Pub Date : 2025-09-17DOI: 10.1016/j.ympev.2025.108472
Han-Yang Lin , Miao Sun , Jian-Jun Jin , Cheng-Xin Fu , Douglas E. Soltis , Pamela S. Soltis , Yun-Peng Zhao
Reticulate evolution and recalcitrant phylogenetic relationships are common in the East Asian evergreen broad-leaved forests (EA-EBLFs),. Hybridization and incomplete lineage sorting (ILS) can both occur during diversification of these forests, yet the extent of ILS has often been overlooked. Among floristic elements in the EA-EBLFs, plant genera that are disjunctly distributed between eastern Asia and eastern North America (EA-ENA disjuncts) provide an excellent system to explore the magnitude of hybridization and ILS after vicariance and long-distance dispersal. Here, we investigated the evolutionary history of Stewartia L. (Theaceae), one of the EA-ENA disjuncts whose major members inhabit the EA-EBLFs (ca. 20 spp. in EA vs. two spp. in ENA) using target enrichment sequence data obtained from Angiosperms353. Based on nearly complete taxon sampling, we recovered two Stewartia clades (the EA deciduous and evergreen clades) in the EA-EBLFs. Our estimates indicate that these two clades started to diversify in the late Miocene, and the evergreen clade showed a higher diversification rate than the deciduous clade. The SNaQ and NANUQ analyses detected hybridization signals within both clades, primarily involving S. serrata and S. tonkinensis, respectively. In addition, the QuIBL analysis revealed co-occurring introgression and ILS in 98/105 and 318/360 tested triplets (Δ BIC < − 10) in the deciduous and evergreen clades, respectively. The Phytop analysis further supported ILS as the primary source of gene-tree discordance. Our study reveals complex phylogenetic and evolutionary patterns in EA-EBLF endemics and highlights the importance of hybridization and ILS in this region.
{"title":"Hybridization and incomplete lineage sorting characterize the evolutionary history of two East Asian clades of Stewartia (Theaceae)","authors":"Han-Yang Lin , Miao Sun , Jian-Jun Jin , Cheng-Xin Fu , Douglas E. Soltis , Pamela S. Soltis , Yun-Peng Zhao","doi":"10.1016/j.ympev.2025.108472","DOIUrl":"10.1016/j.ympev.2025.108472","url":null,"abstract":"<div><div>Reticulate evolution and recalcitrant phylogenetic relationships are common in the East Asian evergreen broad-leaved forests (EA-EBLFs),. Hybridization and incomplete lineage sorting (ILS) can both occur during diversification of these forests, yet the extent of ILS has often been overlooked. Among floristic elements in the EA-EBLFs, plant genera that are disjunctly distributed between eastern Asia and eastern North America (EA-ENA disjuncts) provide an excellent system to explore the magnitude of hybridization and ILS after vicariance and long-distance dispersal. Here, we investigated the evolutionary history of <em>Stewartia</em> L. (Theaceae), one of the EA-ENA disjuncts whose major members inhabit the EA-EBLFs (ca. 20 spp. in EA vs. two spp. in ENA) using target enrichment sequence data obtained from Angiosperms353. Based on nearly complete taxon sampling, we recovered two <em>Stewartia</em> clades (the EA deciduous and evergreen clades) in the EA-EBLFs. Our estimates indicate that these two clades started to diversify in the late Miocene, and the evergreen clade showed a higher diversification rate than the deciduous clade. The SNaQ and NANUQ analyses detected hybridization signals within both clades, primarily involving <em>S. serrata</em> and <em>S. tonkinensis</em>, respectively. In addition, the QuIBL analysis revealed co-occurring introgression and ILS in 98/105 and 318/360 tested triplets (Δ BIC < − 10) in the deciduous and evergreen clades, respectively. The Phytop analysis further supported ILS as the primary source of gene-tree discordance. Our study reveals complex phylogenetic and evolutionary patterns in EA-EBLF endemics and highlights the importance of hybridization and ILS in this region.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108472"},"PeriodicalIF":3.6,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093139","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 : 2025-09-15DOI: 10.1016/j.ympev.2025.108469
Weixuan Ning , Heidi M. Meudt , Antoine N. Nicolas , Gregory M. Plunkett , Peter B. Heenan , William G. Lee , Jennifer A. Tate
Genera with species of multiple ploidy levels provide models to understand successive rounds of whole genome duplication leading to intricate reticulate relationships of polyploid plant species. Here, we studied 17 polyploid taxa (species, subspecies, or varieties) in Azorella (Apiaceae) sections Schizeilema and Stilbocarpa that are mostly endemic to New Zealand. Using phylogenomic approaches, our goals were to resolve species relationships, determine the origins of the higher-level polyploids (6x and 10x), and assess the biogeography of the New Zealand Azorella species. Phylogenomic analysis of Anigosperms353 baits-captured Hyb-Seq data, together with comparison of phylogenies reconstructed using genome-skimming retrieved nrDNA and plastome sequences, showed that species diversification within New Zealand may relate to multiple origins from South America, which has been further shaped by additional rounds of polyploidy as well as hybridization or introgression. The two Azorella sections in New Zealand likely resulted from different biogeographic events from South America − one to the subantarctic islands (section Stilbocarpa) and a second to the South Island (section Schizeilema). In addition, within section Schizeilema, species have dispersed from the South Island (New Zealand) to Australia, the subantarctic islands, and the North Island (New Zealand). Our combined approach of phylogenomic analyses of plastome and nuclear locus-based data, together with SNP-based network approaches allowed us to determine the origins of some higher-level polyploids in New Zealand Azorella and revealed a more complex picture of historical and ongoing polyploidy and hybridization within these lineages.
{"title":"Resolving reticulate evolutionary histories of polyploid species of Azorella (Apiaceae) endemic to New Zealand","authors":"Weixuan Ning , Heidi M. Meudt , Antoine N. Nicolas , Gregory M. Plunkett , Peter B. Heenan , William G. Lee , Jennifer A. Tate","doi":"10.1016/j.ympev.2025.108469","DOIUrl":"10.1016/j.ympev.2025.108469","url":null,"abstract":"<div><div>Genera with species of multiple ploidy levels provide models to understand successive rounds of whole genome duplication leading to intricate reticulate relationships of polyploid plant species. Here, we studied 17 polyploid taxa (species, subspecies, or varieties) in <em>Azorella</em> (Apiaceae) sections <em>Schizeilema</em> and <em>Stilbocarpa</em> that are mostly endemic to New Zealand. Using phylogenomic approaches, our goals were to resolve species relationships, determine the origins of the higher-level polyploids (6<em>x</em> and 10<em>x</em>), and assess the biogeography of the New Zealand <em>Azorella</em> species. Phylogenomic analysis of Anigosperms353 baits-captured Hyb-Seq data, together with comparison of phylogenies reconstructed using genome-skimming retrieved nrDNA and plastome sequences, showed that species diversification within New Zealand may relate to multiple origins from South America, which has been further shaped by additional rounds of polyploidy as well as hybridization or introgression. The two <em>Azorella</em> sections in New Zealand likely resulted from different biogeographic events from South America − one to the subantarctic islands (section <em>Stilbocarpa</em>) and a second to the South Island (section <em>Schizeilema</em>). In addition, within section <em>Schizeilema</em>, species have dispersed from the South Island (New Zealand) to Australia, the subantarctic islands, and the North Island (New Zealand). Our combined approach of phylogenomic analyses of plastome and nuclear locus-based data, together with SNP-based network approaches allowed us to determine the origins of some higher-level polyploids in New Zealand <em>Azorella</em> and revealed a more complex picture of historical and ongoing polyploidy and hybridization within these lineages.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108469"},"PeriodicalIF":3.6,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145082656","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 : 2025-09-14DOI: 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。
{"title":"Argyrolobium legumes from an African centre of endemism associate with novel Bradyrhizobium species harbouring unique sets of symbiosis genes","authors":"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","doi":"10.1016/j.ympev.2025.108471","DOIUrl":"10.1016/j.ympev.2025.108471","url":null,"abstract":"<div><div>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 <em>Argyrolobium</em> 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 (<em>dnaK, glnII, gyrB, recA,</em> and <em>rpoB</em>) separated the 18 <em>Bradyrhizobium</em> strains examined into five well-supported groups. Three of these were conspecific with <em>B. arachidis</em>, <em>B. brasilense/B. australafricanum</em> and <em>B. ivorense</em>, 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 <em>B. spitzkopense</em> sp. nov. (Arg816<sup>Ts</sup>) and <em>B. mpumalangense</em> sp. nov. (Arg237L<sup>Ts</sup>). Phylogenetic analyses of <em>nodA</em> 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 <em>Bradyrhizobium</em> strains nodulating Crotalarieae endemic to this region. Genome-based analyses of data from this and previous studies further showed that strains with these unique <em>nodA</em> alleles typically encode the <em>nodH</em> 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 <em>nodA</em> alleles commonly encountered elsewhere in South Africa and other tropical regions of the world. Also, the genomes of these other strains lacked <em>nodH</em> but encoded <em>nodZ</em>, 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 <em>Bradyrhizobium</em> strains that are distinct from bradyrhizobia nodulating Genisteae in the Mediterranean and the Americas.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108471"},"PeriodicalIF":3.6,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145076650","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 : 2025-09-13DOI: 10.1016/j.ympev.2025.108470
George Sangster , Meritxell Genovart , Tim Guilford , Daniel Oro , Maite Louzao , M. de L. Brooke , José Manuel Arcos
Ferrer Obiol et al. (2023) applied double digest restriction-site associated sequencing (ddRAD-seq) data to delimit species in North Atlantic and Mediterranean Puffinus shearwaters. These authors concluded that the Balearic/Yelkouan shearwaters (P. mauretanicus/P. yelkouan) sister-species pair comprised a single species based on analyses of ddRAD-seq data and a very brief and deficient review of other evidence. While it is clear that reduced representation genomic data are often suitable for the discovery and documentation of species and their relationships, the issue of whether such data are sufficient to falsify hypotheses of species taxa has received only limited attention so far. Here, we note that detection of species in phylogenomic analyses based on reduced representation sequencing methods will be problematic if species differences are only found in a small portion of the genome (so-called ‘genomic islands of differentiation’), as has been documented in multiple case studies. This means that genomic differences between some species may only be detected if (i) entire genomes are sequenced, and (ii) a formal search for islands of differentiation is conducted. Valid species may be overlooked in reduced representation approaches, such as ddRAD sequencing. Consequently, an apparent lack of overall phylogenomic divergence (e.g. lack of reciprocal monophyly, low genome-wide FST) should not be used by taxonomists as evidence that such taxa are not valid species. We conclude that the apparent lack of divergence in the ddRAD-seq data of Ferrer Obiol et al. (2023) does not represent credible evidence that P. mauretanicus and P. yelkouan are conspecific. In addition, we show that the authors misrepresented other available taxonomic data, failing to properly follow an integrative approach.
{"title":"Phylogenomics and the falsification of shearwater species (Puffinus mauretanicus, P. yelkouan) hypotheses: a comment on Ferrer Obiol et al. (2023)","authors":"George Sangster , Meritxell Genovart , Tim Guilford , Daniel Oro , Maite Louzao , M. de L. Brooke , José Manuel Arcos","doi":"10.1016/j.ympev.2025.108470","DOIUrl":"10.1016/j.ympev.2025.108470","url":null,"abstract":"<div><div><span><span>Ferrer Obiol et al. (2023)</span></span> applied double digest restriction-site associated sequencing (ddRAD-seq) data to delimit species in North Atlantic and Mediterranean <em>Puffinus</em> shearwaters. These authors concluded that the Balearic/Yelkouan shearwaters (<em>P. mauretanicus</em>/<em>P. yelkouan</em>) sister-species pair comprised a single species based on analyses of ddRAD-seq data and a very brief and deficient review of other evidence. While it is clear that reduced representation genomic data are often suitable for the discovery and documentation of species and their relationships, the issue of whether such data are sufficient to <em>falsify</em> hypotheses of species taxa has received only limited attention so far. Here, we note that detection of species in phylogenomic analyses based on reduced representation sequencing methods will be problematic if species differences are only found in a small portion of the genome (so-called ‘genomic islands of differentiation’), as has been documented in multiple case studies. This means that genomic differences between some species may only be detected if (i) entire genomes are sequenced, and (ii) a formal search for islands of differentiation is conducted. Valid species may be overlooked in reduced representation approaches, such as ddRAD sequencing. Consequently, an apparent lack of overall phylogenomic divergence (e.g. lack of reciprocal monophyly, low genome-wide <em>F</em><sub>ST</sub>) should not be used by taxonomists as evidence that such taxa are not valid species. We conclude that the apparent lack of divergence in the ddRAD-seq data of <span><span>Ferrer Obiol et al. (2023)</span></span> does not represent credible evidence that <em>P. mauretanicus</em> and <em>P. yelkouan</em> are conspecific. In addition, we show that the authors misrepresented other available taxonomic data, failing to properly follow an integrative approach.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108470"},"PeriodicalIF":3.6,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071309","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 : 2025-09-05DOI: 10.1016/j.ympev.2025.108468
Yuexin Wang , Didi Jin , Xiaopeng Hou , Khaled A.S. Al-Rasheid , Chen Shao , Tengteng Zhang
Early-branching eukaryotes are associated with the early branching events during eukaryogenesis. Understanding their genomic diversity and evolution can provide insights into the origin and speciation of eukaryotes. Ciliated protists (ciliates) are a group of early-branching unicellular eukaryotes with a high biodiversity, making them excellent models for evolutionary studies. However, their genomic diversity and evolution remain insufficiently understood. In this study, the comparative genomic and phylogenomic analyses were conducted using well-annotated macronuclear genomes from 16 bulk-cultured ciliates across four major classes. Our results indicate that: a) ciliates exhibit significant genomic diversity, with genome sizes ranging from 18.4 Mb to 117.1 Mb, extensive stop codon rearrangements, and tens of thousands of nanochromosomes in Spirotrichea and Litostomatea, reflecting dynamic genome architecture and adaptive evolution; b) gene family expansions highlight divergent evolutionary trajectories among ciliate classes, with Heterotrichea enhancing cell division capacity and Spirotrichea focusing on signal transduction; c) phylogenetic and structural analyses of meiosis related zinc finger protein and calcium channel related calmodulin gene families indicate that they predate the divergence of ciliates with functional diversification; d) anaerobic Entodinium caudatum retains abundant ubiquitin-related genes, while halotolerant Fabrea salina enriches anaphase-promoting complex cofactors (a crucial E3 ubiquitin ligase), suggesting that the encystment might be enhanced for both species. In summary, we systematically investigated the genomic landscape of ciliates to broaden our understanding of the genomic diversity and evolutionary patterns of ciliates.
{"title":"An integrated framework for evolution of ciliated protists (Protista, Ciliophora) from the perspective of comparative genomics","authors":"Yuexin Wang , Didi Jin , Xiaopeng Hou , Khaled A.S. Al-Rasheid , Chen Shao , Tengteng Zhang","doi":"10.1016/j.ympev.2025.108468","DOIUrl":"10.1016/j.ympev.2025.108468","url":null,"abstract":"<div><div>Early-branching eukaryotes are associated with the early branching events during eukaryogenesis. Understanding their genomic diversity and evolution can provide insights into the origin and speciation of eukaryotes. Ciliated protists (ciliates) are a group of early-branching unicellular eukaryotes with a high biodiversity, making them excellent models for evolutionary studies. However, their genomic diversity and evolution remain insufficiently understood. In this study, the comparative genomic and phylogenomic analyses were conducted using well-annotated macronuclear genomes from 16 bulk-cultured ciliates across four major classes. Our results indicate that: a) ciliates exhibit significant genomic diversity, with genome sizes ranging from 18.4 Mb to 117.1 Mb, extensive stop codon rearrangements, and tens of thousands of nanochromosomes in Spirotrichea and Litostomatea, reflecting dynamic genome architecture and adaptive evolution; b) gene family expansions highlight divergent evolutionary trajectories among ciliate classes, with Heterotrichea enhancing cell division capacity and Spirotrichea focusing on signal transduction; c) phylogenetic and structural analyses of meiosis related zinc finger protein and calcium channel related calmodulin gene families indicate that they predate the divergence of ciliates with functional diversification; d) anaerobic <em>Entodinium caudatum</em> retains abundant ubiquitin-related genes, while halotolerant <em>Fabrea salina</em> enriches anaphase-promoting complex cofactors (a crucial E3 ubiquitin ligase), suggesting that the encystment might be enhanced for both species. In summary, we systematically investigated the genomic landscape of ciliates to broaden our understanding of the genomic diversity and evolutionary patterns of ciliates.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108468"},"PeriodicalIF":3.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145014485","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 : 2025-09-04DOI: 10.1016/j.ympev.2025.108454
Jing Zhao , Hong Yu , Carl J. Rothfels , Jian-Jun Yang , Shao-Li Fang , Zhao-Rong He , Li-Bing Zhang , Xin-Mao Zhou
The advent of high-throughput genomic sequencing has provided unprecedented access to genome-scale data. This deluge of data has yielded new insights into phylogenetic relationships across the tree of life. However, incongruent results arising from different data partitions or from the use of different analyses have often been overlooked or insufficiently explored. In this study, we analyze the transcriptomes and plastomes of Selaginellaceae, an important land plant lineage and an ideal system to thoroughly explore phylogenomic incongruence. We aimed to reconstruct the most likely phylogenetic relationships in Selaginaceae and to examine the underlying causes of incongruence using various tests. Our major findings include: (1) phylogenomic incongruence in Selaginellaceae is quite common; (2) some plastid genes did not evolve as a linked unit, different from what is generally thought in vascular plants; (3) quantifying phylogenetic signal across different sites and genes that cause significant incongruence is necessary in phylogenomic analysis; (4) cytonuclear discordance and gene-tree conflict can be explained by incomplete lineage sorting, hybridization, and unique plastome traits; and (5) the most likely relationships “true tree” based on different datasets and phylogenetic analyses within Selaginellaceae are (Selaginoidoideae, (Boreoselaginelloideae, (Gymnogynoideae, (Sinoselaginelloideae, (Pulvinielloideae, (Lycopodioidoideae + Selaginelloideae))))). The data-analysis workflows established here might offer a framework for future phylogenomic studies for other complicated lineages.
{"title":"Widespread incongruence in the phylogenomics of the ancient land plant lineage, Selaginellaceae (lycophytes)","authors":"Jing Zhao , Hong Yu , Carl J. Rothfels , Jian-Jun Yang , Shao-Li Fang , Zhao-Rong He , Li-Bing Zhang , Xin-Mao Zhou","doi":"10.1016/j.ympev.2025.108454","DOIUrl":"10.1016/j.ympev.2025.108454","url":null,"abstract":"<div><div>The advent of high-throughput genomic sequencing has provided unprecedented access to genome-scale data. This deluge of data has yielded new insights into phylogenetic relationships across the tree of life. However, incongruent results arising from different data partitions or from the use of different analyses have often been overlooked or insufficiently explored. In this study, we analyze the transcriptomes and plastomes of Selaginellaceae, an important land plant lineage and an ideal system to thoroughly explore phylogenomic incongruence. We aimed to reconstruct the most likely phylogenetic relationships in Selaginaceae and to examine the underlying causes of incongruence using various tests. Our major findings include: (1) phylogenomic incongruence in Selaginellaceae is quite common; (2) some plastid genes did not evolve as a linked unit, different from what is generally thought in vascular plants; (3) quantifying phylogenetic signal across different sites and genes that cause significant incongruence is necessary in phylogenomic analysis; (4) cytonuclear discordance and gene-tree conflict can be explained by incomplete lineage sorting, hybridization, and unique plastome traits; and (5) the most likely relationships “true tree” based on different datasets and phylogenetic analyses within Selaginellaceae are (Selaginoidoideae, (Boreoselaginelloideae, (Gymnogynoideae, (Sinoselaginelloideae, (Pulvinielloideae, (Lycopodioidoideae + Selaginelloideae))))). The data-analysis workflows established here might offer a framework for future phylogenomic studies for other complicated lineages.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108454"},"PeriodicalIF":3.6,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145008676","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 : 2025-09-03DOI: 10.1016/j.ympev.2025.108459
Ivan A. Dvoyashov , Semyon Yu. Bodrov , Tatyana V. Petrova , Nataliya I. Abramson
Cases of intergeneric introgression have been poorly studied. That is why the mito–nuclear discordance in the tribe Clethrionomyini has been confusing and attracted our special attention. The phylogenetic position of the subgenus Aschizomys of rock voles (Alticola) has long been debated: a discussion that has resurfaced after early phylogenetic studies on cytochrome b placed Aschizomys with Clethrionomys (red-backed voles). Subsequent studies based on multiple nuclear markers support the monophyly of rock voles but have left unresolved whether the observed mito–nuclear discordance has resulted from intergeneric introgression or other factors, such as the retention of ancestral polymorphisms. Here, we compiled existing divergence time estimates for transcriptomic and mitochondrial data of both genera and demonstrated that both factors affect the mitochondrial phylogeny of Aschizomys. We then investigated potential traces of nuclear intergeneric introgression corresponding to mitochondrial signals using transcriptomic and quaddRAD sequencing datasets. Despite applying multiple introgression detection approaches, we did not find convincing evidence of nuclear intergeneric introgression. Nonetheless, certain tests produced conflicting outcomes, highlighting potential methodological sensitivities or complex evolutionary signals. Our study represents the first genome-wide investigation of mito–nuclear discordance between Clethrionomys and Alticola, thus contributing to a broader understanding of evolutionary processes in these rodents.
{"title":"Untangling intergeneric mito-nuclear discordance: evidence for ancient introgression in two vole genera, Clethrionomys and Alticola (Rodentia, Cricetidae)","authors":"Ivan A. Dvoyashov , Semyon Yu. Bodrov , Tatyana V. Petrova , Nataliya I. Abramson","doi":"10.1016/j.ympev.2025.108459","DOIUrl":"10.1016/j.ympev.2025.108459","url":null,"abstract":"<div><div>Cases of intergeneric introgression have been poorly studied. That is why the mito–nuclear discordance in the tribe Clethrionomyini has been confusing and attracted our special attention. The phylogenetic position of the subgenus <em>Aschizomys</em> of rock voles (<em>Alticola</em>) has long been debated: a discussion that has resurfaced after early phylogenetic studies on cytochrome <em>b</em> placed <em>Aschizomys</em> with <em>Clethrionomys</em> (red-backed voles). Subsequent studies based on multiple nuclear markers support the monophyly of rock voles but have left unresolved whether the observed mito–nuclear discordance has resulted from intergeneric introgression or other factors, such as the retention of ancestral polymorphisms. Here, we compiled existing divergence time estimates for transcriptomic and mitochondrial data of both genera and demonstrated that both factors affect the mitochondrial phylogeny of <em>Aschizomys</em>. We then investigated potential traces of nuclear intergeneric introgression corresponding to mitochondrial signals using transcriptomic and quaddRAD sequencing datasets. Despite applying multiple introgression detection approaches, we did not find convincing evidence of nuclear intergeneric introgression. Nonetheless, certain tests produced conflicting outcomes, highlighting potential methodological sensitivities or complex evolutionary signals. Our study represents the first genome-wide investigation of mito–nuclear discordance between <em>Clethrionomys</em> and <em>Alticola</em>, thus contributing to a broader understanding of evolutionary processes in these rodents.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108459"},"PeriodicalIF":3.6,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145004701","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 : 2025-09-02DOI: 10.1016/j.ympev.2025.108460
Sara Kafimola , Veronika Horsáková , Markéta Nováková , Eva Mikulášková , Kazuki Kimura , Stefan Meng , Jan Divíšek , Jeffrey C. Nekola , Michal Horsák
The remarkable phenotypic plasticity of land snail shells often results in convergent evolution, leading to frequent taxonomic misidentifications and non-monophyletic classifications. The taxonomy of the Holarctic micro land snails related to Euconulus fulvus has been particularly challenging to resolve. This study integrates mitochondrial and nuclear DNA phylogenetics, geometric morphometrics, and climate suitability modeling to clarify the phylogenetic and taxonomic status of an East Asian lineage within this group. We confirm that this lineage represents a distinct and previously misclassified species, Euconulus harimensis, which was formerly placed within the genus Parakaliella. While standard mtDNA and nDNA markers showed this evolutionary lineage as polyphyletic, two newly developed nuclear markers (ZN507 and TEP1) resolved the lineage, except for one individual, within a single robust clade of E. harimensis. Geometric morphometric analyses revealed significant differences in shell shape, which, along with unique shell microsculpture, further support its taxonomic separation. Although E. harimensis possesses the smallest distribution range of all related species, it exhibits the highest intraspecific genetic diversity. The models of suitable climatic conditions for both the present and the Last Glacial Maximum showed no major shifts, suggesting high climatic stability of the species range during the Pleistocene. This, along with other palaeobiogeographic factors, may have contributed to the unexpectedly high intraspecific genetic diversity of this species despite its limited range. Our findings provide new insights into the evolutionary processes that shape land snail inter- and intraspecific diversity, with implications for their taxonomy, which has often relied on shell morphology only. Additionally, phylogenetic analysis based on the new markers sheds novel light on the taxonomy and evolution of E. fulvus and E. alderi, highlighting the need for further taxonomic research.
{"title":"Integrative taxonomy reveals Parakaliella harimensis (Pilsbry, 1901) as a distinct East Asian Euconulus species with deep genetic structure","authors":"Sara Kafimola , Veronika Horsáková , Markéta Nováková , Eva Mikulášková , Kazuki Kimura , Stefan Meng , Jan Divíšek , Jeffrey C. Nekola , Michal Horsák","doi":"10.1016/j.ympev.2025.108460","DOIUrl":"10.1016/j.ympev.2025.108460","url":null,"abstract":"<div><div>The remarkable phenotypic plasticity of land snail shells often results in convergent evolution, leading to frequent taxonomic misidentifications and non-monophyletic classifications. The taxonomy of the Holarctic micro land snails related to <em>Euconulus fulvus</em> has been particularly challenging to resolve. This study integrates mitochondrial and nuclear DNA phylogenetics, geometric morphometrics, and climate suitability modeling to clarify the phylogenetic and taxonomic status of an East Asian lineage within this group. We confirm that this lineage represents a distinct and previously misclassified species, <em>Euconulus harimensis</em>, which was formerly placed within the genus <em>Parakaliella</em>. While standard mtDNA and nDNA markers showed this evolutionary lineage as polyphyletic, two newly developed nuclear markers (ZN507 and TEP1) resolved the lineage, except for one individual, within a single robust clade of <em>E. harimensis</em>. Geometric morphometric analyses revealed significant differences in shell shape, which, along with unique shell microsculpture, further support its taxonomic separation. Although <em>E. harimensis</em> possesses the smallest distribution range of all related species, it exhibits the highest intraspecific genetic diversity. The models of suitable climatic conditions for both the present and the Last Glacial Maximum showed no major shifts, suggesting high climatic stability of the species range during the Pleistocene. This, along with other palaeobiogeographic factors, may have contributed to the unexpectedly high intraspecific genetic diversity of this species despite its limited range. Our findings provide new insights into the evolutionary processes that shape land snail inter- and intraspecific diversity, with implications for their taxonomy, which has often relied on shell morphology only. Additionally, phylogenetic analysis based on the new markers sheds novel light on the taxonomy and evolution of <em>E. fulvus</em> and <em>E. alderi</em>, highlighting the need for further taxonomic research.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108460"},"PeriodicalIF":3.6,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145002074","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 : 2025-09-02DOI: 10.1016/j.ympev.2025.108455
Carolina Carrizo García , Valentin Heimer , Peter Schönswetter , Claudio Varotto , Božo Frajman , Mingai Li
Among the different mechanisms triggering diversification processes, chromosomal rearrangements that generate karyotypic changes are common in plants. Luzula (Juncaceae) is among the few angiosperm genera with holocentric chromosomes, which can undergo chromosome fission (agmatoploidy) or fusion (symploidy), resulting in karyotypes with different chromosome numbers and sizes. In this study, 3RAD genome-wide sequencing data and plastid sequences were used to explore evolutionary trends and patterns of genetic diversification among diploid taxa of Luzula sect. Luzula centred in the European Alpine System. In addition, we inferred its phylogenetic relationships to other closely related sections, of which several proved to be non-monophyletic. The species of Luzula sect. Luzula are segregated into three lineages, which show contrasting patterns regarding bifurcated branching, reticulation, and levels of coancestry as a result of different evolutionary histories. Agmatoploid species are found in two of these clades, displaying different karyotypes, while the third lineage comprises only L. campestris. Based on a molecular dating reconstruction, at least two putatively independent transitions towards agmatoploidy are estimated, which have occurred between the mid- and late Pleistocene in Luzula sect. Luzula. In addition, several trans-continental migrations, e.g. between Europe and Africa, were inferred. This study provides a new perspective on the complexity of diversification among wood rushes, which may serve as a basis for future exploration of the occurrence of agmatoploidy and its role in species diversification.
{"title":"Contrasting diversification patterns across wood rushes from Luzula sect. Luzula (Juncaceae) revealed by 3RAD genome-wide sequencing","authors":"Carolina Carrizo García , Valentin Heimer , Peter Schönswetter , Claudio Varotto , Božo Frajman , Mingai Li","doi":"10.1016/j.ympev.2025.108455","DOIUrl":"10.1016/j.ympev.2025.108455","url":null,"abstract":"<div><div>Among the different mechanisms triggering diversification processes, chromosomal rearrangements that generate karyotypic changes are common in plants. <em>Luzula</em> (Juncaceae) is among the few angiosperm genera with holocentric chromosomes, which can undergo chromosome fission (agmatoploidy) or fusion (symploidy), resulting in karyotypes with different chromosome numbers and sizes. In this study, 3RAD genome-wide sequencing data and plastid sequences were used to explore evolutionary trends and patterns of genetic diversification among diploid taxa of <em>Luzula</em> sect. <em>Luzula</em> centred in the European Alpine System. In addition, we inferred its phylogenetic relationships to other closely related sections, of which several proved to be non-monophyletic. The species of <em>Luzula</em> sect. <em>Luzula</em> are segregated into three lineages, which show contrasting patterns regarding bifurcated branching, reticulation, and levels of coancestry as a result of different evolutionary histories. Agmatoploid species are found in two of these clades, displaying different karyotypes, while the third lineage comprises only <em>L. campestris</em>. Based on a molecular dating reconstruction, at least two putatively independent transitions towards agmatoploidy are estimated, which have occurred between the mid- and late Pleistocene in <em>Luzula sect. Luzula</em>. In addition, several trans-continental migrations, e.g. between Europe and Africa, were inferred. This study provides a new perspective on the complexity of diversification among wood rushes, which may serve as a basis for future exploration of the occurrence of agmatoploidy and its role in species diversification.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108455"},"PeriodicalIF":3.6,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145002049","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 : 2025-09-01DOI: 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":"2025-09-01","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}
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