Pub Date : 2024-07-08DOI: 10.1016/j.ympev.2024.108139
Littorinoidea is one of the most diverse radiations and the most successful group that evolutionary transitions from marine to terrestrial within Littorinimorpha. With such an unmatched diversity, few phylogenetic investigations have attempted to understand their evolutionary relationships, and existing research has primarily focused on typical intertidal species. To address this gap, we conducted the first phylogenomic analysis of the Littorinoidea, leveraging 35 transcriptomes to investigate their internal relationships. Our analyses revealed significant revisions necessary within the Littorinoidea: 1) Pomatias appears distantly related to Littorinidae, suggesting a potential ancestral origin outside of Littorinoidea, challenging traditional classification. The homology of penial innervation within Littorinoidea warrants reevaluation. 2) Lacuna’s placement indicates a close relationship with Naticidae, prompting consideration for its removal from Littorinidae. 3) Based on the current phylogenetic research, Peasiella may belong to a distinct family separate from Littorinidae. 4) Our findings support revising the placement of Pteropods within the Littorinimorpha, which is situated phylogenetically between the families Littorinoidea and Naticoidea. Additionally, we highlight the impact of site heterogeneity and evolutionary rate variation on phylogenetic inference. Our study provides a robust phylogenomic framework for the Littorinoidea, emphasizing the importance of including microgastropoda taxa in molecular phylogenetic reconstructions of gastropod subgroups.
{"title":"Increased microgastropoda sampling give new insights into the phylogenetic relationships of Littorinoidea (Littorinimorpha)","authors":"","doi":"10.1016/j.ympev.2024.108139","DOIUrl":"10.1016/j.ympev.2024.108139","url":null,"abstract":"<div><p>Littorinoidea is one of the most diverse radiations and the most successful group that evolutionary transitions from marine to terrestrial within Littorinimorpha. With such an unmatched diversity, few phylogenetic investigations have attempted to understand their evolutionary relationships, and existing research has primarily focused on typical intertidal species. To address this gap, we conducted the first phylogenomic analysis of the Littorinoidea, leveraging 35 transcriptomes to investigate their internal relationships. Our analyses revealed significant revisions necessary within the Littorinoidea: 1) <em>Pomatias</em> appears distantly related to Littorinidae, suggesting a potential ancestral origin outside of Littorinoidea, challenging traditional classification. The homology of penial innervation within Littorinoidea warrants reevaluation. 2) <em>Lacuna</em>’s placement indicates a close relationship with Naticidae, prompting consideration for its removal from Littorinidae. 3) Based on the current phylogenetic research, <em>Peasiella</em> may belong to a distinct family separate from Littorinidae. 4) Our findings support revising the placement of Pteropods within the Littorinimorpha, which is situated phylogenetically between the families Littorinoidea and Naticoidea. Additionally, we highlight the impact of site heterogeneity and evolutionary rate variation on phylogenetic inference. Our study provides a robust phylogenomic framework for the Littorinoidea, emphasizing the importance of including microgastropoda taxa in molecular phylogenetic reconstructions of gastropod subgroups.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108139"},"PeriodicalIF":3.6,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581656","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 : 2024-07-08DOI: 10.1016/j.ympev.2024.108146
Yunxiang Liu , Christopher H. Dietrich , Cong Wei
The contributions of divergent selection and spatial isolation to population divergence are among the main focuses of evolutionary biology. Here we employed integrated methods to explore genomic divergence, demographic history and calling-song differentiation in the cicada Subpsaltria yangi, and compared the genotype and calling-song phenotype of different populations occurring in distinct habitats. Our results indicate that this species comprises four main lineages with unique sets of haplotypes and calling-song structure, which are distinctly associated with geographic isolation and habitats. The populations occurring on the Loess Plateau underwent substantial expansion at ∼0.130–0.115 Ma during the Last Interglacial. Geographic distance and host shift between pairs of populations predict genomic divergence, with geographic distance and acoustical signal together explaining > 60% of the divergence among populations. Differences in calling songs could reflect adaptation of populations to novel environments with different host plants, habitats and predators, which may have resulted from neutral divergence at the molecular level followed by natural selection. Geomorphic barriers and climate oscillations associated with Pleistocene glaciation may have been primary factors in shaping the population genetic structure of this species. Ultimately this may couple with a host shift in leading toward allopatric speciation in S. yangi, i.e., isolation by distance. Our findings improve understanding of divergence in allopatry of herbivorous insects, and may inform future studies on the molecular mechanisms underlying the association between genetic/phenotypic changes and adaptation of insects to novel niches and host plants.
分化选择和空间隔离对种群分化的贡献是进化生物学的重点之一。在此,我们采用综合方法探讨了蝉Subpsaltria yangi的基因组分化、人口历史和叫声分化,并比较了发生在不同栖息地的不同种群的基因型和叫声表型。我们的研究结果表明,该物种由四个主要品系组成,具有独特的单倍型和叫声结构,这些单倍型和叫声结构与地理隔离和栖息地有明显的关联。发生在黄土高原的种群在末次冰期的 0.130-0.115 Ma 之间经历了大幅扩张。成对种群之间的地理距离和宿主迁移预示着基因组的分化,地理距离和声学信号共同解释了种群间大于60%的分化。叫声的差异可能反映了种群对不同寄主植物、栖息地和捕食者的新环境的适应,这可能是分子水平的中性分化和自然选择的结果。与更新世冰川作用有关的地貌障碍和气候振荡可能是形成该物种种群遗传结构的主要因素。最终,这可能会与宿主的转变相结合,导致 S. yangi 的同域物种分化,即通过距离实现隔离。我们的发现加深了人们对食草昆虫异地种群分化的理解,并可能为今后研究昆虫基因/表型变化与适应新的生境和寄主植物之间联系的分子机制提供信息。
{"title":"The impact of geographic isolation and host shifts on population divergence of the rare cicada Subpsaltria yangi","authors":"Yunxiang Liu , Christopher H. Dietrich , Cong Wei","doi":"10.1016/j.ympev.2024.108146","DOIUrl":"10.1016/j.ympev.2024.108146","url":null,"abstract":"<div><p>The contributions of divergent selection and spatial isolation to population divergence are among the main focuses of evolutionary biology. Here we employed integrated methods to explore genomic divergence, demographic history and calling-song differentiation in the cicada <em>Subpsaltria yangi</em>, and compared the genotype and calling-song phenotype of different populations occurring in distinct habitats. Our results indicate that this species comprises four main lineages with unique sets of haplotypes and calling-song structure, which are distinctly associated with geographic isolation and habitats. The populations occurring on the Loess Plateau underwent substantial expansion at ∼0.130–0.115 Ma during the Last Interglacial. Geographic distance and host shift between pairs of populations predict genomic divergence, with geographic distance and acoustical signal together explaining > 60% of the divergence among populations. Differences in calling songs could reflect adaptation of populations to novel environments with different host plants, habitats and predators, which may have resulted from neutral divergence at the molecular level followed by natural selection. Geomorphic barriers and climate oscillations associated with Pleistocene glaciation may have been primary factors in shaping the population genetic structure of this species. Ultimately this may couple with a host shift in leading toward allopatric speciation in <em>S. yangi</em>, i.e., isolation by distance. Our findings improve understanding of divergence in allopatry of herbivorous insects, and may inform future studies on the molecular mechanisms underlying the association between genetic/phenotypic changes and adaptation of insects to novel niches and host plants.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108146"},"PeriodicalIF":3.6,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581657","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 : 2024-07-08DOI: 10.1016/j.ympev.2024.108147
Samuel G.S. Costa , Andrei Tolstikov , Alireza Saboori , Dante Batista-Ribeiro , Javad Noei , Mark S. Harvey , Matthew D. Shaw , Pavel B. Klimov , Zhi-Qiang Zhang , Almir R. Pepato
Parasitengona (velvet mites, chiggers and water mites) is a highly diverse and globally distributed mite lineage encompassing over 11,000 described species, inhabiting terrestrial, freshwater and marine habitats. Certain species, such as chiggers (Trombiculidae), have a great medical and veterinary importance as they feed on their vertebrate hosts and vector pathogens. Despite extensive previous research, the classification of Parasitengona is still contentious, particularly regarding the boundaries between superfamilies and families, exacerbated by the absence of a comprehensive phylogeny. The ontogeny of most Parasitengona is distinct by the presence of striking metamorphosis, with parasitic larvae being heteromorphic compared to the predatory free-living deutonymphs and adults. The enigmatic superfamily Allotanaupodoidea is an exception, with larvae and active post-larval stages being morphologically similar, suggesting that the absence of metamorphosis may be either an ancestral state or a secondary reversal. Furthermore, there is disagreement in the literature on whether Parasitengona had freshwater or terrestrial origin. Here, we inferred phylogenetic relationships of Parasitengona (89 species, 36 families) and 307 outgroups using five genes (7,838 nt aligned). This phylogeny suggests a terrestrial origin of Parasitengona and a secondary loss of metamorphosis in Allotanaoupodoidea. We recovered the superfamily Trombidioidea (Trombidioidea sensu lato) as a large, well-supported, higher-level clade including 10 sampled families. We propose a new classification for the terrestrial Parasitengona with three new major divisions (epifamilies) of the superfamily Trombidioidea: Trombelloidae (families Audyanidae, Trombellidae, Neotrombidiidae, Johnstonianidae, Chyzeriidae); Trombidioidae (Microtrombidiidae, Neothrombiidae, Achaemenothrombiidae, Trombidiidae, Podothrombiidae); and Trombiculoidae (=Trombiculidae sensu lato). Adding them to previously recognized superfamilies Allotanaupodoidea, Amphotrombioidea, Calyptostomatoidea, Erythraeoidea, Tanaupodoidae and Yurebilloidae.
寄生螨(绒螨、恙螨和水螨)种类繁多,分布于全球各地,包括 11,000 多个已描述的物种,栖息于陆地、淡水和海洋栖息地。某些种类,如恙螨(Trombiculidae),以脊椎动物宿主和病原体媒介为食,因此在医学和兽医学方面具有重要意义。尽管之前进行了大量研究,但寄生虫分类仍存在争议,尤其是超科和科之间的界限,而缺乏全面的系统发育则加剧了这一争议。大多数寄生藤壶虫的本体发育都有显著的变态现象,寄生幼虫与捕食性的自由生活的脱虫和成虫相比具有异形性。神秘的超科 Allotanaupodoidea 是一个例外,其幼虫和活跃的后幼虫阶段在形态上相似,这表明没有变态可能是一种祖先状态,也可能是一种继发性逆转。此外,关于 Parasitengona 是起源于淡水还是陆地,文献中也存在分歧。在此,我们利用 5 个基因(7838 nt 对齐)推断了 Parasitengona(89 种,36 科)和 307 个外群的系统发生关系。该系统发育表明,Parasitengona起源于陆生,Allotanaoupodoidea次生失去了变态过程。我们复原了超科 Trombidioidea(Trombidioidea sensu lato),它是一个大型的、支持良好的、更高层次的支系,包括 10 个采样科。我们为陆生寄生虫提出了一个新的分类法,即在超科 Trombidioidea 中划分出三个新的主要分支(外科):Trombelloidae(Audyanidae科、Trombellidae科、Neotrombidiidae科、Johnstonianidae科、Chyzeriidae科);Trombidioidae(Microtrombidiidae科、Neothrombiidae科、Achaemenothrombiidae科、Trombidiidae科、Podothrombiidae科);以及Trombiculoidae(=Trombiculidae sensu lato)。将它们加入之前已被确认的超科 Allotanaupodoidea、Amphotrombioidea、Calyptostomatoidea、Erythraeoidea、Tanaupodoidae 和 Yurebilloidae。
{"title":"A comprehensive molecular phylogeny of the terrestrial Parasitengona (Acariformes, Prostigmata) provides insights into the evolution of their metamorphosis, invasion into aquatic habitats and classification","authors":"Samuel G.S. Costa , Andrei Tolstikov , Alireza Saboori , Dante Batista-Ribeiro , Javad Noei , Mark S. Harvey , Matthew D. Shaw , Pavel B. Klimov , Zhi-Qiang Zhang , Almir R. Pepato","doi":"10.1016/j.ympev.2024.108147","DOIUrl":"10.1016/j.ympev.2024.108147","url":null,"abstract":"<div><p>Parasitengona (velvet mites, chiggers and water mites) is a highly diverse and globally distributed mite lineage encompassing over 11,000 described species, inhabiting terrestrial, freshwater and marine habitats. Certain species, such as chiggers (Trombiculidae), have a great medical and veterinary importance as they feed on their vertebrate hosts and vector pathogens. Despite extensive previous research, the classification of Parasitengona is still contentious, particularly regarding the boundaries between superfamilies and families, exacerbated by the absence of a comprehensive phylogeny. The ontogeny of most Parasitengona is distinct by the presence of striking metamorphosis, with parasitic larvae being heteromorphic compared to the predatory free-living deutonymphs and adults. The enigmatic superfamily Allotanaupodoidea is an exception, with larvae and active post-larval stages being morphologically similar, suggesting that the absence of metamorphosis may be either an ancestral state or a secondary reversal. Furthermore, there is disagreement in the literature on whether Parasitengona had freshwater or terrestrial origin. Here, we inferred phylogenetic relationships of Parasitengona (89 species, 36 families) and 307 outgroups using five genes (7,838 nt aligned). This phylogeny suggests a terrestrial origin of Parasitengona and a secondary loss of metamorphosis in Allotanaoupodoidea. We recovered the superfamily Trombidioidea (Trombidioidea <em>sensu lato</em>) as a large, well-supported, higher-level clade including 10 sampled families. We propose a new classification for the terrestrial Parasitengona with three new major divisions (epifamilies) of the superfamily Trombidioidea: Trombelloidae (families Audyanidae, Trombellidae, Neotrombidiidae, Johnstonianidae, Chyzeriidae); Trombidioidae (Microtrombidiidae, Neothrombiidae, Achaemenothrombiidae, Trombidiidae, Podothrombiidae); and Trombiculoidae (=Trombiculidae <em>sensu lato</em>). Adding them to previously recognized superfamilies Allotanaupodoidea, Amphotrombioidea, Calyptostomatoidea, Erythraeoidea, Tanaupodoidae and Yurebilloidae.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108147"},"PeriodicalIF":3.6,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581655","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 : 2024-07-07DOI: 10.1016/j.ympev.2024.108140
Cryptic diversity abounds in many biological species, posing challenges to our understanding of biological diversity, conservation and management. Taking the common coralline algae, the subfamily Lithophylloideae as an illustration, this study delved into the implications of cryptic diversity through global-level phylogenetic and geographical analysis based upon Lithophylloideae molecular data worldwide, as well as a multi-locus time-calibrated phylogeny to elucidate their possible evolutionary process. The multiscale analysis revealed the polyphyly in current concept of the genus Lithophyllum. Geographic isolation resulting from the Tethys terminal event (TTE) has led to two distinct distribution regions for this so-called cosmopolitan genus: one regionally distributed along European coasts/Mediterranean that should include the taxonomical Lithophyllum; others widely distributed, particularly among pan-tropic waters, suggesting at least five groups to be rediscovered within the subfamily Lithophylloideae. Meanwhile, the cryptic genus Titanoderma, lacking morphological identification features with Lithophyllum, exhibited differences in distribution and evolutionary patterns consistent with their ecological habits, thus supporting their separation. This study provided useful hints for cryptic diversity, which advocated an integrative thinking to investigating global cryptic diversity and exploring the broad linkages between phylogenetic relationships and evolutionary origin, biogeography, morphological and ecological traits to achieve a more comprehensive understanding of biodiversity.
{"title":"A multiscale analysis of coralline algae Lithophylloideae (Corallinophycidae, Rhodophyta) shedding new light on understanding cryptic diversity","authors":"","doi":"10.1016/j.ympev.2024.108140","DOIUrl":"10.1016/j.ympev.2024.108140","url":null,"abstract":"<div><p>Cryptic diversity abounds in many biological species, posing challenges to our understanding of biological diversity, conservation and management. Taking the common coralline algae, the subfamily Lithophylloideae as an illustration, this study delved into the implications of cryptic diversity through global-level phylogenetic and geographical analysis based upon Lithophylloideae molecular data worldwide, as well as a multi-locus time-calibrated phylogeny to elucidate their possible evolutionary process. The multiscale analysis revealed the polyphyly in current concept of the genus <em>Lithophyllum</em>. Geographic isolation resulting from the Tethys terminal event (TTE) has led to two distinct distribution regions for this so-called cosmopolitan genus: one regionally distributed along European coasts/Mediterranean that should include the taxonomical <em>Lithophyllum</em>; others widely distributed, particularly among pan-tropic waters, suggesting at least five groups to be rediscovered within the subfamily Lithophylloideae. Meanwhile, the cryptic genus <em>Titanoderma</em>, lacking morphological identification features with <em>Lithophyllum</em>, exhibited differences in distribution and evolutionary patterns consistent with their ecological habits, thus supporting their separation. This study provided useful hints for cryptic diversity, which advocated an integrative thinking to investigating global cryptic diversity and exploring the broad linkages between phylogenetic relationships and evolutionary origin, biogeography, morphological and ecological traits to achieve a more comprehensive understanding of biodiversity.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108140"},"PeriodicalIF":3.6,"publicationDate":"2024-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565144","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 : 2024-07-06DOI: 10.1016/j.ympev.2024.108143
Shahan Derkarabetian , Ligia R. Benavides , Gonzalo Giribet
Cyphophthalmi (the mite harvesters) are a group of Opiliones with broad interest due to their species being classic examples of short-range endemics and displaying model biogeographical patterns for poor dispersers. Cyphophthalmi phylogeny has received attention using morphology, Sanger-based sequencing data, or transcriptomics. Here we turn to a new type of data, ultraconserved elements (UCEs) and provide a first phylogeny for the entire suborder Cyphophthalmi using such data and including representatives from 36 of the 46 currently recognized genera. Phylogenetic analysis of four occupancy matrices (50%, 75%, 90% and 95%), for a total of 840, 567, 129, and 23 loci, respectively, yielded a well resolved phylogeny with monophyly of Pettalidae, Parasironidae, Stylocellidae and Troglosironidae. However, Neogoveidae appeared paraphyletic with respect to Ogoveidae in all datasets and to Troglosironidae in some, and the traditional Sironidae, which was monophyletic, now appeared paraphyletic with respect to the recently erected family Parasironidae. Our phylogenomic results using UCE data resolve the position of several problematic genera (e.g., Pettalus) and add support to other parts of the tree that received low support in Sanger-based phylogenies. Our work also stresses the possibility to add museum samples to phylogenies although methods for optimizing DNA yield from such small-bodied specimens need further improvement. Finally, this backbone phylogeny demonstrates the feasibility of an all-species phylogeny using UCEs for Cyphophthalmi, and by extension, for all Opiliones.
{"title":"Reassessing the phylogeny of Cyphophthalmi with phylogenomics: A UCE-based phylogeny of mite harvesters (Opiliones)","authors":"Shahan Derkarabetian , Ligia R. Benavides , Gonzalo Giribet","doi":"10.1016/j.ympev.2024.108143","DOIUrl":"10.1016/j.ympev.2024.108143","url":null,"abstract":"<div><p>Cyphophthalmi (the mite harvesters) are a group of Opiliones with broad interest due to their species being classic examples of short-range endemics and displaying model biogeographical patterns for poor dispersers. Cyphophthalmi phylogeny has received attention using morphology, Sanger-based sequencing data, or transcriptomics. Here we turn to a new type of data, ultraconserved elements (UCEs) and provide a first phylogeny for the entire suborder Cyphophthalmi using such data and including representatives from 36 of the 46 currently recognized genera. Phylogenetic analysis of four occupancy matrices (50%, 75%, 90% and 95%), for a total of 840, 567, 129, and 23 loci, respectively, yielded a well resolved phylogeny with monophyly of Pettalidae, Parasironidae, Stylocellidae and Troglosironidae. However, Neogoveidae appeared paraphyletic with respect to Ogoveidae in all datasets and to Troglosironidae in some, and the traditional Sironidae, which was monophyletic, now appeared paraphyletic with respect to the recently erected family Parasironidae. Our phylogenomic results using UCE data resolve the position of several problematic genera (e.g., <em>Pettalus</em>) and add support to other parts of the tree that received low support in Sanger-based phylogenies. Our work also stresses the possibility to add museum samples to phylogenies although methods for optimizing DNA yield from such small-bodied specimens need further improvement. Finally, this backbone phylogeny demonstrates the feasibility of an all-species phylogeny using UCEs for Cyphophthalmi, and by extension, for all Opiliones.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108143"},"PeriodicalIF":3.6,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141560460","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 : 2024-07-06DOI: 10.1016/j.ympev.2024.108138
Min Liao , Jun-Yi Zhang , Yu Feng , Zong-Xin Ren , Heng-Ning Deng , Bo Xu
Cypripedioideae (slipper orchids; Orchidaceae) currently consist of ∼200 herbaceous species with a strikingly disjunctive distribution in tropical and temperate regions of both hemispheres. In this study, an updated phylogeny with representatives from all five cypripedioid genera was presented based on maximum likelihood and Bayesian inference of plastome and low-copy nuclear genes. Phylogenomic analyses indicated that each genus is monophyletic, but some relationships (e.g., those among Cypripedium sects. Acaulia, Arietinum, Bifolia, Flabellinervia, Obtusipetala and Palangshanensia) conflict with those in previous studies based on Sanger data. Cypripedioideae appeared to have arisen in South America and/or the adjacent Qinghai-Tibet Plateau and Hengduan Mountains ∼35 Mya. We inferred multiple dispersal events between East Asia and North America in Cypripedium, and between mainland Southeast Asia and the Malay Archipelago in Paphiopedilum. In the Americas, divergences among four genera (except Cypripedium) occurred around 31–20 Mya, long before the closure of the Isthmus of Panama, indicating the importance of long-distance dispersal. Evolutionary patterns between morphological and plastome character evolution suggested several traits, genome size and NDH genes, which are likely to have contributed to the success of slipper orchids in alpine floras and low-elevation forests. Species diversification rates were notably higher in epiphytic clades of Paphiopedilum than in other, terrestrial cypripedioids, paralleling similar accelerations associated with epiphytism in other groups. This study also suggested that sea-level fluctuations and mountain-building processes promoted the diversification of the largest genera, Paphiopedilum and Cypripedium.
{"title":"Phylogenomic insights into the historical biogeography, character-state evolution, and species diversification rates of Cypripedioideae (Orchidaceae)","authors":"Min Liao , Jun-Yi Zhang , Yu Feng , Zong-Xin Ren , Heng-Ning Deng , Bo Xu","doi":"10.1016/j.ympev.2024.108138","DOIUrl":"10.1016/j.ympev.2024.108138","url":null,"abstract":"<div><p>Cypripedioideae (slipper orchids; Orchidaceae) currently consist of ∼200 herbaceous species with a strikingly disjunctive distribution in tropical and temperate regions of both hemispheres. In this study, an updated phylogeny with representatives from all five cypripedioid genera was presented based on maximum likelihood and Bayesian inference of plastome and low-copy nuclear genes. Phylogenomic analyses indicated that each genus is monophyletic, but some relationships (e.g., those among <em>Cypripedium</em> sects. <em>Acaulia</em>, <em>Arietinum</em>, <em>Bifolia</em>, <em>Flabellinervia</em>, <em>Obtusipetala</em> and <em>Palangshanensia</em>) conflict with those in previous studies based on Sanger data. Cypripedioideae appeared to have arisen in South America and/or the adjacent Qinghai-Tibet Plateau and Hengduan Mountains ∼35 Mya. We inferred multiple dispersal events between East Asia and North America in <em>Cypripedium</em>, and between mainland Southeast Asia and the Malay Archipelago in <em>Paphiopedilum</em>. In the Americas, divergences among four genera (except <em>Cypripedium</em>) occurred around 31–20 Mya, long before the closure of the Isthmus of Panama, indicating the importance of long-distance dispersal. Evolutionary patterns between morphological and plastome character evolution suggested several traits, genome size and <em>NDH</em> genes, which are likely to have contributed to the success of slipper orchids in alpine floras and low-elevation forests. Species diversification rates were notably higher in epiphytic clades of <em>Paphiopedilum</em> than in other, terrestrial cypripedioids, paralleling similar accelerations associated with epiphytism in other groups. This study also suggested that sea-level fluctuations and mountain-building processes promoted the diversification of the largest genera, <em>Paphiopedilum</em> and <em>Cypripedium</em>.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108138"},"PeriodicalIF":3.6,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141560459","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 : 2024-07-05DOI: 10.1016/j.ympev.2024.108144
Saskia Wutke , Stephan M. Blank , Jean-Luc Boevé , Brant C. Faircloth , Frank Koch , Catherine R. Linnen , Tobias Malm , Gengyun Niu , Marko Prous , Nathan M. Schiff , Stefan Schmidt , Andreas Taeger , Lars Vilhelmsen , Niklas Wahlberg , Meicai Wei , Tommi Nyman
Phylogenomic approaches have recently helped elucidate various insect relationships, but large-scale comprehensive analyses on relationships within sawflies and woodwasps are still lacking. Here, we infer the relationships and long-term biogeographic history of these hymenopteran groups using a large dataset of 354 UCE loci collected from 385 species that represent all major lineages. Early Hymenoptera started diversifying during the Early Triassic ∼249 Ma and spread all over the ancient supercontinent Pangaea. We recovered Xyeloidea as a monophyletic sister group to other Hymenoptera and Pamphilioidea as sister to Unicalcarida. Within the diverse family Tenthredinidae, our taxonomically and geographically expanded taxon sampling highlights the non-monophyly of several traditionally defined subfamilies. In addition, the recent removal of Athalia and related genera from the Tenthredinidae into the separate family Athaliidae is supported. The deep historical biogeography of the group is characterised by independent dispersals and re-colonisations between the northern (Laurasia) and southern (Gondwana) palaeocontinents. The breakup of these landmasses led to ancient vicariance in several Gondwanan lineages, while interchange across the Northern Hemisphere has continued until the Recent. The little-studied African sawfly fauna is likewise a diverse mixture of groups with varying routes of colonization. Our results reveal interesting parallels in the evolution and biogeography of early hymenopterans and other ancient insect groups.
{"title":"Phylogenomics and biogeography of sawflies and woodwasps (Hymenoptera, Symphyta)","authors":"Saskia Wutke , Stephan M. Blank , Jean-Luc Boevé , Brant C. Faircloth , Frank Koch , Catherine R. Linnen , Tobias Malm , Gengyun Niu , Marko Prous , Nathan M. Schiff , Stefan Schmidt , Andreas Taeger , Lars Vilhelmsen , Niklas Wahlberg , Meicai Wei , Tommi Nyman","doi":"10.1016/j.ympev.2024.108144","DOIUrl":"10.1016/j.ympev.2024.108144","url":null,"abstract":"<div><p>Phylogenomic approaches have recently helped elucidate various insect relationships, but large-scale comprehensive analyses on relationships within sawflies and woodwasps are still lacking. Here, we infer the relationships and long-term biogeographic history of these hymenopteran groups using a large dataset of 354 UCE loci collected from 385 species that represent all major lineages. Early Hymenoptera started diversifying during the Early Triassic ∼249 Ma and spread all over the ancient supercontinent Pangaea. We recovered Xyeloidea as a monophyletic sister group to other Hymenoptera and Pamphilioidea as sister to Unicalcarida. Within the diverse family Tenthredinidae, our taxonomically and geographically expanded taxon sampling highlights the non-monophyly of several traditionally defined subfamilies. In addition, the recent removal of <em>Athalia</em> and related genera from the Tenthredinidae into the separate family Athaliidae is supported. The deep historical biogeography of the group is characterised by independent dispersals and re-colonisations between the northern (Laurasia) and southern (Gondwana) palaeocontinents. The breakup of these landmasses led to ancient vicariance in several Gondwanan lineages, while interchange across the Northern Hemisphere has continued until the Recent. The little-studied African sawfly fauna is likewise a diverse mixture of groups with varying routes of colonization. Our results reveal interesting parallels in the evolution and biogeography of early hymenopterans and other ancient insect groups.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108144"},"PeriodicalIF":3.6,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001362/pdfft?md5=b736e4dfeb4010b7432517a3e51d9a53&pid=1-s2.0-S1055790324001362-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141556093","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 : 2024-07-02DOI: 10.1016/j.ympev.2024.108142
Bing Yang , Xin Zhou , Shanlin Liu
Assigning a query individual animal or plant to its derived population is a prime task in diverse applications related to organismal genealogy. Such endeavors have conventionally relied on short DNA sequences under a phylogenetic framework. These methods naturally show constraints when the inferred population sources are ambiguously phylogenetically structured, a scenario demanding substantially more informative genetic signals. Recent advances in cost-effective production of whole-genome sequences and artificial intelligence have created an unprecedented opportunity to trace the population origin for essentially any given individual, as long as the genome reference data are comprehensive and standardized. Here, we developed a convolutional neural network method to identify population origins using genomic SNPs. Three empirical datasets (an Asian honeybee, a red fire ant, and a chicken datasets) and two simulated populations are used for the proof of concepts. The performance tests indicate that our method can accurately identify the genealogy origin of query individuals, with success rates ranging from 93 % to 100 %. We further showed that the accuracy of the model can be significantly increased by refining the informative sites through filtering. Our method is robust to configurations related to batch sizes and epochs, whereas model learning benefits from the setting of a proper preset learning rate. Moreover, we explained the importance score of key sites for algorithm interpretability and credibility, which has been largely ignored. We anticipate that by coupling genomics and deep learning, our method will see broad potential in conservation and management applications that involve natural resources, invasive pests and weeds, and illegal trades of wildlife products.
{"title":"Tracing the genealogy origin of geographic populations based on genomic variation and deep learning","authors":"Bing Yang , Xin Zhou , Shanlin Liu","doi":"10.1016/j.ympev.2024.108142","DOIUrl":"10.1016/j.ympev.2024.108142","url":null,"abstract":"<div><p>Assigning a query individual animal or plant to its derived population is a prime task in diverse applications related to organismal genealogy. Such endeavors have conventionally relied on short DNA sequences under a phylogenetic framework. These methods naturally show constraints when the inferred population sources are ambiguously phylogenetically structured, a scenario demanding substantially more informative genetic signals. Recent advances in cost-effective production of whole-genome sequences and artificial intelligence have created an unprecedented opportunity to trace the population origin for essentially any given individual, as long as the genome reference data are comprehensive and standardized. Here, we developed a convolutional neural network method to identify population origins using genomic SNPs. Three empirical datasets (an Asian honeybee, a red fire ant, and a chicken datasets) and two simulated populations are used for the proof of concepts. The performance tests indicate that our method can accurately identify the genealogy origin of query individuals, with success rates ranging from 93 % to 100 %. We further showed that the accuracy of the model can be significantly increased by refining the informative sites through <span><math><mrow><msub><mi>F</mi><mrow><mi>ST</mi></mrow></msub></mrow></math></span> filtering. Our method is robust to configurations related to batch sizes and epochs, whereas model learning benefits from the setting of a proper preset learning rate. Moreover, we explained the importance score of key sites for algorithm interpretability and credibility, which has been largely ignored. We anticipate that by coupling genomics and deep learning, our method will see broad potential in conservation and management applications that involve natural resources, invasive pests and weeds, and illegal trades of wildlife products.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"198 ","pages":"Article 108142"},"PeriodicalIF":3.6,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141536108","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 : 2024-07-02DOI: 10.1016/j.ympev.2024.108141
Mauricio Langleib , Javier Calvelo , Alicia Costábile , Estela Castillo , José F. Tort , Federico G. Hoffmann , Anna V. Protasio , Uriel Koziol , Andrés Iriarte
Platyhelminthes, also known as flatworms, is a phylum of bilaterian invertebrates infamous for their parasitic representatives. The classes Cestoda, Monogenea, and Trematoda comprise parasitic helminths inhabiting multiple hosts, including fishes, humans, and livestock, and are responsible for considerable economic damage and burden on human health. As in other animals, the genomes of flatworms have a wide variety of paralogs, genes related via duplication, whose origins could be mapped throughout the evolution of the phylum. Through in-silico analysis, we studied inparalogs, i.e., species-specific duplications, focusing on their biological functions, expression changes, and evolutionary rate. These genes are thought to be key players in the adaptation process of species to each particular niche. Our results showed that genes related with specific functional terms, such as response to stress, transferase activity, oxidoreductase activity, and peptidases, are overrepresented among inparalogs. This trend is conserved among species from different classes, including free-living species. Available expression data from Schistosoma mansoni, a parasite from the trematode class, demonstrated high conservation of expression patterns between inparalogs, but with notable exceptions, which also display evidence of rapid evolution. We discuss how natural selection may operate to maintain these genes and the particular duplication models that fit better to the observations. Our work supports the critical role of gene duplication in the evolution of flatworms, representing the first study of inparalogs evolution at the genome-wide level in this group.
{"title":"Evolutionary analysis of species-specific duplications in flatworm genomes","authors":"Mauricio Langleib , Javier Calvelo , Alicia Costábile , Estela Castillo , José F. Tort , Federico G. Hoffmann , Anna V. Protasio , Uriel Koziol , Andrés Iriarte","doi":"10.1016/j.ympev.2024.108141","DOIUrl":"10.1016/j.ympev.2024.108141","url":null,"abstract":"<div><p>Platyhelminthes, also known as flatworms, is a phylum of bilaterian invertebrates infamous for their parasitic representatives. The classes Cestoda, Monogenea, and Trematoda comprise parasitic helminths inhabiting multiple hosts, including fishes, humans, and livestock, and are responsible for considerable economic damage and burden on human health. As in other animals, the genomes of flatworms have a wide variety of paralogs, genes related via duplication, whose origins could be mapped throughout the evolution of the phylum. Through <em>in-silico</em> analysis, we studied inparalogs, <em>i.e.</em>, species-specific duplications, focusing on their biological functions, expression changes, and evolutionary rate. These genes are thought to be key players in the adaptation process of species to each particular niche. Our results showed that genes related with specific functional terms, such as response to stress, transferase activity, oxidoreductase activity, and peptidases, are overrepresented among inparalogs. This trend is conserved among species from different classes, including free-living species. Available expression data from <em>Schistosoma mansoni</em>, a parasite from the trematode class, demonstrated high conservation of expression patterns between inparalogs, but with notable exceptions, which also display evidence of rapid evolution. We discuss how natural selection may operate to maintain these genes and the particular duplication models that fit better to the observations. Our work supports the critical role of gene duplication in the evolution of flatworms, representing the first study of inparalogs evolution at the genome-wide level in this group.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"199 ","pages":"Article 108141"},"PeriodicalIF":3.6,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141536107","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 : 2024-06-24DOI: 10.1016/j.ympev.2024.108135
Safiqul Islam , Claire Peart , Christian Kehlmaier , Yue-Hua Sun , Fumin Lei , Andreas Dahl , Sylvia Klemroth , Dimitra Alexopoulou , Maria del Mar Delgado , Paola Laiolo , Juan Carlos Illera , Sebastian Dirren , Sabine Hille , Davaa Lkhagvasuren , Till Töpfer , Martin Kaiser , Axel Gebauer , Jochen Martens , Claudia Paetzold , Martin Päckert
Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis).
Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus Pyrgilauda. Misplacement of one species-level taxon (Onychostruthus tazcanowskii) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between M. nivalis and the QTP endemic M. henrici was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera Montifringilla and Pyrgilauda with monotypic Onychostruthus being sister to the latter. The Afghan endemic P. theresae likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with P. ruficollis. Our extended trans-Palearctic sampling for the white-winged snowfinch, M. nivalis, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 – 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.
博物馆收藏的历史标本提供了一个宝贵的材料来源,这些标本也来自偏远地区或冲突地区,而现在的科学家还很难接触到这些地区的标本。通过这项研究,我们利用阿富汗特有物种--阿富汗雪雀(Pyrgilauda theresae)的整张皮上的历史 DNA,提供了一个完整的雪雀分类群系统发育。为了解决以前的系统发育假说之间的强烈冲突,我们利用ddRAD测序技术为青藏高原(QTP)特有的所有现生雪雀物种和中西古北唯一雪雀物种(Montifringilla nivalis)的扩展种内取样生成了选定类群的新型有丝分裂基因组序列和全基因组SNP数据。我们的系统发育重建一致驳斥了之前提出的雪雀属(Pyrgilauda)旁系的观点。一个种级分类群(Onychostruthus tazcanowskii)在以前的雪雀系统发育中的错误定位无疑是由包含异特异性序列信息的嵌合有丝分裂基因组推断出来的。此外,对新的序列数据和以前产生的序列数据进行比较后发现,假定 M. nivalis 与 QTP 特有的 M. henrici 之间的姊妹群关系是基于有缺陷的分类学提出的。基于全基因组 SNP 数据和有丝分裂基因组的系统发育重建结果基本一致,支持 Montifringilla 属和 Pyrgilauda 属互为单系,单型的 Onychostruthus 是后者的姊妹属。阿富汗特有的P. theresae可能起源于上新世的一次相当古老的西藏外扩散,可能与P. ruficollis有共同的祖先。我们对白翅雪雀(M. nivalis)进行的跨北极采样证实,在距今150万-270万年前的一个亚洲支系和一个欧洲支系之间存在着强烈的世系分化。全基因组 SNP 数据表明,来自阿尔卑斯山和坎塔布里亚山脉的欧洲样本之间存在微妙的分化。
{"title":"Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies)","authors":"Safiqul Islam , Claire Peart , Christian Kehlmaier , Yue-Hua Sun , Fumin Lei , Andreas Dahl , Sylvia Klemroth , Dimitra Alexopoulou , Maria del Mar Delgado , Paola Laiolo , Juan Carlos Illera , Sebastian Dirren , Sabine Hille , Davaa Lkhagvasuren , Till Töpfer , Martin Kaiser , Axel Gebauer , Jochen Martens , Claudia Paetzold , Martin Päckert","doi":"10.1016/j.ympev.2024.108135","DOIUrl":"10.1016/j.ympev.2024.108135","url":null,"abstract":"<div><p>Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, <em>Pyrgilauda theresae</em>. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (<em>Montifringilla nivalis</em>).</p><p>Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus <em>Pyrgilauda</em>. Misplacement of one species-level taxon (<em>Onychostruthus tazcanowskii</em>) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between <em>M. nivalis</em> and the QTP endemic <em>M. henrici</em> was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera <em>Montifringilla</em> and <em>Pyrgilauda</em> with monotypic <em>Onychostruthus</em> being sister to the latter. The Afghan endemic <em>P. theresae</em> likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with <em>P. ruficollis</em>. Our extended <em>trans</em>-Palearctic sampling for the white-winged snowfinch, <em>M. nivalis</em>, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 – 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"198 ","pages":"Article 108135"},"PeriodicalIF":3.6,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001271/pdfft?md5=fd6533e17820bc8062aaef2c71923cfa&pid=1-s2.0-S1055790324001271-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460913","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}