Pub Date : 2026-01-01Epub Date: 2025-09-27DOI: 10.1016/j.ympev.2025.108473
David Ferreiro, Elena Pazos, Miguel Arenas
Substitution models of protein evolution describe the rates of evolutionary change among amino acids and are essential for a variety of evolutionary studies, including the reconstruction of phylogenetic histories and ancestral sequences, among others. The earliest substitution models of protein evolution are based on empirical protein sequences and, despite their unrealistic assumptions, are still routinely used in protein phylogenetics. Next, the incorporation of additional parameters that inform about evolutionary constraints on protein stability and protein function provided a significant increase in the accuracy of the modeling. However, despite the wide variety of substitution models of protein evolution that were presented, only a small subset has been implemented in evolutionary frameworks of practical use in phylogenetics. Here, we overview general trends in the development and application of substitution models of protein evolution, including their theoretical fundamentals, goals, areas for improvement, and implementation in phylogenetic frameworks. We also provide detailed practical examples of phylogenetic inference using advanced structurally constrained substitution models.
{"title":"Trends in substitution models of protein evolution for phylogenetic inference","authors":"David Ferreiro, Elena Pazos, Miguel Arenas","doi":"10.1016/j.ympev.2025.108473","DOIUrl":"10.1016/j.ympev.2025.108473","url":null,"abstract":"<div><div>Substitution models of protein evolution describe the rates of evolutionary change among amino acids and are essential for a variety of evolutionary studies, including the reconstruction of phylogenetic histories and ancestral sequences, among others. The earliest substitution models of protein evolution are based on empirical protein sequences and, despite their unrealistic assumptions, are still routinely used in protein phylogenetics. Next, the incorporation of additional parameters that inform about evolutionary constraints on protein stability and protein function provided a significant increase in the accuracy of the modeling. However, despite the wide variety of substitution models of protein evolution that were presented, only a small subset has been implemented in evolutionary frameworks of practical use in phylogenetics. Here, we overview general trends in the development and application of substitution models of protein evolution, including their theoretical fundamentals, goals, areas for improvement, and implementation in phylogenetic frameworks. We also provide detailed practical examples of phylogenetic inference using advanced structurally constrained substitution models.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108473"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145194074","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 : 2026-01-01Epub Date: 2025-10-07DOI: 10.1016/j.ympev.2025.108478
Rui Zhong , Jian Chang , Yunhe Wang , Haixin Zhang , Yu Peng , Ingi Agnarsson , Jie Liu
Ongoing climate change mandates improved understanding of how temperature fluctuations influence organismal evolution and behavior. Detritus-based nest-retreats in spiders have originated multiple times in parallel—hypothesized to be an adaptive response to climatic fluctuations. We investigated the potential role of climate change in shaping the evolution of nest-retreats over geological timescales, and the short-term effect of temperature on the morphology and energy investment of nest-retreats in Campanicola campanulata (Theridiidae). Phylogenetic analyses reconstruct twelve origins of nest-retreats, first appearing in the Eocene, and diversifying during the Late Cenozoic Icehouse period. Spiders respond to experimentally lowered temperatures by making larger nest-retreats, indicating a direct impact of temperature on retreat architecture. Our results for the first time affirm the thermoregulatory function of spider nests and suggest that temperature impacts nest-retreats across both evolutionary and ecological timescales. Nest-retreat spiders can serve as a model to study the origins of thermoregulatory nest-building in animals and how it may be impacted by ongoing climate change.
{"title":"Spider nest-retreat origin, diversification, and architectural plasticity link to historical and current temperature fluctuations","authors":"Rui Zhong , Jian Chang , Yunhe Wang , Haixin Zhang , Yu Peng , Ingi Agnarsson , Jie Liu","doi":"10.1016/j.ympev.2025.108478","DOIUrl":"10.1016/j.ympev.2025.108478","url":null,"abstract":"<div><div>Ongoing climate change mandates improved understanding of how temperature fluctuations influence organismal evolution and behavior. Detritus-based nest-retreats in spiders have originated multiple times in parallel—hypothesized to be an adaptive response to climatic fluctuations. We investigated the potential role of climate change in shaping the evolution of nest-retreats over geological timescales, and the short-term effect of temperature on the morphology and energy investment of nest-retreats in <em>Campanicola campanulata</em> (Theridiidae). Phylogenetic analyses reconstruct twelve origins of nest-retreats, first appearing in the Eocene, and diversifying during the Late Cenozoic Icehouse period. Spiders respond to experimentally lowered temperatures by making larger nest-retreats, indicating a direct impact of temperature on retreat architecture. Our results for the first time affirm the thermoregulatory function of spider nests and suggest that temperature impacts nest-retreats across both evolutionary and ecological timescales. Nest-retreat spiders can serve as a model to study the origins of thermoregulatory nest-building in animals and how it may be impacted by ongoing climate change.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108478"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145253890","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 : 2026-01-01Epub Date: 2025-09-01DOI: 10.1016/j.ympev.2025.108438
Jacob S. Stai , Warren Cardinal-McTeague , Anne Bruneau , Steven B. Cannon
Contradictory lines of evidence have made it difficult to resolve the phylogenetic history of the legume diversification era; this is true for the backbone topology, and for the number and timing of whole genome duplications (WGDs). By analyzing the transcriptomic data for 473 gene families in 76 species covering all six accepted legume subfamilies, we assessed the phylogenetic relationships of the legume backbone and uncovered evidence of independent whole genome duplications in each of the six legume subfamilies. Three subfamilies – Cercidoideae, Dialioideae, and Caesalpinioideae – bear evidence of an allopolyploid duplication pattern suggestive of ancient hybridization. In Cercidoideae and Dialioideae, the hybridization appears to be within-subfamily, with the genera Cercis and Poeppigia apparently unduplicated descendants of one of the parental lineages. In Caesalpinioideae, the hybridization appears to involve a member of the Papilionoideae lineage, and some other lineage, potentially extinct. Several independent lines of evidence converged on a single backbone hypothesis and the above hypotheses of reticulate evolution: phylogenies calculated from both superalignments and from multi-tree coalescent-based analyses; concordance factor analysis of the set of gene family alignments and topologies; and direct inference of reticulation events via maximum pseudo-likelihood implemented by PhyloNet.
{"title":"Complex reticulation in backbone subfamily relationships in Leguminosae","authors":"Jacob S. Stai , Warren Cardinal-McTeague , Anne Bruneau , Steven B. Cannon","doi":"10.1016/j.ympev.2025.108438","DOIUrl":"10.1016/j.ympev.2025.108438","url":null,"abstract":"<div><div>Contradictory lines of evidence have made it difficult to resolve the phylogenetic history of the legume diversification era; this is true for the backbone topology, and for the number and timing of whole genome duplications (WGDs). By analyzing the transcriptomic data for 473 gene families in 76 species covering all six accepted legume subfamilies, we assessed the phylogenetic relationships of the legume backbone and uncovered evidence of independent whole genome duplications in each of the six legume subfamilies. Three subfamilies – Cercidoideae, Dialioideae, and Caesalpinioideae – bear evidence of an allopolyploid duplication pattern suggestive of ancient hybridization. In Cercidoideae and Dialioideae, the hybridization appears to be within-subfamily, with the genera <em>Cercis</em> and <em>Poeppigia</em> apparently unduplicated descendants of one of the parental lineages. In Caesalpinioideae, the hybridization appears to involve a member of the Papilionoideae lineage, and some other lineage, potentially extinct. Several independent lines of evidence converged on a single backbone hypothesis and the above hypotheses of reticulate evolution: phylogenies calculated from both superalignments and from multi-tree coalescent-based analyses; concordance factor analysis of the set of gene family alignments and topologies; and direct inference of reticulation events via maximum pseudo-likelihood implemented by PhyloNet.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108438"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994775","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}
Recent studies have shown the significant role of introgression in evolution, yet the confident evidence of introgression has come from biased taxa. Although the Mollusca were representative taxa to show introgression-driven evolution, conclusive examination has been rare. Here, we investigated the genetic structure and evolutionary history of terrestrial snails in the Euhadra peliomphala species complex (Heterobranchia: Camaenidae). We collected 197 individuals from 196 sites in Japan, covering the entire distribution, and obtained genome-wide single nucleotide polymorphisms (SNPs) using double digest restriction site-associated DNA sequencing. The population genetic analysis showed that the study individuals are clustered into 12 lineages, which are distributed parapatrically. Our hybrid test detected hybrid zones between several pairs of the lineages. Additionally, we reconstructed a phylogenetic network of these lineages and detected three reticulate events, including introgression from an extinct lineage. The ages of the introgression events suggests that geological activity and climate change were involved. We also found human-induced introgression. Overall, the present research showed a highly reticulated evolutionary history of the E. peliomphala species complex, and provided confident evidence of introgression in terrestrial snails. This study should play a major role as a basis for further research on introgression-driven evolution within the E. peliomphala species complex.
{"title":"Reticulate evolution in terrestrial snails of Euhadra peliomphala species complex","authors":"Yasuto Ishii , Shun Ito , Yuichi Kameda , Tsuyoshi Takano , Tsukasa Waki , Satoshi Chiba , Takahiro Hirano","doi":"10.1016/j.ympev.2025.108437","DOIUrl":"10.1016/j.ympev.2025.108437","url":null,"abstract":"<div><div>Recent studies have shown the significant role of introgression in evolution, yet the confident evidence of introgression has come from biased taxa. Although the Mollusca were representative taxa to show introgression-driven evolution, conclusive examination has been rare. Here, we investigated the genetic structure and evolutionary history of terrestrial snails in the <em>Euhadra peliomphala</em> species complex (Heterobranchia: Camaenidae). We collected 197 individuals from 196 sites in Japan, covering the entire distribution, and obtained genome-wide single nucleotide polymorphisms (SNPs) using double digest restriction site-associated DNA sequencing. The population genetic analysis showed that the study individuals are clustered into 12 lineages, which are distributed parapatrically. Our hybrid test detected hybrid zones between several pairs of the lineages. Additionally, we reconstructed a phylogenetic network of these lineages and detected three reticulate events, including introgression from an extinct lineage. The ages of the introgression events suggests that geological activity and climate change were involved. We also found human-induced introgression. Overall, the present research showed a highly reticulated evolutionary history of the <em>E. peliomphala</em> species complex, and provided confident evidence of introgression in terrestrial snails. This study should play a major role as a basis for further research on introgression-driven evolution within the <em>E. peliomphala</em> species complex.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108437"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859934","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 : 2026-01-01Epub Date: 2025-08-31DOI: 10.1016/j.ympev.2025.108457
James Smith , Cara Hastings , Christopher Davidson , Sven Buerki , Stephen Novak , Allan Bornstein
The delimitation of species boundaries has been a constant challenge to the fields of systematics, natural history, and conservation biology. Subtle and minor morphological differences in a widespread species complex make delimiting species boundaries particularly difficult. High throughput targeted sequencing of hundreds of loci has allowed researchers to obtain improved insights into evolutionary processes and resolved previously ambiguous phylogenetic relationships. Piper amalago (subgenus Gonistum) is morphologically similar to, and geographically overlaps with, many other Neotropical Piper species that have narrow restricted distributions, or occur as narrow endemics. Taxonomists have debated whether morphological differences between P. amalago and other similar species merit distinct species status or if these taxa represent a single widespread species exhibiting extensive intraspecific variation. Recent molecular analyses demonstrated that P. amalago is paraphyletic with morphologically similar species, notably P. martensianum, but these findings lack phylogenetic support. This study investigates the phylogenetic relationships of P. amalago and several closely related species using multiple DNA sequences, and seeks to determine whether species can be delimited on the basis of phylogenetic, geographical, and morphological information. The Angiosperms353 bait set was used to retrieve nuclear genes to build maximum likelihood and multispecies coalescent phylogenetic hypotheses. Available DNA sequence data are consistent with the presence of a single, monophyletic, widespread species complex, with considerable morphological variation and some geographic structure. While the drivers of the morphological variation within this complex are not yet fully understood, we have a better understanding of evolutionary relationships and species boundaries within Piper, a giant genus.
{"title":"A single widespread species or multiple narrow endemics: a search for boundaries within the Piper amalago complex (Piperaceae)","authors":"James Smith , Cara Hastings , Christopher Davidson , Sven Buerki , Stephen Novak , Allan Bornstein","doi":"10.1016/j.ympev.2025.108457","DOIUrl":"10.1016/j.ympev.2025.108457","url":null,"abstract":"<div><div>The delimitation of species boundaries has been a constant challenge to the fields of systematics, natural history, and conservation biology. Subtle and minor morphological differences in a widespread species complex make delimiting species boundaries particularly difficult. High throughput targeted sequencing of hundreds of loci has allowed researchers to obtain improved insights into evolutionary processes and resolved previously ambiguous phylogenetic relationships. <em>Piper amalago</em> (subgenus <em>Gonistum</em>) is morphologically similar to, and geographically overlaps with, many other Neotropical <em>Piper</em> species that have narrow restricted distributions, or occur as narrow endemics. Taxonomists have debated whether morphological differences between <em>P. amalago</em> and other similar species merit distinct species status or if these taxa represent a single widespread species exhibiting extensive intraspecific variation. Recent molecular analyses demonstrated that <em>P. amalago</em> is paraphyletic with morphologically similar species, notably <em>P. martensianum</em>, but these findings lack phylogenetic support. This study investigates the phylogenetic relationships of <em>P. amalago</em> and several closely related species using multiple DNA sequences, and seeks to determine whether species can be delimited on the basis of phylogenetic, geographical, and morphological information. The Angiosperms353 bait set was used to retrieve nuclear genes to build maximum likelihood and multispecies coalescent phylogenetic hypotheses. Available DNA sequence data are consistent with the presence of a single, monophyletic, widespread species complex, with considerable morphological variation and some geographic structure. While the drivers of the morphological variation within this complex are not yet fully understood, we have a better understanding of evolutionary relationships and species boundaries within <em>Piper</em>, a giant genus.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108457"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144933763","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 : 2026-01-01Epub Date: 2025-08-29DOI: 10.1016/j.ympev.2025.108450
Leidys Murillo-Ramos , Hamid Reza Ghanavi , Kyung Min Lee , Elina Laiho , Axel Hausmann , Hermann Staude , Egbert Friedrich , Gunnar Brehm , Pasi Sihvonen
Disjunct distribution patterns have long intrigued biogeographers, sparking ongoing debates about the mechanisms driving the current distribution of biodiversity. Among the most discussed patterns are long-distance dispersal and vicariance. While these patterns have been extensively studied in plants, marine taxa, mammals, and some invertebrates, they remain less explored in groups like moths. In this study, we use the Epidesmiinae + Oenochrominae + Desmobathrinae complex—three closely related subfamilies within the Geometridae family—as a model to examine disjunct distribution patterns in Australasian moths. Epidesmiinae + Oenochrominae moths are primarily distributed within the Australasian region, with some taxa being endemic to New Zealand. In contrast, their sister group, Desmobathrinae, exhibits a trans-continental and mainly pantropical distribution. The biogeography and evolution of these subfamilies, which currently have different distribution areas, have not been analysed in an evolutionary context before. To investigate this, we inferred phylogenetic trees using a Maximum-Likelihood approach and used the topology to estimate time-calibrated trees and reconstruct ancestral biogeographical areas using a Bayesian method. Additionally, we explored the diversification rates of these lineages. Our results suggest that the ancestor of the three subfamilies most likely originated in Australasia during the Eocene (∼58 Ma). Bayesian biogeographical analyses suggested dispersal events of the Desmobathrinae into the Indo-Malayan region and other areas, with an important jump to the Neotropics, while Epidesmiinae and Oenochrominae dispersed mainly within Australasia. Diversification analysis revealed no significant shifts in diversification rates, with the phylogeny showing a pattern of declining speciation rates over time. Our study exemplifies how phylogenetics in combination with biogeographical reconstruction uncovers macroevolutionary patterns in moths.
{"title":"Disjunct distributions and evolutionary diversification of Australasian geometrid moths: subfamilies Epidesmiinae, Desmobathrinae and Oenochrominae (Lepidopera)","authors":"Leidys Murillo-Ramos , Hamid Reza Ghanavi , Kyung Min Lee , Elina Laiho , Axel Hausmann , Hermann Staude , Egbert Friedrich , Gunnar Brehm , Pasi Sihvonen","doi":"10.1016/j.ympev.2025.108450","DOIUrl":"10.1016/j.ympev.2025.108450","url":null,"abstract":"<div><div>Disjunct distribution patterns have long intrigued biogeographers, sparking ongoing debates about the mechanisms driving the current distribution of biodiversity. Among the most discussed patterns are long-distance dispersal and vicariance. While these patterns have been extensively studied in plants, marine taxa, mammals, and some invertebrates, they remain less explored in groups like moths. In this study, we use the Epidesmiinae + Oenochrominae + Desmobathrinae complex—three closely related subfamilies within the Geometridae family—as a model to examine disjunct distribution patterns in Australasian moths. Epidesmiinae + Oenochrominae moths are primarily distributed within the Australasian region, with some taxa being endemic to New Zealand. In contrast, their sister group, Desmobathrinae, exhibits a <em>trans</em>-continental and mainly pantropical distribution. The biogeography and evolution of these subfamilies, which currently have different distribution areas, have not been analysed in an evolutionary context before. To investigate this, we inferred phylogenetic trees using a Maximum-Likelihood approach and used the topology to estimate time-calibrated trees and reconstruct ancestral biogeographical areas using a Bayesian method. Additionally, we explored the diversification rates of these lineages. Our results suggest that the ancestor of the three subfamilies most likely originated in Australasia during the Eocene (∼58 Ma). Bayesian biogeographical analyses suggested dispersal events of the Desmobathrinae into the Indo-Malayan region and other areas, with an important jump to the Neotropics, while Epidesmiinae and Oenochrominae dispersed mainly within Australasia. Diversification analysis revealed no significant shifts in diversification rates, with the phylogeny showing a pattern of declining speciation rates over time. Our study exemplifies how phylogenetics in combination with biogeographical reconstruction uncovers macroevolutionary patterns in moths.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108450"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144979904","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 : 2026-01-01Epub Date: 2025-10-24DOI: 10.1016/j.ympev.2025.108484
Li-Sha Jiang , Yu Feng , Jun-Yi Zhang , Xiong Li , Min Liao , Heng-Ning Deng , Qi Yu , Bo Xu
The shrub genus Campylotropis (Fabaceae, trib. Desmodieae, subtrib. Lespedezinae) encompasses approximately 40 species, predominantly distributed across temperate and subtropical East Asia, with its diversity centered in the Hengduan Mountains and southern China. Historical constraints in sampling and methodological approaches have long obscured its evolutionary history and species relationships. This study provides the most comprehensive phylogenomic analysis of Campylotropis to date, incorporating 91 samples representing 40 taxa. Leveraging sequence data from 77 plastid genes and 1,233 single-copy nuclear genes (SCGs), we reconstructed the genus’s phylogenomic framework, estimated divergence times, inferred ancestral area distributions, and traced the evolution of key morphological traits. Our results robustly confirm the monophyly of Campylotropis, distinguishing it from allied genera. We delineated six well-supported clades within the genus and resolved previously unresolved relationships. The conflicts between nuclear and chloroplast phylogenies highlight a complex evolutionary history, likely influenced by chloroplast capture and incomplete lineage sorting (ILS) during rapid radiation. We found that global climate change and tectonic activities since the late Miocene likely shaped lineage diversification, with Quaternary climate oscillations potentially triggering rapid radiation within the genus. Ancestral area reconstruction suggests that Campylotropis originated in the Hengduan Mountains and southern China before dispersing swiftly across adjacent East Asian regions. By integrating extensive sampling with nuclear genomic data, this study elucidates the evolutionary history of Campylotropis and enhances our understanding of diversification processes in biodiversity hotspots.
{"title":"Phylogenomic framework, biogeography and character evolution of the genus Campylotropis (Fabaceae, Papilionoideae)","authors":"Li-Sha Jiang , Yu Feng , Jun-Yi Zhang , Xiong Li , Min Liao , Heng-Ning Deng , Qi Yu , Bo Xu","doi":"10.1016/j.ympev.2025.108484","DOIUrl":"10.1016/j.ympev.2025.108484","url":null,"abstract":"<div><div>The shrub genus <em>Campylotropis</em> (Fabaceae, trib. Desmodieae, subtrib. Lespedezinae) encompasses approximately 40 species, predominantly distributed across temperate and subtropical East Asia, with its diversity centered in the Hengduan Mountains and southern China. Historical constraints in sampling and methodological approaches have long obscured its evolutionary history and species relationships. This study provides the most comprehensive phylogenomic analysis of <em>Campylotropis</em> to date, incorporating 91 samples representing 40 taxa. Leveraging sequence data from 77 plastid genes and 1,233 single-copy nuclear genes (SCGs), we reconstructed the genus’s phylogenomic framework, estimated divergence times, inferred ancestral area distributions, and traced the evolution of key morphological traits. Our results robustly confirm the monophyly of <em>Campylotropis</em>, distinguishing it from allied genera. We delineated six well-supported clades within the genus and resolved previously unresolved relationships. The conflicts between nuclear and chloroplast phylogenies highlight a complex evolutionary history, likely influenced by chloroplast capture and incomplete lineage sorting (ILS) during rapid radiation. We found that global climate change and tectonic activities since the late Miocene likely shaped lineage diversification, with Quaternary climate oscillations potentially triggering rapid radiation within the genus. Ancestral area reconstruction suggests that <em>Campylotropis</em> originated in the Hengduan Mountains and southern China before dispersing swiftly across adjacent East Asian regions. By integrating extensive sampling with nuclear genomic data, this study elucidates the evolutionary history of <em>Campylotropis</em> and enhances our understanding of diversification processes in biodiversity hotspots.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108484"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145416753","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 : 2026-01-01Epub Date: 2025-09-29DOI: 10.1016/j.ympev.2025.108474
Javier Torres , R. Graham Reynolds , Kin Onn Chan , Paul Hime , Richard E. Glor
The Cuban green anoles, members of the Anolis carolinensis species complex, are among the most successful colonizing lineages of anole lizards in the Caribbean. We use ddRAD and Sanger sequence data to clarify the evolutionary relationships among all members of the A. carolinensis species complex (generally called Cuban green anoles), demarcate species boundaries, and explain the geographic origins of this key group of highly dispersive anoles. This study supports the “Out of Cuba” hypothesis involving six or seven independent colonization events from a Cuban source with one possible island-to-island dispersal event between the Cayman Islands and Navassa. Independent colonization events occurred from three main clades delimited by western, central, and eastern Cuba. West Cuban lineages dispersed twice—to the Cay Sal Bank (Bahamas) and to Florida. Central Cuban lineages dispersed twice—to the Bahamas archipelago and the Bay Islands (Honduras), respectively, with the latter seemingly owing to human assistance. East Cuban lineages colonized the Bahamas archipelago once as well as Little Cayman and Navassa, although it is unclear if all these colonizations occurred directly from Cuba. We recommend continued recognition of all species in the complex except A. fairchildi—which we consider a subspecies of A. porcatus—for a total of 8 species in this group: A. allisoni, A. brunneus, A. carolinensis, A. longiceps, A. maynardii, A. porcatus, A. smaragdinus, and A. torresfundorai.
古巴绿变色蜥是卡罗莱纳变色蜥物种复合体的成员，是加勒比地区变色蜥最成功的殖民谱系之一。我们利用ddRAD和Sanger序列数据来澄清A. carolinensis物种复合物（通常称为古巴绿变色蜥）所有成员之间的进化关系，划分物种边界，并解释这一高度分散的变色蜥关键群体的地理起源。这项研究支持“离开古巴”假说，该假说涉及六到七次来自古巴的独立殖民事件，其中一次可能是开曼群岛和纳瓦萨之间的岛屿到岛屿的分散事件。独立的殖民事件发生在古巴西部、中部和东部三个主要分支。西古巴的血统曾两次分散到萨尔滩（巴哈马群岛）和佛罗里达。古巴中部的血统两次分散到巴哈马群岛和海湾群岛（洪都拉斯），后者似乎是由于人类的援助。东古巴血统曾经殖民过巴哈马群岛以及小开曼群岛和纳瓦萨群岛，尽管尚不清楚这些殖民地是否都直接来自古巴。我们建议继续识别除a . fairchildi（我们认为是a . porcati的一个亚种）外的所有物种，该类群共有8种：a . allisoni, a . brunneus, a . carolinensis, a . longiceps, a . maynardii, a . porcatus, a . smaragdinus和a . torresfundai。
{"title":"Overwater dispersal from a single source island shaped the diversity of green anole lizards (Anolis carolinensis subgroup)","authors":"Javier Torres , R. Graham Reynolds , Kin Onn Chan , Paul Hime , Richard E. Glor","doi":"10.1016/j.ympev.2025.108474","DOIUrl":"10.1016/j.ympev.2025.108474","url":null,"abstract":"<div><div>The Cuban green anoles, members of the <em>Anolis carolinensis</em> species complex, are among the most successful colonizing lineages of anole lizards in the Caribbean. We use ddRAD and Sanger sequence data to clarify the evolutionary relationships among all members of the <em>A. carolinensis</em> species complex (generally called Cuban green anoles), demarcate species boundaries, and explain the geographic origins of this key group of highly dispersive anoles. This study supports the “Out of Cuba” hypothesis involving six or seven independent colonization events from a Cuban source with one possible island-to-island dispersal event between the Cayman Islands and Navassa. Independent colonization events occurred from three main clades delimited by western, central, and eastern Cuba. West Cuban lineages dispersed twice—to the Cay Sal Bank (Bahamas) and to Florida. Central Cuban lineages dispersed twice—to the Bahamas archipelago and the Bay Islands (Honduras), respectively, with the latter seemingly owing to human assistance. East Cuban lineages colonized the Bahamas archipelago once as well as Little Cayman and Navassa, although it is unclear if all these colonizations occurred directly from Cuba. We recommend continued recognition of all species in the complex except <em>A. fairchildi—</em>which we consider a subspecies of <em>A. porcatus</em>—for a total of 8 species in this group: <em>A. allisoni</em>, <em>A. brunneus</em>, <em>A. carolinensis</em>, <em>A. longiceps</em>, <em>A. maynardii</em>, <em>A. porcatus</em>, <em>A. smaragdinus</em>, and <em>A. torresfundorai</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108474"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208511","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 : 2026-01-01Epub Date: 2025-10-22DOI: 10.1016/j.ympev.2025.108479
Jie Tang , Ying Jiang , Zhe Hu , Huizhen Zhou , Dawei You , Maurycy Daroch
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Pub Date : 2026-01-01Epub Date: 2025-09-14DOI: 10.1016/j.ympev.2025.108471
Mabodiba M. Maake , Chrizelle W. Beukes , Magriet A. van der Nest , Juanita R. Avontuur , Esther K. Muema , Tomasz Stępkowski , Stephanus N. Venter , Emma T. Steenkamp
Given that several, mainly endemic South African Genisteae genera occupy basal positions in legume phylogenetic trees, this region of Africa is considered a primaeval centre of diversification of this legume tribe. Despite the importance of South Africa in Genisteae evolution, almost all studies have focused on rhizobia nodulating Genisteae in their centres of diversity in either the Mediterranean Basin or the Americas. Therefore, this study aimed to identify and characterize rhizobial strains associated with Argyrolobium species native to areas of the Grassland biome associated with the Great Escarpment, which dominates the subcontinent’s eastern landscape, and compare these to bradyrhizobia nodulating Genisteae in other centres of diversity. Phylogenetic analyses of five housekeeping genes (dnaK, glnII, gyrB, recA, and rpoB) separated the 18 Bradyrhizobium strains examined into five well-supported groups. Three of these were conspecific with B. arachidis, B. brasilense/B. australafricanum and B. ivorense, while the remaining two appeared to be new to science. After confirming their novelty using Average Nucleotide Identity, a metric for genome relatedness, and certain phenotypic traits, we recognized them as novel species for which we proposed the names B. spitzkopense sp. nov. (Arg816Ts) and B. mpumalangense sp. nov. (Arg237LTs). Phylogenetic analyses of nodA gene sequences showed that about half of the strains examined, irrespective of their species identity, harboured alleles known only from the Grassland biome along the Great Escarpment that were previously detected in Bradyrhizobium strains nodulating Crotalarieae endemic to this region. Genome-based analyses of data from this and previous studies further showed that strains with these unique nodA alleles typically encode the nodH gene, the product of which adds a sulfate moiety to the Nod factor (the signalling molecule for establishing the nitrogen-fixing symbiosis). The remaining strains had nodA alleles commonly encountered elsewhere in South Africa and other tropical regions of the world. Also, the genomes of these other strains lacked nodH but encoded nodZ, the gene involved in the fucosylation of the Nod factor. Our findings, therefore, showed that the root nodules of Genisteae (and its sister tribe Crotalarieae) native to the Grassland biome along the Great Escarpment are often related Bradyrhizobium strains that are distinct from bradyrhizobia nodulating Genisteae in the Mediterranean and the Americas.
考虑到几个主要是南非特有的金雀花属占据豆科系统发育树的基础位置，非洲的这一地区被认为是这个豆科部落多样化的原始中心。尽管南非在金雀花科进化中的重要性，但几乎所有的研究都集中在根瘤菌在地中海盆地或美洲的多样性中心的根瘤菌。因此，本研究旨在鉴定和表征与大悬崖相关的草原生物群系相关的根瘤菌菌株，该地区占次大陆东部景观的主导地位，并将其与剩余多样性中心的慢生根瘤菌结核gensteae进行比较。通过对5个清洁基因（dnaK、glnII、gyrB、recA和rpoB）的系统发育分析，将18株慢生根瘤菌分为5个支持良好的类群。其中3种与花生芽孢杆菌、巴西芽孢杆菌/巴西芽孢杆菌同生。australafricum和b.ivorense，而剩下的两个似乎是科学上的新发现。在使用平均核苷酸身份（基因组相关性度量）和某些表型特征确认它们的新颖性后，我们认为它们是新物种，并提出了B. spitzkopense sp. nov （Arg816Ts）和B. mpumalangense sp. nov （arg237lt）的名称。nodA基因序列的系统发育分析表明，无论其物种身份如何，约有一半的被检查菌株含有仅在大悬崖草原生物群系中已知的等位基因，这些等位基因以前在该地区特有的结瘤crotalariae属慢生根瘤菌菌株中检测到。基于基因组的数据分析和先前的研究进一步表明，具有这些独特的nodA等位基因的菌株通常编码nodH基因，其产物在Nod因子（建立固氮共生的信号分子）上增加了硫酸盐部分。剩下的菌株没有在南非和世界其他热带地区常见的da等位基因。此外，他们的基因组缺乏nodH，但编码nodZ基因，该基因参与Nod因子的集中。因此，我们的研究结果表明，原产于大悬崖草原生物群系的Genisteae（及其姊妹部落crotalariae）的根瘤通常与慢生根瘤菌菌株相关，但与地中海和美洲的慢生根瘤菌结核Genisteae不同。
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