Molecular Phylogenetics and Evolution最新文献

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 Ischnocolus Ausserer, 1871. The results suggest that the disjunct distribution of Ischnocolus 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 Ischnocolus 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 Ischnocolus and assess its position within the tarantula phylogeny. As a consequence, we revalidate the genus Luphocemus Denis, 1960, which is endemic to North Africa.

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 (Leiothlypis, 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 Leiothlypis, 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 L. ruficapilla and a three-member clade including L. crissalis. Rather, this pattern was better explained by deep coalescence that arose from nearly simultaneous speciation events for L. ruficapilla and L. crissalis approximately 600,000 years ago. Together, these findings suggest the evolution of Leiothlypis and perhaps other avian radiations are shaped by a complex series of factors that include deep coalescence and ancient hybridization with varied outcomes.

The Levant region is an important recognized biological corridor that unites three major continents, Africa, Asia and Europe. Due to its intersectional positioning, the region has facilitated flora and faunal exchange between four biogeographical elements: Palaearctic, Palaeoeremic, Ethiopian and Oriental. The Levant's unique geological position, along with a distinguishable climate gradient and topographic heterogeneity, has likely contributed to the impressive solifuge biodiversity in a comparatively small area, making it an ideal and important gateway for beginning to interrogate the current solifuge diversity in the Old World. In this region, there are currently six families of solifuges and over 50 species described. However, solifuge taxonomy in the Old World has remained largely stagnant. While there exists a consensus that accurate taxonomic estimates are imperative for conservation efforts, such information is often in reference to undiscovered diversity, rather than the possible taxonomic inflation that may exist in understudied groups such as solifuges. The purpose of this study was to revisit the current standing taxonomic hypotheses using UCE phylogenomics, divergence dating, and analysis of SNPs recovered from solifuge genomes, using both newly generated genomic data derived from natural history collections and previously acquired genomic data. Our primary goal was to reevaluate the solifuge historical taxonomy of this region, with the intent of obtaining a better picture of shallow-level diversity patterns in the six native solifuge families of interest. Our molecular study provides evidence to suggest that the current reported solifuge diversity from this region should be synonymized to about one-third, as they represent junior synonyms of conspecifics. Our findings highlight longstanding taxonomic inaccuracies within Levantine Solifugae and illuminate the extent of unwarranted and excessive taxonomic splitting. Future taxonomic research should prioritize clarifying species boundaries and reorganizing the group based on a comprehensive understanding of what defines a meaningfully stable taxonomic unit, while remaining open to simplified scenarios with fewer taxonomic ranks.

Xinjiang, with extensive mountain systems and desert basins, forms a major biogeographic corridor between East and Central Asia and harbors taxonomically challenging wild Rosa 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 R. beggeriana and tetraploid R. laxa. 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 DRS1 and DCL4). They also linked dense pedicel hair to hot-arid habitats in an arid lineage of R. beggeriana, 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.

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.

Freshwater gastropods are among the most imperiled organisms globally, and taxonomic uncertainty remains a major obstacle to their conservation. Elimia melanoides (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 E. melanoides sensu lato. Our molecular phylogenetic analyses revealed that E. melanoides, as currently conceived, comprises three distinct lineages: E. melanoides sensu stricto, Elimia hydeii (Conrad, 1834) (in part), and Elimia turgida (Haldeman, 1840), which we restore from synonymy. Comparison to historical museum specimens indicates that the extant lineage currently identified as E. melanoides is not conspecific with the taxon described as Anculosa melanoides by Conrad. We propose to follow prevailing usage and retain the name E. melanoides for the extinct taxon described by Conrad. There is no available name for the extant taxon, which we describe here as Elimia mintoni n. sp. Population genomic analyses revealed high genetic structure in E. mintoni n. sp. and E. hydeii, especially in headwater populations, while E. turgida showed no structure across its narrow range but maintains high genetic diversity. These findings have urgent conservation implications: E. mintoni n. sp. and E. turgida 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.

The distribution of vegetation across the Northern Hemisphere has been profoundly shaped by the climatic and geological history of the Cenozoic. An ancient paleotropical vegetation belt, once spanning the Northern Hemisphere, is hypothesized to have facilitated biotic exchange across regions during the early Cenozoic, before its eventual fragmentation and near-complete disappearance. We investigate the evolutionary history of this pattern using the fern subfamily Woodwardioideae (Blechnaceae)-a striking example of disjunction across the Northern Hemisphere. By integrating phylogenetic relationships, divergence times and ancestral range dynamics based on plastid and genome-wide genotyping-by-sequencing markers, complemented by a review of the fossil record, ecological niche modelling and paleoclimate simulations, we reconstruct the spatio-temporal colonization history of this group. Our results suggest a vicariance-driven speciation process facilitated by climatic change. Notably, we identify intracontinental vicariance between the sister species Woodwardia radicans and W. unigemmata across Eurasia in the Pliocene, likely driven by the extinction of intermediate populations, which confined these species to opposite ends of Eurasia, corresponding to late-Cenozoic refugia of the paleotropical (lauroid) element. Extinction in the Western Palearctic appears to have been more severe than in the East, leading continental populations of W. radicans to retreat to the Macaronesian archipelagos, from which they back-colonized small continental and Mediterranean island enclaves in the Pleistocene. These findings underscore the role of islands as both crucial reservoirs for paleotropical-affinity relicts and sources of diversity for adjacent continental enclaves. They also emphasize both island and continental refugia as the last reservoirs of the evolutionary legacy of paleotropical-affinity lineages, and highlight their vulnerability to ongoing climate change.