Pub Date : 2024-06-16DOI: 10.1016/j.ympev.2024.108130
Miranda B. Sherlock , Jeffrey W. Streicher , David J. Gower , Simon T. Maddock , Ronald A. Nussbaum , Oommen V. Oommen , Ana Serra Silva , Julia J. Day , Mark Wilkinson
Unusually for oceanic islands, the granitic Seychelles host multiple lineages of endemic amphibians. This includes an ancient (likely ca. 60 million years) radiation of eight caecilian species, most of which occur on multiple islands. These caecilians have a complicated taxonomic history and their phylogenetic inter-species relationships have been difficult to resolve. Double-digest RAD sequencing (ddRADseq) has been applied extensively to phylogeography and increasingly to phylogenetics but its utility for resolving ancient divergences is less well established. To address this, we applied ddRADseq to generate a genome-wide SNP panel for phylogenomic analyses of the Seychelles caecilians, whose phylogeny has so far not been satisfactorily resolved with traditional DNA markers. Based on 129,154 SNPs, we resolved deep and shallow splits, with strong support. Our findings demonstrate the capability of genome-wide SNPs for evolutionary inference at multiple taxonomic levels and support the recently proposed synonymy of Grandisonia Taylor, 1968 with Hypogeophis Peters, 1879. We revealed three clades of Hypogeophis (large-, medium- and short-bodied) and identify a single origin of the diminutive, stocky-bodied and pointy-snouted phenotype.
对于海洋岛屿来说,塞舌尔群岛的花岗岩质地非常罕见,这里有多个特有的两栖动物品系。其中包括一个古老的(可能约 6000 万年前)八种凯西拉类,它们中的大多数出现在多个岛屿上。这些无尾类有着复杂的分类历史,其物种间的系统发育关系一直难以解决。双位 RAD 测序(ddRADseq)已被广泛应用于系统地理学,并越来越多地应用于系统发育学,但其在解决远古分化方面的实用性还不太成熟。为了解决这个问题,我们应用 ddRADseq 生成了一个全基因组 SNP 面板,用于塞舌尔群岛无尾类的系统发生学分析。基于 129,154 个 SNPs,我们解决了深层和浅层分裂问题,并获得了强有力的支持。我们的研究结果证明了全基因组 SNP 在多个分类水平上的进化推断能力,并支持最近提出的 Grandisonia Taylor, 1968 与 Hypogeophis Peters, 1879 的同义。我们揭示了 Hypogeophis 的三个支系(大体型、中体型和短体型),并确定了体型矮小、体格粗壮和尖嘴表型的单一起源。
{"title":"Genomic SNPs resolve the phylogeny of an ancient amphibian island radiation from the Seychelles","authors":"Miranda B. Sherlock , Jeffrey W. Streicher , David J. Gower , Simon T. Maddock , Ronald A. Nussbaum , Oommen V. Oommen , Ana Serra Silva , Julia J. Day , Mark Wilkinson","doi":"10.1016/j.ympev.2024.108130","DOIUrl":"10.1016/j.ympev.2024.108130","url":null,"abstract":"<div><p>Unusually for oceanic islands, the granitic Seychelles host multiple lineages of endemic amphibians. This includes an ancient (likely ca. 60 million years) radiation of eight caecilian species, most of which occur on multiple islands.<!--> <!-->These caecilians have a complicated taxonomic history and their phylogenetic inter-species relationships have been difficult to resolve. Double-digest RAD sequencing (ddRADseq) has been applied extensively to phylogeography and increasingly to phylogenetics but its utility for resolving ancient divergences is less well established. To address this, we applied ddRADseq to generate a genome-wide SNP panel for phylogenomic analyses of the Seychelles caecilians, whose phylogeny has so far not been satisfactorily resolved with traditional DNA markers. Based on 129,154 SNPs, we resolved deep and shallow splits, with strong support. Our findings demonstrate the capability of genome-wide SNPs for evolutionary inference at multiple taxonomic levels and support the recently proposed synonymy of <em>Grandisonia</em> Taylor, 1968 with <em>Hypogeophis</em> Peters, 1879. We revealed three clades of <em>Hypogeophis</em> (large-, medium- and short-bodied) and identify a single origin of the diminutive, stocky-bodied and pointy-snouted phenotype.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001222/pdfft?md5=ba216c2347ef206daf4433490b1f4493&pid=1-s2.0-S1055790324001222-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141393029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-13DOI: 10.1016/j.ympev.2024.108129
Sara González-Delgado , Paula C. Rodríguez-Flores , Gonzalo Giribet
Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.
{"title":"Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia)","authors":"Sara González-Delgado , Paula C. Rodríguez-Flores , Gonzalo Giribet","doi":"10.1016/j.ympev.2024.108129","DOIUrl":"10.1016/j.ympev.2024.108129","url":null,"abstract":"<div><p>Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141328194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-12DOI: 10.1016/j.ympev.2024.108116
Emanuel M. Fonseca , Bryan C. Carstens
While genetic variation in any species is potentially shaped by a range of processes, phylogeography and landscape genetics are largely concerned with inferring how environmental conditions and landscape features impact neutral intraspecific diversity. However, even as both disciplines have come to utilize SNP data over the last decades, analytical approaches have remained for the most part focused on either broad-scale inferences of historical processes (phylogeography) or on more localized inferences about environmental and/or landscape features (landscape genetics). Here we demonstrate that an artificial intelligence model-based analytical framework can consider both deeper historical factors and landscape-level processes in an integrated analysis. We implement this framework using data collected from two Brazilian anurans, the Brazilian sibilator frog (Leptodactylus troglodytes) and granular toad (Rhinella granulosa). Our results indicate that historical demographic processes shape most the genetic variation in the sibulator frog, while landscape processes primarily influence variation in the granular toad. The machine learning framework used here allows both historical and landscape processes to be considered equally, rather than requiring researchers to make an a priori decision about which factors are important.
虽然任何物种的遗传变异都可能受到一系列过程的影响,但系统地理学和景观遗传学主要关注的是推断环境条件和景观特征如何影响中性的种内多样性。然而,即使这两个学科在过去几十年中都开始利用 SNP 数据,分析方法在很大程度上仍然集中在对历史进程的大范围推断(系统地理学)或对环境和/或景观特征的局部推断(景观遗传学)上。在这里,我们证明了基于人工智能模型的分析框架可以在综合分析中同时考虑更深层次的历史因素和景观层面的过程。我们利用从两种巴西无尾类动物--巴西咝蛙(Leptodactylus troglodytes)和颗粒蟾蜍(Rhinella granulosa)--收集到的数据实施了这一框架。我们的研究结果表明,历史人口统计过程决定了箭蛙的大部分遗传变异,而景观过程则主要影响颗粒蟾蜍的变异。这里使用的机器学习框架允许同时考虑历史和景观过程,而不是要求研究人员先验地决定哪些因素是重要的。
{"title":"Artificial intelligence enables unified analysis of historical and landscape influences on genetic diversity","authors":"Emanuel M. Fonseca , Bryan C. Carstens","doi":"10.1016/j.ympev.2024.108116","DOIUrl":"10.1016/j.ympev.2024.108116","url":null,"abstract":"<div><p>While genetic variation in any species is potentially shaped by a range of processes, phylogeography and landscape genetics are largely concerned with inferring how environmental conditions and landscape features impact neutral intraspecific diversity. However, even as both disciplines have come to utilize SNP data over the last decades, analytical approaches have remained for the most part focused on either broad-scale inferences of historical processes (phylogeography) or on more localized inferences about environmental and/or landscape features (landscape genetics). Here we demonstrate that an artificial intelligence model-based analytical framework can consider both deeper historical factors and landscape-level processes in an integrated analysis. We implement this framework using data collected from two Brazilian anurans, the Brazilian sibilator frog (<em>Leptodactylus troglodytes</em>) and granular toad (<em>Rhinella granulosa</em>). Our results indicate that historical demographic processes shape most the genetic variation in the sibulator frog, while landscape processes primarily influence variation in the granular toad. The machine learning framework used here allows both historical and landscape processes to be considered equally, rather than requiring researchers to make an <em>a priori</em> decision about which factors are important.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141319128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-07DOI: 10.1016/j.ympev.2024.108120
Anna Cho, Gordon Lax, Patrick J. Keeling
Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable groupings with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenetic relationships, and discrete gene properties affect lineages of stramenopiles differently. This is something which may be explored to further our understanding of the molecular evolution of stramenopiles.
{"title":"Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages","authors":"Anna Cho, Gordon Lax, Patrick J. Keeling","doi":"10.1016/j.ympev.2024.108120","DOIUrl":"https://doi.org/10.1016/j.ympev.2024.108120","url":null,"abstract":"<div><p>Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable groupings with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenetic relationships, and discrete gene properties affect lineages of stramenopiles differently. This is something which may be explored to further our understanding of the molecular evolution of stramenopiles.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S105579032400112X/pdfft?md5=0bc2a149c37f34004bf2354c17eee979&pid=1-s2.0-S105579032400112X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141291848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-07DOI: 10.1016/j.ympev.2024.108117
Alexandre M. Fernandes , Mario Cohn-Haft , Luís Fábio Silveira , Alexandre Aleixo , Nathália Nascimento , Urban Olsson
The Least Nighthawk Chordeiles pusillus is widespread wherever there are savannas in the South American tropics, often in isolated patches, such as white-sands savannas in the Amazon rainforest realm. Here, we investigate genetic relationships between populations of the Least Nighthawk to understand historical processes leading to its diversification and to determine dispersal routes between northern and southern savannas by way of three hypothesized dispersal corridors by comparing samples from white-sand savannas to samples from other savannas outside of the Amazon rainforest region. We use 32 mtDNA samples from the range of C. pusillus to infer a dated phylogeny. In a subset of 17 samples, we use shotgun sequences to infer a distance-based phylogeny and to estimate individual admixture proportions. We calculate gene flow and shared alleles between white-sand and non-Amazonian populations using the ABBA-BABA test (D statistics), and Principal Component Analysis (PCA) to examine genetic structure within and between lineages. Finally, we use species distribution modelling (SDM) of conditions during the Last Glacial Maximum (LGM), currently, and in the future (2050–2080) to predict potential species occurrence under a climate change scenario. Two main clades (estimated to have diverged around 1.07 million years ago) were recovered with mtDNA sequences and Single Nucleotide Polymorphism (SNPs) and were supported by NGSadmix and PCA: one in the Amazon basin white-sand savannas, the other in the non-Amazonian savannas. Possible allele sharing between these clades was indicated by the D-statistics between northern non-Amazonian populations and the white-sand savanna population, but this was not corroborated by the admixture analyses. Dispersal among northern non-Amazonian populations may have occurred in a dry corridor between the Guianan and the Brazilian Shield, which has since moved eastward. Our data suggest that the lineages separated well before the Last Glacial Maximum, consequently dispersal could have happened at any earlier time during similar climatic conditions. Subsequently, non-Amazonian lineages became more divergent among themselves, possibly connecting and dispersing across the mouth of the Amazon River across Marajó island during favourable climatic conditions in the Pleistocene.
{"title":"Speciation in savanna birds in South America: The case of the Least Nighthawk Chordeiles pusillus (Aves: Caprimulgidae) in and out of the Amazon","authors":"Alexandre M. Fernandes , Mario Cohn-Haft , Luís Fábio Silveira , Alexandre Aleixo , Nathália Nascimento , Urban Olsson","doi":"10.1016/j.ympev.2024.108117","DOIUrl":"10.1016/j.ympev.2024.108117","url":null,"abstract":"<div><p>The Least Nighthawk <em>Chordeiles pusillus</em> is widespread wherever there are savannas in the South American tropics, often in isolated patches, such as white-sands savannas in the Amazon rainforest realm. Here, we investigate genetic relationships between populations of the Least Nighthawk to understand historical processes leading to its diversification and to determine dispersal routes between northern and southern savannas by way of three hypothesized dispersal corridors by comparing samples from white-sand savannas to samples from other savannas outside of the Amazon rainforest region. We use 32 mtDNA samples from the range of <em>C. pusillus</em> to infer a dated phylogeny. In a subset of 17 samples, we use shotgun sequences to infer a distance-based phylogeny and to estimate individual admixture proportions. We calculate gene flow and shared alleles between white-sand and non-Amazonian populations using the ABBA-BABA test (D statistics), and Principal Component Analysis (PCA) to examine genetic structure within and between lineages. Finally, we use species distribution modelling (SDM) of conditions during the Last Glacial Maximum (LGM), currently, and in the future (2050–2080) to predict potential species occurrence under a climate change scenario. Two main clades (estimated to have diverged around 1.07 million years ago) were recovered with mtDNA sequences and Single Nucleotide Polymorphism (SNPs) and were supported by NGSadmix and PCA: one in the Amazon basin white-sand savannas, the other in the non-Amazonian savannas. Possible allele sharing between these clades was indicated by the D-statistics between northern non-Amazonian populations and the white-sand savanna population, but this was not corroborated by the admixture analyses. Dispersal among northern non-Amazonian populations may have occurred in a dry corridor between the Guianan and the Brazilian Shield, which has since moved eastward. Our data suggest that the lineages separated well before the Last Glacial Maximum, consequently dispersal could have happened at any earlier time during similar climatic conditions. Subsequently, non-Amazonian lineages became more divergent among themselves, possibly connecting and dispersing across the mouth of the Amazon River across Marajó island during favourable climatic conditions in the Pleistocene.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141297399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.1016/j.ympev.2024.108121
Juhong Chen , Kun Jiang , Tianyi Qi , Yanfei Li , Huaxi Liu , Huaijun Xue , Zhen Ye , Shujing Wang , Wenjun Bu
The subgenus Aeschyntelus includes six species that show variations in body color and shape, thus making it difficult to identify them based on morphological identification alone. To date, no genetic study has evaluated species within this genus. Herein, we collected 171 individuals from 90 localities of Rhopalus and employed an integrative taxonomic approach that incorporated morphological data, mitochondrial genomic data (COI, whole mitochondrial data) and nuclear genomic data (18S + 28S rRNAs, nuclear genome-wide SNPs) to delineate species boundaries. Our analyses confirmed the status of nine described species of Rhopalus and proposed the recognition of one new species known as Rhopalus qinlinganus sp. nov., which is classified within the subgenus Aeschyntelus. Discrepancies arising from nuclear and mitochondrial data suggest the presence of mito-nuclear discordance. Specifically, mitochondrial data indicated admixture within Clade A, comprising R. kerzhneri and R. latus, whereas genome-wide SNPs unambiguously identified two separate species, aligning with morphological classification. Conversely, mitochondrial data clearly distinguished Clade B- consisting of R. sapporensis into two lineages, whereas genome-wide SNPs unequivocally identified a single species. Our study also provides insights into the evolutionary history of Aeschyntelus, thus indicating that it likely originated in East Asia during the middle Miocene. The development of Aeschyntelus biodiversity in the southwestern mountains of China occurred via an uplift-driven diversification process. Our findings highlight the necessity of integrating both morphological and multiple molecular datasets for precise species identification, particularly when delineating closely related species. Additionally, it reveals the important role of mountain orogenesis on speciation within the southwestern mountains of China.
Aeschyntelus 亚属包括六个物种,这些物种的体色和体形各不相同,因此很难仅凭形态鉴定来识别它们。迄今为止,还没有基因研究对该属的物种进行评估。在本文中,我们从 Rhopalus 的 90 个地点收集了 171 个个体,并采用了综合分类方法,结合形态学数据、线粒体基因组数据(COI、全线粒体数据)和核基因组数据(18S + 28S rRNAs、核全基因组 SNPs)来划分物种边界。我们的分析确认了 9 个已描述的 Rhopalus 物种的地位,并提议确认一个新物种,即 Rhopalus qinlinganus sp.nov.,将其归入 Aeschyntelus 亚属。核与线粒体数据的不一致表明存在有丝分裂与核分裂不一致的现象。具体来说,线粒体数据表明,在由 R. kerzhneri 和 R. latus 组成的支系 A 中存在混杂现象,而全基因组 SNP 则明确指出了两个独立的物种,与形态学分类一致。相反,线粒体数据清楚地将由 R. sapporensis 组成的支系 B 区分为两个世系,而全基因组 SNP 则明确地确定了一个物种。我们的研究还揭示了Aeschyntelus的进化历史,从而表明它很可能起源于中新世中期的东亚。Aeschyntelus生物多样性在中国西南山区的发展经历了一个隆升驱动的多样化过程。我们的研究结果突显了整合形态学和多种分子数据集进行精确物种鉴定的必要性,尤其是在划分近缘物种时。此外,它还揭示了山地造山运动对中国西南山区物种分化的重要作用。
{"title":"Integrative taxonomy, phylogenetics and historical biogeography of subgenus Aeschyntelus Stål, 1872 (Hemiptera: Heteroptera: Rhopalidae)","authors":"Juhong Chen , Kun Jiang , Tianyi Qi , Yanfei Li , Huaxi Liu , Huaijun Xue , Zhen Ye , Shujing Wang , Wenjun Bu","doi":"10.1016/j.ympev.2024.108121","DOIUrl":"10.1016/j.ympev.2024.108121","url":null,"abstract":"<div><p>The subgenus <em>Aeschyntelus</em> includes six species that show variations in body color and shape, thus making it difficult to identify them based on morphological identification alone. To date, no genetic study has evaluated species within this genus. Herein, we collected 171 individuals from 90 localities of <em>Rhopalus</em> and employed an integrative taxonomic approach that incorporated morphological data, mitochondrial genomic data (<em>COI</em>, whole mitochondrial data) and nuclear genomic data (<em>18S</em> + <em>28S</em> rRNAs, nuclear genome-wide SNPs) to delineate species boundaries. Our analyses confirmed the status of nine described species of <em>Rhopalus</em> and proposed the recognition of one new species known as <em>Rhopalus qinlinganus</em> sp. nov., which is classified within the subgenus <em>Aeschyntelus</em>. Discrepancies arising from nuclear and mitochondrial data suggest the presence of mito-nuclear discordance. Specifically, mitochondrial data indicated admixture within Clade A, comprising <em>R. kerzhneri</em> and <em>R. latus</em>, whereas genome-wide SNPs unambiguously identified two separate species, aligning with morphological classification. Conversely, mitochondrial data clearly distinguished Clade B- consisting of <em>R. sapporensis</em> into two lineages, whereas genome-wide SNPs unequivocally identified a single species. Our study also provides insights into the evolutionary history of <em>Aeschyntelus</em>, thus indicating that it likely originated in East Asia during the middle Miocene. The development of <em>Aeschyntelus</em> biodiversity in the southwestern mountains of China occurred via an uplift-driven diversification process. Our findings highlight the necessity of integrating both morphological and multiple molecular datasets for precise species identification, particularly when delineating closely related species. Additionally, it reveals the important role of mountain orogenesis on speciation within the southwestern mountains of China.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141293943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-05DOI: 10.1016/j.ympev.2024.108096
Ruiyan Zhang , Marine Fau , Christopher Mah , Marc Eléaume , Dongsheng Zhang , Yadong Zhou , Bo Lu , Chunsheng Wang
{"title":"Corrigendum to “Systematics of deep-sea starfish order Brisingida (Echinodermata: Asteroidea), with a revised classification and assessments of morphological characters” [Mol. Phylogenetics Evol. 191 (2024) 107993]","authors":"Ruiyan Zhang , Marine Fau , Christopher Mah , Marc Eléaume , Dongsheng Zhang , Yadong Zhou , Bo Lu , Chunsheng Wang","doi":"10.1016/j.ympev.2024.108096","DOIUrl":"10.1016/j.ympev.2024.108096","url":null,"abstract":"","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324000885/pdfft?md5=d44ae586ca83b37ebccb238f30cbf22f&pid=1-s2.0-S1055790324000885-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141285499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-05DOI: 10.1016/j.ympev.2024.108119
Zhenfu Huang , Hideyuki Chiba , Yanqing Hu , Xiaohua Deng , Wen Fei , Szabolcs Sáfián , Liwei Wu , Min Wang , Xiaoling Fan
Despite considerable research efforts in recent years, the deeper phylogenetic relationships among skipper butterflies (Hesperiidae) remain unresolved. This is primarily because of limited sampling, especially within Asian and African lineages. In this study, we consolidated previous data and extensively sampled Asian and African taxa to elucidate the phylogenetic relationships within Hesperiidae. The molecular dataset comprised sequences from two mitochondrial and two nuclear gene regions from 563 species that represented 353 genera. Our analyses revealed seven subfamilies within Hesperiidae: Coeliadinae, Euschemoninae, Eudaminae, Pyrginae, Heteropterinae, Trapezitinae, and Hesperiinae. The systematics of most tribes and genera aligned with those of prior studies. However, notable differences were observed in several tribes and genera. Overall, the position of taxa assigned to incertae sedis in Hesperiinae is largely clarified in this study. Our results strongly support the monophyly of the tribe Tagiadini (Pyrginae), and the systematics of some genera are clarified with comprehensive discussion. We recognize 15 tribes within the subfamily Hesperiinae. Of these, nine tribes are discussed in detail: Aeromachini, Astictopterini, Erionotini, Unkanini (new status), Ancistroidini, Ismini (confirmed status), Plastingini (new status), Gretnini (confirmed status), and Eetionini (confirmed status). We propose four subtribes within Astictopterini: Hypoleucina subtrib.n., Aclerosina, Cupithina, and Astictopterina. Furthermore, we describe a new genus (Hyarotoidesgen.n.) and reinstate two genera (Zeareinst.stat. and Separeinst.stat.) as valid. Additionally, we propose several new combinations: Zea mythecacomb.n.,Sepa bononiacomb.n. & reinst.stat., and Sepa umbrosacomb.n. This study, with extensive sampling of Asian and African taxa, greatly enhances the understanding of the knowledge of the skipper tree of life.
{"title":"Molecular phylogeny of Hesperiidae (Lepidoptera) with an emphasis on Asian and African genera","authors":"Zhenfu Huang , Hideyuki Chiba , Yanqing Hu , Xiaohua Deng , Wen Fei , Szabolcs Sáfián , Liwei Wu , Min Wang , Xiaoling Fan","doi":"10.1016/j.ympev.2024.108119","DOIUrl":"10.1016/j.ympev.2024.108119","url":null,"abstract":"<div><p>Despite considerable research efforts in recent years, the deeper phylogenetic relationships among skipper butterflies (Hesperiidae) remain unresolved. This is primarily because of limited sampling, especially within Asian and African lineages. In this study, we consolidated previous data and extensively sampled Asian and African taxa to elucidate the phylogenetic relationships within Hesperiidae. The molecular dataset comprised sequences from two mitochondrial and two nuclear gene regions from 563 species that represented 353 genera. Our analyses revealed seven subfamilies within Hesperiidae: Coeliadinae, Euschemoninae, Eudaminae, Pyrginae, Heteropterinae, Trapezitinae, and Hesperiinae. The systematics of most tribes and genera aligned with those of prior studies. However, notable differences were observed in several tribes and genera. Overall, the position of taxa assigned to <em>incertae sedis</em> in Hesperiinae is largely clarified in this study. Our results strongly support the monophyly of the tribe Tagiadini (Pyrginae), and the systematics of some genera are clarified with comprehensive discussion. We recognize 15 tribes within the subfamily Hesperiinae. Of these, nine tribes are discussed in detail: Aeromachini, Astictopterini, Erionotini, Unkanini (new status), Ancistroidini, Ismini (confirmed status), Plastingini (new status), Gretnini (confirmed status), and Eetionini (confirmed status). We propose four subtribes within Astictopterini: Hypoleucina <strong>subtrib.n.</strong>, Aclerosina, Cupithina, and Astictopterina. Furthermore, we describe a new genus (<em>Hyarotoides</em> <strong>gen.n.</strong>) and reinstate two genera (<em>Zea</em> <strong>reinst.stat.</strong> and <em>Sepa</em> <strong>reinst.stat.</strong>) as valid. Additionally, we propose several new combinations: <em>Zea mytheca</em> <strong>comb.n.,</strong> <em>Sepa bononia</em> <strong>comb.n. & reinst.stat.,</strong> and <em>Sepa umbrosa</em> <strong>comb.n.</strong> This study, with extensive sampling of Asian and African taxa, greatly enhances the understanding of the knowledge of the skipper tree of life.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001118/pdfft?md5=219d4a76e376759b942ad88d260c7bd4&pid=1-s2.0-S1055790324001118-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-05DOI: 10.1016/j.ympev.2024.108118
Charlotte Benedict , Alonso Delgado , Isabel Pen , Claudia Vaga , Marymegan Daly , Andrea M. Quattrini
Sea anemones (Order Actiniaria) are a diverse group of marine invertebrates ubiquitous across marine ecosystems. Despite their wide distribution and success, a knowledge gap persists in our understanding of their diversity within tropical systems, owed to sampling bias of larger and more charismatic species overshadowing cryptic lineages. This study aims to delineate the sea anemone diversity in Mo’orea (French Polynesia) with the use of a dataset from the Mo’orea Biocode’s “BioBlitz” initiative, which prioritized the sampling of more cryptic and understudied taxa. Implementing a target enrichment approach, we integrate 71 newly sequenced samples into an expansive phylogenetic framework and contextualize Mo’orea’s diversity within global distribution patterns of sea anemones. Our analysis corroborates the presence of several previously documented sea anemones in French Polynesia and identifies for the first time the occurrence of members of genera Andvakia and Aiptasiomorpha. This research unveils the diverse sea anemone ecosystem in Mo’orea, spotlighting the area’s ecological significance and emphasizing the need for continued exploration. Our methodology, encompassing a broad BLAST search coupled with phylogenetic analysis, proved to be a practical and effective approach for overcoming the limitations posed by the lack of comprehensive sequence data for sea anemones. We discuss the merits and limitations of current molecular methodologies and stress the importance of further research into lesser-studied marine organisms like sea anemones. Our work sets a precedent for future phylogenetic studies stemming from BioBlitz endeavors.
{"title":"Sea anemone (Anthozoa, Actiniaria) diversity in Mo’orea (French Polynesia)","authors":"Charlotte Benedict , Alonso Delgado , Isabel Pen , Claudia Vaga , Marymegan Daly , Andrea M. Quattrini","doi":"10.1016/j.ympev.2024.108118","DOIUrl":"10.1016/j.ympev.2024.108118","url":null,"abstract":"<div><p>Sea anemones (Order Actiniaria) are a diverse group of marine invertebrates ubiquitous across marine ecosystems. Despite their wide distribution and success, a knowledge gap persists in our understanding of their diversity within tropical systems, owed to sampling bias of larger and more charismatic species overshadowing cryptic lineages. This study aims to delineate the sea anemone diversity in Mo’orea (French Polynesia) with the use of a dataset from the Mo’orea Biocode’s “BioBlitz” initiative, which prioritized the sampling of more cryptic and understudied taxa. Implementing a target enrichment approach, we integrate 71 newly sequenced samples into an expansive phylogenetic framework and contextualize Mo’orea’s diversity within global distribution patterns of sea anemones. Our analysis corroborates the presence of several previously documented sea anemones in French Polynesia and identifies for the first time the occurrence of members of genera <em>Andvakia</em> and <em>Aiptasiomorpha</em>. This research unveils the diverse sea anemone ecosystem in Mo’orea, spotlighting the area’s ecological significance and emphasizing the need for continued exploration. Our methodology, encompassing a broad BLAST search coupled with phylogenetic analysis, proved to be a practical and effective approach for overcoming the limitations posed by the lack of comprehensive sequence data for sea anemones. We discuss the merits and limitations of current molecular methodologies and stress the importance of further research into lesser-studied marine organisms like sea anemones. Our work sets a precedent for future phylogenetic studies stemming from BioBlitz endeavors.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001106/pdfft?md5=fa0aef636cb361dc529c36a2e23263da&pid=1-s2.0-S1055790324001106-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-31DOI: 10.1016/j.ympev.2024.108114
Yibo Ding , Hongbo Guo , Xinfang Hong , Qiudi Li , Zhijiang Miao , Qiuwei Pan , Kuiyang Zheng , Wenshi Wang
Chronic infection of hepatitis B virus (HBV) and hepatitis D virus (HDV) causes the most severe form of viral hepatitis. Due to the dependence on HBV, HDV was deemed to co-evolve and co-migrate with HBV. However, we previously found that the naturally occurred HDV/HBV combinations do not always reflect the most efficient virological adaptation (Wang et al., 2021). Moreover, regions with heavy HBV burden do not always correlate with high HDV prevalence (e.g., East Asia), and vice versa (e.g., Central Asia). Herein, we systematically elucidated the spatiotemporal evolutionary landscape of HDV to understand the unique epidemic features of HDV. We found that the MRCA of HDV was from South America around the late 13th century, was globally dispersed mainly via Central Asia, and evolved into eight genotypes from the 19th to 20th century. In contrast, the MRCA of HBV was from Europe ∼23.7 thousand years ago (Kya), globally dispersed mainly via Africa and East Asia, and evolved into eight genotypes ∼1100 years ago. When HDV stepped in, all present-day HBV genotypes had already formed and its global genotypic distribution had stayed stable geographically. Nevertheless, regionalized HDV adapted to local HBV genotypes and human lineages, contributing to the global geographical separation of HDV genotypes. Additionally, a sharp increase in HDV infections was observed after the 20th century. In conclusion, HDV exhibited a distinct spatiotemporal distribution path compared with HBV. This unique evolutionary relationship largely fostered the unique epidemic features we observe nowadays. Moreover, HDV infections may continue to ramp up globally, thus more efforts are urgently needed to combat this disease.
{"title":"The distinct spatiotemporal evolutionary landscape of HBV and HDV largely determines the unique epidemic features of HDV globally","authors":"Yibo Ding , Hongbo Guo , Xinfang Hong , Qiudi Li , Zhijiang Miao , Qiuwei Pan , Kuiyang Zheng , Wenshi Wang","doi":"10.1016/j.ympev.2024.108114","DOIUrl":"10.1016/j.ympev.2024.108114","url":null,"abstract":"<div><p>Chronic infection of hepatitis B virus (HBV) and hepatitis D virus (HDV) causes the most severe form of viral hepatitis. Due to the dependence on HBV, HDV was deemed to co-evolve and co-migrate with HBV. However, we previously found that the naturally occurred HDV/HBV combinations do not always reflect the most efficient virological adaptation (Wang et al., 2021). Moreover, regions with heavy HBV burden do not always correlate with high HDV prevalence (e.g., East Asia), and vice versa (e.g., Central Asia). Herein, we systematically elucidated the spatiotemporal evolutionary landscape of HDV to understand the unique epidemic features of HDV. We found that the MRCA of HDV was from South America around the late 13th century, was globally dispersed mainly via Central Asia, and evolved into eight genotypes from the 19th to 20th century. In contrast, the MRCA of HBV was from Europe ∼23.7 thousand years ago (Kya), globally dispersed mainly via Africa and East Asia, and evolved into eight genotypes ∼1100 years ago. When HDV stepped in, all present-day HBV genotypes had already formed and its global genotypic distribution had stayed stable geographically. Nevertheless, regionalized HDV adapted to local HBV genotypes and human lineages, contributing to the global geographical separation of HDV genotypes. Additionally, a sharp increase in HDV infections was observed after the 20th century. In conclusion, HDV exhibited a distinct spatiotemporal distribution path compared with HBV. This unique evolutionary relationship largely fostered the unique epidemic features we observe nowadays. Moreover, HDV infections may continue to ramp up globally, thus more efforts are urgently needed to combat this disease.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141201286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}