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Phylogenomic insights into the historical biogeography, character-state evolution, and species diversification rates of Cypripedioideae (Orchidaceae) 通过系统发生组学深入了解兰科(Cypripedioideae)植物的历史生物地理学、特征进化和物种多样化率。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-06 DOI: 10.1016/j.ympev.2024.108138
Min Liao , Jun-Yi Zhang , Yu Feng , Zong-Xin Ren , Heng-Ning Deng , Bo Xu

Cypripedioideae (slipper orchids; Orchidaceae) currently consist of ∼200 herbaceous species with a strikingly disjunctive distribution in tropical and temperate regions of both hemispheres. In this study, an updated phylogeny with representatives from all five cypripedioid genera was presented based on maximum likelihood and Bayesian inference of plastome and low-copy nuclear genes. Phylogenomic analyses indicated that each genus is monophyletic, but some relationships (e.g., those among Cypripedium sects. Acaulia, Arietinum, Bifolia, Flabellinervia, Obtusipetala and Palangshanensia) conflict with those in previous studies based on Sanger data. Cypripedioideae appeared to have arisen in South America and/or the adjacent Qinghai-Tibet Plateau and Hengduan Mountains ∼35 Mya. We inferred multiple dispersal events between East Asia and North America in Cypripedium, and between mainland Southeast Asia and the Malay Archipelago in Paphiopedilum. In the Americas, divergences among four genera (except Cypripedium) occurred around 31–20 Mya, long before the closure of the Isthmus of Panama, indicating the importance of long-distance dispersal. Evolutionary patterns between morphological and plastome character evolution suggested several traits, genome size and NDH genes, which are likely to have contributed to the success of slipper orchids in alpine floras and low-elevation forests. Species diversification rates were notably higher in epiphytic clades of Paphiopedilum than in other, terrestrial cypripedioids, paralleling similar accelerations associated with epiphytism in other groups. This study also suggested that sea-level fluctuations and mountain-building processes promoted the diversification of the largest genera, Paphiopedilum and Cypripedium.

拖鞋兰科(Cypripedioideae;Orchidaceae)目前有 200 多个草本物种,分布在两个半球的热带和温带地区,具有明显的不连续性。本研究根据质体基因和低拷贝核基因的最大似然法和贝叶斯推断法,提出了一个最新的系统发生图,其中包括所有五个蝶形花属的代表物种。系统发生组分析表明,每个属都是单系的,但有些关系(如 Cypripedium sects.Acaulia、Arietinum、Bifolia、Flabellinervia、Obtusipetala 和 Palangshanensia)与之前基于 Sanger 数据的研究结果相冲突。Cypripedioideae似乎起源于南美洲和/或邻近的青藏高原和横断山脉∼35 Mya。我们推断Cypripedium在东亚和北美之间、Paphiopedilum在东南亚大陆和马来群岛之间有多次扩散事件。在美洲,4个属之间的分化发生在31-20万年左右,远远早于巴拿马地峡的关闭,这表明了远距离扩散的重要性。形态和质体特征之间的进化模式表明,基因组大小和NDH基因等几种性状很可能有助于拖鞋兰在高山植物区系和低海拔森林中取得成功。木犀草属附生支系的物种多样化率明显高于其他陆生蝶形花科植物,这与其他类群中与附生相关的类似加速现象类似。这项研究还表明,海平面波动和造山运动促进了最大的属--木槿属和芹菜属--的多样化。
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引用次数: 0
Phylogenomics and biogeography of sawflies and woodwasps (Hymenoptera, Symphyta) 锯蝇和木蝉(膜翅目,同翅目)的系统发生组学和生物地理学。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-05 DOI: 10.1016/j.ympev.2024.108144
Saskia Wutke , Stephan M. Blank , Jean-Luc Boevé , Brant C. Faircloth , Frank Koch , Catherine R. Linnen , Tobias Malm , Gengyun Niu , Marko Prous , Nathan M. Schiff , Stefan Schmidt , Andreas Taeger , Lars Vilhelmsen , Niklas Wahlberg , Meicai Wei , Tommi Nyman

Phylogenomic approaches have recently helped elucidate various insect relationships, but large-scale comprehensive analyses on relationships within sawflies and woodwasps are still lacking. Here, we infer the relationships and long-term biogeographic history of these hymenopteran groups using a large dataset of 354 UCE loci collected from 385 species that represent all major lineages. Early Hymenoptera started diversifying during the Early Triassic ∼249 Ma and spread all over the ancient supercontinent Pangaea. We recovered Xyeloidea as a monophyletic sister group to other Hymenoptera and Pamphilioidea as sister to Unicalcarida. Within the diverse family Tenthredinidae, our taxonomically and geographically expanded taxon sampling highlights the non-monophyly of several traditionally defined subfamilies. In addition, the recent removal of Athalia and related genera from the Tenthredinidae into the separate family Athaliidae is supported. The deep historical biogeography of the group is characterised by independent dispersals and re-colonisations between the northern (Laurasia) and southern (Gondwana) palaeocontinents. The breakup of these landmasses led to ancient vicariance in several Gondwanan lineages, while interchange across the Northern Hemisphere has continued until the Recent. The little-studied African sawfly fauna is likewise a diverse mixture of groups with varying routes of colonization. Our results reveal interesting parallels in the evolution and biogeography of early hymenopterans and other ancient insect groups.

系统发生组学方法最近帮助阐明了各种昆虫的关系,但仍然缺乏对锯蝇和木蝉内部关系的大规模综合分析。在这里,我们利用从代表所有主要品系的 385 个物种中收集的 354 个 UCE 位点组成的大型数据集,推断了这些膜翅目昆虫类群的关系和长期生物地理历史。早期膜翅目昆虫在早三叠世(249 Ma)开始分化,遍布古老的盘古大陆。我们发现 Xyeloidea 是其他膜翅目的单系姊妹群,Pamphilioidea 是 Unicalcarida 的姊妹群。在种类繁多的天牛科(Tenthredinidae)中,我们在分类学和地理学上扩大了分类群的取样范围,突出了几个传统定义的亚科的非单系性。此外,最近将 Athalia 及相关属从 Tenthredinidae 科移入单独的 Athaliidae 科的观点也得到了支持。该类的深层历史生物地理学特征是在北部(劳拉西亚)和南部(冈瓦纳)古大陆之间的独立扩散和再殖民。这些大陆的解体导致了冈瓦纳的几个种系在远古时期的沧海桑田,而北半球的交流则一直持续到近代。非洲锯蝇动物群的研究很少,同样也是一个由不同殖民路线的群体组成的多样性混合体。我们的研究结果揭示了早期膜翅目昆虫和其他古老昆虫类群在进化和生物地理学方面有趣的相似之处。
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引用次数: 0
Tracing the genealogy origin of geographic populations based on genomic variation and deep learning 基于基因组变异和深度学习追溯地理种群的谱系起源。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-02 DOI: 10.1016/j.ympev.2024.108142
Bing Yang , Xin Zhou , Shanlin Liu

Assigning a query individual animal or plant to its derived population is a prime task in diverse applications related to organismal genealogy. Such endeavors have conventionally relied on short DNA sequences under a phylogenetic framework. These methods naturally show constraints when the inferred population sources are ambiguously phylogenetically structured, a scenario demanding substantially more informative genetic signals. Recent advances in cost-effective production of whole-genome sequences and artificial intelligence have created an unprecedented opportunity to trace the population origin for essentially any given individual, as long as the genome reference data are comprehensive and standardized. Here, we developed a convolutional neural network method to identify population origins using genomic SNPs. Three empirical datasets (an Asian honeybee, a red fire ant, and a chicken datasets) and two simulated populations are used for the proof of concepts. The performance tests indicate that our method can accurately identify the genealogy origin of query individuals, with success rates ranging from  93 % to 100 %. We further showed that the accuracy of the model can be significantly increased by refining the informative sites through FST filtering. Our method is robust to configurations related to batch sizes and epochs, whereas model learning benefits from the setting of a proper preset learning rate. Moreover, we explained the importance score of key sites for algorithm interpretability and credibility, which has been largely ignored. We anticipate that by coupling genomics and deep learning, our method will see broad potential in conservation and management applications that involve natural resources, invasive pests and weeds, and illegal trades of wildlife products.

将查询到的动物或植物个体归入其衍生种群是与生物系谱相关的各种应用中的首要任务。这些工作通常依赖于系统发育框架下的短 DNA 序列。当推断出的种群来源在系统发育结构上含糊不清时,这些方法自然会受到限制,这种情况下就需要信息量更大的遗传信号。最近,全基因组序列的生产和人工智能在成本效益方面取得的进展,为追溯任何给定个体的种群起源创造了前所未有的机会,只要基因组参考数据是全面和标准化的。在这里,我们开发了一种卷积神经网络方法,利用基因组 SNPs 来识别种群起源。我们使用了三个经验数据集(亚洲蜜蜂、红火蚁和鸡数据集)和两个模拟种群进行概念验证。性能测试表明,我们的方法可以准确识别查询个体的系谱起源,成功率从 > 93 % 到 100 % 不等。我们还进一步证明,通过 FST 过滤提炼信息位点,可以显著提高模型的准确性。我们的方法对与批量大小和历时相关的配置具有鲁棒性,而模型学习则得益于适当预设学习率的设置。此外,我们还解释了关键位点对于算法可解释性和可信度的重要性得分,而这一点在很大程度上被忽视了。我们预计,通过将基因组学与深度学习相结合,我们的方法将在涉及自然资源、入侵害虫和杂草以及野生动物产品非法贸易的保护和管理应用中发挥广泛的潜力。
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引用次数: 0
Evolutionary analysis of species-specific duplications in flatworm genomes 扁形虫基因组中物种特异性重复的进化分析。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-02 DOI: 10.1016/j.ympev.2024.108141
Mauricio Langleib , Javier Calvelo , Alicia Costábile , Estela Castillo , José F. Tort , Federico G. Hoffmann , Anna V. Protasio , Uriel Koziol , Andrés Iriarte

Platyhelminthes, also known as flatworms, is a phylum of bilaterian invertebrates infamous for their parasitic representatives. The classes Cestoda, Monogenea, and Trematoda comprise parasitic helminths inhabiting multiple hosts, including fishes, humans, and livestock, and are responsible for considerable economic damage and burden on human health. As in other animals, the genomes of flatworms have a wide variety of paralogs, genes related via duplication, whose origins could be mapped throughout the evolution of the phylum. Through in-silico analysis, we studied inparalogs, i.e., species-specific duplications, focusing on their biological functions, expression changes, and evolutionary rate. These genes are thought to be key players in the adaptation process of species to each particular niche. Our results showed that genes related with specific functional terms, such as response to stress, transferase activity, oxidoreductase activity, and peptidases, are overrepresented among inparalogs. This trend is conserved among species from different classes, including free-living species. Available expression data from Schistosoma mansoni, a parasite from the trematode class, demonstrated high conservation of expression patterns between inparalogs, but with notable exceptions, which also display evidence of rapid evolution. We discuss how natural selection may operate to maintain these genes and the particular duplication models that fit better to the observations. Our work supports the critical role of gene duplication in the evolution of flatworms, representing the first study of inparalogs evolution at the genome-wide level in this group.

扁形动物(Platyhelminthes),又称扁形动物,是双脊无脊椎动物门的一个分支,因其寄生代表而臭名昭著。绦虫纲(Cestoda)、单精虫纲(Monogenea)和吸虫纲(Trematoda)由寄生蠕虫组成,栖息在鱼类、人类和家畜等多种宿主体内,造成了巨大的经济损失和人类健康负担。与其他动物一样,扁形动物的基因组中也有各种各样的旁系亲属,即通过重复而相关的基因,它们的起源可以在整个扁形动物门的进化过程中找到。通过模拟分析,我们研究了内同源物,即物种特异性复制,重点关注它们的生物学功能、表达变化和进化速度。这些基因被认为是物种适应每个特定生态位过程中的关键角色。我们的研究结果表明,与特定功能术语相关的基因,如应激反应、转移酶活性、氧化还原酶活性和肽酶等,在内切类中的比例较高。这一趋势在不同类别的物种(包括自由生活物种)中是一致的。来自曼氏血吸虫(一种吸虫类寄生虫)的现有表达数据显示,内表型之间的表达模式高度一致,但也有明显的例外,这些例外也显示了快速进化的证据。我们讨论了自然选择是如何维持这些基因的,以及更适合观察结果的特定复制模型。我们的工作证明了基因复制在扁形虫进化过程中的关键作用,这是首次在全基因组水平上研究该类扁形虫的内表型进化。
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引用次数: 0
Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies) Museomics有助于解析雪雀(鸟类,百灵鸟科,Montifringilla及其同属鸟类)的系统发育。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-24 DOI: 10.1016/j.ympev.2024.108135
Safiqul Islam , Claire Peart , Christian Kehlmaier , Yue-Hua Sun , Fumin Lei , Andreas Dahl , Sylvia Klemroth , Dimitra Alexopoulou , Maria del Mar Delgado , Paola Laiolo , Juan Carlos Illera , Sebastian Dirren , Sabine Hille , Davaa Lkhagvasuren , Till Töpfer , Martin Kaiser , Axel Gebauer , Jochen Martens , Claudia Paetzold , Martin Päckert

Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis).

Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus Pyrgilauda. Misplacement of one species-level taxon (Onychostruthus tazcanowskii) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between M. nivalis and the QTP endemic M. henrici was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera Montifringilla and Pyrgilauda with monotypic Onychostruthus being sister to the latter. The Afghan endemic P. theresae likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with P. ruficollis. Our extended trans-Palearctic sampling for the white-winged snowfinch, M. nivalis, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 – 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.

博物馆收藏的历史标本提供了一个宝贵的材料来源,这些标本也来自偏远地区或冲突地区,而现在的科学家还很难接触到这些地区的标本。通过这项研究,我们利用阿富汗特有物种--阿富汗雪雀(Pyrgilauda theresae)的整张皮上的历史 DNA,提供了一个完整的雪雀分类群系统发育。为了解决以前的系统发育假说之间的强烈冲突,我们利用ddRAD测序技术为青藏高原(QTP)特有的所有现生雪雀物种和中西古北唯一雪雀物种(Montifringilla nivalis)的扩展种内取样生成了选定类群的新型有丝分裂基因组序列和全基因组SNP数据。我们的系统发育重建一致驳斥了之前提出的雪雀属(Pyrgilauda)旁系的观点。一个种级分类群(Onychostruthus tazcanowskii)在以前的雪雀系统发育中的错误定位无疑是由包含异特异性序列信息的嵌合有丝分裂基因组推断出来的。此外,对新的序列数据和以前产生的序列数据进行比较后发现,假定 M. nivalis 与 QTP 特有的 M. henrici 之间的姊妹群关系是基于有缺陷的分类学提出的。基于全基因组 SNP 数据和有丝分裂基因组的系统发育重建结果基本一致,支持 Montifringilla 属和 Pyrgilauda 属互为单系,单型的 Onychostruthus 是后者的姊妹属。阿富汗特有的P. theresae可能起源于上新世的一次相当古老的西藏外扩散,可能与P. ruficollis有共同的祖先。我们对白翅雪雀(M. nivalis)进行的跨北极采样证实,在距今150万-270万年前的一个亚洲支系和一个欧洲支系之间存在着强烈的世系分化。全基因组 SNP 数据表明,来自阿尔卑斯山和坎塔布里亚山脉的欧洲样本之间存在微妙的分化。
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引用次数: 0
Complex patterns of gene flow and convergence in the evolutionary history of the spiral-horned antelopes (Tragelaphini) 螺旋角羚羊(Tragelaphini)进化史中基因流动和趋同的复杂模式。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-22 DOI: 10.1016/j.ympev.2024.108131
Andrinajoro R. Rakotoarivelo , Thabelo Rambuda , Ulrike H. Taron , Gabrielle Stalder , Paul O’Donoghue , Jan Robovský , Stefanie Hartmann , Michael Hofreiter , Yoshan Moodley

The Tragelaphini, also known as spiral-horned antelope, is a phenotypically diverse mammalian tribe comprising a single genus, Tragelaphus. The evolutionary history of this tribe has attracted the attention of taxonomists and molecular geneticists for decades because its diversity is characterised by conflicts between morphological and molecular data as well as between mitochondrial, nuclear and chromosomal DNA. These inconsistencies point to a complex history of ecological diversification, coupled by either phenotypic convergence or introgression. Therefore, to unravel the phylogenetic relationships among spiral-horned antelopes, and to further investigate the role of divergence and gene flow in trait evolution, we sequenced genomes for all nine accepted species of the genus Tragelaphus, including a genome each for the highly divergent bushbuck lineages (T. s. scriptus and T. s. sylvaticus). We successfully reconstructed the Tragelaphus species tree, providing genome-level support for the early Pliocene divergence and monophyly of the nyala (T. angasii) and lesser kudu (T. imberbis), the monophyly of the two eland species (T. oryx and T. derbianus) and, importantly, the monophyly of kéwel (T. s. scriptus) and imbabala (T. s. sylvaticus) bushbuck. We found strong evidence for gene flow in at least four of eight nodes on the species tree. Among the six phenotypic traits assessed here, only habitat type mapped onto the species tree without homoplasy, showing that trait evolution was the result of complex patterns of divergence, introgression and convergent evolution.

羚羊科(Tragelaphini),又称螺旋角羚羊,是一个表型多样的哺乳动物部落,由一个属--羚羊属(Tragelaphus)组成。几十年来,该科的进化史一直吸引着分类学家和分子遗传学家的关注,因为其多样性的特点是形态学数据和分子数据之间以及线粒体、核DNA和染色体DNA之间的冲突。这些不一致性表明,该物种的生态多样化历史十分复杂,同时还存在表型趋同或外来引入的情况。因此,为了揭示旋角羚之间的系统发育关系,并进一步研究分化和基因流在性状进化中的作用,我们对旋角羚属所有九个公认物种的基因组进行了测序,包括高度分化的丛林羚系(T. s. scriptus和T. s. sylvaticus)的基因组。我们成功地重建了 Tragelaphus 的物种树,为尼亚拉(T. angasii)和小库杜(T. imberbis)在上新世早期的分化和单系化、两个伊兰种(T. oryx 和 T. derbianus)的单系化以及重要的凯威(T. s. scriptus)和伊姆巴拉(T. s. sylvaticus)丛林巴克的单系化提供了基因组水平的支持。在物种树的八个节点中,我们至少在四个节点上发现了基因流动的有力证据。在本文评估的六个表型特征中,只有栖息地类型映射到物种树上时没有同源现象,这表明特征的进化是复杂的分化、引入和趋同进化模式的结果。
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引用次数: 0
Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae) 矮牵牛及相关属(矮牵牛科,茄科)树种不一致的原因是不完全的世系分类和杂交。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-22 DOI: 10.1016/j.ympev.2024.108136
Pedro H. Pezzi , Lucas C. Wheeler , Loreta B. Freitas , Stacey D. Smith

Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies suggest that hybridization is frequent, the extent of reticulation within Petunia and its closely related genera has never been examined from a phylogenetic perspective. In this study, we used transcriptomic data from 11 Petunia, 16 Calibrachoa, and 10 Fabiana species to illuminate the relationships between these species and investigate whether hybridization played a significant role in the diversification of the clade. We inferred that gene tree discordance within genera is linked to hybridization events along with high levels of ILS due to their rapid diversification. Moreover, network analyses estimated deeper hybridization events between Petunia and Calibrachoa, genera that have different chromosome numbers. Although these genera cannot hybridize at the present time, ancestral hybridization could have played a role in their parallel radiations, as they share the same habitat and life history.

尽管存在物种分化的总体历史,但系统发育研究经常揭示出基因组不同区域的不同拓扑结构。这些基因树不一致的原因多种多样,但不完全系谱分选(ILS)和杂交是其中最具生物学意义的原因。矮牵牛是研究野生杂交的经典系统。虽然野外研究表明杂交很频繁,但牵牛花及其近缘属内部的网状结构程度却从未从系统发育的角度进行过研究。在这项研究中,我们使用了来自 11 个矮牵牛属、16 个萼叶草属和 10 个法比亚娜属的转录组数据来阐明这些物种之间的关系,并研究杂交是否在该支系的多样化过程中发挥了重要作用。我们推断,属内基因树的不一致性与杂交事件有关,同时由于其快速多样化,ILS水平较高。此外,网络分析还估计了矮牵牛属和萼片草属之间更深层次的杂交事件,这两个属的染色体数目不同。虽然这两个属目前还不能杂交,但祖先的杂交可能在它们的平行辐射中起到了一定的作用,因为它们有着相同的栖息地和生活史。
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引用次数: 0
Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki) 利用 RADseq 和 Sanger 测序揭示天鹅绒蠕虫物种复合体(Onychophora: Peripatopsidae: Peripatopsis sedgwicki)中隐性宗族发生的一致模式。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-22 DOI: 10.1016/j.ympev.2024.108132
Angus Macgregor Myburgh , Aaron Barnes , Romina Henriques , Savel R. Daniels

In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259–11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.

本研究利用第一代 DNA 测序(线粒体细胞色素 c 氧化酶亚单位一,COI)和还原代表性基因组 RADseq 数据来了解绒毛虫 Peripatopsis sedgwicki 物种群在南非分布范围内的多样化模式和过程。为了评估该物种群的多样性和系统地理学,我们为 RADseq 数据生成了三个数据集(两个主要数据集和一个补充数据集),对应 1,259-11,468 个 SNPs。利用最大似然法和贝叶斯推断法推断了两个主要数据集的树拓扑结构。利用 COI 数据集进行的系统发育分析在该物种群中检索到四个不同的、支持良好的支系。应用于 COI 数据的五种物种划分方法(ASAP、bPTP、bGMYC、STACEY 和 iBPP)均支持福特斯堡自然保护区标本的区分。在主要的 P. sedgwicki 种群中,物种划分方法揭示了不同数量的可操作分类单元,并高估了推定类群的数量。分化时间估计值、物种的地理排他性和系统地理学结果表明,Plio/Pleistocene时期的宗族发生是最近发生的。在最大似然法框架下,对 RADseq 数据进行了主成分分析和主成分判别分析。后者的结果证实了利用 COI 数据观察到的四个主要支系,然而,应用额外的筛选方法发现了更多的多样性。RADseq 数据与 COI 数据之间的总体一致性很高,这表明第一代序列数据仍然是进化研究的一种廉价而有效的方法,尽管 RADseq 确实能提供更高的当代时空模式分辨率。
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引用次数: 0
Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion 水平转移的苷水解酶 26 可能有助于半翅目昆虫消化植物组织。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-18 DOI: 10.1016/j.ympev.2024.108134
Hunter K. Walt , Seung-Joon Ahn , Federico G. Hoffmann

Glycoside hydrolases are enzymes that break down complex carbohydrates into simple sugars by catalyzing the hydrolysis of glycosidic bonds. There have been multiple instances of adaptive horizontal gene transfer of genes belonging to various glycoside hydrolase families from microbes to insects, as glycoside hydrolases can metabolize constituents of the carbohydrate-rich plant cell wall. In this study, we characterize the horizontal transfer of a gene from the glycoside hydrolase family 26 (GH26) from bacteria to insects of the order Hemiptera. Our phylogenies trace the horizontal gene transfer to the common ancestor of the superfamilies Pentatomoidea and Lygaeoidea, which include stink bugs and seed bugs. After horizontal transfer, the gene was assimilated into the insect genome as indicated by the gain of an intron, and a eukaryotic signal peptide. Subsequently, the gene has undergone independent losses and expansions in copy number in multiple lineages, suggesting an adaptive role of GH26s in some insects. Finally, we measured tissue-level gene expression of multiple stink bugs and the large milkweed bug using publicly available RNA-seq datasets. We found that the GH26 genes are highly expressed in tissues associated with plant digestion, especially in the principal salivary glands of the stink bugs. Our results are consistent with the hypothesis that this horizontally transferred GH26 was co-opted by the insect to aid in plant tissue digestion and that this HGT event was likely adaptive.

糖苷水解酶是一种通过催化水解糖苷键将复杂碳水化合物分解为单糖的酶。由于糖苷水解酶可以代谢富含碳水化合物的植物细胞壁成分,属于各种糖苷水解酶家族的基因从微生物向昆虫进行了多次适应性水平基因转移。在这项研究中,我们描述了糖苷水解酶家族 26(GH26)的一个基因从细菌向半翅目昆虫水平转移的特征。我们的系统发生学将该基因水平转移追溯到了包括蝽和种子蝽在内的五蠹目和姬蛙目超家族的共同祖先。水平转移后,该基因被同化到昆虫基因组中,表现为获得了一个内含子和一个真核信号肽。随后,该基因在多个品系中经历了独立的拷贝数丢失和扩增,这表明 GH26s 在某些昆虫中具有适应性作用。最后,我们利用公开的 RNA-seq 数据集测量了多种蝽类和大型乳草蝽的组织级基因表达。我们发现,GH26 基因在与植物消化相关的组织中高度表达,尤其是在蝽的主要唾液腺中。我们的研究结果符合这样的假设,即这种横向转移的 GH26 被昆虫共同利用来帮助植物组织消化,而且这种 HGT 事件很可能是适应性的。
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引用次数: 0
Phylogenomics and biogeography of the small carpenter bees (Apidae: Xylocopinae: Ceratina) 小木匠蜂(Apidae: Xylocopinae: Ceratina)的系统发生组学和生物地理学。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-06-17 DOI: 10.1016/j.ympev.2024.108133
Trevor J.L. Sless , Michael G. Branstetter , Michael Mikát , Katherine A. Odanaka , Kerrigan B. Tobin , Sandra M. Rehan

Small carpenter bees in the genus Ceratina are behaviourally diverse, species-rich, and cosmopolitan, with over 370 species and a range including all continents except Antarctica. Here, we present the first comprehensive phylogeny of the genus based on ultraconserved element (UCE) phylogenomic data, covering a total of 185 ingroup specimens representing 22 of the 25 current subgenera. Our results support most recognized subgenera as natural groups, but we also highlight several groups in need of taxonomic revision – particularly the nominate subgenus Ceratina sensu stricto – and several clades that likely need to be described as new subgenera. In addition to phylogeny, we explore the evolutionary history of Ceratina through divergence time estimation and biogeographic reconstruction. Our findings suggest that Ceratinini split from its sister tribe Allodapini about 72 million years ago. The common ancestor of Ceratina emerged in the Afrotropical realm approximately 42 million years ago, near the Middle Eocene Climatic Optimum. Multiple subsequent dispersal events led to the present cosmopolitan distribution of Ceratina, with the majority of transitions occurring between the Afrotropics, Indomalaya, and the Palearctic. Additional movements also led to the arrival of Ceratina in Madagascar, Australasia, and a single colonization of the Americas. Dispersal events were asymmetrical overall, with temperate regions primarily acting as destinations for migrations from tropical source regions.

小木匠蜂属(Ceratina)行为多样、物种丰富且具有世界性,有 370 多个物种,分布范围包括除南极洲以外的所有大陆。在此,我们基于超保守元素(UCE)系统发生组数据首次提出了该属的全面系统发生,涵盖了代表目前 25 个亚属中 22 个亚属的总共 185 个内群标本。我们的研究结果支持大多数公认的亚属为自然类群,但我们也强调了几个需要进行分类学修订的类群--特别是严格意义上的提名亚属 Ceratina,以及几个可能需要描述为新亚属的支系。除了系统发育外,我们还通过分歧时间估计和生物地理重建来探索 Ceratina 的进化史。我们的研究结果表明,Ceratinini大约在7200万年前从其姊妹族Allodapini中分离出来。Ceratina 的共同祖先出现在大约 4200 万年前的非洲热带地区,接近中始新世气候最适宜期。随后的多次扩散事件导致了 Ceratina 目前的世界性分布,其中大部分过渡发生在非洲热带地区、印度河流域和古北区之间。其他的迁移还导致 Ceratina 来到马达加斯加、大洋洲和美洲的一次殖民。传播事件总体上是不对称的,温带地区主要是热带来源地区迁徙的目的地。
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Molecular Phylogenetics and Evolution
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