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An ultraconserved element probe set for velvet worms (Onychophora) 绒毛蠕虫(Onychophora)的超保守元素探针集。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-05-27 DOI: 10.1016/j.ympev.2024.108115
Shoyo Sato , Shahan Derkarabetian , Arianna Lord , Gonzalo Giribet

Onychophora are cryptic, soil-dwelling invertebrates known for their biogeographic affinities, diversity of reproductive modes, close phylogenetic relationship to arthropods, and peculiar prey capture mechanism. The 216 valid species of Onychophora are grouped into two families – Peripatopsidae and Peripatidae – and apart from a few relationships among major lineages within these two families, a stable phylogenetic backbone for the phylum has yet to be resolved. This has hindered our understanding of onychophoran biogeographic patterns, evolutionary history, and systematics. Neopatida, the Neotropical clade of peripatids, has proved particularly difficult, with recalcitrant nodes and low resolution, potentially due to rapid radiation of the group during the Cretaceous. Previous studies have had to compromise between number of loci and number of taxa due to limitations of Sanger sequencing and phylotranscriptomics, respectively. Additionally, aspects of their genome size and structure have made molecular phylogenetics difficult and data matrices have been affected by missing data. To address these issues, we leveraged recent, published transcriptomes and the first high quality genome for the phylum and designed a high affinity ultraconserved element (UCE) probe set for Onychophora. This new probe set, consisting of ∼ 20,000 probes that target 1,465 loci across both families, has high locus recovery and phylogenetic utility. Phylogenetic analyses recovered the monophyly of major clades of Onychophora and revealed a novel lineage from the Neotropics that challenges our current understanding of onychophoran biogeographic endemicity. This new resource could drastically increase the power of molecular datasets and potentially allow access to genomic scale data from archival museum specimens to further tackle the issues exasperating onychophoran systematics.

栉水母是隐居在土壤中的无脊椎动物,以其生物地理亲缘关系、繁殖方式的多样性、与节肢动物密切的系统发育关系以及奇特的猎物捕捉机制而闻名。Onychophora 的 216 个有效物种分为两个科 - Peripatopsidae 和 Peripatidae - 除了这两个科内的几个主要品系之间的关系外,该门类的稳定系统发育主干尚未确定。这阻碍了我们对泥鳅生物地理模式、进化史和系统学的了解。Neopatida,即新热带地区的围虫支系,被证明特别困难,其节点顽固,分辨率低,这可能是由于该类群在白垩纪的快速辐射造成的。由于桑格测序法和系统转录组学的限制,以前的研究不得不在基因位点数量和类群数量之间做出妥协。此外,它们的基因组大小和结构也给分子系统学研究带来了困难,数据矩阵也受到缺失数据的影响。为了解决这些问题,我们利用最近发表的转录组和该门的第一个高质量基因组,设计了一套亲和性很高的鬼爪蛙超保留元素(UCE)探针。这套新的探针组由 20,000 个探针组成,针对两个科的 1,465 个位点,具有很高的位点恢复能力和系统发育效用。系统发育分析恢复了缟栉水母主要支系的单系性,并揭示了一个来自新热带地区的新支系,该支系挑战了我们目前对缟栉水母生物地理特有性的理解。这一新资源可大大提高分子数据集的能力,并有可能从档案博物馆标本中获取基因组规模的数据,从而进一步解决困扰缟褶菌系统学的问题。
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引用次数: 0
Phylogenomic analyses revealed widely occurring hybridization events across Elsholtzieae (Lamiaceae) 系统发生组分析表明,Elsholtzieae(苎麻科)中广泛发生杂交事件。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-05-26 DOI: 10.1016/j.ympev.2024.108112
Yan Wang , Xuexue Wu , Yanyi Chen , Chao Xu , Yinghui Wang , Qiang Wang

Obtaining a robust phylogeny proves challenging due to the intricate evolutionary history of species, where processes such as hybridization and incomplete lineage sorting can introduce conflicting signals, thereby complicating phylogenetic inference. In this study, we conducted comprehensive sampling of Elsholtzieae, with a particular focus on its largest genus, Elsholtzia. We utilized 503 nuclear loci and complete plastome sequences obtained from 99 whole-genome sequencing datasets to elucidate the interspecific relationships within the Elsholtzieae. Additionally, we explored various sources of conflicts between gene trees and species trees. Fully supported backbone phylogenies were recovered, and the monophyly of Elsholtzia and Keiskea was not supported. Significant gene tree heterogeneity was observed at numerous nodes, particularly regarding the placement of Vuhuangia and the E. densa clade. Further investigations into potential causes of this discordance revealed that incomplete lineage sorting (ILS), coupled with hybridization events, has given rise to substantial gene tree discordance. Several species, represented by multiple samples, exhibited a closer association with geographical distribution rather than following a strictly monophyletic pattern in plastid trees, suggesting chloroplast capture within Elsholtzieae and providing evidence of hybridization. In conclusion, this study provides phylogenomic insights to untangle taxonomic problems in the tribe Elsholtzieae, especially the genus Elsholtzia.

由于物种的进化历史错综复杂,杂交和不完全世系分类等过程可能会带来相互矛盾的信号,从而使系统发育推断复杂化,因此获得稳健的系统发育具有挑战性。在本研究中,我们对 Elsholtzieae 进行了全面采样,尤其关注其最大的属 Elsholtzia。我们利用从 99 个全基因组测序数据集中获得的 503 个核基因位点和完整的质粒体序列来阐明 Elsholtzieae 的种间关系。此外,我们还探讨了基因树与物种树之间冲突的各种来源。我们恢复了完全支持的骨干系统发生,并否定了 Elsholtzia 和 Keiskea 的单系性。在许多节点上观察到了明显的基因树异质性,尤其是在 Vuhuangia 和 E. densa 支系的位置上。对造成这种不一致性的潜在原因的进一步研究表明,不完全的世系分类(ILS),加上古代和近期的杂交事件,造成了基因树的严重不一致性。由多个样本代表的几个物种表现出与地理分布更密切的联系,而不是在质体树中遵循严格的单系模式,这表明在 Elsholtzieae 中叶绿体的捕获量很大,并提供了杂交的证据。总之,本研究为解开 Elsholtzieae 族,尤其是 Elsholtzia 属的分类问题提供了系统发生学的见解。
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引用次数: 0
Phylogeny and historical biogeography of the swallow family (Hirundinidae) inferred from comparisons of thousands of UCE loci 通过比较数千个 UCE 位点推断燕科(Hirundinidae)的系统发育和历史生物地理学。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-05-25 DOI: 10.1016/j.ympev.2024.108111
Drew R. Schield , Clare E. Brown , Subir B. Shakya , Gina M. Calabrese , Rebecca J. Safran , Frederick H. Sheldon

Swallows (Hirundinidae) are a globally distributed family of passerine birds that exhibit remarkable similarity in body shape but tremendous variation in plumage, sociality, nesting behavior, and migratory strategies. As a result, swallow species have become models for empirical behavioral ecology and evolutionary studies, and variation across the Hirundinidae presents an excellent opportunity for comparative analyses of trait evolution. Exploiting this potential requires a comprehensive and well-resolved phylogenetic tree of the family. To address this need, we estimated swallow phylogeny using genetic data from thousands of ultraconserved element (UCE) loci sampled from nearly all recognized swallow species. Maximum likelihood, coalescent-based, and Bayesian approaches yielded a well-resolved phylogenetic tree to the generic level, with minor disagreement among inferences at the species level, which likely reflect ongoing population genetic processes. The UCE data were particularly useful in helping to resolve deep nodes, which previously confounded phylogenetic reconstruction efforts. Divergence time estimates from the improved swallow tree support a Miocene origin of the family, roughly 13 million years ago, with subsequent diversification of major groups in the late Miocene and Pliocene. Our estimates of historical biogeography support the hypothesis that swallows originated in the Afrotropics and have subsequently expanded across the globe, with major in situ diversification in Africa and a secondary major radiation following colonization of the Neotropics. Initial examination of nesting and sociality indicates that the origin of mud nesting – a relatively rare nest construction phenotype in birds – was a major innovation coincident with the origin of a clade giving rise to over 40% of extant swallow diversity. In contrast, transitions between social and solitary nesting appear less important for explaining patterns of diversification among swallows.

燕子(Hirundinidae)是一个分布于全球的雀形目鸟类家族,它们的体形非常相似,但在羽毛、社会性、筑巢行为和迁徙策略方面却存在巨大差异。因此,燕科物种已成为行为生态学和进化研究的实证模型,燕科的变异为性状进化的比较分析提供了绝佳的机会。要挖掘这一潜力,就需要建立一个全面、清晰的燕科系统发生树。为了满足这一需求,我们利用从几乎所有公认的燕子物种中采样的数千个超保留元素(UCE)位点的遗传数据估算了燕子的系统发生。最大似然法、基于聚合法和贝叶斯法得出的系统发生树在通属水平上得到了很好的解析,在物种水平上的推断之间存在较小的分歧,这可能反映了正在进行的种群遗传过程。UCE 数据在帮助解决深节点方面特别有用,而这些节点以前曾给系统发育重建工作带来困惑。根据改良的燕子树估计的分化时间支持该科起源于中新世,距今约 1300 万年,主要类群随后在中新世晚期和上新世发生了分化。我们对历史生物地理学的估计支持这样的假设,即燕子起源于非洲热带地区,随后扩展到全球各地,主要在非洲就地分化,并在新热带地区殖民化后进行二次大辐射。对筑巢和社会性的初步研究表明,泥巢--一种鸟类中相对罕见的筑巢表型--的起源是一个重大创新,它与产生现存燕子多样性 40% 以上的一个支系的起源相吻合。相比之下,社会性筑巢和独居筑巢之间的过渡对于解释燕子的多样化模式似乎并不那么重要。
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引用次数: 0
Phylogenomic data exploration with increased sampling provides new insights into the higher-level relationships of butterflies and moths (Lepidoptera) 通过增加取样进行系统发生组数据探索,对蝴蝶和蛾类(鳞翅目)的高层关系有了新的认识
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-05-23 DOI: 10.1016/j.ympev.2024.108113
Qi Chen , Min Deng , Xuan Dai , Wei Wang , Xing Wang , Liu-Sheng Chen , Guo-Hua Huang

A robust and stable phylogenetic framework is a fundamental goal of evolutionary biology. As the third largest insect order in the world following Coleoptera and Diptera, Lepidoptera (butterflies and moths) play a central role in almost every terrestrial ecosystem as indicators of environmental change and serve as important models for biologists exploring questions related to ecology and evolutionary biology. However, for such a charismatic insect group, the higher-level phylogenetic relationships among its superfamilies are still poorly resolved. Compared to earlier phylogenomic studies, we increased taxon sampling among Lepidoptera (37 superfamilies and 68 families containing 263 taxa) and acquired a series of large amino-acid datasets from 69,680 to 400,330 for phylogenomic reconstructions. Using these datasets, we explored the effect of different taxon sampling with significant increases in the number of included genes on tree topology by considering a series of systematic errors using maximum-likelihood (ML) and Bayesian inference (BI) methods. Moreover, we also tested the effectiveness in topology robustness among the three ML-based models. The results showed that taxon sampling is an important determinant in tree robustness of accurate lepidopteran phylogenetic estimation. Long-branch attraction (LBA) caused by site-wise heterogeneity is a significant source of bias giving rise to unstable positions of ditrysian groups in phylogenomic reconstruction. Phylogenetic inference showed the most comprehensive framework to reveal the relationships among lepidopteran superfamilies, and presented some newly relationships with strong supports (Papilionoidea was sister to Gelechioidea and Immoidea was sister to Galacticoidea, respectively), but limited by taxon sampling, the relationships within the species-rich and relatively rapid radiation Ditrysia and especially Apoditrysia remain poorly resolved, which need to increase taxon sampling for further phylogenomic reconstruction. The present study demonstrates that taxon sampling is an important determinant for an accurate lepidopteran tree of life and provides some essential insights for future lepidopteran phylogenomic studies.

一个强大而稳定的系统发育框架是进化生物学的基本目标。作为继鞘翅目和双翅目之后的世界第三大昆虫目,鳞翅目(蝶类和蛾类)在几乎所有陆地生态系统中都扮演着重要角色,是环境变化的指标,也是生物学家探索生态学和进化生物学相关问题的重要模型。然而,对于这样一个极具魅力的昆虫类群,其超科之间较高层次的系统发育关系仍然没有得到很好的解决。与早期的系统发生组研究相比,我们增加了鳞翅目昆虫的分类群取样(37 个超科和 68 个科,包含 263 个分类群),并获得了一系列从 69,680 到 400,330 的大型氨基酸数据集,用于系统发生组重建。利用这些数据集,我们采用最大似然法(ML)和贝叶斯推断法(BI),通过考虑一系列系统误差,探索了不同类群取样、所含基因数量显著增加对树拓扑结构的影响。此外,我们还测试了基于 ML 的三种模型在拓扑稳健性方面的有效性。结果表明,分类群取样是准确估计鳞翅目昆虫系统发生树稳健性的重要决定因素。位点异质性引起的长分支吸引(LBA)是导致系统发生重建中二尖杉类群位置不稳定的重要偏差来源。系统发生学推断为揭示鳞翅目超科之间的关系提供了最全面的框架,并提出了一些新的具有强支持的关系(Papilionoidea与Gelechioidea是姊妹科,Immoidea与Galacticoidea是姊妹科),但受分类群取样的限制,物种丰富且辐射相对较快的双翅目(Ditrysia),尤其是钝翅目(Apoditrysia)内部的关系仍然没有得到很好的解析,需要增加分类群取样以进一步重建系统发生学。本研究表明,分类群取样是准确构建鳞翅目生命树的重要决定因素,并为今后的鳞翅目系统发生组学研究提供了一些重要的启示。
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引用次数: 0
Dynamics and timing of diversification events of ciliated eukaryotes from a large phylogenomic perspective 从大型系统发生组的角度看纤毛真核生物多样化事件的动态和时间。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-05-19 DOI: 10.1016/j.ympev.2024.108110
Chuanqi Jiang , Siyu Gu , Tingting Pan , Xueyan Wang , Weiwei Qin , Guangying Wang , Xinxin Gao , Jing Zhang , Kai Chen , Alan Warren , Jie Xiong , Wei Miao

Ciliophora, an exceptionally diverse lineage of unicellular eukaryotes, exhibits a remarkable range of species richness across classes in the ciliate Tree of Life. In this study, we have acquired transcriptome and genome data from 40 representative species in seven ciliate classes. Utilizing 247 genes and 105 taxa, we devised a comprehensive phylogenomic tree for Ciliophora, encompassing over 60 % of orders and constituting the most extensive dataset of ciliate species to date. We established a robust phylogenetic framework that encompasses ambiguous taxa and the major classes within the phylum. Our findings support the monophyly of each of two subphyla (Postciliodesmatophora and Intramacronucleata), along with three subclades (Protocruzia, CONTHREEP, and SAPML) nested within Intramacronucleata, and elucidate evolutionary positions among the major classes within the phylum. Drawing on the robust ciliate Tree of Life and three constraints, we estimated the radiation of Ciliophora around 1175 Ma during the middle of the Proterozoic Eon, and most of the ciliate classes diverged from their sister lineage during the latter half of this period. Additionally, based on the time-calibrated tree and species richness pattern, we investigated net diversification rates of Ciliophora and its classes. The global net diversification rate for Ciliophora was estimated at 0.004979 species/Ma. Heterogeneity in net diversification rates was evident at the class level, with faster rates observed in Oligohymenophorea and Spirotrichea than other classes within the subclades CONTHREEP and SAPML, respectively. Notably, our analysis suggests that variations in net diversification rates, rather than clade ages, appear to contribute to the differences in species richness in Ciliophora at the class level.

纤毛虫是一种异常多样化的单细胞真核生物,在纤毛虫生命树的不同类别中表现出惊人的物种丰富性。在这项研究中,我们获得了 7 个纤毛虫类中 40 个代表性物种的转录组和基因组数据。利用 247 个基因和 105 个类群,我们为纤毛虫设计了一个全面的系统发生树,涵盖了 60% 以上的目,是迄今为止最广泛的纤毛虫物种数据集。我们建立了一个稳健的系统发育框架,涵盖了纤毛虫门中的模糊类群和主要类群。我们的研究结果支持两个亚门(后纤毛虫门(Postciliodesmatophora)和内纤毛虫门(Intramacronucleata))以及嵌套于内纤毛虫门的三个亚支系(Protocruzia、CONTHREEP和SAPML)的单系性,并阐明了纤毛虫门主要类群之间的进化位置。根据强大的纤毛虫生命树和三个约束条件,我们估计纤毛虫的辐射时间约为 1175 Ma,处于原生代中期,大多数纤毛虫类都是在这一时期的后半期从它们的姊妹系分化出来的。此外,根据时间校准树和物种丰富度模式,我们研究了纤毛虫及其类别的净分化率。据估计,纤毛虫的全球净多样化率为 0.004979 种/Ma。净变异率的异质性在类的水平上非常明显,在 CONTHREEP 亚类群和 SAPML 亚类群中,Oligohymenophorea 和 Spirotrichea 的净变异率分别快于其他类群。值得注意的是,我们的分析表明,净变异率的变化,而不是支系年龄的变化,似乎是造成纤毛虫类物种丰富度差异的原因。
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引用次数: 0
Phylogeny and biogeography of harmochirine jumping spiders (Araneae: Salticidae) 哈莫奇林跳蛛(Araneae: Salticidae)的系统发育和生物地理学。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-05-18 DOI: 10.1016/j.ympev.2024.108109
Guilherme H.F. Azevedo , Marshal Hedin , Wayne P. Maddison

We use ultraconserved elements (UCE) and Sanger data to study the phylogeny, age, and biogeographical history of harmochirine jumping spiders, a group that includes the species-rich genus Habronattus, whose remarkable courtship has made it the focus of studies of behaviour, sexual selection, and diversification. We recovered 1947 UCE loci from 43 harmochirine taxa and 4 outgroups, yielding a core dataset of 193 UCEs with at least 50 % occupancy. Concatenated likelihood and ASTRAL analyses confirmed the separation of harmochirines into two major clades, here designated the infratribes Harmochirita and Pellenita. Most are African or Eurasian with the notable exception of a clade of pellenites containing Habronattus and Pellenattus of the Americas and Havaika and Hivanua of the Pacific Islands. Biogeographical analysis using the DEC model favours a dispersal of the clade’s ancestor from Eurasia to the Americas, from which Havaika’s ancestor dispersed to Hawaii and Hivanua’s ancestor to the Marquesas Islands. Divergence time analysis on 32 loci with 85 % occupancy, calibrated by fossils and island age, dates the dispersal to the Americas at approximately 4 to 6 million years ago. The explosive radiation of Habronattus perhaps began only about 4 mya. The phylogeny clarifies both the evolution of sexual traits (e.g., the terminal apophyses was enlarged in Pellenes and not subsequently lost) and the taxonomy. Habronattus is confirmed as monophyletic. Pellenattus is raised to the status of genus, and 13 species moved into it as new combinations. Bianor stepposus Logunov, 1991 is transferred to Sibianor, and Pellenes bulawayoensis Wesołowska, 1999 is transferred to Neaetha. A molecular clock rate estimate for spider UCEs is presented and its utility to inform prior distributions is discussed.

我们利用超保留元件(UCE)基因组数据来研究哈莫奇林跳蛛的系统发育、年龄和生物地理历史,哈莫奇林跳蛛包括物种丰富的哈莫奇林跳蛛属,其非凡的求偶行为使其成为行为、性选择和多样化研究的焦点。我们从 43 个跳蛛类群和 4 个外群中恢复了 1947 个 UCE 位点,得到了一个包含 193 个 UCE 位点的核心数据集,这些位点的占有率至少为 50%。合并似然法和 ASTRAL 分析证实,姬蛙类分为两大支系,即 Harmochirita 下支系和 Pellenita 下支系。除了包含美洲 Habronattus 和 Pellenattus 以及太平洋岛屿 Havaika 和 Hivanua 的 Pellenites 支系之外,大多数支系都属于非洲或欧亚大陆。利用 DEC 模型进行的生物地理学分析表明,该支系的祖先从欧亚大陆扩散到美洲,Havaika 的祖先从美洲扩散到夏威夷,Hivanua 的祖先从夏威夷扩散到马克萨斯群岛。在化石和岛屿年龄的校准下,对 32 个占有率为 85% 的位点进行的发散时间分析表明,向美洲扩散的时间约为 400 万至 600 万年前。Habronattus的爆炸性辐射可能在距今约400万年前才开始。该系统发育阐明了有性特征的进化(例如,Pellenes 的末端骨节增大,随后并未消失)和分类学。Habronattus 被确认为单系。Pellenattus 属被提升为属,13 个物种作为新的组合移入该属。Bianor stepposus Logunov, 1991 被归入 Sibianor,Pellenes bulawayoensis Wesołowska, 1999 被归入 Neaetha。本文对蜘蛛 UCEs 的分子钟速率进行了估计,并讨论了其在提供先验分布信息方面的实用性。
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引用次数: 0
Phylogenomics including new sequence data of phytoplankton-infecting chytrids reveals multiple independent lifestyle transitions across the phylum 包括浮游植物感染糜烂丝虫新序列数据在内的系统发生组学揭示了整个糜烂丝虫门多种独立生活方式的转变。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-05-14 DOI: 10.1016/j.ympev.2024.108103
Pauline C. Thomé , Justyna Wolinska , Silke Van Den Wyngaert , Albert Reñé , Doris Ilicic , Ramsy Agha , Hans-Peter Grossart , Esther Garcés , Michael T. Monaghan , Jürgen F.H. Strassert

Parasitism is the most common lifestyle on Earth and has emerged many times independently across the eukaryotic tree of life. It is frequently found among chytrids (Chytridiomycota), which are early-branching unicellular fungi that feed osmotrophically via rhizoids as saprotrophs or parasites. Chytrids are abundant in most aquatic and terrestrial environments and fulfil important ecosystem functions. As parasites, they can have significant impacts on host populations. They cause global amphibian declines and influence the Earth’s carbon cycle by terminating algal blooms. To date, the evolution of parasitism within the chytrid phylum remains unclear due to the low phylogenetic resolution of rRNA genes for the early diversification of fungi, and because few parasitic lineages have been cultured and genomic data for parasites is scarce. Here, we combine transcriptomics, culture-independent single-cell genomics and a phylogenomic approach to overcome these limitations. We newly sequenced 29 parasitic taxa and combined these with existing data to provide a robust backbone topology for the diversification of Chytridiomycota. Our analyses reveal multiple independent lifestyle transitions between parasitism and saprotrophy among chytrids and multiple host shifts by parasites. Based on these results and the parasitic lifestyle of other early-branching holomycotan lineages, we hypothesise that the chytrid last common ancestor was a parasite of phytoplankton.

寄生是地球上最常见的生活方式,在真核生物生命树上曾多次独立出现。糜生真菌(糜生菌群)是一种早期分支单细胞真菌,通过根状茎吸水或寄生。糜状寄生虫在大多数水生和陆生环境中都很丰富,具有重要的生态系统功能。作为寄生虫,它们会对宿主种群产生重大影响。它们会导致全球两栖动物数量减少,并通过终止藻类大量繁殖来影响地球的碳循环。迄今为止,由于真菌早期多样化的 rRNA 基因的系统发育分辨率较低,而且很少有寄生虫品系被培养出来,寄生虫的基因组数据也很少,因此糜烂菌门内的寄生性进化仍不清楚。在这里,我们将转录组学、独立于培养的单细胞基因组学和系统发生组学方法结合起来,以克服这些局限性。我们对 29 个寄生类群进行了新的测序,并将这些数据与现有数据相结合,为蜱霉菌群的多样化提供了一个强大的骨干拓扑结构。我们的分析揭示了糜状寄生菌在寄生和吸附之间的多种独立生活方式转变,以及寄生虫的多种宿主转移。基于这些结果以及其他早期分支全真菌纲各系的寄生生活方式,我们推测糜皮虫的最后共同祖先是浮游植物的寄生虫。
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引用次数: 0
Substrate specialisation drives an unexpectedly diverse radiation in barking geckos (Ptenopus: Gekkonidae) 底栖生物的特化推动了树皮壁虎(Ptenopus: Gekkonidae)出人意料的多样化辐射。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-05-14 DOI: 10.1016/j.ympev.2024.108104
Francois S. Becker , Graham J. Alexander , Krystal A. Tolley

Barking geckos (genus Ptenopus) are terrestrial, burrowing lizards endemic to southern Africa, currently with three recognised species. Two species are range-restricted (P. kochi and P. carpi) and display clear differences in substrate preference (soft sand vs. hard gravel). The third and most widespread species, P. garrulus, occurs on a variety of substrates of differing hardness, across potential geographic barriers, and over a steep climatic gradient. Variations in morphology and advertisement calls indicates that P. garrulus may be a species complex. Two subspecies of P. garrulus are currently recognised: P. g. maculatus and P. g. garrulus. To investigate species boundaries, we produced the first comprehensive phylogeny for the genus. We used a novel application of multiple regression on matrices models to assess multiple environmental drivers of diversification, as contrasted to isolation by distance. We show that P. kochi, P. carpi, and P. g. garrulus are valid species, but that P. g. maculatus is a paraphyletic complex of five previously unrecognised taxa. Specialisation onto different substrates was likely the main driver of divergence, with parapatric occurrence of two to four clades occurring at each of the three substrate transition zones identified a priori. The region encompasses diverse bioclimatic regions and potential geographic barriers, and these likely played a role in some divergence events.

树皮壁虎(Ptenopus 属)是南部非洲特有的陆生穴居蜥蜴,目前有三个已知物种。其中两个物种(P. kochi 和 P. carpi)的分布范围受到限制,对底质的偏好(软沙与硬砾石)存在明显差异。第三种也是分布最广的一种,P. garrulus,生活在各种不同硬度的基质上,跨越潜在的地理障碍,并具有陡峭的气候梯度。形态和广告叫声的变化表明 P. garrulus 可能是一个物种复合体。目前已确认的 P. garrulus 有两个亚种:g. maculatus 和 P. g. garrulus。为了研究物种界限,我们首次为该属建立了全面的系统进化关系。我们采用了矩阵模型多元回归的新方法来评估物种多样化的多种环境驱动因素,这与通过距离进行隔离的方法形成了鲜明对比。我们发现 P. kochi、P. carpi 和 P. g. garrulus 都是有效的物种,但 P. g. maculatus 是由五个以前未被发现的类群组成的旁系复合体。对不同基质的特化可能是分化的主要驱动因素,在先验确定的三个基质过渡区中,每个过渡区都有 2 到 4 个支系的类群出现。该地区包括不同的生物气候区和潜在的地理障碍,这些可能在某些分化事件中起到了一定的作用。
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引用次数: 0
Population structure in Mixornis tit-babblers across Sunda Shelf matches interfluvia of paleo-rivers 整个巽他陆架的山雀(Mixornis tit-babberers)种群结构与古河口鱼群的界面相吻合。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-05-14 DOI: 10.1016/j.ympev.2024.108105
Laura Marie Berman , Meng Yue Wu , Pratibha Baveja , Emilie Cros , Yong Chee Keita Sin , Dewi M. Prawiradilaga , Frank E. Rheindt

Rivers constitute an important biogeographic divide in vast areas of tropical rainforest, such as the Amazon and Congo Basins. Southeast Asia’s rainforests are currently fragmented across islands divided by sea, which has long obscured their extensive history of terrestrial connectivity as part of a vast (but now submerged) subcontinent – Sundaland – during most of the Quaternary. The role of paleo-rivers in determining population structure in Sundaic rainforests at a time when these forests were connected remains little understood. We examined the coloration of museum skins and used the genomic DNA of museum samples and freshly-collected blood tissue of a pair of Sundaic songbird species, the pin-striped and bold-striped tit-babblers (Mixornis gularis and M. bornensis, respectively), to assess the genetic affinity of populations on small Sundaic islands that have largely been ignored by modern research. Our genomic and morphological results place the populations from the Anambas and Natuna Islands firmly within M. gularis from the Malay Peninsula in western Sundaland, even though some of these islands are geographically much closer to Borneo, where M. bornensis resides. Our results reveal genetic structure consistent with the course of Sundaic paleo-rivers and the location of the interfluvia they formed, and add to a small but growing body of evidence that rivers would have been of equal biogeographic importance in Sundaland’s former connected forest landscape as they are in Amazonia and the Congo Basin today.

河流是亚马逊河流域和刚果河流域等广大热带雨林地区重要的生物地理分界线。东南亚的热带雨林目前分散在被海洋分割的岛屿上,这长期以来掩盖了它们在第四纪的大部分时间里作为一个广阔(但现在已被淹没)次大陆--巽他兰--的一部分而与陆地相连接的广泛历史。在巽他雨林相互连接的时期,古河口动物在决定巽他雨林种群结构方面的作用仍然鲜为人知。我们研究了博物馆皮肤的颜色,并利用博物馆样本和新鲜采集的一对巽他鸣禽物种--细条纹山雀和粗条纹山雀(分别为 Mixornis gularis 和 M. bornensis)--的血液组织的基因组 DNA 来评估巽他小岛上种群的遗传亲缘关系,这些种群在很大程度上被现代研究忽视了。我们的基因组学和形态学结果将阿南巴斯群岛和纳土纳群岛的种群牢牢地归属于来自西巽他半岛马来半岛的M.我们的研究结果与巽他古河流的流向以及它们所形成的交汇处的位置是一致的,并且为越来越多的少量证据增添了新的内容,这些证据表明,在巽他兰曾经相连的森林景观中,河流的生物地理重要性与今天在亚马孙和刚果盆地的河流的生物地理重要性是相同的。
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引用次数: 0
Of sea, rivers and symbiosis: Diversity, systematics, biogeography and evolution of the deeply diverging florideophycean order Hildenbrandiales (Rhodophyta) 海洋、河流与共生:深度分化的花叶目 Hildenbrandiales(红藻纲)的多样性、系统学、生物地理学和进化。
IF 4.1 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-05-13 DOI: 10.1016/j.ympev.2024.108106
Christophe Vieira , Cody M. Brooks , Shingo Akita , Myung Sook Kim , Gary W. Saunders

The Hildenbrandiales, a typically saxicolous red algal order, is an early diverging florideophycean group with global significance in marine and freshwater ecosystems across diverse temperature zones. To comprehensively elucidate the diversity, phylogeny, biogeography, and evolution of this order, we conducted a thorough re-examination employing molecular data derived from nearly 700 specimens. Employing a species delimitation method, we identified Evolutionary Species Units (ESUs) within the Hildenbrandiales aiming to enhance our understanding of species diversity and generate the first time-calibrated tree and ancestral area reconstruction for this order. Mitochondrial cox1 and chloroplast rbcL markers were used to infer species boundaries, and subsequent phylogenetic reconstructions involved concatenated sequences of cox1, rbcL, and 18S rDNA. Time calibration of the resulting phylogenetic tree used a fossil record from a Triassic purportedly freshwater Hildenbrandia species and three secondary time points from the literature. Our species delimitation analysis revealed an astounding 97 distinct ESUs, quintupling the known diversity within this order. Our time-calibration analysis placed the origin of Hildenbrandiales (crown age) in the Ediacaran period, with freshwater species emerging as a monophyletic group during the later Permian to early Triassic. Phylogenetic reconstructions identified seven major clades, experiencing early diversification during the Silurian to Carboniferous period. Two major evolutionary events—colonization of freshwater habitats and obligate systemic symbiosis with a marine fungus—marked this order, leading to significant morphological alterations without a commensurate increase in species diversification. Despite the remarkable newly discovered diversity, the extant taxon diversity appears relatively constrained when viewed against an evolutionary timeline spanning over 800 million years. This limitation may stem from restricted geographic sampling or the prevalence of asexual reproduction. However, species richness estimation and rarefaction analyses suggest a substantially larger diversity yet to be uncovered—potentially four times greater. These findings drastically reshape our understanding of the deeply diverging florideophycean order Hildenbrandiales species diversity, and contribute valuable insights into this order's evolutionary history and ecological adaptations. Supported by phylogenetic, ecological and morphological evidence, we established the genus Riverina gen. nov. to accommodate freshwater species of Hildenbrandiales, which form a monophyletic clade in our analyses. This marks the first step toward refining the taxonomy of the Hildenbrandiales, an order demanding thorough revisions, notably with the creation of several genera to address the polyphyletic status of Hildenbrandia. However, the limited diagnostic features pose a challe

红藻纲(Hildenbrandiales)是一个典型的沙色红藻目,是一个早期分化的花叶藻类,在不同温度带的海洋和淡水生态系统中具有全球意义。为了全面阐明该目藻的多样性、系统发育、生物地理学和进化,我们利用从近 700 个标本中获得的分子数据进行了全面的重新研究。通过物种划分方法,我们确定了 Hildenbrandiales 目中的物种进化单位(ESUs),旨在加强我们对物种多样性的理解,并首次为该目生成了时间校准树和祖先区域重建。线粒体 cox1 和叶绿体 rbcL 标记被用来推断物种边界,随后的系统发育重建涉及 cox1、rbcL 和 18S rDNA 的连接序列。系统发生树的时间校准使用了三叠纪一个据称是淡水的 Hildenbrandia 物种的化石记录和文献中的三个次要时间点。我们的物种划界分析发现了令人震惊的 97 个不同的 ESU,是该目已知多样性的五倍。我们的时间校准分析将 Hildenbrandiales 的起源(冠年龄)置于埃迪卡拉纪,淡水物种在二叠纪晚期至三叠纪早期作为单系群出现。系统发育重建确定了七个主要支系,它们在志留纪至石炭纪期间经历了早期分化。两个主要的进化事件--淡水栖息地的殖民化和与海洋真菌的强制性系统共生--标志着这个类群,导致其形态发生了显著变化,但物种多样性却没有相应增加。尽管新发现的物种多样性令人瞩目,但从跨越 8 亿多年的进化时间轴来看,现存类群的多样性似乎相对有限。这种限制可能源于有限的地理取样或无性繁殖的盛行。然而,物种丰富度估算和稀有度分析表明,还有更大的多样性有待发掘--可能比现在多四倍。这些发现极大地重塑了我们对深度分化的花叶纲物种多样性的认识,并为该纲的进化历史和生态适应性提供了宝贵的见解。在系统发生学、生态学和形态学证据的支持下,我们建立了新河属(Riverina gen. nov.这标志着我们朝着完善 Hildenbrandiales 目分类学迈出了第一步,这项工作需要进行彻底的修订,特别是要建立几个属来解决 Hildenbrandia 的多系地位问题。然而,有限的诊断特征带来了挑战,需要一种全新的方法来定义属。一个潜在的解决方案是采用分子系统学的观点,它可以精确划分分类学的界限。
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引用次数: 0
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Molecular Phylogenetics and Evolution
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