Molecular Phylogenetics and Evolution最新文献_第5页

Multilocus phylogeny of the land snail Helix differs substantially from the mitochondrial gene tree 地螺螺旋的多位点系统发育与线粒体基因树有很大的不同。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-04 DOI: 10.1016/j.ympev.2025.108516

Ondřej Korábek , Bernhard Hausdorf

The phylogeny of the western Palaearctic land snail genus Helix was previously studied using only a few partial mitochondrial genes. The mitochondrial phylogeny was not well resolved, and frequent mitochondrial introgressions indicated that the mitochondrial phylogeny may not correspond to the species tree. We analysed genome-wide ddRAD data to obtain a reliable species tree and re-analysed the mitochondrial phylogeny with mitogenome-scale data from selected species to investigate the extent and causes of mitonuclear discordance. The ddRAD phylogeny resolved the position of previously problematic species, elucidated the biogeographic history of the genus, and confirmed the monophyly of some species that was not unambiguously supported by the mitochondrial data. Helix arnautorum is shown here to be a distinct species, separate from Helix dormitoris. Mitochondrial introgressions indeed cause discordances between the mitochondrial and species trees. The most significant case, the nearly complete replacement of the original mitochondrion of Helix buchii, is associated with relaxed selection and accelerated substitution rate in the original mitochondrial lineage. However, robustly estimating the mitochondrial phylogeny turned out to be difficult even with complete mitochondrial genomes. This is probably due to a combination of short internal branches and variation in substitution rate and nucleotide composition. Alignment filtering and site-heterogeneous mixture models yielded estimates more concordant with the species tree than partitioned analysis of complete protein-coding sequences.

在此之前，人们仅利用少数部分线粒体基因研究了古北缘西部陆地蜗牛属Helix的系统发育。线粒体系统发育未得到很好的解决，频繁的线粒体渗入表明线粒体系统发育可能与物种树不对应。我们分析了全基因组的ddRAD数据，以获得可靠的物种树，并使用来自选定物种的有丝分裂基因组规模数据重新分析了线粒体系统发育，以研究有丝分裂核不一致的程度和原因。ddRAD系统发育解决了以前有问题的物种的位置，阐明了该属的生物地理历史，并证实了一些线粒体数据不明确支持的物种的单系性。此处显示的螺旋arnautorum是一个独特的物种，与螺旋宿舍分开。线粒体渗入确实导致线粒体树和物种树之间的不一致。最显著的例子是，Helix buchii的原始线粒体几乎完全被替换，这与原始线粒体谱系中的宽松选择和加速替换率有关。然而，即使有完整的线粒体基因组，也很难可靠地估计线粒体系统发育。这可能是由于短的内部分支和取代率和核苷酸组成的变化的结合。比对滤波和位点异质混合模型比完整蛋白质编码序列的分割分析更符合物种树的估计。

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引用次数: 0

Genomic data reveals cryptic diversity and suggests five putative species in the broad-snouted caiman in South America 基因组数据揭示了南美洲宽吻凯门鳄的神秘多样性，并提出了五个假定的物种。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-03 DOI: 10.1016/j.ympev.2025.108507

Iago Silva Ornellas , Felipe Eduardo Alves Coelho , Felipe de Medeiros Magalhães , Yhuri Cardoso Nobrega , Leonora Pires Costa , Marcelo Gehara

The inclusion of molecular data in evolutionary studies revealed a vast underestimation of species richness and allowed for assessing the relative importance of landscape features on the evolutionary history of species with different ecological requirements. Here, we used genomic-scale data to assess the genetic diversity of the crocodylian Caiman latirostris, exploring drivers of diversification. Using phylogenomic analysis, we identified five deeply diverged populations that are putative new species under C. latirostris. Genetic structure is coherent with South American watersheds, with evolutionary significant units/unconfirmed candidate species occurring mainly in the Atlantic Eastern Northeast Coast, São Francisco, Atlantic Southeastern, Atlantic South, and Paraná watersheds. Populations also show congruence with freshwater ecoregions, suggesting that not only watersheds, but also other landscape features, may act on species diversification. This is reinforced by a low migration rate between populations separated by mountain ranges. We highlight the need for separate management plans for each population of this historically threatened species due to their unique evolutionary history and genetic diversity. Future studies focusing on possible morphological and ecological differences, as well as demographic history, may reinforce the existence of putative species.

在进化研究中纳入分子数据揭示了物种丰富度的严重低估，并允许评估景观特征对不同生态需求物种进化史的相对重要性。在这里，我们使用基因组尺度的数据来评估鳄鱼凯门鳄的遗传多样性，探索多样化的驱动因素。通过系统基因组分析，我们确定了5个深度分化的居群，这些居群被认为是latirostris下的新种。遗传结构与南美流域一致，进化重要单位/未证实的候选物种主要发生在大西洋东东北海岸、旧金山、大西洋东南部、大西洋南部和帕拉南流域。种群与淡水生态区也表现出一致性，这表明不仅是流域，还有其他景观特征可能对物种多样化起作用。被山脉隔开的人口之间的低迁移率加强了这一点。由于其独特的进化历史和遗传多样性，我们强调需要对每个历史上受到威胁的物种进行单独的管理计划。未来的研究聚焦于可能的形态和生态差异，以及人口统计学历史，可能会加强假设物种的存在。

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引用次数: 0

Deep diversification in Lampropsar tanagrinus (Aves:Icteridae) illustrates hidden diversity and its implication to biogeographic inferences in the Neotropics tanagrinus的深度多样化揭示了新热带地区潜在的多样性及其对生物地理推断的意义

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-03 DOI: 10.1016/j.ympev.2025.108505

Eduardo D. Schultz , Joel Cracraft , Mateus Ferreira , Camila C. Ribas

Neotropical biodiversity is highly underestimated. Even in allegedly well-known taxonomic groups like birds, recent revisions reveal inaccurate taxonomic arrangements that conceal complex evolutionary histories. In this study, we present a complementary molecular and morphometric revision of the taxonomy of the Velvet-fronted Grackle, Lampropsar tanagrinus, a specialist to the floodplains of northern South America. Our results show that across its described distribution, individuals present enough molecular and morphologic differences to be classified as three separate species that partially match described subspecies, including L. tanagrinus, L. violaceus and L. guianensis that occupy the floodplains of, respectively, the Orinoco, the Amazon and the Beni river basins. We show that previous adoption of subspecies status was influenced by an undetected west-east cline in the size of birds in the Amazon basin which nevertheless corresponds to a single taxon. Based on these results, we interpret the diversification history of Lampropsar taxa in the context of the evolution of the Northern South American landscape. Finally, we use our findings to discuss how taxonomic practices in Neotropical ornithology repeatedly lead to misleading interpretation of the evolutionary and biogeographic history of the taxa and the landscape in the region.

新热带生物多样性被严重低估。即使是在鸟类等据称众所周知的分类群体中，最近的修订也揭示了不准确的分类安排，这些安排掩盖了复杂的进化历史。在这项研究中，我们提出了一个互补的分子和形态测量学修订的天鹅绒前Grackle， Lampropsar tanagrinus，一个专家的南美北部洪泛平原的分类。我们的研究结果表明，在其描述的分布中，个体表现出足够的分子和形态差异，可以将其分类为三个独立的物种，这些物种部分匹配所描述的亚种，包括分别占据奥里诺科河、亚马逊河和贝尼河流域洪泛区的L. tanagrinus、L. violaceus和L. guianensis。我们表明，先前的亚种地位的采用受到未被发现的亚马逊盆地鸟类大小的西向东倾斜的影响，然而这对应于一个单一的分类单元。基于这些结果，我们在南美北部景观演变的背景下解释了Lampropsar分类群的多样化历史。最后，我们利用我们的发现讨论了新热带鸟类学的分类实践如何反复导致对该分类群的进化和生物地理历史以及该地区景观的误导性解释。

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引用次数: 0

Phylogenomics provides insights into the phylogeny of Liliales and the evolution of colchicine biosynthesis genes 系统基因组学为百合科植物的系统发育和秋水仙碱生物合成基因的进化提供了新的视角

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-01 DOI: 10.1016/j.ympev.2025.108506

Wenfang Zheng , Diego F. Morales-Briones , Zhanjiang Zhang , Jingyu Tian , Ying Hu , Xiaomei Wei , Wenda Zhang , Na Zhang , Duoyuan Chen , Xinya Hemu , Chienhsun Huang , Lingyun Chen

Liliales comprises many species of ecological, ornamental, and medicinal importance, yet its evolutionary relationships remain controversial. In particular, the origin and evolution of genes involved in colchicine biosynthesis are poorly understood. Here, we aimed to investigate phylogenetic uncertainties within Liliales and the evolution of colchicine-related genes. We sampled 203 transcriptomes (179 species), including 51 newly generated, representing eight families of Liliales. Then, we performed phylogenomic analyses including species tree inference, hybridization detection, and whole-genome duplication (WGD) assessment. We detected extensive phylogenetic conflict driven by incomplete lineage sorting and hybridization, and identified five WGD events across the order. Metabolite profiling confirmed colchicine in Colchicaceae species, and molecular analyses revealed that genes in its biosynthetic pathway are widely present in Liliales. Gene copy number, positive selection analyses, and molecular docking suggested that gene expansion and amino acid change (genes ABH1 and NAT1) contributed to colchicine biosynthesis. These findings indicate that WGDs and subsequent gene evolution contributed to the diversification of Liliales. This study provides new insights into the evolution of Liliales and the molecular basis of colchicine biosynthesis.

百合属植物包括许多种类的生态，观赏和药用的重要性，但其进化关系仍然存在争议。特别是，参与秋水仙碱生物合成的基因的起源和进化尚不清楚。本研究旨在探讨百合属植物系统发育的不确定性以及秋水仙碱相关基因的进化。本研究共采集了百合科8科共203个转录组（179种），其中新生成51个。然后，我们进行了系统基因组分析，包括物种树推断、杂交检测和全基因组重复（WGD）评估。我们发现了由不完整的谱系分类和杂交驱动的广泛的系统发育冲突，并在整个顺序中确定了五个WGD事件。代谢谱分析证实了秋水仙碱在秋水仙科物种中的存在，分子分析表明其生物合成途径的基因在百合属植物中广泛存在。基因拷贝数、阳性选择分析和分子对接表明，基因扩增和氨基酸变化（ABH1和NAT1基因）参与了秋水仙碱的生物合成。这些结果表明，WGDs和随后的基因进化促进了百合科植物的多样化。该研究为百合科植物的进化和秋水仙碱生物合成的分子基础提供了新的认识。

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引用次数: 0

Slippery slopes: Montane isolation and elevational shifts shape the evolution and diversity of Iberolacerta lizards 滑坡：山地隔离和海拔变化塑造了伊比利亚蜥蜴的进化和多样性。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-11-26 DOI: 10.1016/j.ympev.2025.108502

Christophe Dufresnes , Sven Gippner , Sylvia Hofmann , Spartak Litvinchuk , Anamarija Žagar , Daniel Jablonski , Gilles Pottier , Rodrigo Megía-Palma , Gregorio Sánchez-Montes , Octavio Jiménez Robles , Enrique Ayllón , Pierre-André Crochet , ĺñigo Martínez-Solano

Understanding the processes driving the diversity of mountain herpetofauna requires a comprehensive examination of species diversification across evolutionary scales. Here, we investigate the phylogeography of Iberolacerta, a genus of eight lizard species mainly restricted to high elevations in southwestern Europe. Using genomic data, we reconstructed a nuclear phylogeny that aligns with mitochondrial evidence in supporting the divergence of all currently recognized species. Notably, we detect historical nuclear gene flow between I. cyreni and I. martinezricai in Central Spain, suggesting past range overlap, reminiscent of previously observed mitochondrial introgression between I. galani and I. monticola, and the lack of divergence between disjoint populations of I. monticola. Bioclimatic projections accordingly depict broader historical ranges during the last glacial maximum compared to interglacial and current conditions. At the intraspecific level, genomic analyses of four high-elevation species reveal that genetic structure is mainly shaped by isolation-by-distance and, in I. cyreni, by separation among mountain ranges, while heterozygosity generally decreases with elevation. These findings are consistent with the impact of glacial-interglacial cycles on the genetic diversity of montane taxa: populations experience genetic isolation and altitudinal bottlenecks during interglacial periods, but are reconnected and admix in lowland areas during glacial periods. These processes are expected to leave contrasting signatures between the mitochondrial and nuclear genomes, as well as between slow- and fast-evolving molecular markers. From a conservation perspective, our results highlight that the genetically richest – and potentially most adaptive – populations occur at the lowland edges of the species’ ranges, where they are also most vulnerable to climate change.

理解驱动山地爬行动物多样性的过程需要对物种多样性在进化尺度上的全面研究。本文对主要生活在欧洲西南部高海拔地区的八种伊比利亚蜥蜴进行了系统地理学研究。利用基因组数据，我们重建了一个核系统发育，与线粒体证据一致，支持所有目前公认的物种的分歧。值得注意的是，我们在西班牙中部发现了I. cyreni和I. martinezricai之间的历史核基因流动，这表明过去的范围重叠，让人想起之前观察到的I. galani和I. monticola之间的线粒体渗入，以及I. monticola不相交的种群之间缺乏分化。因此，与间冰期和当前条件相比，生物气候预估在末次极盛期描绘了更广泛的历史范围。在种内水平上，对4个高海拔物种的基因组分析表明，遗传结构主要是由距离隔离形成的，在cyreni中，遗传结构主要是由山脉间的分离形成的，而杂合性通常随着海拔的升高而降低。这些发现与冰期-间冰期旋回对山地类群遗传多样性的影响是一致的：种群在间冰期经历遗传隔离和高度瓶颈，但在冰期在低地地区重新连接和混合。这些过程预计会在线粒体和核基因组之间，以及在缓慢和快速进化的分子标记之间留下对比的特征。从保护的角度来看，我们的研究结果强调，基因最丰富的种群——也可能是最具适应性的种群——出现在物种分布范围的低地边缘，在那里它们也最容易受到气候变化的影响。

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引用次数: 0

Phylogeny and evolutionary history of the tribe Scymnini Mulsant, 1846 (Coleoptera: Coccinellidae) based on a multi-locus dataset, with emphasis on the Asian lineage 基于多位点数据的Scymnini Mulsant部落的系统发育和进化史（鞘翅目：Coccinellidae），重点研究了亚洲谱系

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-11-25 DOI: 10.1016/j.ympev.2025.108504

Weidong Huang , Jiamin Zhuang , Xinyue Liang , Wenjing Li , Xingmin Wang , Xiaosheng Chen

The tribe Scymnini Mulsant, 1846 (Coleoptera: Coccinellidae) is a species-rich and ecologically diverse group widely recognized for its role as a biocontrol agent against homopterous insects, including aphids, psyllids, mealybugs, and whiteflies. However, the phylogenetic relationships within Scymnini and their evolutionary history remain poorly understood. We present what is, to our knowledge, the first most taxonomically comprehensive molecular phylogeny of the tribe to date, with emphasis on the Asian lineage, aiming to establish a framework for future studies on this ecologically significant insect group. Phylogenetic trees were inferred using maximum likelihood and Bayesian approaches based on five nuclear and three mitochondrial markers, comprising a total of 4,935 bp. The ingroup included 94 Scymnini taxa, complemented by 40 outgroup species representing diverse coccinellid subfamilies and tribes, to test the phylogenetic relationships among Asian Scymnini. Our results indicate that the Asian Scymnini is paraphyletic, with Axinoscymnus, Slipinskiscymnus, and Clitostethus forming a distinct clade separate from the main Asian Scymnini lineage. Despite this, the analysis strongly supports the monophyly of these genera, along with Nephus, Sasajiscymnus, Nephaspis, and Horniolus. Additionally, the Asian Scymnus was recovered as paraphyletic, as two species of the subgenus Scymnus (Orthoscymnus) Canepari formed a well-supported clade distinct from the main Scymnus lineage. Molecular dating based on fossil record suggests that generic diversification within the Asian Scymnini occurred between the Paleocene and Miocene, while the common ancestor of Coccinellidae dates back to the Early Cretaceous, approximately 143 Ma. Our results provide a novel phylogenetic framework for revising Scymnini classification and offer new insights into its evolutionary history, with broader implications for understanding Coccinellidae phylogeny.

Scymnini Mulsant, 1846（鞘翅目：瓢虫科）是一个物种丰富、生态多样的类群，被广泛认为是一种生物防治剂，可防治同型昆虫，包括蚜虫、木虱、粉虱和白蝇。然而，Scymnini的系统发育关系及其进化史仍然知之甚少。据我们所知，这是迄今为止第一个在分类学上最全面的部落分子系统发育，重点是亚洲血统，旨在为未来研究这一生态意义重大的昆虫类群建立一个框架。基于5个核标记和3个线粒体标记，使用最大似然和贝叶斯方法推断系统发育树，共包含4,935 bp。内群包括94个伞虫分类群，外加40个代表不同伞虫亚科和部落的外群种，以检验亚洲伞虫的系统发育关系。我们的研究结果表明，亚洲scymninus具有副系，axinoscymus、Slipinskiscymnus和cliitostethus形成了一个与亚洲scymninus主要谱系分离的独立分支。尽管如此，该分析强烈支持这些属的单系性，以及Nephus， Sasajiscymnus， Nephaspis和Horniolus。此外，亚洲Scymnus被恢复为副属，因为Scymnus (Orthoscymnus) Canepari亚属的两个种形成了一个与主要scymus谱系不同的良好支持的分支。基于化石记录的分子定年研究表明，亚洲星尾虫属的多样性发生在古新世至中新世之间，而星尾虫科的共同祖先可以追溯到早白垩世，大约143ma。我们的研究结果为修正球虫分类提供了一个新的系统发育框架，并对其进化史提供了新的见解，对理解球虫科的系统发育具有更广泛的意义。

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引用次数: 0

Leaping between branches: Hybridisation and the tangled evolutionary history of true lemurs 在树枝间跳跃：杂交和真正狐猴的复杂进化史

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-11-25 DOI: 10.1016/j.ympev.2025.108503

Giacomo Mercuri , Giovanni Merici , Kyle Kai-How Farh , Lukas F.K. Kuderna , Jeffrey Rogers , Tomàs Marques-Bonet , Giuseppe Donati , Riccardo Percudani , Cristian Capelli

The true lemurs (genus Eulemur) are a genetically diverse and spatially widespread group of species inhabiting most of Madagascar’s forests. Including 12 recognized species, the genus can be divided into four major evolutionary groups: E. rubriventer, E. mongoz, the Brown Lemur Species Complex (BLSC), and the coronatus-macaco-flavifrons complex (CMFC), although monophyly for the CMFC is not always supported. Recent genome-based studies highlighted topological and chronological differences between nuclear and mitochondrial phylogenies of true lemurs, which could be explained by events of hybridisation. In order to reconstruct the evolutionary history of the genus, we test for gene-flow between Eulemur clades using a set of whole genome sequences representative of the diversity of the genus. Events of hybridization among true lemurs clades were identified, explaining discordances between mitochondrial and nuclear phylogenies and providing the context for mito-nuclear co-evolution, which we detected for E. rubriventer. Overall, by directly testing for hybridization among Eulemur species, we developed an evolutionary model that deepens our understanding of the unique and complex history of the genus Eulemur, and sets it as a starting point for future research.

真正的狐猴（狐猴属）是一种基因多样化且在空间上广泛分布的物种，栖息在马达加斯加的大部分森林中。该属包括12个已知物种，可分为四个主要进化群：E. rubriventer， E. mongoz，褐狐猴物种复合体（BLSC）和冠状猴-猕猴-黄酮类复合体（CMFC），尽管CMFC的单系性并不总是得到支持。最近基于基因组的研究强调了真狐猴的核和线粒体系统发育之间的拓扑和时间差异，这可以用杂交事件来解释。为了重建该属的进化历史，我们使用一组代表该属多样性的全基因组序列来测试Eulemur分支之间的基因流动。鉴定了真狐猴分支间的杂交事件，解释了线粒体和核系统发育之间的不一致，并为我们在rubriventer中检测到的核-核共同进化提供了背景。总的来说，通过直接测试Eulemur物种之间的杂交，我们建立了一个进化模型，加深了我们对Eulemur属独特而复杂的历史的理解，并将其作为未来研究的起点。

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引用次数: 0

Multiple origins, singular success: genomic evidence for past recurrent hybridization in Chenopodium album s. str. (Amaranthaceae) 多重起源，单一成功：过去在苋菜科藜属（Chenopodium album s. Str.）反复杂交的基因组证据。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-11-13 DOI: 10.1016/j.ympev.2025.108500

Bohumil Mandák , Farzaneh Habibi , Dijana Čortan , Alexander Belyayev , David E. Jarvis , Eric N. Jellen , Peter J. Maughan , Sergei L. Mosyakin , Pertti Uotila , Karol Krak

Polyploidy, particularly allopolyploidy resulting from interspecific hybridization followed by chromosome duplication, plays a key role in plant diversification and ecological success. Chenopodium album s. str. is one of the world’s most widespread and morphologically variable weeds, yet the timing and mechanism of its origin as an allohexaploid (2n = 6x = 54) remained unresolved. Using RADseq data, this study investigated the origin of ‘BBCCDD’ allohexaploid C. album s. str. and closely related hexaploid taxa by analyzing their relationship to putative diploid progenitors with the ‘BB’ genome (C. ficifolium, C. suecicum, C. ucrainicum) and tetraploid species with the ‘CCDD’ subgenomic combination (C. betaceum, C. glaucophyllum, C. novopokrovskyanum, C. striatiforme). The genomic sequences were mapped to the chromosome-scale reference genome of C. formosanum, a closely related allohexaploid. Results reveal that C. album s. str. does not genetically align with contemporary diploid or tetraploid taxa, suggesting its origin from extinct ancestors rather than ongoing hybridization. Both its ‘BB’ and ‘CCDD’ subgenomes show higher or comparable number of genetic lineages, respectively, than its extant di- and tetraploid relatives, implying conservation of ancestral variation in the allohexaploid. Furthermore, 16 distinct subgenomic combinations were identified within C. album s. str., confirming its polytopic and repeated origin across geographic regions. This explains the remarkable morphological and ecological plasticity observed across its range. This research underscores C. album s. str. as an ancient, stabilized, and globally invasive polyploid, shaped by multiple hybridization events and fixed heterozygosity, offering parallels with other polyploid species such as Triticum/Aegilops complex.

多倍体，特别是由种间杂交和染色体复制引起的异源多倍体，在植物多样化和生态成功中起着关键作用。Chenopodium album s. str.是世界上分布最广、形态最多变的杂草之一，但其作为异源六倍体（2n = 6x = 54）起源的时间和机制尚未明确。本研究利用RADseq数据，通过分析“BBCCDD”异源六倍体C. album s.str .及其近缘六倍体类群与具有“BB”基因组的二倍体祖先（C. ficifolium、C. suecicum、C. ucrainicum）和具有“CCDD”亚基因组组合的四倍体物种（C. betaceum、C. glaucophyllum、C. novopokrovskyanum、C. striatiformme）的关系，探讨了它们的起源。基因组序列被定位到近缘异源六倍体的参比基因组。结果表明，C. album s. str.与当代二倍体或四倍体类群在遗传上不一致，表明其起源于已灭绝的祖先，而不是正在进行的杂交。它的“BB”和“CCDD”亚基因组分别显示出比其现有的二倍体和四倍体亲属更高或相当数量的遗传谱系，这意味着同种异体六倍体祖先变异的保存。此外，在C. album s. str.中鉴定出16种不同的亚基因组组合，证实了其在不同地理区域的多变性和重复起源。这解释了在其分布范围内观察到的显著的形态和生态可塑性。本研究强调C. album s.s r r是一种古老的、稳定的、具有全球入侵性的多倍体，由多次杂交事件和固定杂合性形成，与其他多倍体物种如Triticum/Aegilops复合体有相似之处。

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引用次数: 0

Different expansion events of the actin and tubulin gene families within spirotrichean ciliates (Alveolate, Ciliophora) 肌动蛋白和微管蛋白基因家族在螺旋体纤毛虫（Alveolate, Ciliophora）中的不同扩增事件。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-10-31 DOI: 10.1016/j.ympev.2025.108489

Hua Su, Zengyu Song, Guoling Chai, Fangfang He, Yize Li, Yuxuan Qian, Xuefen Lu, Qi Zhang, Zhenzhen Yi

Actin and tubulin are important components of eukaryotic cytoskeletons that participate in many fundamental cellular processes. As unicellular eukaryotes with abundant cytoskeletons, ciliates offer an excellent model for exploring the origin and evolution of these two gene families. Nonetheless, it remains unclear whether the evolutionary relationships between actin and tubulin subfamilies are consistent across closely related species. Additionally, previous studies inferred the evolutionary patterns of these gene families using different methods, therefore, evaluating the consistency of their results is necessary. Here, we analyzed the evolutionary histories of cytoskeletal subfamilies ActI, ActII, and β-Tub in spirotrichean ciliates based on PCR products and omics data. The results showed: (1) Early PCR-based Sanger sequencing provided valuable insights into evolutionary patterns of ciliate gene families, but primer biases may have limited coverage to certain gene family members. Omics data, though potentially incomplete for some species, offer a more comprehensive approach for future evolutionary studies by minimizing primer biases. (2) Actin and tubulin gene subfamilies exhibited distinct evolutionary patterns, with their histories diverging even within the same species. Expansions of different subfamilies occurred independently in various ancestral groups, and divergent evolutionary patterns between gene families may be associated their distinct biological functions. (3) Subfamilies ActI and ActII underwent different lineag-specific expansion events across spirotrichean groups. ActI expanded at least twice in Euplotia but not in other groups, whereas Euplotia and Hypotrichia each underwent a single ActII expansion. Collectively, these findings provided important insights into the complex evolutionary patterns of eukaryotic cytoskeletons.

肌动蛋白和微管蛋白是真核细胞骨架的重要组成部分，参与许多基本的细胞过程。纤毛虫作为具有丰富细胞骨架的单细胞真核生物，为探索这两个基因家族的起源和进化提供了一个很好的模型。尽管如此，目前尚不清楚肌动蛋白和微管蛋白亚科之间的进化关系是否在密切相关的物种中是一致的。此外，以往的研究使用不同的方法推断了这些基因家族的进化模式，因此评估其结果的一致性是必要的。在此，我们基于PCR产物和组学数据分析了螺旋体纤毛虫细胞骨架亚家族ActI、ActII和β-Tub的进化历史。结果表明：(1)早期基于pcr的Sanger测序提供了对基因家族进化模式的宝贵见解，但引物偏差可能对某些基因家族成员的覆盖范围有限。组学数据虽然对某些物种来说可能不完整，但通过减少引物偏差，为未来的进化研究提供了更全面的方法。(2)肌动蛋白和微管蛋白基因亚家族表现出不同的进化模式，即使在同一物种内，它们的历史也存在分歧。不同亚科的扩展在不同的祖先群体中独立发生，基因家族之间不同的进化模式可能与它们不同的生物学功能有关。(3) ActII亚家族和ActII亚家族在螺旋体类群中发生了不同的谱系特异性扩增事件。ActII在整倍体中至少扩增两次，而在其他组中不扩增，而整倍体和低毛体各扩增一次。总的来说，这些发现为真核细胞骨架的复杂进化模式提供了重要的见解。

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引用次数: 0

Synchronous Miocene radiations and geographic-dependent diversification of pantropical Xylopia (Annonaceae) 泛热带木桐科植物中新世同步辐射与地理依赖多样性。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-10-30 DOI: 10.1016/j.ympev.2025.108485

Francis J. Nge , David M. Johnson , Nancy A. Murray , Laura Holzmeyer , Keegan Floyd , Gregory Stull , Vincent R.C. Soule , Pierre Sepulchre , Delphine Tardif , Carlos Rodrigues-Vaz , Thomas L.P. Couvreur

Aim

The evolutionary drivers of hyperdiversity in tropical rain forests are complex and multifaceted. We used the pantropical Xylopia (Annonaceae) genus to address the diversification of rain forest lineages through time, across different regions, and into novel non-rain forest habitats with a comparative phylogenetic approach.

Location

Global (pantropical).

Methods

We generated a time-calibrated phylogeny of Xylopia using hybrid capture sequence data, including 88% (168/191 spp.) of species within the genus. Diversification analyses were conducted to test for the presence of rate heterogeneity (BAMM, ClaDS, CoMET) and environmental-dependent (RPANDA), geographic-dependent, and habitat dependent (GeoHiSSE) diversification in Xylopia.

Results

Significant diversification rate heterogeneity was detected along the backbone of the core Xylopia clade, leading to near synchronous radiations across tropical regions globally in the Miocene, with higher diversification rates in Africa, Central America, and Madagascar, and lower rates in Australia + New Guinea. Transitions from rain forest to subhumid habitats led to lower diversification rates, whereas transitions to ultramafic habitats lead to higher rates. Regional diversification models indicate sea-level changes as an important driver for Asian, Australian, Pacific, and Neotropical clades and regional temperature changes as the main diversification driver for an African clade of Xylopia.

Main conclusions

Our study shows that despite synchronous radiations across regions, different regional environmental drivers have affected the diversification of Xylopia across tropical regions globally. A noteworthy example includes radiations of all five Malagasy clades c. 7 Ma coinciding with the establishment of heavy seasonal rainfall linked with the Indian monsoon. The diversification dynamics of rain forests are complex and heterogenous, with different clade-dependent and region-dependent environmental drivers.

目的：热带雨林超多样性的进化驱动因素是复杂和多方面的。我们使用泛热带木杉属（Annonaceae）来解决随着时间的推移，不同地区的雨林谱系的多样化，并采用比较系统发育的方法进入新的非雨林栖息地。方法：我们使用杂交捕获序列数据生成了一个时间校准的木藻系统发育，其中包括该属内88%（168/191种）的物种。通过多样性分析，检验了木本植物中是否存在速率异质性（BAMM、ClaDS、CoMET）和环境依赖性（RPANDA）、地理依赖性和生境依赖性（GeoHiSSE）多样性。结果：沿Xylopia核心分支主干检测到显著的多样化率异质性，导致中新世全球热带地区的辐射几乎同步，非洲、中美洲和马达加斯加的多样化率较高，澳大利亚 + 新几内亚的多样化率较低。从雨林到半湿润生境的过渡导致较低的多样化率，而向超湿润生境的过渡导致较高的多样化率。区域多样化模式表明，海平面变化是亚洲、澳大利亚、太平洋和新热带分支的重要驱动因素，区域温度变化是木藻非洲分支多样化的主要驱动因素。主要结论：研究表明，尽管热带地区的辐射是同步的，但不同的区域环境驱动因素影响了热带地区木藻的多样性。一个值得注意的例子包括马达加斯加所有五个分支c. 7 Ma的辐射，同时与印度季风有关的强季节性降雨的建立相吻合。热带雨林的多样性动态是复杂和异质性的，具有不同的枝系和区域依赖的环境驱动因素。

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引用次数: 0