生中的不一致程度。研究发现,在多个历史上难以解决的系统发育位置上,基因树的不一致性较高。特别是,蝶冠附近的物种关系和一个快速多样化的亚支系(英雄群)内的物种关系仍然难以解决,这表明ILS和基因流掩盖了该属的进化。这些发现对该蝶类的分类学及其多样化历史的研究具有重要意义。此外,这项工作还为越来越多的证据提供了支持,这些证据表明,即使使用了大量数据,由生物过程驱动的基因冲突也会混淆系统发生学。
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引用次数: 0
Genomic and transcriptomic perspectives on the origin and evolution of NUMTs in Orthoptera 从基因组和转录组角度看直翅目 NUMTs 的起源和进化。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-23 DOI: 10.1016/j.ympev.2024.108221
Nuclear mitochondrial pseudogenes (NUMTs) result from the transfer of mitochondrial DNA (mtDNA) to the nuclear genome. NUMTs, as “frozen” snapshots of mitochondria, can provide insights into diversification patterns. In this study, we analyzed the origins and insertion frequency of NUMTs using genome assembly data from ten species in Orthoptera. We found divergences between NUMTs and contemporary mtDNA in Orthoptera ranging from 0 % to 23.78 %. The results showed that the number of NUMT insertions was significantly positively correlated with the content of transposable elements in the genome. We found that 39.09 %-68.65 % of the NUMTs flanking regions (2,000 bp) contained retrotransposons, and more NUMTs originated from mitochondrial rDNA regions. Based on the analysis of the mitochondrial transcriptome, we found a potential mechanism of NUMT integration: mitochondrial transcripts are reverse transcribed into double-stranded DNA and then integrated into the genome. The probability of this mechanism occurring accounts for 0.30 %-1.02 % of total mitochondrial nuclear transfer events. Finally, based on the phylogenetic tree constructed using NUMTs and contemporary mtDNA, we provide insights into ancient evolutionary events such as species-specific “autaponumts” and “synaponumts” shared among different species, as well as post-integration duplication events.
核线粒体假基因(NUMTs)是线粒体DNA(mtDNA)转移到核基因组的结果。NUMTs作为线粒体的 "冷冻 "快照,可以让人们深入了解线粒体的多样化模式。在这项研究中,我们利用直翅目 10 个物种的基因组组装数据分析了 NUMTs 的起源和插入频率。我们发现 NUMTs 与直翅目当代 mtDNA 之间的差异从 0 % 到 23.78 % 不等。结果表明,NUMT插入的数量与基因组中转座元件的含量呈显著正相关。我们发现,39.09%-68.65%的NUMTs侧翼区域(2000 bp)含有反转座子,更多的NUMTs来源于线粒体rDNA区域。根据对线粒体转录本组的分析,我们发现了 NUMT 整合的潜在机制:线粒体转录本反向转录为双链 DNA,然后整合到基因组中。这种机制发生的概率占线粒体核转移事件总数的 0.30%-1.02%。最后,根据利用 NUMTs 和当代 mtDNA 构建的系统发生树,我们深入了解了古老的进化事件,如不同物种之间共享的物种特异性 "自聚体 "和 "合聚体",以及整合后的复制事件。
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引用次数: 0
Jumping through hoops: Structural rearrangements and accelerated mutation rates on Dendrodorididae (Mollusca: Nudibranchia) mitogenomes rumble their evolution 跳过圈圈:石斛科(软体动物门:裸鳃纲)有丝分裂基因组的结构重排和加速突变率推动了它们的进化。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-17 DOI: 10.1016/j.ympev.2024.108218
The systematics of the family Dendrodorididae, with only three valid genera, is a challenge for integrative taxonomists. Its members lack hard structures for morphological comparisons and their mitochondrial and nuclear markers provide contradictory phylogenetic signals, making phylogenetic reconstructions difficult. This molecular discordance has been hypothesized to be the result of nuclear pseudogenes or exogenous contamination. However, these hypotheses have not been tested. Here, we assembled the first genome drafts of seven Dendrodorididae species to investigate the evolutionary processes of this family. Two of the mitogenomes displayed an identical structural rearrangement involving the translocation of three coding genes and five tRNAs, described for the first time in nudibranchs. In addition, we found particularly high dN and dN/dS values and multiple insertions and deletions on the mitochondrial genes of smooth Dendrodoris. In contrast, nuclear single-copy ortholog genes showed no such mutational differences. Models of protein structures from mitochondrial genes are conserved, suggesting conserved functionality. Phylogenies using mitogenomic and nuclear data showed that species with rearranged mitogenomes form a clade, although Dendrodorididae relationships remained unresolved. The present study provides novel evidence for accelerated mutation rates in the mitogenomes of Dendrodorididae, which presumably have implications on respiratory adaptation, and highlights the importance of using genomic data to unveil rare evolutionary processes, crucial for correctly inferring phylogenies.
石斛科仅有三个有效属,其系统学研究对综合分类学家来说是一个挑战。其成员缺乏用于形态学比较的坚硬结构,其线粒体和核标记提供了相互矛盾的系统发育信号,使得系统发育重建变得困难。这种分子上的不一致被假定为核假基因或外源污染的结果。然而,这些假设尚未得到验证。在这里,我们收集了 7 个树枝蛙科物种的首个基因组草案,以研究该科的进化过程。其中两个有丝分裂基因组显示了相同的结构重排,涉及三个编码基因和五个tRNA的易位,这在裸鳃亚目中还是首次被描述。此外,我们还发现光滑斛鱼的线粒体基因具有特别高的 dN 值和 dN/dS 值以及多个插入和缺失。相比之下,核单个拷贝同源基因没有显示出这种突变差异。线粒体基因的蛋白质结构模型是保守的,这表明其功能是保守的。利用有丝分裂基因组和核数据进行的系统发育显示,有丝分裂基因组重新排列的物种形成了一个支系,但鼠斛科的关系仍未解决。本研究提供了新的证据,证明石斛科的有丝分裂基因组突变率加快,这可能对呼吸适应有影响,并强调了利用基因组数据揭示罕见进化过程的重要性,这对正确推断系统进化至关重要。
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引用次数: 0
Phylogenomic insights into the worldwide evolutionary relationships of the stingless bees (Apidae, Meliponini) 无刺蜜蜂(Apidae, Meliponini)全球进化关系的系统发生学见解。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-15 DOI: 10.1016/j.ympev.2024.108219
Stingless bees (tribe Meliponini) are remarkable for their characteristically large social colonies, their capacity to produce honey and other useful products, and their morphological and behavioral diversity. They have a disjunct pan-tropical distribution, primarily occurring in warm and humid environments in the Neotropical, Afrotropical, and Indo-Australasian regions. Even though phylogenetic hypotheses have been proposed for Meliponini based on morphology and molecular data, many questions are still unsolved regarding the evolutionary relationships and systematics of the tribe. In this contribution, we present a large phylogenomic dataset comprising over 2500 ultra-conserved element (UCE) loci sequenced for 153 species of Meliponini, representing all known genera of stingless bees. The genera Camargoia, Paratrigonoides, Plectoplebeia, Cleptotrigona, Ebaiotrigona, Papuatrigona, Pariotrigona, Platytrigona, and Sahulotrigona were included in molecular phylogenetic analyses for the first time. Concatenated and species-tree analyses were performed using different partitioning strategies and summary methods. We performed gene-genealogy interrogation (GGI) on several recalcitrant nodes to resolve discordances among recovered tree topologies. Results were mostly consistent among analyses, recovering three main lineages of Meliponini congruent with the biogeographic domains to which they are associated. Within major clades, discordances were found in relation to previous works. The genus Frieseomelitta was recovered as paraphyletic in relation to Trichotrigona, and the genus Lepidotrigona was revealed to be composed of two independent lineages. Even though concatenated and weighted ASTRAL analyses were mostly effective in recovering the relationships favored by GGI, they retrieved different results in relation to the phylogenetic placements of Oxytrigona and Cephalotrigona. The most favored hypothesis in GGI analyses was not found in any other analyses, being more congruent with morphological evidence and highlighting the relevance of exploring the support given to alternative hypotheses through topological tests. Recent advances in our capacity to generate molecular sequences from old specimens using modern sequencing methods allowed for unparalleled sampling across genera, yielding a backbone for the phylogenetic relationships of stingless bees, which will further investigations into their systematics and evolution.
无刺蜜蜂(蜜蜂科)以其特有的大型社会性蜂群、生产蜂蜜和其他有用产品的能力以及形态和行为的多样性而引人注目。它们在泛热带地区分布不均,主要分布在新热带、非洲热带和印度-澳大利亚地区的温暖潮湿环境中。尽管已根据形态学和分子数据提出了 Meliponini 的系统发育假说,但关于该族的进化关系和系统学仍有许多问题尚未解决。在这篇论文中,我们展示了一个大型的系统发生组数据集,该数据集由超过 2,500 个超保守元素(UCE)位点组成,测序了 Meliponini 的 153 个物种,代表了所有已知的无刺蜂属。Camargoia属、Paratrigonoides属、Plectoplebeia属、Cleptotrigona属、Ebaiotrigona属、Papuatrigona属、Pariotrigona属、Platytrigona属和Sahulotrigona属首次被纳入分子系统学分析。我们使用不同的分区策略和总结方法进行了并列分析和物种树分析。我们对几个难以解决的节点进行了基因-谱系查询(GGI),以解决恢复的树拓扑之间的不一致问题。不同分析的结果基本一致,所恢复的 Meliponini 的三个主要支系与其相关的生物地理区域一致。在主要支系中,发现了与以前工作不一致的地方。Frieseomelitta 属被认为是与 Trichotrigona 属相关的旁系,而 Lepidotrigona 属被认为是由两个独立的支系组成。尽管合并分析和加权 ASTRAL 分析大多能有效地恢复 GGI 所支持的关系,但它们在 Oxytrigona 和 Cephalotrigona 的系统发育位置上得到了不同的结果。在 GGI 分析中最受青睐的假说在其他分析中都没有发现,它与形态学证据更为一致,突出表明了通过拓扑学检验探索替代假说支持度的意义。最近,我们利用现代测序方法从古老标本中生成分子序列的能力有了长足的进步,这使得我们可以在各属之间进行无与伦比的取样,从而为无刺蜂的系统发生关系提供了一个基础,这将进一步推动对无刺蜂系统学和进化的研究。
{"title":"Phylogenomic insights into the worldwide evolutionary relationships of the stingless bees (Apidae, Meliponini)","authors":"","doi":"10.1016/j.ympev.2024.108219","DOIUrl":"10.1016/j.ympev.2024.108219","url":null,"abstract":"<div><div>Stingless bees (tribe Meliponini) are remarkable for their characteristically large social colonies, their capacity to produce honey and other useful products, and their morphological and behavioral diversity. They have a disjunct pan-tropical distribution, primarily occurring in warm and humid environments in the Neotropical, Afrotropical, and Indo-Australasian regions. Even though phylogenetic hypotheses have been proposed for Meliponini based on morphology and molecular data, many questions are still unsolved regarding the evolutionary relationships and systematics of the tribe. In this contribution, we present a large phylogenomic dataset comprising over 2500 ultra-conserved element (UCE) loci sequenced for 153 species of Meliponini, representing all known genera of stingless bees. The genera <em>Camargoia</em>, <em>Paratrigonoides</em>, <em>Plectoplebeia, Cleptotrigona</em>, <em>Ebaiotrigona</em>, <em>Papuatrigona</em>, <em>Pariotrigona</em>, <em>Platytrigona</em>, and <em>Sahulotrigona</em> were included in molecular phylogenetic analyses for the first time. Concatenated and species-tree analyses were performed using different partitioning strategies and summary methods. We performed gene-genealogy interrogation (GGI) on several recalcitrant nodes to resolve discordances among recovered tree topologies. Results were mostly consistent among analyses, recovering three main lineages of Meliponini congruent with the biogeographic domains to which they are associated. Within major clades, discordances were found in relation to previous works. The genus <em>Frieseomelitta</em> was recovered as paraphyletic in relation to <em>Trichotrigona</em>, and the genus <em>Lepidotrigona</em> was revealed to be composed of two independent lineages. Even though concatenated and weighted ASTRAL analyses were mostly effective in recovering the relationships favored by GGI, they retrieved different results in relation to the phylogenetic placements of <em>Oxytrigona</em> and <em>Cephalotrigona</em>. The most favored hypothesis in GGI analyses was not found in any other analyses, being more congruent with morphological evidence and highlighting the relevance of exploring the support given to alternative hypotheses through topological tests. Recent advances in our capacity to generate molecular sequences from old specimens using modern sequencing methods allowed for unparalleled sampling across genera, yielding a backbone for the phylogenetic relationships of stingless bees, which will further investigations into their systematics and evolution.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Genome-wide species delimitation and quantification of the extent of introgression in eriophyoid mite Epitrimerus sabinae complex (Acariformes: Eriophyoidea) 全基因组范围的物种划分以及eriophyoid螨Epitrimerus sabinae复合体(螨形目:Eriophyoidea)引种程度的量化。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-15 DOI: 10.1016/j.ympev.2024.108220
Species complex hinders the exploration of terrestrial species diversity, particularly in small arthropod lineages that are morphologically indistinguishable from each other. The Epitrimerus sabinae complex in the Eriophyoidea provides a valuable case study in species complex delimitation, as they exhibit limited morphological variations. In this study, we obtained thousands of nuclear genomic single-nucleotide polymorphisms via whole-genome sequencing from 55 E. sabinae complex specimens, covering their potential all known distribution ranges. We implemented a framework to infer cryptic speciation, which involved phylogenetic and genetic clustering to identify potential species, followed by population demographic assessment to confirm lineage independence (and thus species status). Our results demonstrate that the E. sabinae complex comprises ten distinct species. These species range from highly divergent, genetically isolated lineages, to differentiated populations involving gene flow. This gene flow is widespread across species boundaries, indicating potential genetic introgression among them. Additionally, demographic analyses revealed that the ten species have followed unique trajectories in size change during the Quaternary period. Time-calibrated phylogenies further showed that speciation in the E. sabinae complex occurred rapidly, resulting in a rapid radiation during the Neogene period. Collectively, parallelism/convergence and recent divergence involving multiple gene flows may explain the homoplasy of E. sabinae complex. Our results highlight the integrated approach in species complex delimitation.
物种复合体阻碍了对陆生物种多样性的探索,尤其是在形态上无法相互区分的小型节肢动物类群中。Eriophyoidea 中的 Epitrimerus sabinae 复合体为物种复合体的划分提供了一个有价值的案例研究,因为它们表现出有限的形态变异。在这项研究中,我们通过全基因组测序从 55 个 E. sabinae 复合体标本中获得了数千个核基因组单核苷酸多态性,涵盖了它们潜在的所有已知分布范围。我们建立了一个推断隐性物种的框架,其中包括通过系统发育和遗传聚类来确定潜在物种,然后通过种群人口学评估来确认种系的独立性(进而确定物种地位)。我们的研究结果表明,E. sabinae 复合体包括 10 个不同的物种。这些物种既有高度分化、基因隔离的品系,也有涉及基因流动的分化种群。这种基因流跨越物种边界的现象非常普遍,表明它们之间存在潜在的基因导入。此外,人口学分析表明,这十个物种在第四纪期间的大小变化轨迹独特。时间校准系统进化进一步表明,E. sabinae复合体的物种分化发生得很快,导致了新近纪时期的快速辐射。总之,平行/融合和涉及多基因流的近期分化可能解释了沙棘藻复合体的同源现象。我们的研究结果凸显了物种复合体划分的综合方法。
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引用次数: 0
Revisiting evolutionary relationships of Antrodiaetus (Araneae, Mygalomorphae, Antrodiaetidae) using phylogenomics; implications for species diversity and biogeography of a persistent Holarctic lineage 利用系统发生组学重新审视蚁龙(Antrodiaetus)(鹤形目,蚁龙科,Antrodiaetidae)的进化关系;对物种多样性和一个持续存在的全北区系的生物地理学的影响。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-12 DOI: 10.1016/j.ympev.2024.108206
Antrodiaetus is a lineage of mygalomorph spider (Mygalomorphae: Antrodiaetidae) that has persisted since the late Cretaceous and has a disjunct Holarctic distribution and strong morphological conservatism. These folding-door spiders possess a life history (i.e., limited dispersal, conserved environmental niche) that closely ties their evolution to geology. This study produces a robust, well-supported phylogenomic inference of all currently recognized Antrodiaetus species using UCEs (Ultraconserved Elements), corroborates previous biogeographical hypotheses, and proposes new hypotheses about diversification patterns. We also confirm that previously suspected cryptic diversity within A. pacificus is underestimated, as this nominal species comprises multiple divergent and cryptic lineages. Our phylogeny now serves as a foundation for understanding Antrodiaetus species relationships, biogeography, and speciation.
蚁蜘蛛(Antrodiaetus)是自白垩纪晚期以来一直存在的贻贝目蜘蛛(贻贝目:Antrodiaetidae)的一个品系,在全北极地区分布不均,形态上具有很强的保守性。这些折门蜘蛛的生活史(即有限的散布、保留的环境生态位)将它们的进化与地质密切联系在一起。这项研究利用超保守元素(UCEs)对所有目前已知的蚁蛛物种进行了稳健、可靠的系统进化推断,证实了之前的生物地理学假说,并对其多样化模式提出了新的假说。我们还证实,之前怀疑的太平洋杓鹬内部的隐性多样性被低估了,因为这一标称物种由多个不同的隐性世系组成。现在,我们的系统发育为理解蚂蚁的物种关系、生物地理学和物种分化奠定了基础。
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引用次数: 0
A multi-gene phylogeny of the Asian kukri snakes (Oligodon Fitzinger, 1826): Sharpening the blade of the second largest serpent radiation (Reptilia: Squamata: Colubridae) 亚洲库克里蛇(Oligodon Fitzinger,1826 年)的多基因系统发育:将第二大蛇类辐射(爬行纲:有鳞目:眼镜蛇科)的刀刃磨得更锋利。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-11 DOI: 10.1016/j.ympev.2024.108215
With 90 recognized species, kukri snakes in the genus Oligodon Fitzinger constitute the second largest snake radiation in the world. Oligodon species are collectively distributed across the Asian continent and possess several ecological and morphological attributes that are unique amongst other snakes. Despite their high levels of species richness, evolutionary relationships within Oligodon are poorly understood due to a limited number of samples and genetic markers available in earlier phylogenies. In this study, we assembled the largest molecular dataset of Oligodon to date, which we use to assess the systematics and biogeography of the entire genus. Based on a combination of maximum likelihood and Bayesian phylogenies using fragments of three mitochondrial genes (12 s, 16 s, CytB) and three nuclear genes (Rag1, C-mos, BDNF), we identify eight deeply divergent clades within Oligodon, of which only two correspond with species groupings that were recognized by previous morphological classifications. Four species delimitation methods employed on the mitochondrial portion of the dataset resulted in dramatically divergent estimations of molecular operational taxonomic units (mOTUs). When combined, all four methods support the existence of unrecognized species-level lineages, but also indicate that several other Oligodon species are poorly differentiated genetically and require additional integrative taxonomic research to properly resolve. Based on divergence dating, we demonstrate that Oligodon began to diversify during the early Neogene and hypothesize that the most recent common ancestor of the genus originated in mainland Southeast Asia. We conclude by recognizing eight phylogenetically defined species groups and identify sampling gaps that require further investigation once new data becomes available. This study contributes to a greater understanding of snake evolution on the Asian continent and acts as a baseline for future studies of this speciose genus.
乌梢蛇属(Oligodon Fitzinger)拥有 90 个公认的物种,是世界上第二大蛇类分布区。Oligodon物种集体分布于亚洲大陆,拥有其他蛇类所独有的几种生态和形态特征。尽管 Oligodon 的物种丰富度很高,但由于早期系统进化中的样本和遗传标记数量有限,人们对其内部的进化关系知之甚少。在这项研究中,我们收集了迄今为止最大的 Oligodon 分子数据集,用来评估整个蛇属的系统学和生物地理学。基于最大似然法和贝叶斯系统发育法(使用三个线粒体基因片段(12 s、16 s、CytB)和三个核基因片段(Rag1、C-mos、BDNF)),我们在 Oligodon 中发现了八个深度分化的支系,其中只有两个支系与之前形态学分类所确认的物种组相对应。对数据集线粒体部分采用的四种物种划分方法得出的分子操作分类单元(mOTUs)估计值差异巨大。综合这四种方法,我们发现了一些未被确认的种系的存在,但同时也表明其他几种 Oligodon 在遗传学上的分化程度很低,需要进行更多的综合分类研究才能正确分辨。根据分化年代测定,我们证明 Oligodon 在新近纪早期开始分化,并假设该属最近的共同祖先起源于东南亚大陆。最后,我们确认了八个系统发育明确的物种群,并指出了取样缺口,一旦有了新的数据,就需要进一步调查。这项研究有助于加深对亚洲大陆蛇类进化的了解,并为今后对这一多物种蛇属的研究奠定了基础。
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引用次数: 0
A step in the deep evolution of Alvinellidae (Annelida: Polychaeta): A phylogenomic comparative approach based on transcriptomes Alvinellidae (Annelida: Polychaeta) 深度进化的一步:基于转录组的系统进化比较方法。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-10 DOI: 10.1016/j.ympev.2024.108207
The Alvinellidae are a family of worms that are endemic to deep-sea hydrothermal vents in the Pacific and Indian Oceans. These annelid worms, a sister group to the Ampharetidae, occupy a wide range of thermal habitats. The family includes the most thermotolerant marine animals described to date such as the Pompeii worm Alvinella pompejana, and other species living at much lower temperatures such as Paralvinella grasslei or Paralvinella pandorae. The phylogeny of this family has not been studied extensively. It is, however, a complex case where molecular phylogenies have given conflicting results, especially concerning the monophyletic or polyphyletic nature of the genus Paralvinella.
We carried out a comprehensive study of the phylogeny of this family using the best molecular data currently available from RNAseq datasets, leading to several hundred orthologous transcripts for 11 of the 14 species currently described or in description. The results obtained by the two most popular phylogenetic inference models (using either gene concatenation with maximum likelihood, or a coalescent-based model from gene trees) were compared using a series of ampharetid and terebellid outgroups.
Our study shows that the global phylogenetic signal favors the hypothesis of paraphyly for the Paralvinella genus, with P. pandorae being sister species of the other Alvinellidae.
However, a high number of gene trees also supports the hypothesis of alternative trees in which the monophyly of the Paralvinella genus, as initially proposed by Desbruyères and Laubier, is valid with the species P. pandorae and Paralvinella unidentata being sister species. According to molecular dating, the radiation of the Alvinellidae was rapid and took place in a short period of time between 80 and 110 million years ago. This is reflected at the genomic scale by gene trees equally separated between different phylogenetic hypothesis, showing high rates of incomplete lineage sorting between the first lineages of the Alvinellidae and probable gene transfers. Although different genomic regions seem to have different phylogenetic stories in the early step of the alvinellid radiation, our study supports the view that the two P. pandorae species can be grouped into a separate genus (possibly Nautalvinella) and that the Miralvinella subgenus, defined by Desbruyères and Laubier, is not valid anymore.
Alvinellidae 是太平洋和印度洋深海热液喷口特有的蠕虫科。这些无环蠕虫是热液虫科(Ampharetidae)的姊妹科,占据着广泛的热栖息地。该科包括迄今为止所描述的最耐高温的海洋动物,如庞贝虫 Alvinella pompejana,以及生活在更低温度下的其他物种,如 Paralvinella grasslei 或 Paralvinella pandorae。该科的系统发育尚未得到广泛研究。然而,这是一个复杂的例子,分子系统发育给出了相互矛盾的结果,特别是关于 Paralvinella 属的单系或多系性质。我们利用目前可从 RNAseq 数据集获得的最佳分子数据,对该科的系统发生进行了全面研究,为目前已描述或正在描述的 14 个物种中的 11 个物种找到了数百个同源转录本。我们使用一系列两栖类和小脑类外群,比较了两种最流行的系统发生推断模型(使用最大似然法的基因串联或基于基因树的聚合模型)得出的结果。我们的研究表明,总体系统发生信号倾向于 Paralvinella 属的旁系假说,P. pandorae 是其他 Alvinellidae 的姊妹种。然而,大量的基因树也支持替代树的假说,在这些替代树中,Desbruyères 和 Laubier 最初提出的 Paralvinella 属的单系是有效的,P. pandorae 和 Paralvinella unidentata 是姐妹种。根据分子年代测定,阿尔文贝科的辐射非常迅速,发生在 8000 万年前到 1.1 亿年前的短时间内。这反映在基因组尺度上,不同系统发育假说之间的基因树相等分离,表明阿尔文鱼科第一世系之间的不完全世系分类率很高,而且可能存在基因转移。尽管不同的基因组区域在阿尔文贝类辐射的早期阶段似乎有不同的系统发育故事,但我们的研究支持这样一种观点,即两个 P. pandorae 物种可归入一个单独的属(可能是 Nautalvinella 属),而 Desbruyères 和 Laubier 所定义的 Miralvinella 亚属已不再有效。
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引用次数: 0
Phylogenomic analyses of the pantropical Platycerium Desv. (Platycerioideae) reveal their complex evolution and historical biogeography 泛热带桔梗科(Platycerioideae)的系统发生组分析揭示了其复杂的进化和历史生物地理学。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-10 DOI: 10.1016/j.ympev.2024.108213
Platycerium is a genus of pantropical epiphytic ferns consisting of ca. 18 species and are highly sought after by horticultural enthusiasts. Although the monophyly of this genus has been well supported in previous molecular studies, as an intercontinentally disjunct genus, the origin and distribution pattern of Platycerium were elusive and controversial. This is mainly due to limited taxon sampling, a plastid representing only a single coalescent history, the lack of fossil evidence, and so on. Here, by utilizing genome-skimming sequencing, transcriptome sequencing, and flow cytometry, we integrated chloroplast genomes, data of single-copy nuclear genes, ploidy levels, morphology, and geographic distribution to understand the species phylogeny and the evolutionary and biogeographic history of Platycerium. Our major results include: (1) based on both plastid and nuclear datasets, Platycerium is consistently resolved into three fully supported clades: the Afro-American (AA) clade, the Javan-Australian (JA) clade, and the Malayan-Asian (MA) clade. The AA clade and MA clade are further divided into three and two subclades, respectively; (2) a large amount of gene tree conflict, as well as cytonuclear discordance, was found and can be explained by hybridization and incomplete lineage sorting, and most of the hybridization hypotheses represented ancient hybridization events; (3) through molecular dating, the crown age of Platycerium is determined to be at approximately 32.79 Ma based on the plastid dataset or 29.08 Ma based on the nuclear dataset in the Middle Oligocene; (4) ancestral area reconstruction analysis from different datasets showed that Platycerium most likely originated from Indochina; (5) current distribution patterns are resultant from long-distance dispersals, ancient orogeny, and an ancient climate event; and (6) species diversification was driven by polyploidization, dispersal, and hybridization. This study presented here will help understand the evolution of tropical plant flora and provide a reference for the cultivation and breeding of staghorn ferns.
桔梗属(Platycerium)是泛热带附生蕨类植物,约有 18 个种,深受园艺爱好者的喜爱。虽然该属的单系性在以前的分子研究中得到了很好的支持,但作为一个洲际间不相连的属,Platycerium 的起源和分布模式一直难以捉摸并存在争议。这主要是由于分类群取样有限、质体仅代表单一的聚合历史、缺乏化石证据等原因造成的。在此,我们利用基因组脱脂测序、转录组测序和流式细胞仪,整合了叶绿体基因组、单拷贝核基因数据、倍性水平、形态学和地理分布,以了解桔梗的物种系统发育、进化和生物地理历史。我们的主要成果包括(1)基于质粒和核数据集,Platycerium被一致解析为三个完全支持的支系:非洲-美洲支系(AA)、爪哇-澳大利亚支系(JA)和马来亚-亚洲支系(MA)。AA支系和MA支系又分别分为3个亚支系和2个亚支系;(2)发现了大量的基因树冲突以及细胞核的不一致性,可以用杂交和不完全的世系分类来解释,大多数杂交假说代表了古老的杂交事件;(3)通过分子测年,确定桔梗的冠龄约为32.3)通过分子测年,根据质粒数据集确定桔梗的冠年龄约为 32.79 Ma,根据核数据集确定其冠年龄约为 29.08 Ma,位于中新世;(4)通过不同数据集的祖先区域重建分析表明,桔梗很可能起源于印度支那;(5)目前的分布模式是远距离扩散、古造山运动和古气候事件的结果;(6)物种多样化是由多倍体化、扩散和杂交驱动的。本研究有助于了解热带植物群的演化过程,并为鹿角蕨类植物的栽培和育种提供参考。
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引用次数: 0
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Molecular Phylogenetics and Evolution
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