Molecular Phylogenetics and Evolution最新文献

{"title":"Genomic insights into the transition from saprophytic to parasitic lifestyles in Hymenochaetales.","authors":"Ji-Hang Jiang, Xue-Wei Wang, Zi-Qi Shen, Qiu-Shi Li, Shi-Liang Liu, Li-Wei Zhou","doi":"10.1016/j.ympev.2026.108632","DOIUrl":"https://doi.org/10.1016/j.ympev.2026.108632","url":null,"abstract":"<p><p>Macrofungi play key roles in forest ecosystems by forming symbiotic, saprophytic, and parasitic associations with various plant species. Although previous genomic studies have investigated the transitions between these modes of nutrition, limited attention has been paid to the transition from saprophytic to parasitic ecological lifestyles. Hymenochaetales originated as a saprophytic species, and subsequently transitioned to parasitism on multiple occasions. In this study, we sequenced and compared 27 high-quality genomes of the Hymenochaetales. We identified differences in transposable element content and secretome composition between the saprophyte and parasite species. Specifically, the insertion of long-terminal repeat retrotransposons shortly after parasite speciation may drive the transition from saprophytic to parasitic ecological types. Additionally, the close genomic proximity of TEs to CAZymes and SSPs, along with the higher content in several CAZyme and protease families and SSPs in parasites may contribute to shaping host and substrate preferences. Notably, the Ser/Thr protein kinase was postulated to be crucial for the interaction between parasitic species and their host plants. In conclusion, we provide new insights into the molecular mechanisms underlying the transition from saprotrophy to parasitism in Hymenochaetales.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108632"},"PeriodicalIF":3.6,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147864665","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":"Molecular phylogeography of the riffle beetle Urumaelmis uenoi (Coleoptera: Elmidae) in the Ryukyu Islands, Japan.","authors":"Takumi Yoshida, Masakazu Hayashi, Masaki Takenaka, Koji Tojo","doi":"10.1016/j.ympev.2026.108631","DOIUrl":"https://doi.org/10.1016/j.ympev.2026.108631","url":null,"abstract":"<p><p>Islands are regarded as \"nature's laboratories\" and are important model systems for examining biological phenomena. In phylogeographic studies of continental islands, estimating divergence periods has often been used to examine the relationship between island formation history and species evolution. However, when only post-island-formation events are used for calibration, earlier geological processes may be overlooked, potentially introducing bias into divergence- period estimates and their interpretation. In this study, we investigated the relationship between evolutionary history and the formation history of the Ryukyu Islands using the riffle beetle Urumaelmis uenoi (Elmidae), which inhabits river systems in the Ryukyu Islands. Divergence-period estimation was conducted using multiple DNA markers and analytical approaches. Three major geographically distinct lineages (Northern Ryukyu, Amami Iss. and Okinawa Iss.) were identified within U. uenoi, one of which was separated by the Tokara Gap between the Palearctic and Oriental regions. Mito-nuclear discordance was detected in the phylogenetic relationships of U. uenoi and its related species, and mitochondrial DNA did not support species-level monophyly of U. uenoi. In contrast, nuclear DNA supported species-level monophyly and suggested that divergence among intraspecific lineages predates the formation of the Ryukyu Islands. These results indicate that geological history prior to island formation, as well as post-formation inter-island dispersal, played important roles in shaping genetic structure. Our findings highlight the importance of integrating multiple DNA markers, including related species, as well as carefully selecting calibration points, in phylogeographic studies of continental islands. In addition, this study is the first to apply genome-wide SNPs to the Elmidae.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108631"},"PeriodicalIF":3.6,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147846572","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":"Limitations of molecular dating using constant birth–death rate priors in deep time reflected in Brachiopoda evolution","authors":"Luyan Li ,&nbsp;Joëlle Barido-Sottani ,&nbsp;Daniele Silvestro","doi":"10.1016/j.ympev.2026.108557","DOIUrl":"10.1016/j.ympev.2026.108557","url":null,"abstract":"<div><div>Molecular dating often struggles to align with fossil records when divergence times are estimated in deep evolutionary history, particularly during the Palaeozoic era. This discrepancy may arise because of the assumptions embedded in constant birth–death rate priors, which oversimplify complex evolutionary dynamics and remain the default setting in most analyses. In the present study, we tested the impact of different models and priors on phylogenetic inference on a dataset of Rhynchonellata (Brachiopoda), and explored whether the divergence times inferred from molecular clocks and fossils can be reconciled. In particular, we addressed rate heterogeneity, that is, variation in speciation (λ) and extinction (μ) rates over time, in divergence time estimation by incorporating the birth–death rates inferred independently from fossil occurrence data as rate priors and calibration points. These were reviewed using Marshall’s temporal calibration method and ancestral state reconstruction. We showed that using the birth–death skyline model as a tree prior significantly reduces the gap between age estimates. Furthermore, to assess the generality of these patterns beyond a deeply diverging clade, we conducted a robustness check using Lingulidae, a comparatively young, re-diversified lineage, and determined that skyline models also produced divergence-time estimates more consistent with those inferred from the fossil record in this dataset. Overall, we showed that using a constant birth–death rate prior, which ignores rate heterogeneity, can affect the accuracy of the resulting phylogenetic trees. Our results revealed that when the lineages used for molecular dating persisted through the Cambrian explosion, Ordovician extinction, and Permian-Triassic (P-T) boundary, caution should be implemented in the interpretation of phylogenetic inferences as the data from molecular alignments alone and standard model assumptions may not reflect the significant shifts in diversification dynamics that occurred during these time periods. These findings highlight the inadequacy of constant birth–death rate priors in the presence of rate heterogeneity across deep time, thus limiting their reliability for studying lineages with complex evolutionary histories. Our analyses showed that informative priors from independent analyses of the fossil occurrences can improve the quality of molecular clock analyses, indicating the requirement of more flexible models to improve the precision of molecular dating in deep-time research.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"218 ","pages":"Article 108557"},"PeriodicalIF":3.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146159503","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":"Out of North Africa: Evolution and biogeography of Afro-Arabian dwarf tarantulas (Theraphosidae, Ischnocolinae)","authors":"Jan Korba,&nbsp;Vera Opatova","doi":"10.1016/j.ympev.2026.108559","DOIUrl":"10.1016/j.ympev.2026.108559","url":null,"abstract":"<div><div>Large-scale vicariant events are expected to create congruent phylogeographic patterns among unrelated taxa. A continental-wide disjunction displayed by unrelated plant taxa across Afro-Arabia (the RAND flora pattern) has been traditionally explained as a consequence of late Miocene aridification of the region and the formation of the Sahara Desert. We implement genomic data (UCE), divergence time estimation and biogeographic analyses to uncover the origins of RAND pattern distribution in dwarf tarantula genus <em>Ischnocolus</em> <span><span>Ausserer, 1871</span></span>. The results suggest that the disjunct distribution of <em>Ischnocolus</em> resulted from ecological vicariance driven by the Middle Miocene climate cooling, predating the timing of the aridification of the region. Our results thus bring evidence of phylogeographic discordance of the RAND pattern origins among different taxa. Conserved lifestyle and the preference for humid environments among the early diverging <em>Ischnocolus</em> lineages also suggest that dispersal across Afro-Arabia was likely catalyzed by interspecific competitive exclusion. Subsequent lifestyle switches, that enabled the dwarf tarantulas to successfully colonize dry environments, evolved repeatedly in the group’s evolution. Additionally, we delimit the boundaries of the genus <em>Ischnocolus</em> and assess its position within the tarantula phylogeny. As a consequence, we revalidate the genus <em>Luphocemus</em> Denis, 1960, which is endemic to North Africa.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"218 ","pages":"Article 108559"},"PeriodicalIF":3.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146137692","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":"Structural dynamics of chloroplast genome in Paphiopedilum (Orchidaceae): in response to natural hybridization","authors":"Xue-Ying Wei ,&nbsp;Ai-Qun Hu ,&nbsp;Jin Zhou ,&nbsp;Jiang-Ping Shu ,&nbsp;Wei-Yue Sun ,&nbsp;Li-Qiang Li ,&nbsp;Jian-Wen Shao ,&nbsp;Hui Wang ,&nbsp;Yue-Hong Yan","doi":"10.1016/j.ympev.2025.108521","DOIUrl":"10.1016/j.ympev.2025.108521","url":null,"abstract":"<div><div>Chloroplast genomes, once considered highly conserved, have been shown to exhibit significant structural variations, though the underlying mechanisms remain unclear. In this study, we investigated the chloroplast genome structure of eight populations comprising 76 individuals of <em>Paphiopedilum barbigerum</em>, <em>P. helenae</em>, and <em>P. vejvarutianum</em>. By using chloroplast genome sequences and 15,924 nuclear SNP loci, we conducted analyses and validations of chloroplast genome structural recombination and natural hybridization. Our key findings include the following: (1) Structural variations in the chloroplast genomes were found to be stable and heritable across populations. (2) In <em>P. barbigerum</em>, populations exhibiting structural variation contained an unidentified insertion sequence in the SSC region, which was associated with a significant reduction in GC content within this region. (3) The presence of non-LTR retrotransposons suggests their potential role in the expansion and contraction of the IR region in <em>Paphiopedilum</em>, with this chloroplast variation potentially linked to natural hybridization events. (4) The incongruent phylogenetic relationships, gene flow and gene introgression among <em>P. barbigerum</em>, <em>P. helenae</em>, and <em>P. vejvarutianum</em> point to a history of hybridization within these species. Our study proposes that both transposon activity and hybridization play crucial roles in driving chloroplast structural variations. For the first time, the structural variations of chloroplasts have been linked to transposons and natural hybridization, breaking the traditional stereotype of chloroplasts being highly conserved. This discovery enhances our understanding of how natural hybridization contributes to species formation and provides a basis for exploring the evolutionary mechanisms of chloroplast genomes.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"218 ","pages":"Article 108521"},"PeriodicalIF":3.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145745409","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":"Phylotranscriptomics reveals conflicts of deep nodes in Saxifragales","authors":"Hui-Ling Li ,&nbsp;Hong Chang ,&nbsp;Huan-Huan Xie ,&nbsp;Lei Zhang ,&nbsp;Guo-Qian Hao ,&nbsp;Dimitar Dimitrov ,&nbsp;Peng-Chuan Sun ,&nbsp;Nathanael Walker-Hale ,&nbsp;Jia-Liang Li ,&nbsp;Xiao-Ting Xu","doi":"10.1016/j.ympev.2026.108553","DOIUrl":"10.1016/j.ympev.2026.108553","url":null,"abstract":"<div><div>Saxifragales comprises 15 families in five well-supported clades: Paeoniaceae, Peridiscaceae, the woody clade, Cynomoriaceae, and the core Saxifragales. Relationships among these groups—particularly the placements of Paeoniaceae and Cynomoriaceae, and family-level relationships within the woody clade—remain uncertain. Here, we analyzed transcriptomes from 88 species (13 families) and plastomes from 14 families (with limited plastid genes retained in the parasitic Cynomoriaceae). Phylogenomic analyses of 1,113 BUSCO single-copy nuclear genes and 78 plastid genes consistently recovered Paeoniaceae as sister to the woody clade (Paeoniaceae + Woody clade, PWC) and supported Cynomoriaceae as sister to the core Saxifragales (Cynomoriaceae + Core Saxifragales, CCS). We detected widespread phylogenetic conflict and cytonuclear discordance, largely driven by pervasive gene flow and, to a lesser extent, incomplete lineage sorting (ILS). Gene tree error contributed to the unstable placement of Cynomoriaceae, while ILS dominated conflicts involving Cercidiphyllaceae. Future work integrating chromosome-level genomes and karyotype evolution may clarify woody clade relationships, and account for horizontal gene transfer in Cynomoriaceae.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"218 ","pages":"Article 108553"},"PeriodicalIF":3.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146127526","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":"Unraveling the complex systematics of Malagasy Donella species (Sapotaceae) using herbarium phylogenomics","authors":"T. Kiedaisch ,&nbsp;L. Gautier ,&nbsp;C.G. Boluda ,&nbsp;C. Pouchon ,&nbsp;Y. Naciri","doi":"10.1016/j.ympev.2026.108569","DOIUrl":"10.1016/j.ympev.2026.108569","url":null,"abstract":"<div><div><em>Donella</em> is a genus of tropical trees distributed across Africa and Madagascar with a single species in Asia. While a recent taxonomic revision provided a genus-wide morphological framework, the circumscription of the Malagasy taxa remained difficult, hindering conservation assessments in this high-diversity region.</div><div>We employed a phylogenomic framework to delimit species boundaries and infer evolutionary relationships within the <em>Donella</em> lineage. A set of 99 specimens, selected to capture the breadth of morphological and geographic variation of the Malagasy species from ∼ 230 unique collection numbers, was analysed using a target enrichment approach. We inferred phylogenetic relationships on nearly 800 nuclear loci using both species-tree and network analyses, assessed genome-wide heterozygosity levels, and implemented species delimitation models as well as niche modelling.</div><div>All Malagasy taxa, except <em>Donella guereliana</em>, form a clade, characterized by a radiation-like topology. Results across analytical approaches are largely congruent and agree with morphological differentiation and geographic structuring. <em>Donella lanceolata</em>, previously thought to occur in Madagascar, is resolved as sister to the Malagasy clade, with the Malagasy specimens representing a distinct species, here recognized as <em>D. malagassica</em> comb. et stat. nov. Two species are newly described, <em>D. ricardorum</em> sp. nov. and <em>D. cryptica</em> sp. nov.; <em>D. sambiranensis</em> is reinstated; <em>D. humbertii</em> is synonymized under <em>D. analalavensis</em>; and <em>D. guereliana</em> is excluded from the genus.</div><div>The taxonomic changes proposed here refine the circumscription of the genus <em>Donella</em> and its Malagasy species, while demonstrating that 73% of the species in Madagascar are threatened according to IUCN criteria, highlighting the urgent need of targeted conservation measures.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"218 ","pages":"Article 108569"},"PeriodicalIF":3.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146159445","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":"Integrative morphological and genomic analyses reveal diversity, reticulate evolution, and adaptation in diploid and tetraploid Rosa species from Xinjiang","authors":"Zhongyu Tang ,&nbsp;Zhenlong Liang ,&nbsp;Hengning Deng ,&nbsp;Liangying Li ,&nbsp;Jian Ru ,&nbsp;Shiqi Li ,&nbsp;Jia Miao ,&nbsp;Cheng Zhang ,&nbsp;Xinfen Gao","doi":"10.1016/j.ympev.2026.108555","DOIUrl":"10.1016/j.ympev.2026.108555","url":null,"abstract":"<div><div>Xinjiang, with extensive mountain systems and desert basins, forms a major biogeographic corridor between East and Central Asia and harbors taxonomically challenging wild <em>Rosa</em> species. We analyzed 252 accessions (159 diploids, 93 tetraploids) and integrated morphometrics, ploidy estimates, and whole-genome resequencing. PCA of 14 quantitative traits revealed extensive overlap, especially between diploid <em>R. beggeriana</em> and tetraploid <em>R. laxa</em>. In contrast, mixed-trait clustering based on Gower distance was consistent with the genomic backbone, while Random Forest and linear discriminant analysis (LDA) identified ten diagnostic traits that improved discrimination (86.2% accuracy). This integrated framework helped delineate lineage boundaries and attribute persistent phenotypic overlap to reticulate evolution. Diploid resequencing yielded 4.77 million SNPs and revealed deep lineage structure and pervasive introgression, including a multi-species admixed lineage with mosaic ancestry. Genome scans and trait–environment associations highlighted stress-related candidate loci (including signals overlapping <em>DRS1</em> and <em>DCL4</em>). They also linked dense pedicel hair to hot–arid habitats in an arid lineage of <em>R. beggeriana</em>, pending functional validation. Phylogenies inferred from 240 plastomes and 5,641 single-copy nuclear genes revealed strong cytonuclear discordance and gene-tree discordance, consistent with rapid divergence and incomplete lineage sorting and further shaped by introgression and plastid capture. For tetraploids, integrative evidence supported recent autopolyploidization and ongoing gene exchange, although short-read data limited dosage-aware inference. Overall, our results clarify reticulate evolutionary histories of Xinjiang roses and provide a lineage-informed basis for conservation and germplasm utilization.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"218 ","pages":"Article 108555"},"PeriodicalIF":3.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146133571","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":"Ancient gene flow shapes phylogenetic discordance in a genus of wood-warblers (Aves: Parulidae: Leiothlypis)","authors":"Ari A. Rice,&nbsp;Joseph D. Manthey","doi":"10.1016/j.ympev.2026.108558","DOIUrl":"10.1016/j.ympev.2026.108558","url":null,"abstract":"<div><div>The use of whole-genome data has been revelatory towards our understanding of organisms’ evolutionary relationships. However, these perceived relationships will sometimes lack uniform support across genomes, with different genomic regions telling different stories. For taxa that arose through rapid radiations, this phylogenetic discordance is especially common due to gene flow, deep coalescence, or both processes interacting with natural selection and genomic architecture such as coding content or chromosome size. Here, we used whole genomes to determine relationships in a genus of Parulid warblers (<em>Leiothlypis</em>, Parulidae: Aves) and identified causes of phylogenetic discordance by measuring interspecific gene flow and modeling the demographic history of the genus. We found evidence for three separate gene flow events in <em>Leiothlypis</em>, with one event disproportionately affecting phylogenetic inference near the ends of chromosomes and another representing a potential case of adaptive introgression in a small (3 Mbp) autosomal region. Surprisingly, the extent of gene flow and discordance in genomic regions showed little to no correlation with amounts of coding or repetitive elements. Moreover, none of the gene flow events sufficiently explained the low support for a sister relationship between <em>L. ruficapilla</em> and a three-member clade including <em>L. crissalis</em>. Rather, this pattern was better explained by deep coalescence that arose from nearly simultaneous speciation events for <em>L. ruficapilla</em> and <em>L. crissalis</em> approximately 600,000 years ago. Together, these findings suggest the evolution of <em>Leiothlypis</em> and perhaps other avian radiations are shaped by a complex series of factors that include deep coalescence and ancient hybridization with varied outcomes.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"218 ","pages":"Article 108558"},"PeriodicalIF":3.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146137670","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":"Molecular data and museum collections reframe Pleuroceridae (Gastropoda: Cerithioidea) diversity and conservation priorities in an overlooked freshwater biodiversity hotspot","authors":"Nathan V. Whelan ,&nbsp;Annika Baldwin ,&nbsp;Jeffrey T. Garner ,&nbsp;Paul D. Johnson ,&nbsp;Ellen E. Strong","doi":"10.1016/j.ympev.2026.108556","DOIUrl":"10.1016/j.ympev.2026.108556","url":null,"abstract":"<div><div>Freshwater gastropods are among the most imperiled organisms globally, and taxonomic uncertainty remains a major obstacle to their conservation. <em>Elimia melanoides</em> (Conrad, 1834), previously presumed extinct, was rediscovered in the Black Warrior River drainage of Alabama, prompting renewed interest in its conservation status. However, persistent taxonomic uncertainty has hindered listing under the U.S. Endangered Species Act. We used integrative taxonomy—including extensive field sampling, 3RAD-based phylogenomics, and morphological analysis of museum specimens—to resolve the taxonomy of <em>E. melanoides sensu lato</em>. Our molecular phylogenetic analyses revealed that <em>E. melanoides</em>, as currently conceived, comprises three distinct lineages: <em>E. melanoides sensu stricto</em>, <em>Elimia hydeii</em> (Conrad, 1834) (in part), and <em>Elimia turgida</em> (Haldeman, 1840), which we restore from synonymy. Comparison to historical museum specimens indicates that the extant lineage currently identified as <em>E. melanoides</em> is not conspecific with the taxon described as <em>Anculosa melanoides</em> by Conrad. We propose to follow prevailing usage and retain the name <em>E. melanoides</em> for the extinct taxon described by Conrad. There is no available name for the extant taxon, which we describe here as <em>Elimia mintoni</em> n. sp. Population genomic analyses revealed high genetic structure in <em>E. mintoni</em> n. sp. and <em>E. hydeii</em>, especially in headwater populations, while <em>E. turgida</em> showed no structure across its narrow range but maintains high genetic diversity. These findings have urgent conservation implications: <em>E. mintoni</em> n. sp. and <em>E. turgida</em> are valid, range-restricted species with low redundancy and representation. Our study underscores the necessity of taxonomic resolution for accurate biodiversity assessments and effective conservation planning.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"218 ","pages":"Article 108556"},"PeriodicalIF":3.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146120549","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}