Molecular Phylogenetics and Evolution最新文献_第2页

Diversity, phylogeny, and biogeography of the subgenus Japonigekko (Gekkonidae: Gekko) 壁虎亚属（壁虎科：壁虎）的多样性、系统发育和生物地理学。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-04-01 Epub Date: 2026-01-07 DOI: 10.1016/j.ympev.2025.108530

Jing Cao , Nikolay A. Poyarkov , Pingfan Wei , Minhua Tie , Tomoya Matsukoji , Chatmongkon Suwannapoom , Renda Ai , Wenzhu Lu , Phuping Sucharitakul , Haotian Wang , Siriwadee Chomdej , Zhiyong Yuan , Fang Yan

The subgenus Japonigekko, a monophyletic lineage, represents the most ecologically and morphologically diverse group within the genus Gekko, with a wide distribution across East Asia. Given the ecological significance and high diversity of Japonigekko, understanding its true species diversity and biogeographic history is crucial for biodiversity conservation in East Asia. However, research on this subgenus remains limited compared to other well-studied vertebrate groups such as mammals and amphibians. In this study, we conducted extensive sampling and integrated molecular data from 34 of the 38 known Japonigekko species using barcoding techniques for 331 samples from 129 sites, systematically elucidating their phylogenetic relationships. Further genomic analysis addressed longstanding taxonomic controversies, revealed previously underestimated species diversity, and clarified the historical biogeography of this group. Ultimately, we identified nine candidate new species. Phylogenetic analyses and ancestral area reconstructions suggest that Japonigekko originated in the Indochina Peninsula and southern China, subsequently dispersing northward and eastward during the Miocene in response to geological events and climatic fluctuations. The recurrent formation and disappearance of land bridges between the mainland and East Asian islands provided critical opportunities for both dispersal and isolation, revealing a unidirectional mainland-to-island dispersal pattern. These findings support to the “Ancient Species Divergence Hypothesis” in East Asia.

壁虎亚属是壁虎属中生态和形态最多样化的类群，在东亚地区分布广泛。鉴于日本虎的生态意义和高度多样性，了解其真实的物种多样性和生物地理历史对东亚生物多样性保护至关重要。然而，与哺乳动物和两栖动物等其他研究充分的脊椎动物群体相比，对这一亚属的研究仍然有限。在本研究中，我们利用条形码技术对已知的38种日本虎中的34种进行了广泛的采样和分子数据整合，系统地阐明了它们的系统发育关系。进一步的基因组分析解决了长期存在的分类学争议，揭示了以前被低估的物种多样性，并澄清了该类群的历史生物地理学。最终，我们确定了9个候选的新物种。系统发育分析和祖先区域重建表明，日本虎起源于印度支那半岛和中国南部，随后在中新世期间因地质事件和气候波动而向北和向东分散。大陆和东亚岛屿之间陆桥的反复形成和消失为扩散和隔离提供了重要机会，揭示了大陆到岛屿的单向扩散模式。这些发现支持了东亚“古物种分化假说”。

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引用次数: 0

Continental diversification and insular speciation in a widespread passerine (Troglodytes musculus) in southern South America 南美洲南部一种广泛分布的雀形目动物（肌肉类人猿）的大陆多样化和岛屿物种形成。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-04-01 Epub Date: 2026-01-08 DOI: 10.1016/j.ympev.2026.108544

Maria Recuerda , Cecilia Kopuchian , Pablo Andrés Fracas , Pablo Luis Tubaro , Leonardo Campagana , Darío Alejandro Lijtmaer

Understanding how the evolutionary dynamics of widespread species unfold in space and time is critical for uncovering the processes shaping biodiversity. We integrated mitochondrial DNA and genome-wide SNPs to investigate the diversification of the widespread Southern House Wren (Troglodytes musculus) in southern South America and its insular relative, Cobb’s Wren (T. cobbi) from the Malvinas/Falkland Islands (MFI). We aim to reveal processes shaping their evolutionary history and potentially that of other co-distributed taxa. Our analyses indicate a pattern of latitudinal divergence, with an initial split between northern populations (Bolivia, Northern and Central Argentina, Uruguay) and southern populations from Patagonia and the MFI. Shortly after, further diversification occurred, including the colonization of the MFI from Patagonia, where the insular population became isolated, and a split between an Andean lineage and a widespread lowland lineage. Both the timing of these splits and the mitochondrial and genomic patterns suggest a major role of glaciations, particularly the Great Patagonian Glaciation, in the diversification of these species in the southern Neotropics. The colonization of the MFI and negligible gene flow with the continent led to the formation of T. cobbi, contrasting with the notable post-glacial gene flow between the continental northern and southern lineages, although with reduced gene flow between Andean and lowland populations. These results underscore how historical divergence, ecological barriers, and secondary contact jointly shape population structure and genetic diversity, with implications for understanding diversification in widespread species.

了解广泛物种的进化动态如何在空间和时间上展开，对于揭示形成生物多样性的过程至关重要。我们整合了线粒体DNA和全基因组snp，以调查南美洲南部广泛分布的南方家鹪鹩（Troglodytes musculus）及其岛屿亲戚，来自马尔维纳斯群岛/福克兰群岛（MFI）的科布鹪鹩（T. cobbi）的多样化。我们的目标是揭示形成其进化史的过程，以及其他共同分布的分类群的潜在过程。我们的分析表明了一种纬度分化的模式，最初在北部种群（玻利维亚、阿根廷北部和中部、乌拉圭）和南部种群（来自巴塔哥尼亚和小额信贷国家）之间分裂。不久之后，进一步的多样化发生了，包括来自巴塔哥尼亚的MFI的殖民化，在那里岛上的人口被隔离，安第斯血统和广泛的低地血统之间的分裂。这些分裂的时间以及线粒体和基因组模式都表明，冰川作用，特别是巴塔哥尼亚大冰川，在南部新热带地区这些物种的多样化中发挥了重要作用。MFI的殖民化和与大陆的可忽略的基因流动导致了ofT的形成。尽管安第斯和低地种群之间的基因流动减少，但冰川后大陆北部和南部谱系之间的基因流动显著。这些结果强调了历史分化、生态屏障和次生接触如何共同塑造种群结构和遗传多样性，对理解广布物种的多样性具有重要意义。

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引用次数: 0

Phylogenomics of poachers (Agonidae) and the evolution of armor in cottoid fishes (Perciformes: Cottoidei) 盗猎者（Agonidae）的系统基因组学与壳类鱼类（Perciformes: cotoidei）的盔甲进化。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-04-01 Epub Date: 2026-01-23 DOI: 10.1016/j.ympev.2026.108552

Megan L. Vandenberg , Zach Heiple , Matthew A. Kolmann , Thaddaeus Buser , Adam P. Summers , Fernando Meléndez-Vazquez , Dahiana Arcila , Katherine P. Maslenikov , Luke Tornabene

Cottoid fishes represent a morphologically diverse radiation of perciforms, yet their phylogenetic relationships and higher-level taxonomy remain unstable. In particular, the limits of the family Agonidae (poachers) and the placement of closely related lineages have remained uncertain. Here, we used genomic and morphological data to reconstruct relationships across major cottoid clades, and to assess the evolution of dermal armor across this group. Our analyses support a monophyletic Agonidae only when restricted to fully armored poachers and resolve seven well-supported subfamilies. Ancestral-state reconstructions reveal multiple gains of armor plates following a transition from scales to minute dermal spines. These gains coincide with ecological transitions onto continental shelf habitats, where armor likely provided protection from predators and the environment. Given the high diversity of armor morphology in Agonidae, this study enables fine-scalemapping of armor traits and provides a basis for testing the selective pressure shaping performance.

舌形鱼是一种形态多样的鳍形鱼类，但它们的系统发育关系和高级分类仍然不稳定。特别是，猎蝽科（偷猎者）的范围和密切相关的谱系的位置仍然不确定。在这里，我们使用基因组和形态学数据来重建主要子囊分支之间的关系，并评估该群体皮肤盔甲的进化。我们的分析仅在仅限于全副武装的偷猎者时才支持单系的Agonidae，并解决了七个支持良好的亚科。祖先状态的重建揭示了从鳞片到微小的真皮棘过渡后盔甲板的多重增益。这些收获与向大陆架栖息地的生态过渡相吻合，在那里，盔甲可能提供了对捕食者和环境的保护。考虑到甲类动物甲壳形态的高度多样性，本研究为甲壳特征的精细制图提供了可能，并为测试选择性压力成形性能提供了基础。

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引用次数: 0

Phylogenetic analysis of the New Guinean forest wallabies, Dorcopsis and Dorcopsulus reveals cryptic divergent lineages impacted by highland and lowland barriers 新几内亚森林小袋鼠，Dorcopsis和Dorcopsulus的系统发育分析揭示了受高地和低地屏障影响的隐分化谱系。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-04-01 Epub Date: 2026-01-18 DOI: 10.1016/j.ympev.2026.108542

Mark D.B. Eldridge , Matthew J. Phillips , Renae C. Pratt , Linda E. Neaves , Kristofer M. Helgen , Sally Potter

Amongst the Macropodidae (kangaroos and wallabies) the morphologically distinct forest wallabies are the most poorly studied. Modern forest wallabies are confined to the rainforests of New Guinea, with three species inhabiting the lowlands (Dorcopsis), two species in the highlands (Dorcopsulus), and one satellite island endemic (Dorcopsis atrata). Due to limited sampling in previous studies, our understanding of the evolutionary history and systematics of these genera is unresolved. We obtained tissue samples from 17 individual Dorcopsis and 26 Dorcopsulus including representatives from five of the six currently recognised species. DNA sequence data was generated from up to three mitochondrial (3116 bp) and five nuclear (4097 bp) loci. Phylogenetic analysis resolved six major lineages and showed that Dorcopsulus was embedded within Dorcopsis, making the latter paraphyletic. Within Dorcopsis, two lineages corresponded to D. hageni and D. muelleri, which were sister taxa. Another two divergent lineages were identified within sampled D. luctuosa, both of which appear to represent distinct species. Within Dorcopsulus, two major lineages were present, distributed north and south of the Central Ranges, at odds with current taxonomy. Major diversification within Dorcopsis/Dorcopsulus occurred during the late Miocene and the mid-Pliocene, the latter likely associated in New Guinea with lowland barriers and orogenic processes including the uplift of the Central Ranges. The paraphyly of Dorcopsis and detection of divergent lineages within some sampled species indicate that some adjustments to current taxonomy are warranted. We recommend the recognition of a single genus of forest wallabies (Dorcopsis) and provisionally recognise seven species.

在袋鼠科（袋鼠和小袋鼠）中，形态独特的森林小袋鼠是研究得最少的。现代森林小袋鼠局限于新几内亚的热带雨林，有三种生活在低地（Dorcopsis），两种生活在高地（Dorcopsulus），一种特有的卫星岛（Dorcopsis atrata）。由于以往的研究样本有限，我们对这些属的进化历史和系统分类学的理解尚未解决。我们获得了17个Dorcopsis个体和26个Dorcopsulus的组织样本，其中包括6个目前已知物种中的5个。DNA序列数据从多达3个线粒体位点（3116 bp）和5个核位点（4097 bp）生成。系统发育分析确定了6个主要谱系，并表明Dorcopsulus嵌套在Dorcopsis中，使后者成为副系。在dorcopaceae中，有2个谱系对应于D. hageni和D. muelleri，它们是姐妹类群。另外两个不同的谱系被确定在采样的D. luctuosa，两者似乎代表不同的物种。在Dorcopsulus中，存在两个主要的谱系，分布在中央山脉的北部和南部，与目前的分类不一致。Dorcopsis/Dorcopsulus的主要多样化发生在中新世晚期和上新世中期，后者可能与新几内亚的低地屏障和造山过程有关，包括中央山脉的隆起。在一些样本物种中发现了不同的谱系，表明对目前的分类有必要进行一些调整。我们建议承认森林小袋鼠（Dorcopsis）的一个属，暂时承认七个物种。

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引用次数: 0

Phylogenomics reveals the backbone phylogeny of Systellognatha (Insecta: Plecoptera) 系统基因组学揭示了系统蝗的骨干系统发育（昆虫纲：翼翅目）。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-04-01 Epub Date: 2026-01-11 DOI: 10.1016/j.ympev.2026.108547

Xiao Yang , Yehao Wang , Qing-Bo Huo , Abdur Rehman , Scott A. Grubbs , Chenyang Cai , Yu-Zhou Du

Phylogenomics has greatly deepened our understanding of insect evolution, yet significant gaps remain in certain ancient and fast-evolving lineages. Plecoptera (stoneflies), one of the earliest-diverging groups of winged insects with fossil records dating back to the Carboniferous, remain underrepresented in nuclear genomic studies. Within Plecoptera, the suborder Systellognatha, which accounts for nearly half of extant stonefly diversity, has long presented challenges for phylogenetic resolution due to limited taxon sampling and conflicting signals from different molecular datasets. In this study, we performed low-coverage whole-genome sequencing on 16 Systellognatha specimens from China representing nine genera across five families, including the first-ever nuclear genomic data for the understudied family Styloperlidae. Combined with public transcriptomic datasets, our analysis comprises 68 species and covers all seven families of Systellognatha. Phylogenomic analyses using both site-homogeneous and site-heterogeneous models consistently reject the monophyly of Pteronarcyoidea and identify Styloperlidae as the earliest-diverging lineage within the suborder. Meanwhile, comparative analysis based on molecular systematics and morphology indicates that the number of common derived features during the differentiation process of Pteronarcyidae and Perloidea has decreased sharply. However, Pteronarcyidae exhibits ancestral characteristics. This study not only clarifies key evolutionary relationships within Systellognatha with exceptional certainty but also develops a comprehensive phylogenomic framework that will serve as a resource for future global studies on Plecoptera systematics, biogeography, and early insect evolution in general.

系统基因组学极大地加深了我们对昆虫进化的理解，但在某些古老和快速进化的谱系中仍然存在重大差距。翅目（石蝇）是最早分化的有翼昆虫群体之一，其化石记录可以追溯到石炭纪，但在核基因组研究中仍然缺乏代表性。在斑翅目中，系统蝇亚目占现存石蝇多样性的近一半，由于分类群采样有限和来自不同分子数据集的相互矛盾的信号，长期以来一直面临着系统发育分辨率的挑战。在这项研究中，我们对来自中国的16个系统蜥标本进行了低覆盖全基因组测序，这些标本来自5个科9个属，包括首次获得未被充分研究的Styloperlidae科的核基因组数据。结合公开的转录组数据集，我们的分析包括68个物种，涵盖了7个科。使用位点同质和位点异质模型的系统基因组分析一致地拒绝了翼龙科的单一性，并确定柱茎科是该亚目中最早分化的谱系。同时，基于分子系统学和形态学的比较分析表明，在翼元科和翼元科分化过程中，共同衍生特征的数量急剧减少。然而，翼螨科表现出祖先的特征。本研究不仅明确了系统翅目昆虫的主要进化关系，而且还建立了一个全面的系统基因组框架，为未来全球范围内的系统分类学、生物地理学和早期昆虫进化研究提供了资源。

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引用次数: 0

Diversification and biogeographic history of African dormice (genus Graphiurus) revealed by ultraconserved elements and mitochondrial data 超保守元素和线粒体数据揭示非洲睡鼠（Graphiurus属）的多样性和生物地理历史。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-04-01 Epub Date: 2026-01-19 DOI: 10.1016/j.ympev.2026.108549

Kenneth Otieno Onditi , Terrence C. Demos , Julian C. Kerbis Peterhans , Violaine Nicolas , Ondřej Mikula , Anna Bryjová , Amétépé Hounmavo , Ara Monadjem , Josef Bryja

The sub-Saharan Africa endemic dormouse genus Graphiurus is a morphologically diverse group of rodents that has lacked a genus-wide genetic framework, hindering inference of their evolution and biogeography. Here, we assembled the first comprehensive, range-wide genomic dataset for Graphiurus, including ultraconserved elements and the cytochrome b gene. We used phylogenetic reconstruction, divergence-time estimation, and ancestral area reconstruction to clarify biogeographic histories and evaluate how historical range dynamics may have influenced lineage diversification. Graphiurus is the earliest-diverging lineage within Gliridae sister to all other extant genera. Within Graphiurus, we recovered 24 molecular operational taxonomic units (MOTUs) forming two reciprocally monophyletic, deeply divergent clades: a West African lineage comprising three MOTUs and a pan-sub-Saharan Africa lineage comprising 21 MOTUs. Genetic distances between these clades are equal to or greater than those used to distinguish genera. Diversification within Graphiurus started in the middle Miocene, peaking in a rapid radiation during the Plio-Pleistocene. These diversification events coincided with increased climatic instability that fragmented forests into isolated refugia. Ancestral-area reconstructions suggest a Graphiurus origin in the Upper Guinean rainforest, followed by jump dispersal across the Afrotropics, with most subsequent divergences occurring in East Africa. As the first comprehensive phylogenetic analysis of Graphiurus, our study underscores the urgent need for an integrated taxonomic revision of the genus that couples genomic data with detailed morphology and critical re-examination of type material to resolve species limits and formally describe the recovered MOTUs. Many MOTUs appear range restricted, underscoring vulnerability to ongoing habitat loss within montane refugia.

撒哈拉以南非洲特有的睡鼠属Graphiurus是一种形态多样的啮齿类动物，长期以来缺乏全属遗传框架，阻碍了对其进化和生物地理学的推断。在这里，我们组装了第一个全面的，范围广泛的Graphiurus基因组数据集，包括超保守元件和细胞色素b基因。我们使用系统发育重建、分化时间估计和祖先区域重建来澄清生物地理历史，并评估历史范围动态如何影响谱系多样化。Graphiurus是Gliridae中分化最早的分支，是所有现存属的姐妹。在Graphiurus中，我们恢复了24个分子操作分类单位（motu），形成了两个相互单系，深度分化的分支：西非谱系包括3个motu，泛撒哈拉以南非洲谱系包括21个motu。这些分支之间的遗传距离等于或大于用来区分属的距离。Graphiurus内部的多样化始于中新世中期，在上新世-更新世期间快速辐射达到顶峰。这些多样化事件与气候不稳定加剧相吻合，气候不稳定使森林破碎成孤立的避难所。祖先区域重建表明，笔龙起源于上几内亚雨林，随后在非洲热带地区跳跃扩散，随后大多数分化发生在东非。作为第一个全面的系统发育分析，我们的研究强调了迫切需要对该属进行综合分类修订，将基因组数据与详细的形态学结合起来，并对模式材料进行关键的重新检查，以解决物种限制并正式描述恢复的MOTUs。许多motu的活动范围受到限制，这突出了山区避难所不断丧失栖息地的脆弱性。

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引用次数: 0

UCE phylogenomics reveals orogenic vicariance and introgression shaping diversification in the montane Mexican lizard genus Barisia (Squamata: Anguidae) UCE系统基因组学揭示了山地墨西哥壁虎属Barisia的造山带变异和渐入形成多样化。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-04-01 Epub Date: 2026-01-05 DOI: 10.1016/j.ympev.2026.108531

E. Karen López-Estrada , Alejandro Zaldívar-Riverón , Jovana M. Jasso-Martínez , Ernesto Samacá-Sáenz , Jorge Gutiérrez-Rodríguez , Pilar Benites , Valeria B. Salinas-Ramos , John E. McCormack , Robert W. Bryson Jr.

The Mexican Transition Zone is a biogeographic area where the Nearctic and Neotropical regions overlap, encompassing mountain ranges formed during different geological periods. Its complex geological and paleoclimatic history has promoted evolutionary processes such as introgression through hybridization, which can bias phylogenetic inferences and species delimitation. Here, we investigated evolutionary relationships among species of the endemic Mexican lizard genus Barisia using nuclear ultraconserved elements (UCEs). We analyzed samples largely overlapping with a previous study based on mitochondrial DNA (mtDNA) and compared topologies to evaluate mito-nuclear discordance. We also examined population structure, introgression, species boundaries, and biogeographic history of Barisia using molecular dating and ancestral area reconstruction. The strongly supported UCE phylogeny challenges the current species classification of the genus, revealing lineages structured by mountain ranges. Both UCE and previous mtDNA datasets revealed introgression between populations of B. imbricata and B. ciliaris in the southern Central Mexican Plateau and between B. imbricata and B. jonesi in the western Trans-Mexican Volcanic Belt (TMVB), which was further supported by structure and introgression analyses. Our results support the recognition of seven species within Barisia, with the reassignment of populations of B. imbricata, B. ciliaris, and B. jonesi. Overall, diversification within the genus was primarily driven by orogenic vicariance. This study highlights the utility of UCEs for reconstructing robust phylogenies, assessing species limits and genetic structure, as well as to inferring biogeographic patterns.

墨西哥过渡带是一个生物地理区域，新北极和新热带地区重叠，包括不同地质时期形成的山脉。其复杂的地质和古气候历史促进了杂交渗入等进化过程，这可能会影响系统发育推断和物种划分。本文利用核超保守元素（UCEs）研究了墨西哥特有的Barisia蜥蜴属物种间的进化关系。我们分析了与先前基于线粒体DNA （mtDNA）的研究大部分重叠的样本，并比较了拓扑结构以评估mito-nuclear不一致性。利用分子定年和祖先区重建等方法，研究了巴利沙蚤的种群结构、入侵、物种边界和生物地理历史。强有力的支持UCE系统发育挑战了目前属的物种分类，揭示了由山脉结构的谱系。UCE和mtDNA数据均显示，中墨西哥高原南部地区的brbricata和B. ciliaris种群之间以及西部跨墨西哥火山带（TMVB）地区的brbricata和B. jonesi种群之间存在渐近现象，结构和渐近分析进一步支持了这一结论。我们的研究结果支持在Barisia中对7个物种的识别，并重新分配了B. brbricata、B. ciliaris和B. jonesi的种群。总体而言，属内的多样化主要是由造山带变异驱动的。本研究强调了UCEs在重建强健的系统发育、评估物种限制和遗传结构以及推断生物地理模式方面的效用。

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引用次数: 0

Large-scale phylogenomics reveals convergent genome evolution across repeated transitions to endosymbiosis in Enterobacterales 大规模系统基因组学揭示了肠杆菌在重复过渡到内共生过程中的趋同基因组进化。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-04-01 Epub Date: 2026-01-05 DOI: 10.1016/j.ympev.2026.108532

Giobbe Forni , Jacopo Martelossi , Benoit Morel , Dario Pistone , Claudio Bandi , Matteo Montagna

Symbiogenesis stands among the major transitions in the history of life on Earth. Over the past three decades, extensive research has focused on specific host-symbiont associations to investigate their genome evolution. However, the idiosyncratic sequence evolution of endosymbionts has made it challenging to establish a robust phylogenetic framework for identifying broad-scale evolutionary patterns. Here, we establish the first genome-scale phylogenomic resolution for the Enterobacterales order, encompassing both free-living and endosymbiont species, and provide an analysis of gene loss and acquisition dynamics at scale. By examining over 200 genomes, we show remarkable consistency in phenomena previously known from scattered observations: a spike in gene loss invariably accompanies the shift to endosymbiosis, followed by a slower but continuous rate of gene erosion; gene acquisition processes are reduced after the lifestyle shift. Furthermore, convergence in gene family loss across independent and distantly related symbiotic lineages is observed, with genes having conserved functions and evolving under strong constraints lost at lower rates. Our results unify scattered observations into a broad-scale view of the consequences of endosymbiont genome evolution and highlight the roles of gene essentiality and dispensability in shaping convergent evolutionary trajectories.

共生现象是地球生命史上的重大转变之一。在过去的三十年里，广泛的研究集中在特定的宿主-共生体关联上，以研究它们的基因组进化。然而，内共生体的特殊序列进化使得建立一个强大的系统发育框架来识别大范围的进化模式具有挑战性。在这里，我们建立了肠杆菌目的第一个基因组尺度的系统基因组分辨率，包括自由生活和内共生物种，并提供了大规模的基因丢失和获得动力学分析。通过对200多个基因组的研究，我们发现了先前从分散观察中所知道的现象的显著一致性：基因丢失的峰值总是伴随着向内共生的转变，随后是一个缓慢但持续的基因侵蚀速率；改变生活方式后，基因获取过程减少。此外，在独立的和远亲的共生谱系中观察到基因家族丢失的趋同，具有保守功能和在强约束下进化的基因以较低的速率丢失。我们的研究结果将分散的观察结果统一为内共生体基因组进化后果的广泛观点，并强调了基因的必要性和可有可无在形成趋同进化轨迹中的作用。

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引用次数: 0

Diversification of kangaroos and broader turnover among marsupial terrestrial herbivores coincided with emerging aridification then incipient grasslands 袋鼠的多样化和有袋陆生食草动物之间更广泛的更替与出现的干旱化和早期草原相吻合。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-04-01 Epub Date: 2026-01-08 DOI: 10.1016/j.ympev.2026.108543

Clélia Gauthier , William G. Dodt , Manuela Cascini , Maria A. Nilsson , Stephen C. Donnellan , Sally Potter , Mark D.B. Eldridge , Zachary K. Stewart , Vera Weisbecker , Peter J. Prentis , Matthew J. Phillips

Kangaroos and their relatives diverged from arboreal possum-like ancestors and descended into terrestrial or semi-fossorial foraging niches prior to their oldest fossil records from the Late Oligocene (∼25 Ma). However, the most recognisable and speciose sub-family, the Macropodinae, did not appear until the late Miocene and rapidly diversified, presenting a six-clade polytomy that has been impervious to phylogenetic resolution. In this study we have sequenced complete mitochondrial genomes and eleven nuclear loci to further illuminate macropodine evolution. Among the three macropodine tribes, the New Guinean forest wallabies (Dorcopsini) diverge from the base of Macropodinae, leaving Dendrolagini (pademelons, rock-wallabies and tree-kangaroos) as sister to the open habitat Macropodini, among which nail-tail wallabies (Onychogalea), quokka (Setonix), and hare-wallabies (Lagorchestes) diverge successively closer to the ‘Macropus’ clade (Macropus, Osphranter, Wallabia and Notamacropus). Macropodine diversification has been linked to rainforest fragmentation and open habitat expansion, which closely followed the Middle Miocene Climatic Optimum. Our molecular dates instead place macropodine diversification five million years later (from ∼8.5 Ma), concurrent with increasing aridity, habitat heterogeneity, and the decline of all but the largest (or burrowing) vombatiform terrestrial herbivores. The most prominent spike in macropodine diversification (∼4.5 Ma) closely coincides with initial grass expansion during the Early Pliocene and corresponds to the basal diversification of ‘Macropus’ and the crown origins of many macropodine genera. We examine fossil records to consider how faunal turnover among macropodiform and vombatiform terrestrial herbivores may have been facilitated by environmental changes shifting the balance of competition between species.

在晚渐新世最古老的化石记录（~ 25 Ma）之前，袋鼠及其近亲从树栖负鼠类祖先分化而来，并下降到陆生或半化石觅食生态位。然而，直到中新世晚期才出现了最具辨识度和物种特征的巨足亚科，并迅速多样化，呈现出一种不受系统发育分辨率影响的六枝多分支。在这项研究中，我们测序了完整的线粒体基因组和11个核位点，以进一步阐明大足类动物的进化。在三个大足动物部落中，新几内亚森林小袋鼠（Dorcopsini）从大足动物科的基部分化而来，留下了Dendrolagini （pademelons，岩小袋鼠和树袋鼠）作为开放栖息地大足动物的姐妹，其中甲尾小袋鼠（Onychogalea），短尾小袋鼠（Setonix）和兔小袋鼠（Lagorchestes）依次向“大足动物”分支（Macropus, Osphranter， Wallabia和Notamacropus）分化。大足虫的多样化与雨林破碎化和开阔生境的扩张密切相关，这与中新世中期气候最适宜期密切相关。相反，我们的分子日期将大足类动物多样化的时间定在500万年之后（从~ 8.5 Ma开始），与此同时，干旱加剧，栖息地异质性加剧，除了最大的（或穴居的）蝶形陆生食草动物外，其他所有动物都在减少。大足纲植物多样化最显著的峰值（~ 4.5 Ma）与上新世早期草的初始扩张密切相关，与“巨足纲”的基部多样化和许多大足纲植物属的冠源相对应。我们研究了化石记录，以考虑环境变化如何改变物种之间的竞争平衡，从而促进了大足形和蝶形陆生食草动物之间的动物更替。

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引用次数: 0

Hyper-specialized primates possess a reduced suite of xenobiotic-metabolizing cytochrome P450 genes 高度特化的灵长类动物拥有一套减少的外源代谢细胞色素P450基因。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-04-01 Epub Date: 2026-01-22 DOI: 10.1016/j.ympev.2026.108550

Morgan E. Chaney , Anthony J. Tosi , Christina M. Bergey

Subfamilies of cytochrome P450 proteins have been strongly linked to the metabolism of physiologically disruptive compounds such as alkaloids, terpenoids, and other xenobiotics. Consistent with this function, these genes have adaptively evolved in response to environmental pressures exerted on animals, such as herbivores, that consume elevated amounts of toxic xenobiotics or plant secondary metabolites (PSMs). Theory on evolutionary tradeoffs predicts that highly specialized herbivores should exhibit a relatively narrow toolkit of adaptations to accommodate the concomitantly narrow arrays of PSMs in their diets. The bamboo lemurs of Madagascar (genera Prolemur and Hapalemur) represent an interesting test case for this theory because of their dietary hyper-specialization, as these lemurs consume bamboo and grasses at rates otherwise unseen in the order Primates. To test whether the hyper-specialized folivory of these primates is reflected in a similarly specialized and narrow P450 gene suite, we assembled a dataset of confidently assembled CYP1-3 genes for two species of bamboo lemur as well as additional lemur species. We tested the predictions that bamboo lemurs would exhibit, first, greater rates of gene loss for xenobiotic-metabolizing P450s and, second, relaxed selection on xenobiotic-metabolizing P450 subfamilies relative to lemurs without such dietary hyper-specialization. We found support for the first prediction, related to gene loss, in the CYP2B, CYP2C, CYP2D, CYP2J, and CYP3A subfamilies, all of which encode xenobiotic metabolizers. We additionally inferred relaxation of selection for the CYP2F and CYP2J subfamilies. The evolution of the P450 genes in bamboo lemurs provides support for the evolutionary tradeoff hypothesis, and we further hypothesize that, rather than adapting to a general array of PSMs, bamboo lemurs have instead adapted to the primary toxin in their diet, the highly potent poison cyanide.

细胞色素P450蛋白亚家族与生理破坏性化合物（如生物碱、萜类和其他异种生物）的代谢密切相关。与这一功能相一致的是，这些基因已经适应了施加在动物身上的环境压力，例如食草动物，它们消耗了大量的有毒外源物或植物次生代谢物（psm）。进化权衡理论预测，高度特化的食草动物应该表现出相对狭窄的适应工具包，以适应其饮食中伴随而来的狭窄的psm阵列。马达加斯加的竹狐猴（Prolemur属和Hapalemur属）为这一理论提供了一个有趣的测试案例，因为它们的饮食高度专业化，因为这些狐猴以灵长类动物中前所未闻的速度消耗竹子和草。为了测试这些灵长类动物的高度专门化folivory是否反映在类似的专门化和狭窄的P450基因套件中，我们组装了一个自信地组装了两种竹狐猴以及其他狐猴物种的CYP1-3基因的数据集。我们对竹狐猴的预测进行了测试，首先，竹狐猴会表现出更高的外源代谢P450基因失失率，其次，相对于没有这种饮食高度专业化的狐猴，竹狐猴对外源代谢P450亚家族的选择更放松。我们在CYP2B、CYP2C、CYP2D、CYP2J和CYP3A亚家族中发现了与基因丢失有关的第一种预测，这些亚家族都编码异种代谢物。我们还推断CYP2F和CYP2J亚家族的选择放松。竹狐猴P450基因的进化为进化权衡假说提供了支持，我们进一步假设，与其说竹狐猴适应了一系列的psm，不如说是适应了它们饮食中的主要毒素，即剧毒氰化物。

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引用次数: 0