Pub Date : 2025-08-25DOI: 10.1016/j.ympev.2025.108452
Julia Canitz , Frank Kirschbaum , David L.J. Vendrami , Victor Mamonekene , Ralph Tiedemann
The African weakly electric fish genus Campylomormyrus belongs to the species-rich family Mormyridae and comprises 15 described species. Previous species trees that focus on the genus, have included at most ten species. The resulting phylogenies have been used to explain the evolution of the species-specific electrical organ discharge (EOD) and interpreted in the context of sympatric speciation caused by disruptive selection. However, available molecular phylogenies that are focused on the Campylomormyrus genus rely only on a limited number of genetic markers. Here, we used ddRAD sequencing to genotype 65 individuals from twelve Campylomormyrus species and Gnathonemus petersii at more than 8,000 SNPs. We reconstruct a robust species tree that is suggestive of ancient introgression events between different species, which might affect both genetic and trait variability in the genus. Different levels of genetic and EOD diversity in two significant Campylomormyrus clades reveals that i) certain species might be in early stages of their speciation process, ii) that hybridization/introgression occurs in mormyrids and iii) that EOD-related genes could be potential speciation genes. Our genomic approach demonstrates the significance of these findings in understanding the evolution of Campylomormyrus.
{"title":"Phylogenetic reconstruction of African weakly electric fish (Campylomormyrus spp.) is suggestive of ancient introgression events","authors":"Julia Canitz , Frank Kirschbaum , David L.J. Vendrami , Victor Mamonekene , Ralph Tiedemann","doi":"10.1016/j.ympev.2025.108452","DOIUrl":"10.1016/j.ympev.2025.108452","url":null,"abstract":"<div><div>The African weakly electric fish genus <em>Campylomormyrus</em> belongs to the species-rich family Mormyridae and comprises 15 described species. Previous species trees that focus on the genus, have included at most ten species. The resulting phylogenies have been used to explain the evolution of the species-specific electrical organ discharge (EOD) and interpreted in the context of sympatric speciation caused by disruptive selection. However, available molecular phylogenies that are focused on the <em>Campylomormyrus</em> genus rely only on a limited number of genetic markers. Here, we used ddRAD sequencing to genotype 65 individuals from twelve <em>Campylomormyrus</em> species and <em>Gnathonemus petersii</em> at more than 8,000 SNPs. We reconstruct a robust species tree that is suggestive of ancient introgression events between different species, which might affect both genetic and trait variability in the genus. Different levels of genetic and EOD diversity in two significant <em>Campylomormyrus</em> clades reveals that i) certain species might be in early stages of their speciation process, ii) that hybridization/introgression occurs in mormyrids and iii) that EOD-related genes could be potential speciation genes. Our genomic approach demonstrates the significance of these findings in understanding the evolution of <em>Campylomormyrus</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108452"},"PeriodicalIF":3.6,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144979872","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 : 2025-08-25DOI: 10.1016/j.ympev.2025.108447
Lazarus Mavima , Emma T. Steenkamp , Chrizelle W. Beukes , Marike Palmer , Sofie E. De Meyer , Euan K. James , Stephanus N. Venter , Martin P.A. Coetzee
The nitrogen-fixing and nodule-forming symbionts of legumes, which belong to the class Betaproteobacteria, are informally known as beta-rhizobia. Thus far, members of this group have only been found in the genera Paraburkholderia, Trinickia and Cupriavidus. In this study, we investigate the poorly characterized evolutionary history of this trait in the predominant beta-rhizobial genus, Paraburkholderia. This was determined in the context of the current evolutionary theories and date estimates of rhizobia, the genus Paraburkholderia and the earth. Evolutionary divergence dates of rhizobial Paraburkholderia as well as their ancestral nodulation states were estimated using over 800 diverse proteobacterial genomes. Molecular dating was carried out using the software BEAST (Bayesian Evolutionary Analysis Sampling Trees) and APE (using the ‘chronopl’ function). Our results showed that the most recent common ancestor (MRCA) of the extant beta-rhizobial species emerged between 2744 and 1752 million years ago (Ma) and later (2135–514 Ma) diverged into the lineages Cupriavidus, Trinickia and Paraburkholderia. However, major diversifications of rhizobial Paraburkholderia occurred in three phases: (i) during the Permian and Triassic periods (400–200 Ma) when Pangaea was fully assembled and its landmass filling up with flora and fauna, (ii) during the Jurassic period (200–150 Ma) when fauna and flora were flourishing in Pangaea, and (iii) during the Cretaceous and Paleogene periods (150–23 Ma) when Gondwana was breaking up. Furthermore, Paraburkholderia were estimated to have acquired their precursor nodulation loci that evolved into their current nodulation loci from different sources between 103 and 48 Ma. Accordingly, our study describes the evolutionary history of rhizobial Paraburkholderia, thus enabling us to understand the past environmental factors that shaped the current geographical distribution of these agriculturally important bacteria, and to identify locations potentially rich in beta-rhizobia.
{"title":"Estimated timeline for the evolution of symbiotic nitrogen fixing Paraburkholderia","authors":"Lazarus Mavima , Emma T. Steenkamp , Chrizelle W. Beukes , Marike Palmer , Sofie E. De Meyer , Euan K. James , Stephanus N. Venter , Martin P.A. Coetzee","doi":"10.1016/j.ympev.2025.108447","DOIUrl":"10.1016/j.ympev.2025.108447","url":null,"abstract":"<div><div>The nitrogen-fixing and nodule-forming symbionts of legumes, which belong to the class <em>Betaproteobacteria,</em> are informally known as beta-rhizobia. Thus far, members of this group have only been found in the genera <em>Paraburkholderia, Trinickia</em> and <em>Cupriavidus</em>. In this study, we investigate the poorly characterized evolutionary history of this trait in the predominant beta-rhizobial genus, <em>Paraburkholderia</em>. This was determined in the context of the current evolutionary theories and date estimates of rhizobia, the genus <em>Paraburkholderia</em> and the earth. Evolutionary divergence dates of rhizobial <em>Paraburkholderia</em> as well as their ancestral nodulation states were estimated using over 800 diverse proteobacterial genomes. Molecular dating was carried out using the software BEAST (Bayesian Evolutionary Analysis Sampling Trees) and APE (using the ‘chronopl’ function). Our results showed that the most recent common ancestor (MRCA) of the extant beta-rhizobial species emerged between 2744 and 1752 million years ago (Ma) and later (2135–514 Ma) diverged into the lineages <em>Cupriavidus</em>, <em>Trinickia</em> and <em>Paraburkholderia</em>. However, major diversifications of rhizobial <em>Paraburkholderia</em> occurred in three phases: (i) during the Permian and Triassic periods (400–200 Ma) when Pangaea was fully assembled and its landmass filling up with flora and fauna, (ii) during the Jurassic period (200–150 Ma) when fauna and flora were flourishing in Pangaea, and (iii) during the Cretaceous and Paleogene periods (150–23 Ma) when Gondwana was breaking up. Furthermore, <em>Paraburkholderia</em> were estimated to have acquired their precursor nodulation loci that evolved into their current nodulation loci from different sources between 103 and 48 Ma. Accordingly, our study describes the evolutionary history of rhizobial <em>Paraburkholderia</em>, thus enabling us to understand the past environmental factors that shaped the current geographical distribution of these agriculturally important bacteria, and to identify locations potentially rich in beta-rhizobia.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108447"},"PeriodicalIF":3.6,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144911662","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 : 2025-08-25DOI: 10.1016/j.ympev.2025.108449
Dongqing Yan , Yanyan Fan , Xiaoru Jiang , Yang Ma , Kejian Lin , Zhenhua Dang , Jianming Niu
Understanding the evolutionary history of the Eurasian steppe is crucial for restoring severely degraded ecosystems and mitigating the impact of future climate change. Stipa species, which demonstrate zonal and extrazonal distribution patterns across the eastern Eurasian steppe, serve as a noteworthy example for elucidating the evolution of this biome. In this paper, we explored the phylogeny of the genus Stipa using transcriptome data, while examined the genetic differentiation, demographic history, and adaptive evolution of S. baicalensis, S. grandis, and S. krylovii using RAD-seq data. We found that from mid-Miocene to early-Pliocene, the Qinghai-Tibet Plateau (QTP) uplift triggered the formation of the Asian monsoon and progressive aridification of Asian interior, fostering Stipa species emergence and out-of-QTP. During the Pleistocene, glacial-interglacial cycles and East Asian monsoon fluctuations led to alternations of cold-dry and warm-wet climate, facilitating the differentiation and migration of these three species across Mongolian Plateau, Loess Plateau, and Central Asia. These climatic oscillations shaped distinct genetic variations among these species in different geographical regions. Furthermore, annual precipitation and total soil nitrogen content were the primary drivers of their adaptive evolution. Noticeably, the evolution of Stipa species exhibits prominent spatio-temporal integration characteristics. Conclusively, we proposed a comprehensive regional evolution framework for plants in the eastern Eurasian steppe. Our research fills gaps in understanding the evolutionary history of the entire Eurasian steppe and the impact of evolutionary processes on contemporary plant distributions, which is vital for assessing steppe vegetation shifts and plant genomic vulnerability under climate change scenarios.
{"title":"Diversification and differentiation of Stipa species shed light on the regional evolutionary history of the eastern Eurasian steppe","authors":"Dongqing Yan , Yanyan Fan , Xiaoru Jiang , Yang Ma , Kejian Lin , Zhenhua Dang , Jianming Niu","doi":"10.1016/j.ympev.2025.108449","DOIUrl":"10.1016/j.ympev.2025.108449","url":null,"abstract":"<div><div>Understanding the evolutionary history of the Eurasian steppe is crucial for restoring severely degraded ecosystems and mitigating the impact of future climate change. <em>Stipa</em> species, which demonstrate zonal and extrazonal distribution patterns across the eastern Eurasian steppe, serve as a noteworthy example for elucidating the evolution of this biome. In this paper, we explored the phylogeny of the genus <em>Stipa</em> using transcriptome data, while examined the genetic differentiation, demographic history, and adaptive evolution of <em>S. baicalensis</em>, <em>S. grandis</em>, and <em>S. krylovii</em> using RAD-seq data. We found that from mid-Miocene to early-Pliocene, the Qinghai-Tibet Plateau (QTP) uplift triggered the formation of the Asian monsoon and progressive aridification of Asian interior, fostering <em>Stipa</em> species emergence and out-of-QTP. During the Pleistocene, glacial-interglacial cycles and East Asian monsoon fluctuations led to alternations of cold-dry and warm-wet climate, facilitating the differentiation and migration of these three species across Mongolian Plateau, Loess Plateau, and Central Asia. These climatic oscillations shaped distinct genetic variations among these species in different geographical regions. Furthermore, annual precipitation and total soil nitrogen content were the primary drivers of their adaptive evolution. Noticeably, the evolution of <em>Stipa</em> species exhibits prominent spatio-temporal integration characteristics. Conclusively, we proposed a comprehensive regional evolution framework for plants in the eastern Eurasian steppe. Our research fills gaps in understanding the evolutionary history of the entire Eurasian steppe and the impact of evolutionary processes on contemporary plant distributions, which is vital for assessing steppe vegetation shifts and plant genomic vulnerability under climate change scenarios.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108449"},"PeriodicalIF":3.6,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144911631","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 : 2025-08-25DOI: 10.1016/j.ympev.2025.108451
Michael W. Sandel , Andres Aguilar , Sergei Kirilchik , David A. Neely , Bakhtiar E. Bogdanov , Kayla M. Fast , Joshua D. Millwood
Lake Baikal ranks among the world’s most species-rich freshwater ecosystems; however, the evolutionary histories of endemic taxa remain poorly understood. The unique abiotic environments of Lake Baikal include the only bathybenthic, bathypelagic, and deep hydrothermal vent communities in freshwater, each of which supports species with derived morphological and physiological traits. As the only known vertebrate radiation endemic to a non-tropical ancient lake, Baikal sculpins represent an underappreciated resource for investigating evolutionary processes that underlie adaptive radiation. We examined morphological and ecological diversity among Baikal sculpins and present the first interspecific phylogeny inferred from dense nuclear genomic sampling (ddRADseq). The new phylogeny supports a holarctic lotic ancestor to a limnetic radiation and reveals reticulate adaptations to lotic, bathyal, and pelagic habitats.
We apply the new phylogeny to revise Baikal sculpin taxonomy, and we resurrect Uranidea as a monotypic sister-group to the Baikal sculpin radiation. Our data support independent evolution of pelagic and bathypelagic ecomorphs and multiple invasions of aphotic habitats. Concordant ecomorphological shifts involved dramatic modification of skeletal elements, sensory systems, and reproductive mode. Habitat depth is highlighted as an important abiotic factor associated with adaptive radiation, but more research is needed to address potentially confounding effects of thermal and photic zonation. We discuss the geoclimatic processes that may explain this rapid radiation, and conclude by highlighting the anthropogenic changes that threaten this irreplaceable natural resource.
{"title":"Sink or swim: Phylogenomic analysis of Baikal sculpins reveals multiple transformations to pelagic, bathybenthic, and lotic ecomorphologies","authors":"Michael W. Sandel , Andres Aguilar , Sergei Kirilchik , David A. Neely , Bakhtiar E. Bogdanov , Kayla M. Fast , Joshua D. Millwood","doi":"10.1016/j.ympev.2025.108451","DOIUrl":"10.1016/j.ympev.2025.108451","url":null,"abstract":"<div><div>Lake Baikal ranks among the world’s most species-rich freshwater ecosystems; however, the evolutionary histories of endemic taxa remain poorly understood. The unique abiotic environments of Lake Baikal include the only bathybenthic, bathypelagic, and deep hydrothermal vent communities in freshwater, each of which supports species with derived morphological and physiological traits. As the only known vertebrate radiation endemic to a non-tropical ancient lake, Baikal sculpins represent an underappreciated resource for investigating evolutionary processes that underlie adaptive radiation. We examined morphological and ecological diversity among Baikal sculpins and present the first interspecific phylogeny inferred from dense nuclear genomic sampling (ddRADseq). The new phylogeny supports a holarctic lotic ancestor to a limnetic radiation and reveals reticulate adaptations to lotic, bathyal, and pelagic habitats.</div><div>We apply the new phylogeny to revise Baikal sculpin taxonomy, and we resurrect <em>Uranidea</em> as a monotypic sister-group to the Baikal sculpin radiation. Our data support independent evolution of pelagic and bathypelagic ecomorphs and multiple invasions of aphotic habitats. Concordant ecomorphological shifts involved dramatic modification of skeletal elements, sensory systems, and reproductive mode. Habitat depth is highlighted as an important abiotic factor associated with adaptive radiation, but more research is needed to address potentially confounding effects of thermal and photic zonation. We discuss the geoclimatic processes that may explain this rapid radiation, and conclude by highlighting the anthropogenic changes that threaten this irreplaceable natural resource.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108451"},"PeriodicalIF":3.6,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144911663","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 : 2025-08-25DOI: 10.1016/j.ympev.2025.108448
Kamryn Carter , Claudio Reyes-Olivares , Jonathan Eubanks , Hayden Hanna , Stuart V. Nielsen , Damien Esquerré
Quantifying and delimiting biodiversity is a critical challenge in modern biology, particularly in taxa where species boundaries are unclear or poorly defined. In many cases, traditional morphological approaches are insufficient or even misleading when delimiting taxonomic units. Modern genomic methods offer a powerful tool to gain an in-depth perspective of evolutionary history and genetic variation across populations. The Chilean Marked Geckos (genus Garthia) currently comprise two species, G. gaudichaudii and G. penai, endemic to the semi-arid coastal regions of North-Central Chile. Although additional species/subspecies have been proposed, a recent study went so far as to suggest that just one species should be recognized. However, no study to date has evaluated their diversity using genetic tools. For the first time, we used phylogenomic and population genetic methods to better understand diversity across the entire distribution of Garthia. Using both mtDNA and nDNA data, we reconstruct the phylogeny, assess population structure, and delimit species. Our phylogenetic analyses reveal deep evolutionary divergence strongly supporting the existence of at least the two nominate species. However, our species delimitation and population structure analyses suggest alpha-level diversity could be even higher, with evidence supporting a cryptic species complex of between three and eleven species, including deep divergences between geographically proximate populations. We discuss the impact these findings have on our understanding of Chilean gecko diversity and biogeographic patterns in the world’s driest desert.
{"title":"Hidden diversity in the driest desert on Earth: genomics unveils cryptic diversity in an ancient South American gecko lineage (Phyllodactylidae, Garthia)","authors":"Kamryn Carter , Claudio Reyes-Olivares , Jonathan Eubanks , Hayden Hanna , Stuart V. Nielsen , Damien Esquerré","doi":"10.1016/j.ympev.2025.108448","DOIUrl":"10.1016/j.ympev.2025.108448","url":null,"abstract":"<div><div>Quantifying and delimiting biodiversity is a critical challenge in modern biology, particularly in taxa where species boundaries are unclear or poorly defined. In many cases, traditional morphological approaches are insufficient or even misleading when delimiting taxonomic units. Modern genomic methods offer a powerful tool to gain an in-depth perspective of evolutionary history and genetic variation across populations. The Chilean Marked Geckos (genus <em>Garthia</em>) currently comprise two species, <em>G. gaudichaudii</em> and <em>G. penai,</em> endemic to the semi-arid coastal regions of North-Central Chile. Although additional species/subspecies have been proposed, a recent study went so far as to suggest that just one species should be recognized. However, no study to date has evaluated their diversity using genetic tools. For the first time, we used phylogenomic and population genetic methods to better understand diversity across the entire distribution of <em>Garthia</em>. Using both mtDNA and nDNA data, we reconstruct the phylogeny, assess population structure, and delimit species. Our phylogenetic analyses reveal deep evolutionary divergence strongly supporting the existence of at least the two nominate species. However, our species delimitation and population structure analyses suggest alpha-level diversity could be even higher, with evidence supporting a cryptic species complex of between three and eleven species, including deep divergences between geographically proximate populations. We discuss the impact these findings have on our understanding of Chilean gecko diversity and biogeographic patterns in the world’s driest desert.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108448"},"PeriodicalIF":3.6,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144911664","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 : 2025-08-22DOI: 10.1016/j.ympev.2025.108445
Benjamin M. Anderson , Todd G.B. McLay , Carolyn F. Wilkins , Kelly A. Shepherd
The tribe Lasiopetaleae (Malvaceae subfamily Byttnerioideae) consists of nine genera largely distributed in Australia. Boundaries between genera have historically been contentious, with many species being described in one genus and variously transferred to others. Previous phylogenetic studies using morphology and plastid DNA have mostly resolved relationships within the tribe except for a group of genera allied to Lasiopetalum. To clarify generic boundaries and the phylogeny of this group, we generated and analyzed target sequence capture data for 144 samples across 8 genera, focusing on denser sampling within Guichenotia, Lasiopetalum, Lysiosepalum and Thomasia, using two bait sets: Angiosperms353 and OzBaits. Sequences for 388 nuclear loci were assembled using two approaches: HybPiper and SECAPR (with some modifications), and results were compared. We used concatenation and coalescent analyses, with and without putative hybrids, to generate new phylogenetic hypotheses for the group. Potential hybrids were investigated using HybPhaser and by assembling phased high-copy portions of the genome, as well as by quantifying potential parentage from heterozygous sites in alignments. Our results indicate that current genera in the group are paraphyletic, and there are examples of hybridization within and between them. Gene concordance for backbone relationships in the group was low, likely caused by gene tree estimation error and taxon instability among closely-related species as well as incomplete lineage sorting during rapid diversification. Despite discordance and hybridization, morphologically diagnosable genomic clades could be recognized. Paraphyly might be resolved by expanding one or two existing genera substantially (subsuming c. 108 taxa) or, for less taxonomic disruption, reinstating two former genera and recognizing two new genera.
{"title":"Target sequence capture informs generic delimitation and hybridization in the tribe Lasiopetaleae (Malvaceae)","authors":"Benjamin M. Anderson , Todd G.B. McLay , Carolyn F. Wilkins , Kelly A. Shepherd","doi":"10.1016/j.ympev.2025.108445","DOIUrl":"10.1016/j.ympev.2025.108445","url":null,"abstract":"<div><div>The tribe Lasiopetaleae (Malvaceae subfamily Byttnerioideae) consists of nine genera largely distributed in Australia. Boundaries between genera have historically been contentious, with many species being described in one genus and variously transferred to others. Previous phylogenetic studies using morphology and plastid DNA have mostly resolved relationships within the tribe except for a group of genera allied to <em>Lasiopetalum</em>. To clarify generic boundaries and the phylogeny of this group, we generated and analyzed target sequence capture data for 144 samples across 8 genera, focusing on denser sampling within <em>Guichenotia</em>, <em>Lasiopetalum</em>, <em>Lysiosepalum</em> and <em>Thomasia</em>, using two bait sets: Angiosperms353 and OzBaits. Sequences for 388 nuclear loci were assembled using two approaches: HybPiper and SECAPR (with some modifications), and results were compared. We used concatenation and coalescent analyses, with and without putative hybrids, to generate new phylogenetic hypotheses for the group. Potential hybrids were investigated using HybPhaser and by assembling phased high-copy portions of the genome, as well as by quantifying potential parentage from heterozygous sites in alignments. Our results indicate that current genera in the group are paraphyletic, and there are examples of hybridization within and between them. Gene concordance for backbone relationships in the group was low, likely caused by gene tree estimation error and taxon instability among closely-related species as well as incomplete lineage sorting during rapid diversification. Despite discordance and hybridization, morphologically diagnosable genomic clades could be recognized. Paraphyly might be resolved by expanding one or two existing genera substantially (subsuming <em>c</em>. 108 taxa) or, for less taxonomic disruption, reinstating two former genera and recognizing two new genera.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108445"},"PeriodicalIF":3.6,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144911630","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 : 2025-08-17DOI: 10.1016/j.ympev.2025.108446
Luana S. Soares , Aureliano Bombarely , Loreta B. Freitas
Several processes influence species establishment in nature, with evolutionary radiations playing a critical role in biodiversity evolution. Ecological adaptation, progenitor-derivative speciation, pollinator shifts, and geographic isolation followed by local adaptation can lead to plant radiations in montane systems. This study investigated the rapid divergence and migration of highland Petunia species. Employing reduced representation genome sequencing and a genomic population approach, we focused on detecting structuration, ecological inference, hybridization/introgression, and evolutionary patterns. Our findings revealed an intricate and complex array of factors, including ecological adaptation without marked genetic diversity, hybridization, and geographic isolation, which led to species divergence in a short period. Ancestral polymorphism sharing maintained genetic diversity could facilitate rapid divergence among the highland species by providing variation to natural selection. During the Pleistocene, Petunia species expanded and contracted their ranges in response to the alternance of climate cycles. This period of environmental changes was pivotal in promoting rapid speciation through geographic isolation. Here, we highlight the multifaceted nature of species diversification, influenced by a confluence of geographic distribution, demographic history, and hybridization. The interplay of these factors highlights the diverse and dynamic pathways to speciation in a model plant genus, thereby contributing to a deeper understanding of species diversification and the role of genetic and environmental factors in shaping biodiversity.
{"title":"Geographic isolation, ecological adaptation, and hybridization influenced fast divergence of a Solanaceae plant group from subtropical highland grasslands","authors":"Luana S. Soares , Aureliano Bombarely , Loreta B. Freitas","doi":"10.1016/j.ympev.2025.108446","DOIUrl":"10.1016/j.ympev.2025.108446","url":null,"abstract":"<div><div>Several processes influence species establishment in nature, with evolutionary radiations playing a critical role in biodiversity evolution. Ecological adaptation, progenitor-derivative speciation, pollinator shifts, and geographic isolation followed by local adaptation can lead to plant radiations in montane systems. This study investigated the rapid divergence and migration of highland <em>Petunia</em> species. Employing reduced representation genome sequencing and a genomic population approach, we focused on detecting structuration, ecological inference, hybridization/introgression, and evolutionary patterns. Our findings revealed an intricate and complex array of factors, including ecological adaptation without marked genetic diversity, hybridization, and geographic isolation, which led to species divergence in a short period. Ancestral polymorphism sharing maintained genetic diversity could facilitate rapid divergence among the highland species by providing variation to natural selection. During the Pleistocene, <em>Petunia</em> species expanded and contracted their ranges in response to the alternance of climate cycles. This period of environmental changes was pivotal in promoting rapid speciation through geographic isolation. Here, we highlight the multifaceted nature of species diversification, influenced by a confluence of geographic distribution, demographic history, and hybridization. The interplay of these factors highlights the diverse and dynamic pathways to speciation in a model plant genus, thereby contributing to a deeper understanding of species diversification and the role of genetic and environmental factors in shaping biodiversity.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108446"},"PeriodicalIF":3.6,"publicationDate":"2025-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863498","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 : 2025-08-15DOI: 10.1016/j.ympev.2025.108442
Christopher Blair , Carlos J. Pavón-Vázquez , Qaantah Rana , Keaka Farleigh , Erika Crispo , Thomas Panzera , Felipe de Medeiros Magalhães , Britt White , Uri Omar Garcia-Vazquez
The Southwestern US and northern Mexico continue to serve as ideal regions to elucidate the suite of ecological and evolutionary processes influencing lineage diversification. The complex geological history of arid North America, coupled with paleoclimate change during the Pleistocene and diverse ecoregions makes a multipronged approach to hypothesis testing necessary. We combine thousands of loci from a genotyping-by-sequencing (GBS) approach along with mitochondrial DNA (mtDNA) sequences from the Greater Earless Lizard (Cophosaurus texanus) to examine diversity and test for cryptic population structure. We also apply recently developed coalescent approaches in a Bayesian framework to estimate migration rates. Population genomic and phylogenomic analyses support the existence of multiple lineages of C. texanus, with divergence following a southeast to northwest pattern. The geographic distribution of lineages, coupled with estimated divergence times, suggest a complex evolutionary history shaped by a combination of geomorphological shifts and ecological divergence in the Neogene. Our results also support the existence of a biogeographic barrier at the Continental Divide dating to the Pleistocene and the importance of isolation by distance. Migration rates between lineages are low, and multiple species delimitation analyses further support the distinctiveness of lineages. Species tree analyses show that C. texanus texanus is nested within lineages of C. texanus scitulus, supporting the hypothesis that this system may constitute a species complex in need of revision. In sum, we find evidence for multiple processes influencing lineage divergence, indicating that additional multipronged phylogeographic studies using genomic data are needed on diverse, widespread taxa throughout arid western North America.
{"title":"Isolation and divergence of Greater Earless Lizards (Phrynosomatidae: Cophosaurus) in western North America support multiple diversification processes and a complex demographic history","authors":"Christopher Blair , Carlos J. Pavón-Vázquez , Qaantah Rana , Keaka Farleigh , Erika Crispo , Thomas Panzera , Felipe de Medeiros Magalhães , Britt White , Uri Omar Garcia-Vazquez","doi":"10.1016/j.ympev.2025.108442","DOIUrl":"10.1016/j.ympev.2025.108442","url":null,"abstract":"<div><div>The Southwestern US and northern Mexico continue to serve as ideal regions to elucidate the suite of ecological and evolutionary processes influencing lineage diversification. The complex geological history of arid North America, coupled with paleoclimate change during the Pleistocene and diverse ecoregions makes a multipronged approach to hypothesis testing necessary. We combine thousands of loci from a genotyping-by-sequencing (GBS) approach along with mitochondrial DNA (mtDNA) sequences from the Greater Earless Lizard (<em>Cophosaurus texanus</em>) to examine diversity and test for cryptic population structure. We also apply recently developed coalescent approaches in a Bayesian framework to estimate migration rates. Population genomic and phylogenomic analyses support the existence of multiple lineages of <em>C. texanus</em>, with divergence following a southeast to northwest pattern. The geographic distribution of lineages, coupled with estimated divergence times, suggest a complex evolutionary history shaped by a combination of geomorphological shifts and ecological divergence in the Neogene. Our results also support the existence of a biogeographic barrier at the Continental Divide dating to the Pleistocene and the importance of isolation by distance. Migration rates between lineages are low, and multiple species delimitation analyses further support the distinctiveness of lineages. Species tree analyses show that <em>C. texanus texanus</em> is nested within lineages of <em>C. texanus scitulus</em>, supporting the hypothesis that this system may constitute a species complex in need of revision. In sum, we find evidence for multiple processes influencing lineage divergence, indicating that additional multipronged phylogeographic studies using genomic data are needed on diverse, widespread taxa throughout arid western North America.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108442"},"PeriodicalIF":3.6,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876971","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}
Hydrobiidae is the most diverse and species-rich freshwater gastropod family in the Palearctic. Their diversity in the Caucasus region remains largely unexplored and the phylogenetic relationships with European taxa have not been clarified yet. The primary objective of this study is to perform a molecular phylogenetic analysis of the stygobiotic Hydrobiidae of the Caucasus with an increased taxon sampling and incorporation of multiple molecular markers. We show that the Caucasian hydrobiids are represented by three distinct lineages of a subfamily rank: (1) Caucasopsiinae subfam.nov., comprises most of the stygobiotic hydrobiid genera endemic to Caucasus; (2) Belgrandiellinae includes a single stygobiotic genus Sitnikovia and a complex of crenobiotic genera; (3) Islamiinae is represented by a single monotypic genus. The Caucasian stygobiotic hydrobiids are represented by 13 genera, five of which were identified as new for science, and at least 37 species, including a significant number (20 species) of putative new taxa. Analysis of the soft-body anatomy revealed that the female reproductive system showed the best congruence with the phylogenetic relationships. Shell morphology showed high variability at both inter- and intrageneric level, questioning the generic assignment of species based on empty shells. The Caucasian stygobiotic Hydrobiidae show high endemism at all taxonomical levels from species to subfamilies, which probably reflects their long evolution in relative isolation from the hydrobiid clades inhabiting other regions.
{"title":"Little treasures hidden in the darkness: diversity and phylogeny of stygobiotic hydrobiidae (Mollusca: Gastropoda) of the Caucasus","authors":"Elizaveta Chertoprud , Irina Ekimova , Dmitry Palatov , Jozef Grego , Levan Mumladze , Maxim Vinarski","doi":"10.1016/j.ympev.2025.108439","DOIUrl":"10.1016/j.ympev.2025.108439","url":null,"abstract":"<div><div>Hydrobiidae is the most diverse and species-rich freshwater gastropod family in the Palearctic. Their diversity in the Caucasus region remains largely unexplored and the phylogenetic relationships with European taxa have not been clarified yet. The primary objective of this study is to perform a molecular phylogenetic analysis of the stygobiotic Hydrobiidae of the Caucasus with an increased taxon sampling and incorporation of multiple molecular markers. We show that the Caucasian hydrobiids are represented by three distinct lineages of a subfamily rank: (1) Caucasopsiinae <strong>subfam.nov.</strong>, comprises most of the stygobiotic hydrobiid genera endemic to Caucasus; (2) Belgrandiellinae includes a single stygobiotic genus <em>Sitnikovia</em> and a complex of crenobiotic genera; (3) Islamiinae is represented by a single monotypic genus. The Caucasian stygobiotic hydrobiids are represented by 13 genera, five of which were identified as new for science, and at least 37 species, including a significant number (20 species) of putative new taxa. Analysis of the soft-body anatomy revealed that the female reproductive system showed the best congruence with the phylogenetic relationships. Shell morphology showed high variability at both inter- and intrageneric level, questioning the generic assignment of species based on empty shells. The Caucasian stygobiotic Hydrobiidae show high endemism at all taxonomical levels from species to subfamilies, which probably reflects their long evolution in relative isolation from the hydrobiid clades inhabiting other regions.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108439"},"PeriodicalIF":3.6,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144862739","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 : 2025-08-14DOI: 10.1016/j.ympev.2025.108435
Waleska Barbosa , Romina Batista , Eduardo D. Schultz , Camila C. Ribas
The genus Sakesphorus (Aves: Thamnophilidae) includes two species that are floodplain specialists within Amazonia. While S. luctuosus occupies floodplains of southeastern Amazonia and extends south along riparian habitats in central Brazil, S. canadensis occupies northern Amazonian floodplains and extends to other habitat types in northern South America, including mangroves, deciduous forests, and savannas. We reconstruct the historical diversification of the genus to investigate the landscape history of the Amazonian floodplains and their relationships with adjacent environments. We used reduced representation genomic data obtained with Ultra conserved Elements (UCE) probes and mtDNA from 26 S. canadensis and 30 S. luctuosus individuals. The phylogenetic analyses recovered each species as a well-supported clade. The split between the two species dates to 2.67 Ma (CI: 1.66–3.91), with a crown age of 620 Kya (CI: 0.37–0.91) for S. canadensis and 330 (CI: 0.2–0.49) Kya for S. luctuosus. Sakesphorus canadensis comprises three populations with low migration rates between them. Demographic expansion was unequivocal only for the Branco River population (S. c. fumosus), suggesting an association with the evolution of the Branco River drainage. Pleistocene diversification of the genus corroborates the dynamism of the Amazonian fluvial system during this period, affecting connectivity along Amazonian floodplains and driving population differentiation. Connectivity with adjacent biomes through riparian corridors was important for the evolution of Amazonian floodplain biodiversity and should be protected.
{"title":"Population dynamics and evolutionary history of the genus Sakesphorus (Aves: Thamnophilidae) in the Amazonian floodplains","authors":"Waleska Barbosa , Romina Batista , Eduardo D. Schultz , Camila C. Ribas","doi":"10.1016/j.ympev.2025.108435","DOIUrl":"10.1016/j.ympev.2025.108435","url":null,"abstract":"<div><div>The genus <em>Sakesphorus</em> (Aves: Thamnophilidae) includes two species that are floodplain specialists within Amazonia. While <em>S. luctuosus</em> occupies floodplains of southeastern Amazonia and extends south along riparian habitats in central Brazil, <em>S. canadensis</em> occupies northern Amazonian floodplains and extends to other habitat types in northern South America, including mangroves, deciduous forests, and savannas. We reconstruct the historical diversification of the genus to investigate the landscape history of the Amazonian floodplains and their relationships with adjacent environments. We used reduced representation genomic data obtained with Ultra conserved Elements (UCE) probes and mtDNA from 26 <em>S. canadensis</em> and 30 <em>S. luctuosus</em> individuals. The phylogenetic analyses recovered each species as a well-supported clade. The split between the two species dates to 2.67 Ma (CI: 1.66–3.91), with a crown age of 620 Kya (CI: 0.37–0.91) for <em>S. canadensis</em> and 330 (CI: 0.2–0.49) Kya for <em>S. luctuosus</em>. <em>Sakesphorus canadensis</em> comprises three populations with low migration rates between them. Demographic expansion was unequivocal only for the Branco River population (<em>S. c. fumosus)</em>, suggesting an association with the evolution of the Branco River drainage. Pleistocene diversification of the genus corroborates the dynamism of the Amazonian fluvial system during this period, affecting connectivity along Amazonian floodplains and driving population differentiation. Connectivity with adjacent biomes through riparian corridors was important for the evolution of Amazonian floodplain biodiversity and should be protected.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108435"},"PeriodicalIF":3.6,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144852538","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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