Molecular Phylogenetics and Evolution最新文献_第4页

Molecular phylogenetic and estimation of evolutionary divergence and biogeography of the family Schizoparmaceae and allied families (Diaporthales, Ascomycota) Schizoparmaceae 科及其相关科（Diaporthales, Ascomycota）的分子系统发育和进化分异及生物地理学估计。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-10-03 DOI: 10.1016/j.ympev.2024.108211

Taichang Mu , Yongsheng Lin , Huili Pu , Nemat O. Keyhani , Yuxiao Dang , Huajun Lv , Zhiying Zhao , Zhiang Heng , Ziyi Wu , Chengjie Xiong , Longbing Lin , Yuxi Chen , Hailan Su , Xiayu Guan , Junzhi Qiu

The Diaporthales includes 32 families, many of which are important plant pathogens, endophytes and saprobes, e.g., members of the families Pseudoplagiostomataceae, Pyrisporaceae and Schizoparmaceae. Nucleotide sequences derived from five genetic loci including: ITS, LSU, TEF1-α, TUB2 and RPB2 were used for Bayesian evolutionary analysis to determine divergence times and evolutionary relationships within the Schizoparmaceae. Molecular clock analyses revealed that the ancestor of Schizoparmaceae split during the Upper Cretaceous period approximately 75.7 Mya (95 % highest posterior density of 60.3–91.3 Mya). Reconstructing ancestral state in phylogenies (RASP) with using the Bayesian Binary Markov chain Monte Carlo (BBM) Method to reconstruct the historical biogeography for the family Schizoparmaceae indicated its most likely origin in Africa. Based on taxonomic and phylogenetic analyses, the Pseudoplagiostomataceae and Pyrisporaceae relationships were clarified and a total of four species described herein. For Pseudoplagiostomataceae, three new species and one known species that include, Pseudoplagiostoma fafuense sp. nov., Ps. ilicis sp. nov., Ps. sanmingense sp. nov. and Ps. bambusae are described and a key of Pseudoplagiostomataceae is provided. With respect to Pyrisporaceae, we considered Pseudoplagiostoma castaneae to be a synonym of Pyrispora castaneae. In addition, a new species of Schizoparmaceae, Coniella fujianensis sp. nov. is described and illustrated.

Diaporthales 包括 32 个科，其中许多科都是重要的植物病原体、内生菌和酵母菌，如假柄菌科、锈菌科和五味子科的成员。核苷酸序列来自五个基因位点，包括ITS, LSU, TEF1-α, TUB2 和 RPB2 等五个基因位点的核苷酸序列被用于贝叶斯进化分析，以确定五味子科的分化时间和进化关系。分子钟分析表明，五味子科的祖先分裂于上白垩纪，约75.7百万年（95%最高后验密度为60.3-91.3百万年）。利用贝叶斯二元马尔科夫链蒙特卡洛法（BBM）重建系统发育中的祖先状态（RASP），重建了五味子科的历史生物地理学，表明其最有可能起源于非洲。根据分类学和系统发生学分析，明确了假柄孢科（Pseudoplagiostomataceae）和糙叶孢科（Pyrisporaceae）的关系，共描述了 4 个物种。在假柄孢科方面，描述了三个新种和一个已知种，包括 Ps.关于拟盘孢科，我们认为 Pseudoplagiostoma castaneae 是 Pyrispora castaneae 的异名。此外，我们还描述了 Schizoparmaceae 的一个新种 Coniella fujianensis sp.

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引用次数: 0

Transcriptomic data support phylogenetic congruence and reveal genomic changes associated with the repeated evolution of annualism in aplocheiloid killifishes (Cyprinodontiformes) 转录组数据支持系统发育的一致性，并揭示了与鲤形目鳉鱼一年生反复进化相关的基因组变化。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-10-02 DOI: 10.1016/j.ympev.2024.108209

Andrew W. Thompson , Amanda C. Black , Yu Huang , Qiong Shi , Andrew I. Furness , Ingo Braasch , Federico G. Hoffmann , Guillermo Ortí

Repeated evolution of novel life histories that are correlated with ecological variables offers opportunities to study convergence in genetic, developmental, and metabolic features. Nearly half of the 800 species of Aplocheiloid killifishes, a clade of teleost fishes with a circumtropical distribution, are “annual” or seasonal species that survive in ephemeral bodies of water that desiccate and are unfeasible for growth, reproduction, or survival for weeks to months every year. But the repeated evolution of adaptations that are key features of the annual life history among these fishes remains poorly known without a robust phylogenetic framework. We present a large-scale phylogenomic reconstruction of aplocheiloid killifishes evolution using newly sequenced transcriptomes obtained from a diversity of killifish lineages representing putative independent origins of annualism. Ancestral state estimation shows that developmental dormancy (diapause), a key trait of the killifish annual life cycle, may have originated up to seven times independently among African and South American lineages. To further explore the genetic basis of this unique trait, we measure changes in evolutionary rates among orthologous genes across the killifish tree of life by quantifying codon evolution using dN/dS ratios. We show that some genes have higher dN/dS ratios in lineages leading to species with annual life history. Many of them constitute key developmental genes or nuclear-encoded metabolic genes that control oxidative phosphorylation. Lastly, we compare these genes with higher ω to genes previously associated to developmental dormancy and metabolic shifts in killifishes and other vertebrates, and thereby identify molecular evolutionary signatures of repeated transitions to extreme environments.

与生态变量相关的新生活史的重复进化为研究遗传、发育和代谢特征的趋同提供了机会。鳉鱼（Aplocheiloid killifishes）是分布在环热带地区的跃层鱼类的一个支系，在其 800 个物种中，有近一半是 "年生 "或季节性物种，它们生存在短暂的水体中，这些水体每年都会干涸数周至数月，无法生长、繁殖或生存。但是，如果没有一个强大的系统发育框架，人们对这些鱼类一年生活史的关键特征--适应性的反复进化仍然知之甚少。我们利用从代表年生生活的可能独立起源的不同杀鱼系中获得的新测序的转录组，提出了一个大规模的无尾杀鱼进化系统发生组重建。对始祖状态的估计表明，发育休眠（休眠期）是鳉鱼一年生活周期中的一个关键特征，可能在非洲和南美洲的鱼系中独立起源了多达七次。为了进一步探索这一独特性状的遗传基础，我们通过使用 dN/dS 比值量化密码子进化来测量整个鳉鱼生命树中同源基因之间进化率的变化。我们发现，在导致年生活史物种的世系中，一些基因的 dN/dS 比值较高。其中许多基因构成了关键的发育基因或控制氧化磷酸化的核编码代谢基因。最后，我们将这些ω较高的基因与之前在鳉鱼和其他脊椎动物中与发育休眠和代谢转变相关的基因进行了比较，从而确定了重复过渡到极端环境的分子进化特征。

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引用次数: 0

Museomics reveal origins of East African Pleophylla forest chafers and Miocene forest connectivity Museomics揭示了东非Pleophylla森林糠虾的起源和中新世森林的连通性。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-10-02 DOI: 10.1016/j.ympev.2024.108210

Lars Dietz , Sandra Kukowka , Jonas Eberle , Christoph Mayer , Oliver Niehuis , Lars Podsiadlowski , Dirk Ahrens

Here we present a nearly complete species-level phylogeny including 23 of the 25 known species of the forest-dwelling herbivorous scarab chafer beetle genus Pleophylla (Coleoptera: Scarabaeidae: Sericinae), based on the analysis of 950 nuclear genes (metazoan-level universal single-copy orthologs; mzl-USCOs). DNA sequences were obtained from freshly collected, ethanol-preserved samples and from dried museum specimens by target enrichment or genome shotgun sequencing. Alignment completeness of mzl-USCOs newly obtained here by target DNA enrichment of ethanol samples were very heterogenous and lower (29–62 %) than in Dietz et al. (2023a), while that of sequences recovered from dried samples was even lower (∼19 %). Alignment completeness of the sequences obtained from low coverage shotgun sequencing was highest (∼92 %), although the average coverage was much lower than for the target enrichment samples. We used the resulting phylogeny to reconstruct the historical biogeography of the group. To estimate a time-calibrated tree, we combined the mzl-USCO data of Pleophylla with a nucleotide alignment from an available transcriptomic dataset of Scarabaeoidea and used two different sets of secondary calibration points. Despite the problems associated with the capture rate of mzl-USCO sequences from museum specimens, we were able to infer a well-resolved phylogeny of the genus Pleophylla that also provided reliable estimates of the phylogenetic position of species for which we had little sequence data. Our study clearly identified South Africa as the geographic origin of Pleophylla. Timing and biogeographic history confirm a persistent fragmentation of forests since the Eocene. The occurrence of only one long-distance dispersal event from southern Africa to the Eastern African Arc even during the Miocene highlights the limited dispersal possibilities for these forest-adapted chafers, which do not seem to have had important northerly range expansions along hypothetical forest corridors during the Pleistocene.

在此，我们基于对950个核基因（元类动物级通用单拷贝直向同源物；mzl-USCOs）的分析，提出了一个近乎完整的物种级系统发育，其中包括25个已知物种中的23个。通过目标富集或基因组猎枪测序，从新鲜采集、乙醇保存的样本和干燥的博物馆标本中获得了 DNA 序列。与 Dietz 等人（2023a）的研究相比，本研究通过对乙醇样本进行目标 DNA 富集而新获得的 mzl-USCOs 序列的比对完整性非常不均匀且较低（29-62 %），而从干燥样本中获得的序列比对完整性更低（∼19 %）。从低覆盖率枪式测序中获得的序列的比对完整性最高（∼ 92 %），尽管平均覆盖率远低于目标富集样本。我们利用所得到的系统发生重建了该类群的历史生物地理学。为了估算时间校准树，我们将Pleophylla的mzl-USCO数据与Scarabaeoidea现有转录组数据集的核苷酸比对结合起来，并使用了两套不同的次级校准点。尽管博物馆标本的 mzl-USCO 序列捕获率存在问题，但我们仍能推断出一个清晰的 Pleophylla 属系统发生，同时还能对序列数据较少的物种的系统发生位置提供可靠的估计。我们的研究清楚地确定了南非是 Pleophylla 的地理起源地。时间和生物地理历史证实了自始新世以来森林的持续破碎化。即使在中新世期间，也只有一次从南部非洲到东非弧的长距离扩散事件，这突出表明了这些适应森林的螯足类的扩散可能性有限，在更新世期间，它们似乎并没有沿着假定的森林走廊向北扩展重要的分布区。

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引用次数: 0

Phylogeny and evolution of dissimilatory sulfite reduction in prokaryotes 原核生物中异氨亚硫酸盐还原的系统发育和进化。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-09-27 DOI: 10.1016/j.ympev.2024.108208

Yuxin Tao , Zichao Zeng , Yuhui Deng , Menghan Zhang , Fengping Wang , Yinzhao Wang

Sulfate is the second most common nonmetallic ion in modern oceans, as its concentration dramatically increased alongside tectonic activity and atmospheric oxidation in the Proterozoic. Microbial sulfate/sulfite metabolism, involving organic carbon or hydrogen oxidation, is linked to sulfur and carbon biogeochemical cycles. However, the coevolution of microbial sulfate/sulfite metabolism and Earth’s history remains unclear. Here, we conducted a comprehensive phylogenetic analysis to explore the evolutionary history of the dissimilatory sulfite reduction (Dsr) pathway. The phylogenies of the Dsr-related genes presented similar branching patterns but also some incongruencies, indicating the complex origin and evolution of Dsr. Among these genes, dsrAB is the hallmark of sulfur-metabolizing prokaryotes. Our detailed analyses suggested that the evolution of dsrAB was shaped by vertical inheritance and multiple horizontal gene transfer events and that selection pressure varied across distinct lineages. Dated phylogenetic trees indicated that key evolutionary events of dissimilatory sulfur-metabolizing prokaryotes were related to the Great Oxygenation Event (2.4–2.0 Ga) and several geological events in the “Boring Billion” (1.8–0.8 Ga), including the fragmentation of the Columbia supercontinent (approximately 1.6 Ga), the rapid increase in marine sulfate (1.3–1.2 Ga), and the Neoproterozoic glaciation event (approximately 1.0 Ga). We also proposed that the voluminous iron formations (approximately 1.88 Ga) might have induced the metabolic innovation of iron reduction. In summary, our study provides new insights into Dsr evolution and a systematic view of the coevolution of dissimilatory sulfur-metabolizing prokaryotes and the Earth’s environment.

硫酸盐是现代海洋中第二常见的非金属离子，因为在新生代，随着构造活动和大气氧化，硫酸盐的浓度急剧增加。涉及有机碳或氢氧化的微生物硫酸盐/亚硫酸盐代谢与硫和碳的生物地球化学循环有关。然而，微生物硫酸盐/亚硫酸盐代谢与地球历史的共同演化仍不清楚。在此，我们进行了全面的系统发育分析，以探索亚硫酸盐还原（Dsr）途径的进化历史。Dsr相关基因的系统发育呈现出相似的分支模式，但也存在一些不一致的地方，表明Dsr的起源和进化十分复杂。在这些基因中，dsrAB是硫代谢原核生物的标志。我们的详细分析表明，dsrAB 的进化是由垂直遗传和多个水平基因转移事件决定的，不同品系的选择压力也各不相同。有年代的系统发生树表明，异嗜硫代谢原核生物的关键进化事件与大富氧作用事件（2.4-2.0 Ga）和 "Boring Billion"（1.8-0.8 Ga）中的几个地质事件有关，包括哥伦比亚超大陆的破碎（约 1.6 Ga）、海洋硫酸盐的迅速增加（1.3-1.2 Ga）和新元古代冰川事件（约 1.0 Ga）。我们还提出，大量铁形成（约 1.88 Ga）可能诱发了铁还原的新陈代谢创新。总之，我们的研究为 Dsr 的演化提供了新的视角，并系统地揭示了异嗜硫代谢原核生物与地球环境的共同演化。

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引用次数: 0

Disentangling conflicting molecular phylogenetic signals in nuclear and plastid DNA of the western Eurasian-Mediterranean grass genus Cynosurus and its relatives (Poaceae subtribes Cynosurinae and Parapholiinae) 厘清欧亚-地中海西部禾本科草属（Cynosurus）及其近缘种（Poaceae 亚种 Cynosurinae 和 Parapholiinae）核DNA 和质粒 DNA 中相互矛盾的分子系统发育信号。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-09-26 DOI: 10.1016/j.ympev.2024.108204

Natalia Tkach , Sirus Leonard Rasti , Martin Röser

The western Eurasian-Mediterranean grass genus Cynosurus, comprising about 11 species, is morphologically well delimited by the regular occurrence of conspicuous sterile spikelets distal to the fertile ones on the outer, abaxial side of the inflorescences. However, our molecular phylogenetic study using nuclear ribosomal DNA (ITS, ETS) and plastid DNA sequences (trnL–F, matK) has shown that the genus is not monophyletic in its current delimitation, but consists of three distinct lineages. These lineages were found to be closely related to a group of 6–7 genera taxonomically assigned to the subtribe Parapholiinae. These Parapholiinae genera were consistently monophyletic in our analyses, but the suggested relationships to the three lineages of Cynosurus varied depending on the particular DNA region examined. This was the case for both plastid and nuclear DNA, with cytonuclear discordance and ‘chloroplast capture’ indicating earlier hybridization. Interestingly, hybridization also proved to be the most likely explanation even with regard to the 18S–26S cistrons of the nuclear ribosomal DNA, where an exceptional evolutionary divergence between ITS and ETS was found. The results highlight and illustrate the important role of hybridization in the evolution of grasses. In terms of taxonomy, our findings argue against maintaining a polyphyletic genus Cynosurus s.l. but instead argue for dividing it into three monophyletic genera: Cynosurus s.s., Falona, which is reestablished here, and Ciliochloa, which is described as a new genus. In addition, it is proposed that the two subtribes Cynosurinae and Parapholiinae be combined into a single subtribe Cynosurinae, which is also monophyletic. The possible genetic background of the formation of sterile spikelets and the occasional occurrence of inflorescences with consistently fertile spikelets are discussed. New combinations are Ciliochloa effusa, C. effusa var. obliquata, C. effusa var. fertilis, C. elegans, C. gracilis, C. turcomanica and Falona colorata.

西欧亚-地中海禾本科草属（Cynosurus）约有 11 个种，在花序外侧、背面的可育小穗远端经常出现明显的不育小穗，这在形态上很好地划分了该属。然而，我们利用核核糖体 DNA（ITS、ETS）和质体 DNA 序列（trnL-F、matK）进行的分子系统学研究表明，该属目前的划分不是单系的，而是由三个不同的系组成。研究发现，这些支系与在分类学上被归入 Parapholiinae 亚族的 6-7 个属密切相关。在我们的分析中，这些 Parapholiinae 属始终是单系的，但与 Cynosurus 的三个系的关系因所研究的 DNA 区域而异。质体和核 DNA 的情况都是如此，细胞核不一致和 "叶绿体捕获 "表明杂交较早。有趣的是，即使在核核糖体 DNA 的 18S-26S 三元组方面，杂交也被证明是最有可能的解释，因为在核核糖体 DNA 的 18S-26S 三元组中，ITS 和 ETS 之间存在特殊的进化差异。这些结果突出说明了杂交在禾本科植物进化过程中的重要作用。在分类学方面，我们的研究结果反对保留 Cynosurus s.l.这一多系属，而主张将其分为三个单系属：Cynosurus s.s.、Falona（在此重新确立）和 Ciliochloa（描述为一个新属）。此外，还建议将 Cynosurinae 和 Parapholiinae 两个亚族合并为单一的 Cynosurinae 亚族，该亚族也是单系的。讨论了不育小穗形成的可能遗传背景以及偶尔出现的具有持续可育小穗的花序。C. effusa var. obliquata、C. effusa var. fertilis、C. elegans、C. gracilis、C. turcomanica 和 Falona colorata。

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引用次数: 0

Historical biogeography and the evolution of habitat preference in the North American camel spider family, Eremobatidae (Arachnida:Solifugae) 北美骆驼蜘蛛科 Eremobatidae（蛛形纲： Solifugae）的历史生物地理学和栖息地偏好进化。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-09-19 DOI: 10.1016/j.ympev.2024.108193

Erika L. Garcia , Paula E. Cushing

Abiotic variables can influence species distributions, often restricting taxa to an acquired climatic signature or conversely, related species are conserved in the same ecological space over millions of years. An investigation into how abiotic change has shaped geographic distributions of taxa may be key to understanding diversification of lineages, and in the absence of reliable morphological characteristics, such information may support taxonomic units at multiple scales.

Here, we examine the historical biogeography and patterns of habitat preference within the North American solifuge family, Eremobatidae. A previous study demonstrated that a major taxonomic revision of Eremobatidae is warranted, however recent studies demonstrate high levels of morphological convergence within the group, thus a re-classification of generic boundaries using additional information must be prioritized before we can formally begin solid revisionary efforts. In this study, we aimed to reconstruct a well-resolved phylogenetic hypothesis of Eremobatidae by filtering UCE loci based on informativeness, by mitigating the effect of cogenic UCE on phylogenetic estimation, and by supplementing our curated UCE loci with mitochondrial information. Using our preferred topology, in conjunction with published estimated divergence dates for Eremobatidae, we inferred a time-calibrated phylogenetic hypothesis to inform the historical biogeography and patterns of habitat preference. The two major habitat types that were observed for Eremobatidae were warm deserts for early diverging taxa and a subsequent evolution to cold deserts and Mediterranean California ecoregions for later diverging taxa. Eremobatid niche space, determined by temperature and precipitation, has been conserved for at least 25 million years in North America, supporting a warm desert origin, and thus supporting high species richness in the Sonoran and Mexican Plateau. Overall, our study provides support for new generic level designations within Eremobatidae.

非生物变量会影响物种的分布，通常会将类群限制在后天的气候特征中，或者相反，相关物种在数百万年中保存在同一生态空间中。研究非生物变化如何影响类群的地理分布可能是了解类群多样化的关键，在缺乏可靠的形态特征的情况下，此类信息可能支持多种尺度的分类单元。在此，我们研究了北美溶岩科（Eremobatidae）的历史生物地理学和栖息地偏好模式。之前的一项研究表明，有必要对Eremobatidae进行一次重大的分类学修订，但最近的研究表明，该类群内部存在高度的形态学趋同，因此在正式开始扎实的修订工作之前，必须优先利用更多的信息对属界进行重新分类。在本研究中，我们根据信息量筛选 UCE 位点，减轻同源 UCE 对系统发育估计的影响，并利用线粒体信息补充我们策划的 UCE 位点，从而重建了 Eremobatidae 的系统发育假说。利用我们首选的拓扑结构，并结合已发表的 Eremobatidae 的估计分化日期，我们推断出了一个经过时间校准的系统发育假说，为历史生物地理学和栖息地偏好模式提供了信息。我们观察到 Eremobatidae 的两种主要栖息地类型：早期分化类群的栖息地是温暖的沙漠，而后期分化类群的栖息地则演变为寒冷的沙漠和地中海加利福尼亚生态区。由温度和降水决定的Eremobatid生态位空间在北美洲至少保存了2500万年，支持了温暖沙漠的起源，从而支持了索诺拉和墨西哥高原的高物种丰富性。总之，我们的研究为 Eremobatidae 新的属级命名提供了支持。

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引用次数: 0

The small and inconspicuous majority: Revealing the megadiversity and historical biogeography of the Pristimantis unistrigatus species group (Anura, Strabomantidae) 小而不起眼的大多数：揭示 Pristimantis unistrigatus 物种群（无脊椎动物门，Strabomantidae）的巨型多样性和历史生物地理学。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-09-19 DOI: 10.1016/j.ympev.2024.108203

Alexander Tamanini Mônico , Esteban Diego Koch , Miquéias Ferrão , Igor Yuri Fernandes , Giselle Moura Guimarães Marques , Juan Carlos Chaparro , Miguel Trefaut Rodrigues , Albertina Pimentel Lima , Antoine Fouquet

With more than 600 recognized species, the genus Pristimantis is already the most diverse among vertebrates, but described species only represent a fraction of the actual diversity in this clade. This genus is widely distributed throughout the Neotropics and represents an interesting model for biogeographic studies because Pristimantis spp. are direct developing and generally have narrow ecological niches and low dispersal abilities. The P. unistrigatus species group is one of the most important components in the genus (ca. 200 recognized species) and has been supported by morphological but not by molecular evidence. We assessed the species boundaries and distribution in the P. unistrigatus species group and infer spatiotemporal patterns of diversification related to historical landscape changes in the Neotropics. We gathered three mitochondrial, and two nuclear DNA loci from 416 specimens throughout the range of the group, and including 68 nominal species. We redefine the group based on the obtained phylogeny and found 151 candidate species that composes it, with 83 of these remaining undescribed. We recovered 11 major clades within the group that diverged before 13 Ma. The diversification of the group started during the early Miocene most likely in northwestern South America, currently corresponding to western Amazonia and northern Andes. The other neotropical areas subsequently acted as sinks, receiving lineages mostly during the last 10 Ma, after the demise of the Pebas System and the setup of the modern Amazonian hydrographic system.

Pristimantis 属拥有 600 多个公认的物种，已经成为脊椎动物中物种最丰富的属，但已描述的物种仅占该支系实际多样性的一小部分。该属广泛分布于整个新热带地区，是生物地理学研究的一个有趣模型，因为 Pristimantis 属是直接发育的，通常具有狭窄的生态位和较低的变异性。P. unistrigatus物种组是该属最重要的组成部分之一（约有 200 个公认的物种），已得到形态学证据的支持，但未得到分子证据的支持。我们评估了 P. unistrigatus 物种群的物种边界和分布情况，并推断了与新热带地区历史景观变化有关的物种多样化时空模式。我们从该物种群分布区的 416 个标本中收集了三个线粒体和两个核 DNA 位点，其中包括 68 个标称物种。我们根据所获得的系统发生重新定义了该类群，并发现了 151 个候选物种，其中 83 个物种仍未被描述。我们在该类群中发现了 11 个在 13 Ma 年前分化的主要支系。该类群的分化很可能始于中新世早期的南美洲西北部，目前相当于亚马孙西部和安第斯北部。其他新热带地区随后成为吸收汇，主要在最近 10 Ma 期间，即佩巴斯系统消亡和现代亚马逊水文系统建立之后接受了该类群。

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引用次数: 0

A global blueberry phylogeny: Evolution, diversification, and biogeography of Vaccinieae (Ericaceae) 全球蓝莓系统发育：蓝莓科（Ericaceae）的进化、多样化和生物地理学。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-09-15 DOI: 10.1016/j.ympev.2024.108202

Anna L. Becker , Andrew A. Crowl , James L. Luteyn , Andre S. Chanderbali , Walter S. Judd , Paul S. Manos , Douglas E. Soltis , Stephen A. Smith , Deise J.P. Goncalves , Christopher W. Dick , William N. Weaver , Pamela S. Soltis , Nico Cellinese , Peter W. Fritsch

Vaccinieae is a morphologically diverse and species-rich (∼1430 species) tribe in Ericaceae. Although the majority of diversity is tropical, Vaccinieae are best known for temperate crops (i.e., blueberries, cranberries, and lingonberries) in Vaccinium. Vaccinium itself (∼500 species) has been previously suggested as highly polyphyletic and taxonomic boundaries among many of the other genera in the tribe remain uncertain. We assessed the evolutionary history of Vaccinieae with phylogenomic analyses based on a target-enrichment dataset containing 256 low-copy nuclear loci and 210 species representing 30 of the 35 genera in the tribe and 25 of the 29 sections of Vaccinium. We conducted time-calibrated biogeographic analyses and diversification analyses to explore the area of origin and global dispersal history of the tribe. The analysis recovered a temperate North American origin for Vaccinieae approximately 30 million years ago. Tropical diversity of Vaccinieae was inferred to result from multiple, independent movements into the tropics from north-temperate ancestors. Diversification rate increases corresponded to radiation into the Andes and SE Asia. The pseudo-10-locular ovary evolved once in the tribe from the five-locular state, coinciding with the diversification of a major clade that includes most Asian Vaccinium and the group from which commercial blueberries are derived (V. sect. Cyanococcus). A reconstruction from available chromosome counts suggests that a major polyploid event predated the evolution of nearly half the diversity of Vaccinieae. The extent of polyphyly in Vaccinium documented here supports the need for a generic reclassification of the tribe.

越橘科（Vaccinieae）是唇形科（Ericaceae）中一个形态多样、物种丰富（∼1430 种）的科属。虽然其多样性主要集中在热带地区，但越橘科最著名的是越橘属的温带作物（如蓝莓、小红莓、越橘、越橘）。Vaccinium 本身（∼500 种）曾被认为具有高度多态性，而该族中许多其他属之间的分类界限仍不确定。我们基于目标富集数据集评估了 Vaccinieae 的进化历史，该数据集包含 256 个低拷贝核位点和 210 个物种，代表了该族 35 个属中的 30 个属和 Vaccinium 29 个分支中的 25 个分支。我们进行了时间校准生物地理学分析和多样化分析，以探索该族的起源地区和全球扩散历史。分析结果表明， Vaccinieae起源于大约3000万年前的北美温带地区。推断 Vaccinieae 的热带多样性来自于从北温带祖先向热带的多次独立迁移。多样化率的增加与向安第斯山脉和东南亚的辐射相对应。假十室子房在该族中由五室进化而来，与包括大多数亚洲越橘和商业蓝莓（V. sect. Cyanococcus）的一个主要支系的分化相吻合。根据现有的染色体数目重建的结果表明，在越橘科近一半的多样性进化之前，发生了一次重大的多倍体事件。这里所记录的 Vaccinium 的多倍体程度支持了对该族进行重新分类的需要。

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引用次数: 0

Deciphering the evolution and biogeography of ant-ferns Lecanopteris s.s 解密蚁翅目 Lecanopteris s.s 的进化和生物地理学

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-09-14 DOI: 10.1016/j.ympev.2024.108199

Li-Ju Jiang , Jing Zhao , Jia-Guan Wang , Sven Landrein , Ji-Pu Shi , Chuan-Jie Huang , Miao Luo , Xin-Mao Zhou , Hong-Bin Niu , Zhao-Rong He

Southeast Asia is a biodiversity hotspot characterized by a complex paleogeography, and its Polypodiopsida flora is particularly diverse. While hybridization is recognized as common in ferns, further research is needed to investigate the relationship between hybridization events and fern diversity. Lecanopteris s.s., an ant-associated fern, has been subject to debate regarding species delimitations primarily due to limited DNA markers and species sampling. Our study integrates 22 newly generated plastomes, 22 transcriptomes, and flow cytometry of all native species along with two cultivated hybrids. Our objective is to elucidate the reticulate evolutionary history within Lecanopteris s.s. through the integration of phylobiogeographic reconstruction, gene flow inference, and genome size estimation. Key findings of our study include: (1) An enlarged plastome size (178–187 Kb) in Lecanopteris s.s., attributed to extreme expansion of the Inverted Repeat (IR) regions; (2) The traditional ‘pumila’ and ‘crustacea’ groups are paraphyletic; (3) Significant cytonuclear discordance attributed to gene flow; (4) Natural hybridization and introgression in the ‘pumila’ and ‘darnaedii’ groups; (5) L. luzonensis is the maternal parent of L. ‘Yellow Tip’, with L. pumila suggested as a possible paternal parent; (6) L. ‘Tatsuta’ is a hybrid between L. luzonensis and L. crustacea; (7) Lecanopteris s.s. first diverged during the Neogene and then during the middle Miocene climatic optimum in the Indochina and Sundaic regions. In conclusion, the biogeographic history and speciation of Lecanopteris have been profoundly shaped by past climate changes and geodynamics of Southeast Asia. Dispersals, hybridization and introgression between species act as pivotal factors in the evolutionary trajectory of Lecanopteris s.s.. This research provides a robust framework for further exploration and understanding of the complex dynamics driving the diversification and distribution patterns within Polypodiaceae subfamily Microsoroideae.

东南亚是一个生物多样性热点地区，其特点是古地理环境复杂，其多褶蕨类植物群的多样性尤为突出。虽然杂交在蕨类植物中很常见，但还需要进一步研究杂交事件与蕨类植物多样性之间的关系。Lecanopteris s.s.是一种与蚂蚁相关的蕨类植物，由于DNA标记和物种取样有限，它的物种划分一直存在争议。我们的研究整合了 22 个新生成的质粒组、22 个转录组，以及所有本地物种和两个栽培杂交种的流式细胞仪。我们的目标是通过植物生物地理重建、基因流推断和基因组大小估算的整合，阐明Lecanopteris s.s.的网状进化史。我们研究的主要发现包括(1) Lecanopteris s.s.的质体体积增大（178-187 Kb）、(2)传统的 "pumila "和 "crustacea "类群为旁系；(3)基因流导致细胞核显著不一致；(4) "pumila "和 "darnaedii "类群存在自然杂交和引种；(5)L.L. 'Tatsuta'是 L. luzonensis 和 L. crustacea 的杂交种；（7）Lecanopteris s.s.首先在新近纪分化，然后在中新世中期印度支那和巽他地区气候最适宜时期分化。总之，Lecanopteris 的生物地理历史和物种分化受到东南亚过去气候变化和地球动力学的深刻影响。物种间的扩散、杂交和引种是 Lecanopteris s.s.进化轨迹的关键因素。这项研究为进一步探索和理解驱动多足亚科小蔷薇属植物多样化和分布模式的复杂动态提供了一个强有力的框架。

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引用次数: 0

Shining new light on naupliar eyes: A novel molecular phylogeny for Pleuromamma (Family: Metridinidae) and the characterization of luciferase and opsin expression 为稚虫的眼睛带来新的启示：Pleuromamma（Family: Metridinidae）新的分子系统发育以及荧光素酶和虹彩素表达的特征。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-09-13 DOI: 10.1016/j.ympev.2024.108200

Tom Iwanicki , Jessica W. Chen , Junya Hirai , Hunter DeTurk , Mireille Steck , Erica Goetze , Megan L. Porter

Pleuromamma (Giesbrecht, 1898) is a cosmopolitan genus of metridinid copepods, with species that perform remarkable diel vertical migrations (DVM) and emit a bioluminescent secretion when disturbed that varies both spectrally and kinetically. Copepod bioluminescence is autogenic and uses luciferase enzymes that catalyze a luciferin, coelenterazine, to produce light. Pleuromamma possess naupliar eyes, relatively simple photosensitive structures used for many visually-guided behaviors. Yet the fundamental molecular unit for vision, the opsin protein, has not been previously described for the family. The light producers and detectors are important to study because DVM is a behavior that mediates significant active elemental fluxes between the upper ocean and midwaters across vast stretches of oceanic habitat, and DVM is guided by visual behaviors, with animals tracking an isolume. Here we provide the first fully resolved molecular phylogeny for Pleuromamma (Family: Metridinidae) and describe the luciferase and opsin gene diversity and expression using de novo assembled transcriptomes. We successfully sequenced and assembled transcriptomes for 10 of 11 described species of Pleuromamma as well as two other metridinid species: Metridia longa and Gaussia princeps. In all species, we obtained coding sequences of one putative rhabdomeric middle wavelength sensitive visual opsin gene, as well as several non-visual opsins – a c-type pteropsin and a tetra-opsin type peropsin. Furthermore, Pleuromamma express luciferases from each of two main evolutionary clades (Luc1 and Luc2), and a single paralog (Luc2a) dominates expression throughout the group. The variation in luciferase number, sequence, and expression among species could lead to different spectral and kinetic properties of bioluminescence and aid in congener recognition.

Pleuromamma（Giesbrecht，1898 年）是一种世界性的甲壳纲桡足类，其物种可进行显著的昼夜垂直洄游（DVM），并在受到干扰时发出生物发光分泌物，这种分泌物在光谱和动力学上都会发生变化。桡足类的生物发光是自发的，利用荧光素酶催化一种荧光素--腔肠素来发光。Pleuromamma 拥有稚虫眼，这是一种相对简单的光敏结构，可用于许多视觉引导的行为。然而，视觉的基本分子单位--视蛋白，在该家族中还没有被描述过。光产生器和探测器的研究非常重要，因为DVM是一种在海洋栖息地广阔的上层海洋和中层海洋之间介导大量活性元素通量的行为，而且DVM是由视觉行为引导的，动物会追踪孤立体。在这里，我们首次提供了完全解析的Pleuromamma（科：Metridinidae）的分子系统进化，并利用从头组装的转录组描述了荧光素酶和光学蛋白基因的多样性和表达。我们成功地测序并组装了11个已描述的Pleuromamma物种中的10个物种的转录组，以及另外两个蝶形目物种的转录组：Metridia longa和Gaussia princeps。在所有物种中，我们都获得了一个推定的横纹肌中间波长敏感的视觉蛋白基因的编码序列，以及几种非视觉蛋白--一种c型翼状蛋白和一种四眼型眼球蛋白的编码序列。此外，Pleuromamma 还表达来自两个主要进化支系（Luc1 和 Luc2）的荧光素酶，其中一个旁系亲属（Luc2a）的表达在整个群体中占主导地位。物种间荧光素酶数量、序列和表达的差异可能会导致生物发光的光谱和动力学特性不同，并有助于同类识别。

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引用次数: 0