Molecular Phylogenetics and Evolution最新文献

{"title":"Argyrolobium legumes from an African centre of endemism associate with novel Bradyrhizobium species harbouring unique sets of symbiosis genes","authors":"Mabodiba M. Maake ,&nbsp;Chrizelle W. Beukes ,&nbsp;Magriet A. van der Nest ,&nbsp;Juanita R. Avontuur ,&nbsp;Esther K. Muema ,&nbsp;Tomasz Stępkowski ,&nbsp;Stephanus N. Venter ,&nbsp;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^Ts) and <em>B. mpumalangense</em> sp. nov. (Arg237L^Ts). 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":"2026-01-01","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}

{"title":"Resolving reticulate evolutionary histories of polyploid species of Azorella (Apiaceae) endemic to New Zealand","authors":"Weixuan Ning ,&nbsp;Heidi M. Meudt ,&nbsp;Antoine N. Nicolas ,&nbsp;Gregory M. Plunkett ,&nbsp;Peter B. Heenan ,&nbsp;William G. Lee ,&nbsp;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":"2026-01-01","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}

{"title":"The evolutionary history of insect-associated xinmoviruses","authors":"Luis Hernández-Pelegrín","doi":"10.1016/j.ympev.2025.108453","DOIUrl":"10.1016/j.ympev.2025.108453","url":null,"abstract":"<div><div>Viruses are ubiquitous biological entities that shape host evolution and ecosystem dynamics. Among them, negative-sense single-stranded RNA (−ssRNA) viruses form a diverse group that includes well-characterized vertebrate pathogens and an expanding repertoire of invertebrate-infecting viruses. Recent advances in high-throughput sequencing have revealed numerous insect-associated −ssRNA viruses, reshaping our understanding of their diversity, transmission, and ecological significance.</div><div>This study identified 22 novel xinmoviruses, expanding the known host range of this viral family to include Lepidoptera and Plecoptera for the first time. Additionally, xinmovirus-derived non-retroviral endogenous viral elements (nrEVEs) were identified in multiple insect lineages, expanding previous findings that were limited to mosquitoes. Phylogenetic analysis of the <em>Xinmoviridae</em> family revealed host-driven evolutionary patterns with potential cross-order transmission events. Similarly, nrEVEs provided evidence of specific viral-host interactions, with nrEVEs showing greater similarity to exogenous viruses infecting the same insect order and, in some cases, the same insect species.</div><div>Together, these findings significantly expand the known diversity and evolutionary landscape of xinmoviruses. By uncovering new hosts, viral lineages, and genomic integrations, this study provides a more comprehensive framework for understanding their ecological distribution, transmission dynamics, and potential biological functions.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108453"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994762","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}

{"title":"Genome-based phylogenetics and species delimitation for the narrowly distributed Pachyhynobius salamander (Caudata: Hynobiidae) reveal cryptic biodiversity","authors":"Yongxuan Xiao ,&nbsp;Tingli Hu ,&nbsp;Suxin Shi ,&nbsp;Hui Wang ,&nbsp;Caiwen Zhang ,&nbsp;Dapeng Pang ,&nbsp;Yinfan Cai ,&nbsp;Tao Pan ,&nbsp;Pablo Orozco-terWengel ,&nbsp;Baowei Zhang","doi":"10.1016/j.ympev.2025.108458","DOIUrl":"10.1016/j.ympev.2025.108458","url":null,"abstract":"<div><div>Species delimitation is a challenging issue in taxonomy, especially in the absence of clear diagnostic morphological characters, a particular problem for cryptic species. In recent years, the rapid development of high-throughput sequencing technologies, when combined with genomic species delimitation methods such as the multispecies coalescent, has significantly improved the ability to resolve cryptic species. However, traditional methods like Bayesian phylogenetics and phylogeography often result in over-splitting due to their failure to fully consider factors such as gene flow. This study focuses on the genus <em>Pachyhynobius</em>, endemic to China, utilizing specific-locus amplified fragment sequencing technology to construct a high-quality nuclear genome SNP dataset. Systematic genomics combined with various species delimitation methods that incorporate the genealogical differentiation index and the isolation by distance model for geographic information was used to systematically evaluate the species boundaries of this genus. The results show that <em>Pachyhynobius</em> consists of four genetically independent, geographically disjunct lineages with deep genetic differentiation occurring over millions of years. Although these lineages have relatively close geographic distributions, long-term ecological niche conservatism and the sky island effect may be key driving forces responsible for their continued isolation and independent evolutionary paths. Multi-method species delimitation analysis further provides a comprehensive evaluation of the potentially distinct genetic lineages within the group, identifying them as potential cryptic species. Although new species have not yet been formally named, the evidence provided offers a new example for understanding the identification and evolutionary mechanisms of cryptic species in geographically restricted habitats.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108458"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144926744","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}

{"title":"Untangling intergeneric mito-nuclear discordance: evidence for ancient introgression in two vole genera, Clethrionomys and Alticola (Rodentia, Cricetidae)","authors":"Ivan A. Dvoyashov ,&nbsp;Semyon Yu. Bodrov ,&nbsp;Tatyana V. Petrova ,&nbsp;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":"2026-01-01","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}

{"title":"Target sequence capture informs generic delimitation and hybridization in the tribe Lasiopetaleae (Malvaceae)","authors":"Benjamin M. Anderson ,&nbsp;Todd G.B. McLay ,&nbsp;Carolyn F. Wilkins ,&nbsp;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":"2025-12-01","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}

{"title":"Whole-genome resequencing unveils the phylogeographic coevolution of Oncomelania hupensis with Yangtze River dynamics in China","authors":"Lei Duan ,&nbsp;Fang Luo ,&nbsp;Qin Liu ,&nbsp;Shen Chen ,&nbsp;Xia Tian ,&nbsp;Wen-Wen Lv ,&nbsp;Lu He ,&nbsp;Zi-Rui Ren ,&nbsp;Jing Xu ,&nbsp;Xiao-Nong Zhou ,&nbsp;Shi-Zhu Li ,&nbsp;Shan Lv ,&nbsp;Wei Hu","doi":"10.1016/j.ympev.2025.108440","DOIUrl":"10.1016/j.ympev.2025.108440","url":null,"abstract":"<div><div>The freshwater snail <em>Oncomelania hupensis</em> is the only intermediate host of <em>Schistosoma japonicum</em> and is currently mainly distributed in the middle and lower reaches of the Yangtze River in China. To explore the evolutionary history and adaptations of <em>O. hupensis</em>, we re-sequenced 283<em>O. hupensis</em> accessions from 30 geographic locations across the middle and lower Yangtze River. Our study raises and proves an intriguing hypothesis: <em>O. hupensis</em> has its distribution and adaptation closely tied to the geological evolution of the Yangtze River. Despite varying degrees of isolation and differentiation, lake-type snail populations in the middle and lower reaches may migrate westward to eastward (from middle to lower reaches) via water flow, while hill ecotype snails in the middle reaches potentially disperse from hilly region to lake areas. Population genetics and evolutionary analyses revealed that <em>O. hupensis</em> exhibits a gradual dispersal history from hilly region to downstream areas, closely mirroring the Yangtze River’s flow and geological evolution. Compared to hill ecotype populations, lake populations displayed higher genetic diversity, consistent with dynamic habitats and increased gene flow. This west-to-east migration pattern may be driven by the Yangtze River’s geological dynamics and associated climatic-ecological shifts. Notably, we found genes under strong positive selection differed between lake and hill ecotype populations. Our study provides comprehensive insights into the population dynamics and genetic architecture of <em>O. hupensis</em>, underscoring its coevolution with the Yangtze River’s geological history. These findings advance the genetic understanding of <em>O. hupensis</em> adaptation to different ecological environments and inform schistosomiasis control strategies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108440"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144828299","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}

{"title":"Phylogenomics of African Labeo (Cypriniformes: Cyprinidae) emphasizing central African species","authors":"Tobit L.D. Liyandja ,&nbsp;Brian T. Smith ,&nbsp;S. Elizabeth Alter ,&nbsp;Brian L. Sidlauskas ,&nbsp;Melanie L.J. Stiassny","doi":"10.1016/j.ympev.2025.108427","DOIUrl":"10.1016/j.ympev.2025.108427","url":null,"abstract":"<div><div><em>Labeo</em> constitutes the largest genus within the cyprinid tribe Labeonini with over 110 recognized species in Africa and Asia. The clade comprises a major component of the herbivore/detritivore guild with considerable socio-economic importance to artisanal and commercial fisheries. A pan-African distribution and wide variety of habitat occupancy make the group a model to investigate diversification patterns, eco-phenotypic variation, and biogeographical events underpinning their radiation at a continental scale. However, previous attempts to elucidate <em>Labeo</em> systematics using either molecular or morphological data have failed to produce congruent and robust results, and much taxonomic and nomenclatural confusion remains. Here we present the first phylogenomic analysis of the genus using 2,187 ultraconserved elements from 85 taxa, including 56 recognized species, 27 cryptic (candidate) species, and outgroups from the Asian Labeonini. Both concatenated and coalescence-based phylogenetic analyses strongly support monophyly of African <em>Labeo</em> and recover three major clades comprising at least nine species groups. Two main clades are pan-African, while the third is restricted to four ichthyofaunal provinces. With the single exception of the <em>L. umbratus</em> group, none of the previously proposed morphological groupings are resolved as monophyletic, suggesting rampant morphological convergence across the radiation. In this study, interspecific relationships are well resolved and time calibration results corroborate the key role of the Miocene in the radiation of African freshwater fishes. We identify numerous previously unrecognized taxa, and our study provides a much-needed framework for the taxonomic revision of <em>Labeo</em>, a task critical for the development of sound management of these important food fishes.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108427"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144796254","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}

{"title":"Diversification and differentiation of Stipa species shed light on the regional evolutionary history of the eastern Eurasian steppe","authors":"Dongqing Yan ,&nbsp;Yanyan Fan ,&nbsp;Xiaoru Jiang ,&nbsp;Yang Ma ,&nbsp;Kejian Lin ,&nbsp;Zhenhua Dang ,&nbsp;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":"2025-12-01","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}

{"title":"Estimated timeline for the evolution of symbiotic nitrogen fixing Paraburkholderia","authors":"Lazarus Mavima ,&nbsp;Emma T. Steenkamp ,&nbsp;Chrizelle W. Beukes ,&nbsp;Marike Palmer ,&nbsp;Sofie E. De Meyer ,&nbsp;Euan K. James ,&nbsp;Stephanus N. Venter ,&nbsp;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":"2025-12-01","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}