Pub Date : 2024-10-15DOI: 10.1016/j.ympev.2024.108220
Liang-Fei Yao, Zi-Kai Shao, Ni Li, Yue Hu, Xiao-Feng Xue
Species complex hinders the exploration of terrestrial species diversity, particularly in small arthropod lineages that are morphologically indistinguishable from each other. The Epitrimerus sabinae complex in the Eriophyoidea provides a valuable case study in species complex delimitation, as they exhibit limited morphological variations. In this study, we obtained thousands of nuclear genomic single-nucleotide polymorphisms via whole-genome sequencing from 55 E. sabinae complex specimens, covering their potential all known distribution ranges. We implemented a framework to infer cryptic speciation, which involved phylogenetic and genetic clustering to identify potential species, followed by population demographic assessment to confirm lineage independence (and thus species status). Our results demonstrate that the E. sabinae complex comprises ten distinct species. These species range from highly divergent, genetically isolated lineages, to differentiated populations involving gene flow. This gene flow is widespread across species boundaries, indicating potential genetic introgression among them. Additionally, demographic analyses revealed that the ten species have followed unique trajectories in size change during the Quaternary period. Time-calibrated phylogenies further showed that speciation in the E. sabinae complex occurred rapidly, resulting in a rapid radiation during the Neogene period. Collectively, parallelism/convergence and recent divergence involving multiple gene flows may explain the homoplasy of E. sabinae complex. Our results highlight the integrated approach in species complex delimitation.
{"title":"Genome-wide species delimitation and quantification of the extent of introgression in eriophyoid mite Epitrimerus sabinae complex (Acariformes: Eriophyoidea)","authors":"Liang-Fei Yao, Zi-Kai Shao, Ni Li, Yue Hu, Xiao-Feng Xue","doi":"10.1016/j.ympev.2024.108220","DOIUrl":"10.1016/j.ympev.2024.108220","url":null,"abstract":"<div><div>Species complex hinders the exploration of terrestrial species diversity, particularly in small arthropod lineages that are morphologically indistinguishable from each other. The <em>Epitrimerus sabinae</em> complex in the Eriophyoidea provides a valuable case study in species complex delimitation, as they exhibit limited morphological variations. In this study, we obtained thousands of nuclear genomic single-nucleotide polymorphisms via whole-genome sequencing from 55 <em>E. sabinae</em> complex specimens, covering their potential all known distribution ranges. We implemented a framework to infer cryptic speciation, which involved phylogenetic and genetic clustering to identify potential species, followed by population demographic assessment to confirm lineage independence (and thus species status). Our results demonstrate that the <em>E. sabinae</em> complex comprises ten distinct species. These species range from highly divergent, genetically isolated lineages, to differentiated populations involving gene flow. This gene flow is widespread across species boundaries, indicating potential genetic introgression among them. Additionally, demographic analyses revealed that the ten species have followed unique trajectories in size change during the Quaternary period. Time-calibrated phylogenies further showed that speciation in the <em>E. sabinae</em> complex occurred rapidly, resulting in a rapid radiation during the Neogene period. Collectively, parallelism/convergence and recent divergence involving multiple gene flows may explain the homoplasy of <em>E. sabinae</em> complex. Our results highlight the integrated approach in species complex delimitation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108220"},"PeriodicalIF":3.6,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481853","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 : 2024-10-12DOI: 10.1016/j.ympev.2024.108206
Erik Ciaccio , Jason E. Bond , Marshal Hedin , Chris A. Hamilton
Antrodiaetus is a lineage of mygalomorph spider (Mygalomorphae: Antrodiaetidae) that has persisted since the late Cretaceous and has a disjunct Holarctic distribution and strong morphological conservatism. These folding-door spiders possess a life history (i.e., limited dispersal, conserved environmental niche) that closely ties their evolution to geology. This study produces a robust, well-supported phylogenomic inference of all currently recognized Antrodiaetus species using UCEs (Ultraconserved Elements), corroborates previous biogeographical hypotheses, and proposes new hypotheses about diversification patterns. We also confirm that previously suspected cryptic diversity within A. pacificus is underestimated, as this nominal species comprises multiple divergent and cryptic lineages. Our phylogeny now serves as a foundation for understanding Antrodiaetus species relationships, biogeography, and speciation.
{"title":"Revisiting evolutionary relationships of Antrodiaetus (Araneae, Mygalomorphae, Antrodiaetidae) using phylogenomics; implications for species diversity and biogeography of a persistent Holarctic lineage","authors":"Erik Ciaccio , Jason E. Bond , Marshal Hedin , Chris A. Hamilton","doi":"10.1016/j.ympev.2024.108206","DOIUrl":"10.1016/j.ympev.2024.108206","url":null,"abstract":"<div><div><em>Antrodiaetus</em> is a lineage of mygalomorph spider (Mygalomorphae: Antrodiaetidae) that has persisted since the late Cretaceous and has a disjunct Holarctic distribution and strong morphological conservatism. These folding-door spiders possess a life history (i.e., limited dispersal, conserved environmental niche) that closely ties their evolution to geology. This study produces a robust, well-supported phylogenomic inference of all currently recognized <em>Antrodiaetus</em> species using UCEs (Ultraconserved Elements), corroborates previous biogeographical hypotheses, and proposes new hypotheses about diversification patterns. We also confirm that previously suspected cryptic diversity within <em>A. pacificus</em> is underestimated, as this nominal species comprises multiple divergent and cryptic lineages. Our phylogeny now serves as a foundation for understanding <em>Antrodiaetus</em> species relationships, biogeography, and speciation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108206"},"PeriodicalIF":3.6,"publicationDate":"2024-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481854","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 : 2024-10-11DOI: 10.1016/j.ympev.2024.108215
Justin L. Lee , Platon V. Yushchenko , Chatmongkon Suwannapoom , Parinya Pawangkhanant , L. Lee Grismer , Tan Van Nguyen , V. Deepak , Surya Narayanan , Sandeep Das , Thy Neang , H.T. Lalremsanga , Jian-Huan Yang , Daniel Jablonski , Mustafa Erkaya , Gernot Vogel , Aaron M. Bauer , Nikolay A. Poyarkov
With 90 recognized species, kukri snakes in the genus Oligodon Fitzinger constitute the second largest snake radiation in the world. Oligodon species are collectively distributed across the Asian continent and possess several ecological and morphological attributes that are unique amongst other snakes. Despite their high levels of species richness, evolutionary relationships within Oligodon are poorly understood due to a limited number of samples and genetic markers available in earlier phylogenies. In this study, we assembled the largest molecular dataset of Oligodon to date, which we use to assess the systematics and biogeography of the entire genus. Based on a combination of maximum likelihood and Bayesian phylogenies using fragments of three mitochondrial genes (12 s, 16 s, CytB) and three nuclear genes (Rag1, C-mos, BDNF), we identify eight deeply divergent clades within Oligodon, of which only two correspond with species groupings that were recognized by previous morphological classifications. Four species delimitation methods employed on the mitochondrial portion of the dataset resulted in dramatically divergent estimations of molecular operational taxonomic units (mOTUs). When combined, all four methods support the existence of unrecognized species-level lineages, but also indicate that several other Oligodon species are poorly differentiated genetically and require additional integrative taxonomic research to properly resolve. Based on divergence dating, we demonstrate that Oligodon began to diversify during the early Neogene and hypothesize that the most recent common ancestor of the genus originated in mainland Southeast Asia. We conclude by recognizing eight phylogenetically defined species groups and identify sampling gaps that require further investigation once new data becomes available. This study contributes to a greater understanding of snake evolution on the Asian continent and acts as a baseline for future studies of this speciose genus.
{"title":"A multi-gene phylogeny of the Asian kukri snakes (Oligodon Fitzinger, 1826): Sharpening the blade of the second largest serpent radiation (Reptilia: Squamata: Colubridae)","authors":"Justin L. Lee , Platon V. Yushchenko , Chatmongkon Suwannapoom , Parinya Pawangkhanant , L. Lee Grismer , Tan Van Nguyen , V. Deepak , Surya Narayanan , Sandeep Das , Thy Neang , H.T. Lalremsanga , Jian-Huan Yang , Daniel Jablonski , Mustafa Erkaya , Gernot Vogel , Aaron M. Bauer , Nikolay A. Poyarkov","doi":"10.1016/j.ympev.2024.108215","DOIUrl":"10.1016/j.ympev.2024.108215","url":null,"abstract":"<div><div>With 90 recognized species, kukri snakes in the genus <em>Oligodon</em> Fitzinger constitute the second largest snake radiation in the world. <em>Oligodon</em> species are collectively distributed across the Asian continent and possess several ecological and morphological attributes that are unique amongst other snakes. Despite their high levels of species richness, evolutionary relationships within <em>Oligodon</em> are poorly understood due to a limited number of samples and genetic markers available in earlier phylogenies. In this study, we assembled the largest molecular dataset of <em>Oligodon</em> to date, which we use to assess the systematics and biogeography of the entire genus. Based on a combination of maximum likelihood and Bayesian phylogenies using fragments of three mitochondrial genes (12 s, 16 s, CytB) and three nuclear genes (Rag1, C-mos, BDNF), we identify eight deeply divergent clades within <em>Oligodon</em>, of which only two correspond with species groupings that were recognized by previous morphological classifications. Four species delimitation methods employed on the mitochondrial portion of the dataset resulted in dramatically divergent estimations of molecular operational taxonomic units (mOTUs). When combined, all four methods support the existence of unrecognized species-level lineages, but also indicate that several other <em>Oligodon</em> species are poorly differentiated genetically and require additional integrative taxonomic research to properly resolve. Based on divergence dating, we demonstrate that <em>Oligodon</em> began to diversify during the early Neogene and hypothesize that the most recent common ancestor of the genus originated in mainland Southeast Asia. We conclude by recognizing eight phylogenetically defined species groups and identify sampling gaps that require further investigation once new data becomes available. This study contributes to a greater understanding of snake evolution on the Asian continent and acts as a baseline for future studies of this speciose genus.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108215"},"PeriodicalIF":3.6,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481850","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 : 2024-10-10DOI: 10.1016/j.ympev.2024.108207
Pierre-Guillaume Brun , Stéphane Hourdez , Marion Ballenghien , Yadong Zhou , Jean Mary , Didier Jollivet
The Alvinellidae are a family of worms that are endemic to deep-sea hydrothermal vents in the Pacific and Indian Oceans. These annelid worms, a sister group to the Ampharetidae, occupy a wide range of thermal habitats. The family includes the most thermotolerant marine animals described to date such as the Pompeii worm Alvinella pompejana, and other species living at much lower temperatures such as Paralvinella grasslei or Paralvinella pandorae. The phylogeny of this family has not been studied extensively. It is, however, a complex case where molecular phylogenies have given conflicting results, especially concerning the monophyletic or polyphyletic nature of the genus Paralvinella.
We carried out a comprehensive study of the phylogeny of this family using the best molecular data currently available from RNAseq datasets, leading to several hundred orthologous transcripts for 11 of the 14 species currently described or in description. The results obtained by the two most popular phylogenetic inference models (using either gene concatenation with maximum likelihood, or a coalescent-based model from gene trees) were compared using a series of ampharetid and terebellid outgroups.
Our study shows that the global phylogenetic signal favors the hypothesis of paraphyly for the Paralvinella genus, with P. pandorae being sister species of the other Alvinellidae.
However, a high number of gene trees also supports the hypothesis of alternative trees in which the monophyly of the Paralvinella genus, as initially proposed by Desbruyères and Laubier, is valid with the species P. pandorae and Paralvinella unidentata being sister species. According to molecular dating, the radiation of the Alvinellidae was rapid and took place in a short period of time between 80 and 110 million years ago. This is reflected at the genomic scale by gene trees equally separated between different phylogenetic hypothesis, showing high rates of incomplete lineage sorting between the first lineages of the Alvinellidae and probable gene transfers. Although different genomic regions seem to have different phylogenetic stories in the early step of the alvinellid radiation, our study supports the view that the two P. pandorae species can be grouped into a separate genus (possibly Nautalvinella) and that the Miralvinella subgenus, defined by Desbruyères and Laubier, is not valid anymore.
{"title":"A step in the deep evolution of Alvinellidae (Annelida: Polychaeta): A phylogenomic comparative approach based on transcriptomes","authors":"Pierre-Guillaume Brun , Stéphane Hourdez , Marion Ballenghien , Yadong Zhou , Jean Mary , Didier Jollivet","doi":"10.1016/j.ympev.2024.108207","DOIUrl":"10.1016/j.ympev.2024.108207","url":null,"abstract":"<div><div>The Alvinellidae are a family of worms that are endemic to deep-sea hydrothermal vents in the Pacific and Indian Oceans. These annelid worms, a sister group to the Ampharetidae, occupy a wide range of thermal habitats. The family includes the most thermotolerant marine animals described to date such as the Pompeii worm <em>Alvinella pompejana</em>, and other species living at much lower temperatures such as <em>Paralvinella grasslei</em> or <em>Paralvinella pandorae</em>. The phylogeny of this family has not been studied extensively. It is, however, a complex case where molecular phylogenies have given conflicting results, especially concerning the monophyletic or polyphyletic nature of the genus <em>Paralvinella</em>.</div><div>We carried out a comprehensive study of the phylogeny of this family using the best molecular data currently available from RNAseq datasets, leading to several hundred orthologous transcripts for 11 of the 14 species currently described or in description. The results obtained by the two most popular phylogenetic inference models (using either gene concatenation with maximum likelihood, or a coalescent-based model from gene trees) were compared using a series of ampharetid and terebellid outgroups.</div><div>Our study shows that the global phylogenetic signal favors the hypothesis of paraphyly for the <em>Paralvinella</em> genus, with <em>P. pandorae</em> being sister species of the other Alvinellidae.</div><div>However, a high number of gene trees also supports the hypothesis of alternative trees in which the monophyly of the <em>Paralvinella</em> genus, as initially proposed by Desbruyères and Laubier, is valid with the species <em>P. pandorae</em> and <em>Paralvinella unidentata</em> being sister species. According to molecular dating, the radiation of the Alvinellidae was rapid and took place in a short period of time between 80 and 110 million years ago. This is reflected at the genomic scale by gene trees equally separated between different phylogenetic hypothesis, showing high rates of incomplete lineage sorting between the first lineages of the Alvinellidae and probable gene transfers. Although different genomic regions seem to have different phylogenetic stories in the early step of the alvinellid radiation, our study supports the view that the two <em>P. pandorae</em> species can be grouped into a separate genus (possibly <em>Nautalvinella</em>) and that the <em>Miralvinella</em> subgenus, defined by Desbruyères and Laubier, is not valid anymore.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108207"},"PeriodicalIF":3.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407274","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 : 2024-10-10DOI: 10.1016/j.ympev.2024.108205
Peter A. Scott , Elnaz Najafi-Majd , Elif Yıldırım Caynak , Müge Gidiş , Uğur Kaya , H. Bradley Shaffer
Salamanders of the genus Lyciasalamandra are represented by as many as 20 narrow-range endemic taxa inhabiting the Mediterranean coast of Turkey and a handful of Aegean Islands. Despite recent molecular phylogenetic studies, the genus is rife with uncertainty about the number of contained species and their phylogenetic relationships, both of which can interfere with needed conservation actions. To test species limits and infer interrelationships we generated as many as 113,176 RAD loci containing 229,427 single nucleotide polymorphisms (SNPs), for 110 specimens of Lyciasalamandra representing 19 of the 20 described taxa. Through a conservative species delimitation approach, we found support for eight species in the genus which broadly agree with currently described species-level diversity. We then use multiple coalescent-based species tree methods to resolve relationships in this relatively old, synchronous species radiation. We recommend synonymization of the largely over-split subspecific taxa, and the elevation of L. luschani finikensis to full species status as L. finikensis. Our hope is that this revised taxonomic framework provides a stable foundation for conservation management in these fragile, microendemic taxa.
Lyciasalamandra 属蝾螈有多达 20 个狭窄范围的特有类群，栖息于土耳其地中海沿岸和少数爱琴海岛屿。尽管最近进行了分子系统发育研究，但该属所含物种的数量及其系统发育关系仍充满不确定性，这两者都会干扰所需的保护行动。为了测试物种限制和推断相互关系，我们为 110 个 Lyciasalamandra 标本生成了多达 113,176 个 RAD 位点，包含 229,427 个单核苷酸多态性（SNPs），这些标本代表了 20 个已描述类群中的 19 个。通过保守的物种划分方法，我们发现该属有 8 个物种，与目前描述的物种多样性基本一致。然后，我们使用多种基于聚合的物种树方法来解决这一相对古老的同步物种辐射中的关系问题。我们建议对大部分过度分裂的亚种类群进行异名化，并将 L. luschani finikensis 提升为正式种，即 L. finikensis。我们希望修订后的分类框架能为这些脆弱的小地方类群的保护管理提供一个稳定的基础。
{"title":"Phylogenomics reveal species limits and inter-relationships in the narrow-range endemic lycian salamanders","authors":"Peter A. Scott , Elnaz Najafi-Majd , Elif Yıldırım Caynak , Müge Gidiş , Uğur Kaya , H. Bradley Shaffer","doi":"10.1016/j.ympev.2024.108205","DOIUrl":"10.1016/j.ympev.2024.108205","url":null,"abstract":"<div><div>Salamanders of the genus <em>Lyciasalamandra</em> are represented by as many as 20 narrow-range endemic taxa inhabiting the Mediterranean coast of Turkey and a handful of Aegean Islands. Despite recent molecular phylogenetic studies, the genus is rife with uncertainty about the number of contained species and their phylogenetic relationships, both of which can interfere with needed conservation actions. To test species limits and infer interrelationships we generated as many as 113,176 RAD loci containing 229,427 single nucleotide polymorphisms (SNPs), for 110 specimens of <em>Lyciasalamandra</em> representing 19 of the 20 described taxa<em>.</em> Through a conservative species delimitation approach, we found support for eight species in the genus which broadly agree with currently described species-level diversity. We then use multiple coalescent-based species tree methods to resolve relationships in this relatively old, synchronous species radiation. We recommend synonymization of the largely over-split subspecific taxa, and the elevation of <em>L. luschani finikensis</em> to full species status as <em>L. finikensis.</em> Our hope is that this revised taxonomic framework provides a stable foundation for conservation management in these fragile, microendemic taxa.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"202 ","pages":"Article 108205"},"PeriodicalIF":3.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407276","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 : 2024-10-10DOI: 10.1016/j.ympev.2024.108213
Jing Zhao , Chuan-Jie Huang , Li-Ju Jiang , Zhao-Rong He , Shuai Yang , Zhang-Ming Zhu , Liang Zhang , Hong Yu , Xin-Mao Zhou , Jia-Guan Wang
Platycerium is a genus of pantropical epiphytic ferns consisting of ca. 18 species and are highly sought after by horticultural enthusiasts. Although the monophyly of this genus has been well supported in previous molecular studies, as an intercontinentally disjunct genus, the origin and distribution pattern of Platycerium were elusive and controversial. This is mainly due to limited taxon sampling, a plastid representing only a single coalescent history, the lack of fossil evidence, and so on. Here, by utilizing genome-skimming sequencing, transcriptome sequencing, and flow cytometry, we integrated chloroplast genomes, data of single-copy nuclear genes, ploidy levels, morphology, and geographic distribution to understand the species phylogeny and the evolutionary and biogeographic history of Platycerium. Our major results include: (1) based on both plastid and nuclear datasets, Platycerium is consistently resolved into three fully supported clades: the Afro-American (AA) clade, the Javan-Australian (JA) clade, and the Malayan-Asian (MA) clade. The AA clade and MA clade are further divided into three and two subclades, respectively; (2) a large amount of gene tree conflict, as well as cytonuclear discordance, was found and can be explained by hybridization and incomplete lineage sorting, and most of the hybridization hypotheses represented ancient hybridization events; (3) through molecular dating, the crown age of Platycerium is determined to be at approximately 32.79 Ma based on the plastid dataset or 29.08 Ma based on the nuclear dataset in the Middle Oligocene; (4) ancestral area reconstruction analysis from different datasets showed that Platycerium most likely originated from Indochina; (5) current distribution patterns are resultant from long-distance dispersals, ancient orogeny, and an ancient climate event; and (6) species diversification was driven by polyploidization, dispersal, and hybridization. This study presented here will help understand the evolution of tropical plant flora and provide a reference for the cultivation and breeding of staghorn ferns.
{"title":"Phylogenomic analyses of the pantropical Platycerium Desv. (Platycerioideae) reveal their complex evolution and historical biogeography","authors":"Jing Zhao , Chuan-Jie Huang , Li-Ju Jiang , Zhao-Rong He , Shuai Yang , Zhang-Ming Zhu , Liang Zhang , Hong Yu , Xin-Mao Zhou , Jia-Guan Wang","doi":"10.1016/j.ympev.2024.108213","DOIUrl":"10.1016/j.ympev.2024.108213","url":null,"abstract":"<div><div><em>Platycerium</em> is a genus of pantropical epiphytic ferns consisting of ca. 18 species and are highly sought after by horticultural enthusiasts. Although the monophyly of this genus has been well supported in previous molecular studies, as an intercontinentally disjunct genus, the origin and distribution pattern of <em>Platycerium</em> were elusive and controversial. This is mainly due to limited taxon sampling, a plastid representing only a single coalescent history, the lack of fossil evidence, and so on. Here, by utilizing genome-skimming sequencing, transcriptome sequencing, and flow cytometry, we integrated chloroplast genomes, data of single-copy nuclear genes, ploidy levels, morphology, and geographic distribution to understand the species phylogeny and the evolutionary and biogeographic history of <em>Platycerium</em>. Our major results include: (1) based on both plastid and nuclear datasets, <em>Platycerium</em> is consistently resolved into three fully supported clades: the Afro-American (AA) clade, the Javan-Australian (JA) clade, and the Malayan-Asian (MA) clade. The AA clade and MA clade are further divided into three and two subclades, respectively; (2) a large amount of gene tree conflict, as well as cytonuclear discordance, was found and can be explained by hybridization and incomplete lineage sorting, and most of the hybridization hypotheses represented ancient hybridization events; (3) through molecular dating, the crown age of <em>Platycerium</em> is determined to be at approximately 32.79 Ma based on the plastid dataset or 29.08 Ma based on the nuclear dataset in the Middle Oligocene; (4) ancestral area reconstruction analysis from different datasets showed that <em>Platycerium</em> most likely originated from Indochina; (5) current distribution patterns are resultant from long-distance dispersals, ancient orogeny, and an ancient climate event; and (6) species diversification was driven by polyploidization, dispersal, and hybridization. This study presented here will help understand the evolution of tropical plant flora and provide a reference for the cultivation and breeding of staghorn ferns.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108213"},"PeriodicalIF":3.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407275","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 : 2024-10-09DOI: 10.1016/j.ympev.2024.108212
Robert Hadfield , Teagan Mulford , Makani L. Fisher , Abigail Borgmeier , Diego A. Ardon , Andrew D. Suchomel , Judicaël Fomekong-Lontchi , Laura Sutherland , Madison Huie , Pungki Lupiyaningdyah , Sierra Nichols , Ying Fei Lin , Nopparat Anantaprayoon , Steven D. Leavitt
The northern North American Cordillera is a globally significant center of endemism. In western North America, imperiled arid steppe habitats support a number of unique species, including several endemic lichens. However, processes driving diversification and endemism in this region remain unclear. In this study, we investigate diversity and phylogeography of the threatened wanderlust lichens (mycobiont = Rhizoplaca species) which occur unattached on calcareous soils in steppe habitats. Wanderlust lichens comprise three species of lichen-forming fungi (LFF) – Rhizoplaca arbuscula, R. haydenii, and R. idahoensis (endangered, IUCN Red List) – which occur in fragmented populations in Idaho and Wyoming, with more limited populations in southern Montana and northern Utah. These lichens reproduce almost exclusively via large, asexual vegetative propagules. Here, our aims were to (i) assess the evolutionary origin of this group and identify phylogeographic structure, (ii) infer ancestral geographic distributions for lineages within this clade, and (iii) use species distribution modeling to better understand the distribution of contemporary populations. Using a genome-skimming approach, we generated a 19.1Mb alignment, spanning ca. half of the complete LFF genome, from specimens collected throughout the entire range of wanderlust lichens. Based on this phylogeny, we investigated phylogeographic patterns using RASP. Finally, we used MaxEnt to estimate species distribution models for R. arbuscula and R. haydenii. We inferred a highly structured topology, with clades corresponding to distinct geographic regions and morphologies collected throughout the group’s distribution. We found that R. robusta, a sexually reproducing taxon, is clearly nested within the vagrant Rhizoplaca clade. Phylogeographic analyses suggest that both dispersal and vicariance played significant roles throughout the evolutionary history of the vagrant Rhizoplaca clade, with most of the dispersal events originating from the Salmon Basin in eastern Idaho – the center of diversity for this group. Despite the fact that wanderlust lichens are dispersal limited due to large, unspecialized vegetative propagules, we inferred multiple dispersal events crossing the Continental Divide. Comparing herbarium records with species distribution models suggests that wanderlust lichens don’t fully occupy the areas of highest distribution probability. In fact, documented records often occur in areas predicted to be only marginally suitable. These data suggest a potential mismatch between contemporary habitats outside of the center of diversity in eastern Idaho with the most suitable habitat, adding to the vulnerability of this imperiled complex of endemic lichens.
{"title":"Imperiled wanderlust lichens in steppe habitats of western North America comprise geographically structured mycobiont lineages and a reversal to sexual reproduction within this asexual clade","authors":"Robert Hadfield , Teagan Mulford , Makani L. Fisher , Abigail Borgmeier , Diego A. Ardon , Andrew D. Suchomel , Judicaël Fomekong-Lontchi , Laura Sutherland , Madison Huie , Pungki Lupiyaningdyah , Sierra Nichols , Ying Fei Lin , Nopparat Anantaprayoon , Steven D. Leavitt","doi":"10.1016/j.ympev.2024.108212","DOIUrl":"10.1016/j.ympev.2024.108212","url":null,"abstract":"<div><div>The northern North American Cordillera is a globally significant center of endemism. In western North America, imperiled arid steppe habitats support a number of unique species, including several endemic lichens. However, processes driving diversification and endemism in this region remain unclear. In this study, we investigate diversity and phylogeography of the threatened wanderlust lichens (mycobiont = <em>Rhizoplaca</em> species) which occur unattached on calcareous soils in steppe habitats. Wanderlust lichens comprise three species of lichen-forming fungi (LFF) – <em>Rhizoplaca arbuscula</em>, <em>R. haydenii</em>, and <em>R. idahoensis</em> (endangered, IUCN Red List) – which occur in fragmented populations in Idaho and Wyoming, with more limited populations in southern Montana and northern Utah. These lichens reproduce almost exclusively via large, asexual vegetative propagules. Here, our aims were to (i) assess the evolutionary origin of this group and identify phylogeographic structure, (ii) infer ancestral geographic distributions for lineages within this clade, and (iii) use species distribution modeling to better understand the distribution of contemporary populations. Using a genome-skimming approach, we generated a 19.1Mb alignment, spanning ca. half of the complete LFF genome, from specimens collected throughout the entire range of wanderlust lichens. Based on this phylogeny, we investigated phylogeographic patterns using RASP. Finally, we used MaxEnt to estimate species distribution models for <em>R. arbuscula</em> and <em>R. haydenii</em>. We inferred a highly structured topology, with clades corresponding to distinct geographic regions and morphologies collected throughout the group’s distribution. We found that <em>R. robusta</em>, a sexually reproducing taxon, is clearly nested within the vagrant <em>Rhizoplaca</em> clade. Phylogeographic analyses suggest that both dispersal and vicariance played significant roles throughout the evolutionary history of the vagrant <em>Rhizoplaca</em> clade, with most of the dispersal events originating from the Salmon Basin in eastern Idaho – the center of diversity for this group. Despite the fact that wanderlust lichens are dispersal limited due to large, unspecialized vegetative propagules, we inferred multiple dispersal events crossing the Continental Divide. Comparing herbarium records with species distribution models suggests that wanderlust lichens don’t fully occupy the areas of highest distribution probability. In fact, documented records often occur in areas predicted to be only marginally suitable. These data suggest a potential mismatch between contemporary habitats outside of the center of diversity in eastern Idaho with the most suitable habitat, adding to the vulnerability of this imperiled complex of endemic lichens.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108212"},"PeriodicalIF":3.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395622","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 : 2024-10-09DOI: 10.1016/j.ympev.2024.108216
Alison Cloutier , David Tsz Chung Chan, Emily Shui Kei Poon , Simon Yung Wa Sin
Studies of widely distributed species can inform our understanding of how past demographic events tied to historic glaciation and ongoing population genetic processes interact to shape contemporaneous patterns of biodiversity at a continental scale. In this study, we used whole-genome resequencing to investigate the current population structure and genetic signatures of past demographic events in the widespread migratory American goldfinch (Spinus tristis). Phylogenetic relationships inferred from whole mitochondrial genomes were poorly resolved. In contrast, a genome-wide panel of > 4.5 million single nucleotide polymorphisms (SNPs) strongly supported the existence of eastern and western populations separated by western mountain ranges and additional population structuring within the western clade. Demographic modeling estimated that the eastern and western populations diverged approximately one million years ago, and both populations experienced subsequent population bottlenecks during the last glacial period. Species distribution models showed a severe contraction of suitable habitat for the American goldfinch during this period, with predicted discontinuities that are consistent with multiple, isolated glacial refugia that coincide with present-day population structure. Low overall genetic differentiation between the eastern and western populations (FST ∼ 0.01) suggests ongoing gene flow accompanied divergence, and individuals with admixed genomic signatures were sampled along a potential contact zone. Nevertheless, outlier SNPs were identified near genes associated with feather color, song, and migratory behavior and provide strong candidates for further study of the mechanisms underlying reproductive isolation and speciation in birds.
{"title":"The genetic consequences of historic climate change on the contemporary population structure of a widespread temperate North American songbird","authors":"Alison Cloutier , David Tsz Chung Chan, Emily Shui Kei Poon , Simon Yung Wa Sin","doi":"10.1016/j.ympev.2024.108216","DOIUrl":"10.1016/j.ympev.2024.108216","url":null,"abstract":"<div><div>Studies of widely distributed species can inform our understanding of how past demographic events tied to historic glaciation and ongoing population genetic processes interact to shape contemporaneous patterns of biodiversity at a continental scale. In this study, we used whole-genome resequencing to investigate the current population structure and genetic signatures of past demographic events in the widespread migratory American goldfinch (<em>Spinus tristis</em>). Phylogenetic relationships inferred from whole mitochondrial genomes were poorly resolved. In contrast, a genome-wide panel of > 4.5 million single nucleotide polymorphisms (SNPs) strongly supported the existence of eastern and western populations separated by western mountain ranges and additional population structuring within the western clade. Demographic modeling estimated that the eastern and western populations diverged approximately one million years ago, and both populations experienced subsequent population bottlenecks during the last glacial period. Species distribution models showed a severe contraction of suitable habitat for the American goldfinch during this period, with predicted discontinuities that are consistent with multiple, isolated glacial refugia that coincide with present-day population structure. Low overall genetic differentiation between the eastern and western populations (F<sub>ST</sub> ∼ 0.01) suggests ongoing gene flow accompanied divergence, and individuals with admixed genomic signatures were sampled along a potential contact zone. Nevertheless, outlier SNPs were identified near genes associated with feather color, song, and migratory behavior and provide strong candidates for further study of the mechanisms underlying reproductive isolation and speciation in birds.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108216"},"PeriodicalIF":3.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395623","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 : 2024-10-09DOI: 10.1016/j.ympev.2024.108217
Juan F. Alzate , Favio A. González , Natalia Pabón-Mora
The systematics of the holoendoparasitic flowering plant families Apodanthaceae and Rafflesiaceae has been discussed for over two centuries. The morphological reduction of roots, shoots and leaves in all members of both families, resulting in a cryptic mycelium-like vegetative body, has been interpreted either as a key common feature, or as a result of convergent evolution due to full dependence upon their hosts. Historically, the two families have been placed together due to similar morphological features, but recent analyses based on few mitochondrial and ribosomal gene markers placed them in the distantly related orders Cucurbitales and Malpighiales. Here we reevaluate the affinities of the Apodanthaceae and the Rafflesiaceae using a phylogenomic approach. We present (1) a historical account on their affinities over the last 200 years; (2) phylogenetic analyses reinstating their sister group relationship as part of the order Malpighiales, based on over 1000 single-copy nuclear protein-coding loci; and (3) a comprehensive list of putative morphoanatomical and developmental synapomorphies in light of the phylogenomic results, with emphasis on shared reproductive traits regardless of dramatic differences in floral size.
{"title":"Back together: Over 1000 single-copy nuclear loci and reproductive features support the holoendoparasitic Apodanthaceae and Rafflesiaceae as sister lineages in the order Malpighiales","authors":"Juan F. Alzate , Favio A. González , Natalia Pabón-Mora","doi":"10.1016/j.ympev.2024.108217","DOIUrl":"10.1016/j.ympev.2024.108217","url":null,"abstract":"<div><div>The systematics of the holoendoparasitic flowering plant families Apodanthaceae and Rafflesiaceae has been discussed for over two centuries. The morphological reduction of roots, shoots and leaves in all members of both families, resulting in a cryptic mycelium-like vegetative body, has been interpreted either as a key common feature, or as a result of convergent evolution due to full dependence upon their hosts. Historically, the two families have been placed together due to similar morphological features, but recent analyses based on few mitochondrial and ribosomal gene markers placed them in the distantly related orders Cucurbitales and Malpighiales. Here we reevaluate the affinities of the Apodanthaceae and the Rafflesiaceae using a phylogenomic approach. We present (1) a historical account on their affinities over the last 200 years; (2) phylogenetic analyses reinstating their sister group relationship as part of the order Malpighiales, based on over 1000 single-copy nuclear protein-coding loci; and (3) a comprehensive list of putative morphoanatomical and developmental synapomorphies in light of the phylogenomic results, with emphasis on shared reproductive traits regardless of dramatic differences in floral size.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108217"},"PeriodicalIF":3.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395621","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 : 2024-10-04DOI: 10.1016/j.ympev.2024.108214
Irina A. Ekimova , Dimitry M. Schepetov , Brenna Green , Maria V. Stanovova , Tatiana I. Antokhina , Terrence Gosliner , Manuel Antonio E. Malaquias , Ángel Valdés
Nudibranch molluscs Coryphella are widely distributed and species-rich gastropod group lacking fossil record and displaying a complex distribution across both Southern and Northern hemispheres. In this paper we provide a detailed review of the morphology, ecology, and distribution of Coryphella, estimation of divergence times between species, an ancestral area reconstruction, and a population analysis of widely distributed trans-Arctic species Coryphella verrucosa to investigate the evolution, phylogeographic patterns and reconstruct possible historical routes of oceanic dispersal. The inclusion of a larger sample size and five molecular markers has revealed a complex evolutionary history of Coryphella, shaped by transgression, vicariance, and dietary shifts, and overall driven by the pervasive effect of glacial cycles. We also revealed the presence of additional cryptic diversity, which suggests that further sampling may produce additional species in this group of nudibranchs. Tree calibration indicates the genus Coryphella originates in the middle Miocene in the Pacific Ocean and the early divergence within this group also occurred in the Pacific, specifically in different regions of the North Pacific. The ancestral area reconstruction inferred five independent instances of transgression from the Pacific Ocean to the Atlantic via different migration routes, including the Panamanian seaway and the Bering Strait. Among them, we identified three cases of successful transition to the Arctic waters from the North Pacific via the Bering Strait, associated with interglacial conditions of middle Pleistocene. Consequently, Pleistocene glacial cycles likely prompted pulses of boreal faunal elements to disperse southwards followed by range disjunction and temporary isolation of distant populations and resulting in allopatric speciation. Evidence from the population structure of contemporary trans-Arctic species suggests an occurrence of independent recolonization pathways of Arctic waters from both southernly and northernly refugia after the Last Glacial Maximum.
{"title":"Scaling the high latitudes: evolution, diversification, and dispersal of Coryphella nudibranchs across the Northern Hemisphere","authors":"Irina A. Ekimova , Dimitry M. Schepetov , Brenna Green , Maria V. Stanovova , Tatiana I. Antokhina , Terrence Gosliner , Manuel Antonio E. Malaquias , Ángel Valdés","doi":"10.1016/j.ympev.2024.108214","DOIUrl":"10.1016/j.ympev.2024.108214","url":null,"abstract":"<div><div>Nudibranch molluscs <em>Coryphella</em> are widely distributed and species-rich gastropod group lacking fossil record and displaying a complex distribution across both Southern and Northern hemispheres. In this paper we provide a detailed review of the morphology, ecology, and distribution of <em>Coryphella,</em> estimation of divergence times between species, an ancestral area reconstruction, and a population analysis of widely distributed trans-Arctic species <em>Coryphella verrucosa</em> to investigate the evolution, phylogeographic patterns and reconstruct possible historical routes of oceanic dispersal. The inclusion of a larger sample size and five molecular markers has revealed a complex evolutionary history of <em>Coryphella</em>, shaped by transgression, vicariance, and dietary shifts, and overall driven by the pervasive effect of glacial cycles. We also revealed the presence of additional cryptic diversity, which suggests that further sampling may produce additional species in this group of nudibranchs. Tree calibration indicates the genus <em>Coryphella</em> originates in the middle Miocene in the Pacific Ocean and the early divergence within this group also occurred in the Pacific, specifically in different regions of the North Pacific. The ancestral area reconstruction inferred five independent instances of transgression from the Pacific Ocean to the Atlantic via different migration routes, including the Panamanian seaway and the Bering Strait. Among them, we identified three cases of successful transition to the Arctic waters from the North Pacific via the Bering Strait, associated with interglacial conditions of middle Pleistocene. Consequently, Pleistocene glacial cycles likely prompted pulses of boreal faunal elements to disperse southwards followed by range disjunction and temporary isolation of distant populations and resulting in allopatric speciation. Evidence from the population structure of contemporary trans-Arctic species suggests an occurrence of independent recolonization pathways of Arctic waters from both southernly and northernly refugia after the Last Glacial Maximum.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108214"},"PeriodicalIF":3.6,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142382493","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}
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