The expansion of arid and dry ecosystems during the Miocene played a key role in the diversification of succulent plants; however, the relative contributions of biotic traits and environmental factors linked to aridity remain unclear. We investigate diversification in the cactus tribe Cereeae by integrating phylogenomic, biogeographic, and trait-based diversification analyses. We reconstructed a time-calibrated phylogeny and inferred ancestral ranges through biogeographic process-based modeling. We assessed diversification rate heterogeneity and evaluated the impacts of biotic traits and environmental variables using machine learning and trait-dependent diversification analyses. Our results indicate that Cereeae diverged in the late Miocene (∼9 Ma), with ancestral range spanning from the Central and Southern Andes to Espinhaço Mountain Range in Southeastern Brazil. Vicariance events, likely driven by marine transgressions and the assembly of the Cerrado savanna, promoted isolation of taxa across the Andes and Southeastern Brazil. Eastern Brazil was recolonized via jump dispersal during the Miocene-Pliocene transition. Diversification rates were strongly associated with rupicolous substrate preference and globose growth form, while environmental variables showed a negligible correlation with diversification. Our findings underscore the Southern Andes as a likely source of xerophytic lineages and highlight ecological specialization as the dominant driver of Cereeae radiation. This study demonstrates how integrative approaches can disentangle complex evolutionary processes, revealing that morphological innovation prevailed over environmental filtering in shaping the diversification of Cereeae in dry habitats.

Phylogenomic discordance is widespread across plants, but its evolutionary significance is often obscured when conflict is treated primarily as analytical noise rather than as evidence of underlying processes. In woody lineages in particular, incomplete lineage sorting, introgression, and genome duplication can interact over long timescales to produce complex genomic histories that are not adequately summarized by a strictly bifurcating tree. Here, we use Malus as a model woody genus to investigate how these processes structure conflict across a genus-scale, accession-based phylogenomic framework. Using broad taxon sampling, hundreds of nuclear loci, plastid genomes, and genome-wide SNP summaries, we reconstruct a robust nuclear backbone for sampled Malus lineages and evaluate where discordance is concentrated and which processes best explain it. Nuclear analyses resolve eight major clades, whereas conflict is non-random and localized to recurrent hotspots rather than evenly distributed across the tree. Cytonuclear discordance is similarly concentrated, especially around Clade H, represented by sampled accessions of M. tschonoskii, where localized plastid-nuclear disagreement is consistent with candidate plastid capture or organellar introgression. Multiple complementary analyses further indicate that the strongest conflict is not explained by ILS alone, but instead reflects lineage-structured introgression, while polyploid complexes represent additional localized sources of evolutionary complexity. Together, these results provide evidence for a reticulate genomic backbone in Malus and show how integrating nuclear, plastid, and genome-wide conflict analyses can help distinguish background discordance from process-specific signals in woody plant radiations. Several lineage-level reticulation hypotheses identified here should now be tested with broader population-level sampling and curated reference accessions.

Target capture is a common method of generating high throughput DNA sequencing data for phylogenetic reconstruction of species relationships, for which single copy genes are usually most informative. However, a pervasive problem with target capture is that putatively single copy genes may in fact be paralogs resulting from gene duplication, which are problematic for phylogenetic inference because their evolutionary history may differ from the divergence history of species. Here, we use as a case study a target enrichment dataset of 88 species of Detarioideae (Leguminosae) with a focus on the Sindora clade to examine approaches for handling paralogs, including the built-in paralog handling functions in HybPiper and CAPTUS, plus subsequent steps using Putative Paralog Detection and the tree-based Yang & Smith orthology inference approach. We compare the paralogs flagged using these methods and verify their performance with BLAST mapping against a reference genome sequence of Sindora glabra, and then subsequently compare the species tree topologies produced across these methods. Our comparisons of paralogs flagged across the Sindora clade show that the Putative Paralog Detection pipeline was the most accurate in identifying paralogs in terms of its similarity to the BLAST mapping, followed by the built-in paralog identification function of CAPTUS. However, the results we recovered for the Detarioideae subfamily suggest that the largest differences in species tree topology resulted from the use of paralog-filtered alignments (such as with the Putative Paralog Detection pipeline and the Yang & Smith orthology inference approaches) rather than just by removing the sequences of identified paralogous genes. This was the true for HybPiper-assembled datasets but was not seen in CAPTUS-assembled datasets. In all comparisons, the topological differences caused by different paralog handling methods tended to be confined to clades where processes such as hybridisation and introgression are prevalent. Our study provides a roadmap to establish the best approach to identify, eliminate or separate paralogs in the absence of a chromosomally contiguous reference genome for a study group, and highlights the importance of careful data inspection and processing in addition to understanding the extent of paralogy and paralog characteristics (e.g. sequence divergence between copies) for their study group.

The generic-level classification of the bee tribe Megachilini (Megachilidae) has remained controversial due to poor phylogenetic resolution at the base of the group, particularly among the brood parasitic genera and the numerous dauber ("Chalicodoma s. l.") lineages. We present a phylogenomic analysis of Megachilini based on ultraconserved elements (UCEs), sampling 52 ingroup taxa with emphasis on the dauber lineages. We also present a combined UCE + six-gene analysis to improve taxon coverage, resulting in a dataset with 127 ingroup taxa. Maximum likelihood, coalescent, and Bayesian analyses of multiple UCE matrices recover largely congruent topologies with substantially improved support relative to previous studies. Our results strongly support the monophyly of Megachilini, the early divergence of Noteriades and Gronoceras, and a single origin of brood parasitism. All remaining non-parasitic Megachilini form a moderately supported clade sister to the brood parasitic lineage. The leafcutter bees are monophyletic and nested within dauber lineages. Several major dauber clades are consistently recovered, including an exclusively Australian clade corresponding to the Hackeriapis group of subgenera, while several recognized subgenera are paraphyletic. The lineage known as Morphella, previously placed in synonymy with the subgenus Callomegachile, was not closely related to that subgenus and is here treated as a valid subgenus. Divergence-time analyses place the crown age of Megachilini in the late Eocene to early Oligocene, with major extant lineages diversifying during the Miocene. Limited morphological diagnosability of several clades indicates that splitting non-parasitic lineages into numerous genera would result in an impractical classification that would widen the gap between taxonomists and non-specialists and exacerbate the taxonomic impediment in bees. We therefore advocate retaining a single genus Megachile for non-parasitic Megachilini (excluding Noteriades and Gronoceras), as the classification best supported by phylogenomic evidence and most robust to future taxon sampling.

Eunicid polychaetes are often found in association with Cold Water Corals (CWCs), even establishing symbiotic relationships, such as those described between Desmophyllum pertusum and Eunice norvegica. While genetic connectivity of CWCs across the North Atlantic has been widely studied, little is known about their associated fauna in this regard. Here, we present a study combining a focused analysis of the genetic connectivity of E. norvegica with a regional assessment of the distribution and evolutionary relationships of three CWC-associated eunicid species from the Cantabrian Sea and the North of the United Kingdom (190-1,230 m depth). An integrative approach using genetic (16S, COI and 18S), morphological and ecological data allowed the identification of the eunicids studied, with new records of Eunice cf. nicidioformis and Eunice cf. antarctica in the Cantabrian Sea, as well as previously undocumented associations with CWC species. In addition, RADseq data contributed to the delimitation of the closely related species E. norvegica and Eunice philocorallia. Moreover, the genetic connectivity of E. norvegica was studied trough a RADseq (1,067 neutral SNPs) approach. Our results indicate a single panmictic population across approximately 2,000 km, suggesting that oceanographic currents facilitate passive dispersal of E. norvegica lecithotrophic larvae, aided by coral host stepping-stones. The connectivity patterns observed for E. norvegica mirror those of D. pertusum, on which the worm is ecologically dependent. Our study highlights the importance of using integrated genetic, morphological and ecological data to characterise and delineate understudied CWC-associated species and improve our understanding of their dispersal capabilities and genetic connectivity to inform future conservation recommendations.

Isidoidae Heestand Saucier, France & Watling, 2021 is a rare octocoral family currently represented by a single genus and species, Isidoides armataNutting, 1910 recorded in the western Pacific Ocean. The taxonomic status and diversity of Isidoides is unclear, due to the lack of diagnostic taxonomic features and limited taxon sampling. Based on 23 Isidoides specimens obtained from the northwestern to southwestern Pacific, we carried out morphological and phylogenetic analyses to reveal the taxonomic status of new species and develop reliable features for species identification. The 23 specimens could be classified into four well-supported clades by the phylogenomic analysis of ultraconserved elements (UCEs), four groups by 28S rDNA, and two groups by mtMutS-cox1. Integrating morphology and molecular data, we uncovered unexpected diversity of Isidoides composed of the known species Isidoides armata and three new species, viz., I. elegans sp. nov., I. gracilis sp. nov. and I. pseudarmata sp. nov. The morphological analysis showed high intraspecific morphological variation in colony color and the size, shape and arrangement of polyps. By contrast, sclerite forms with their surface sculpturing are more diagnostic features for species identification. Our phylogenetic and species delimitation analyses indicate that UCEs have higher resolution than the nuclear 28S rDNA and the mitochondrial genes mtMutS and cox1 for species discrimination within Isidoidae. ZooBank: urn:lsid:zoobank.org:pub:392485F5-502E-4383-B153-45B167571190.

Since the circumscription of Pleurospermum sensu stricto, the taxonomic status of the remaining Pleurospermum sensu lato species has remained unresolved. Our phylogenomic analyses using plastome (150 sequences), nrDNA (156), and nrITS (244) datasets recover a strongly supported monophyletic lineage within Tribe Komarovieae, sister to the Tongoloa Group and clearly distinct from both Pleurospermum s.str. (Pleurospermeae) and true Hymenidium (Hymenidium Clade). Principal Coordinates Analysis of 16 morphological characters quantitatively separates this lineage from its relatives (94.23% variance explained by the first two axes), with rib winging, calyx teeth, and vittae number emerging as the primary discriminants. Based on this integrative evidence, we formally establish Callibractia ZiX.Li, C.Peng & X.J.He, gen. nov., diagnosed by almost entirely membranous bracts and bracteoles, conspicuous calyx teeth, and mericarps with narrowly winged ribs, 3 vittae per furrow, and 6 vittae on the commissure. The genus comprises eight alpine species (>3,600 m) distributed from the Sino-Himalaya to Central Asia, two of which are newly described species. Biogeographic reconstruction traces the origins of subfamily Apioideae to the Tethyan region (ca. 76.53 Ma) and its subsequent assembly in the Pan-Tibetan Highlands. Within this broader evolutionary context, Callibractia originated in the Oligocene (ca. 24.64 Ma), and its crown diversification in the Mid-Miocene was shaped by the phased uplift of the Pan-Tibetan Highlands and monsoon evolution, followed by rapid Pleistocene speciation in the Hengduan Mountains' Sky Island habitats. Our findings resolve a persistent taxonomic uncertainty and provide a transferable framework for resolving similar taxonomic complexities within Apiaceae.

Resolving species relationships in rapidly radiating lineages remains a major challenge in evolutionary biology, particularly when hybridization obscures phylogenetic signals. Here, we present a chromosome-level, haplotype-resolved genome assembly for Triplophysa pseudoscleroptera, a species residing at the Qinghai-Tibet Plateau, and integrate it with eight other Triplophysa genomes and resequencing data from 57 Triplophysa individuals to reconstruct a robust phylogeny of the genus. We uncovered extensive discordance between mitochondrial and nuclear phylogenies, driven by both ancient and recent introgression. Notably, the individual selected for genome assembly was found to have undergone a recent hybridization event, retaining ∼ 22% introgressed genomic segments. These introgressed segments are phylogenetically closer to T. dalaica, and their inclusion in concatenated whole-genome alignments was sufficient to mislead species tree inference. Empirical genomic resampling analyses demonstrate that as little as 14% introgression is sufficient to result in incorrect phylogenetic inference in our focal system. Our findings provide a cautionary example that reliance on a single individual genome can lead to erroneous phylogenetic conclusions, when a moderate proportion of introgressed segments is present. We therefore advocate chromosome-scale and window-based phylogenomic approaches as essential practices for reconstructing species relationships in systems shaped by reticulate evolution.

The pantropical genus Diospyros L. (Ebenaceae) includes many economically valuable species prized for ebony timber and edible fruits. However, its high species diversity and morphological similarity pose significant challenges for understanding its evolutionary history. Previous phylogenetic studies have suggested a rapid adaptive radiation in Diospyros, but relationships among major lineages remain poorly resolved. Here, we reconstruct a comprehensive species-level phylogeny for Chinese Diospyros using whole genome sequencing data from 69 individuals representing 65 species. Phylogenomic analyses of a concatenated nuclear SNP matrix recovered six strongly supported major clades. Notably, we found substantial cytonuclear discordance between nuclear and plastid phylogenies. To investigate this conflict, we conducted extensive gene-tree concordance analyses (Phytop, MSCquartets) and quantified introgression and incomplete lineage sorting (ILS) using Dsuite, QuIBL, and PhyloNet. These analyses revealed widespread, statistically significant gene-tree conflict, particularly at deep nodes. Our results demonstrate that the evolutionary history of Chinese Diospyros has been likely shaped by deep ILS-a probable genomic signature of rapid early radiation-alongside localized ancient hybridization, most prominently within the morphologically diverse Asian clade F. Recent gene flow appears to have played a limited role, although the relative contributions of ILS and introgression remain challenging to fully disentangle. These findings provide insights into the drivers of cytonuclear discordance and offer a robust phylogenetic framework for understanding the mechanistic role of ILS in diversification, with implications for adaptive radiation dynamics in species-rich tropical lineages.

Claws are strongly sclerotised elements of tardigrade exoskeleton of a great phylogenetic and taxonomic importance. Although several general claw curvatures and anatomies can be distinguished within Eutardigrada, some more subtle differences in claw architecture have evaded the attention of taxonomists and have caused profound errors in species classification. Our study exposes a particularly deceitful morphotype and has widespread consequences for parachelan systematics, affecting two of the three major superfamilies in the order. Specifically, we analysed integratively 26 populations representing the Ursulinius cameruni complex from India and multiple locations in Australasia. Our genetic and morphological analyses demonstrate that this evolutionary lineage does not belong in Isohypsibioidea, but in Hypsibioidea. Moreover, some other taxa previously classified in different hypsibioid families are transferred to the new lineage. Specifically, Synonyxidae fam. nov. and Synonyxgen. nov. are established to accommodate the unique claw and cuticular morphotype of the Ursulinius cameruni complex. Also, Synonyx panjurliisp. nov., the type species for the new genus, is described from India, and two further hypsibioidean species are transferred from other genera to Synonyxgen. nov.: S. antonovaecomb. nov. (formerly Hypsibiidae: Hypsibius) and S. gibbosuscomb. nov. (formerly Acutuncidae: Mixibius). All these systematic changes clearly reflect the difficulties associated with a proper interpretation of claw structure in this peculiar phylogenetic linage. The evolution of Synonyxidae fam. nov. in Hypsibioidea is discussed in detail. Additionally, we elaborate on the taxonomic status and composition of Mixibius.

Speciation is often considered as a prolonged, continuous and complex process shaped by interactions among multiple evolutionary forces, including both biotic and abiotic factors. Robust species delimitation is fundamental for understanding the basic biology and ecology of organisms and of course the implementation of effective conservation policies. The red bamboo ratsnake (Oreocryptophis porphyraceus) is a polytypic species in the family Colubridae widely distributed across Asia with a subspecific taxonomy has long been complex and controversial. Here, we integrated double-digest restriction-site associated DNA sequencing (ddRAD-Seq) with mitochondrial DNA (mtDNA) data to re-evaluate the subspecific taxonomy of this species primarily using samples from China and Vietnam. Phylogenetic relationships, population structure, tests of gene flow and species delimitation analyses consistently revealed that the species comprises at least four highly divergent, geographically structured lineages (five in the mtDNA phylogeny). Notably, these distinct evolutionary lineages are inconsistent with current taxonomic classifications. We propose a revised taxonomy that integrates genomic evidence with morphological data, and we discuss the distribution boundaries for each delineated species.

The origin and maintenance of marine biodiversity remain poorly understood, particularly in highly connected oceanic environments where extensive dispersal is expected to limit population differentiation. Evolutionary processes driving population divergence or speciation frequently depend on a proper knowledge of species' life history and its interaction with major environmental variables. Using a genome-wide approach, we investigated the global population structure of the cosmopolitan pelagic fish Coryphaena hippurus Linnaeus, 1758, generating a dataset of 8.7 million SNPs and complete mitochondrial genomes. Our results reveal, for the first time, four genetically differentiated populations, corresponding to major oceanic basins: Atlantic, Pacific, Indian and Mediterranean Sea. The Mediterranean population exhibited a distinct genomic signature, likely resulting from historical isolation and restricted contemporary exchange through the strait of Gibraltar. Despite this structure, genome-wide analyses uncovered extensive signals of historical connectivity among basins. D-statistics and f4-ratio tests detected significant excess allele sharing, particularly between Indo-Pacific and Atlantic populations, while phylogenetic network reconstruction in TreeMix supported multiple migration events, highlighting the role of ancestral gene flow in shaping global genetic patterns. At finer scales, a limited but significant intra-oceanic structure was detected within both Atlantic and Pacific basins. Seascape genomic analyses revealed that environmental gradients such as salinity, phosphate concentration, light availability (PAR, Kd), and pH are significantly associated with genomic variation, suggesting that ecological factors contribute to population differentiation across heterogeneous marine environments.

The phylogenetic relationships between Procladiini and Tanypodini (Chironomidae, Tanypodinae) remain unresolved. Here, we recovered an average of 2,432 universal single-copy orthologous genes (USCOs) per species from 29 taxa and used occupancy-filtered USCO datasets to reconstruct their phylogenetic relationships, providing the first USCO-based phylogenomic framework for Tanypodinae. Maximum likelihood and multispecies coalescent analyses recovered consistent and strongly supported topologies. Djalmabatista was recovered as a distinct lineage within Procladiini and as sister to Procladius, supporting its status. as a valid genus. In contrast, Saetheromyia was recovered as sister to Tanypus, rather than within Procladiini. Independent morphological evidence indicates that Saetheromyia exhibits a unique combination of characters absent in other tribes, supporting the establishment of a new tribe, Saetheromyiini Xiao, trib. nov.. Divergence time estimation using fossil calibrations indicates that major Tanypodinae tribes originated in the Early Cretaceous (ca. 123.9-104.0 million years ago, Ma), with the split between Procladiini and Tanypodini in the Late Cretaceous (ca. 96.1-78.2 Ma), followed by diversification of Procladiini from the Late Cretaceous to the Eocene and of Tanypodini primarily during the Miocene. These results provide a robust phylogenomic framework for understanding the evolutionary history and higher classification of Tanypodinae.

Obtaining large and well-resolved phylogenetic trees for neotropical clades is challenging, as many species inhabit remote regions, and sampling often relies on herbarium specimens with highly degraded DNA. Target capture provides an effective solution for recovering molecular data from fragmentary material. However, data processing using tools generally designed for diploid organisms and single-copy loci is also challenging, particularly when events such as genome duplication and hybridisation have shaped lineage evolution. We used dual-hybridisation to integrate Ochnaceae-specific and universal probes to reconstruct the phylogenetic relationships of Sauvagesieae, a pantropical clade with ca. 90 species mainly distributed in the northern Andes, the Brazilian Espinhaço Range, and the Amazon-Guyana region. We tested different filtering strategies involving missing data and paralogs to assess probable sources of tree discordance and topological uncertainty. We found no significant benefit in reducing tree discordance after removing entire genes due to the presence of paralogs or a high amount of missing data. Removing fragmentary sequences instead improved alignments and increased branch support of gene trees. By quantifying the proportion of single nucleotide polymorphisms (SNPs), analysing the distribution of the allele frequencies, and gene-tree quartet frequencies, we found signals of polyploidisation and hybridisation, which could reduce resolution at internal nodes, particularly in mountain clades. Our results underscore the importance of exploring the complexities of target-capture data, not only to improve phylogenetic resolution but also to understand the sources of phylogenetic conflict and the underlying molecular evolutionary processes.

Genomic gigantism is rare and reaches its extreme in fork ferns (genus Tmesipteris, Psilotaceae, Psilotales), whose unresolved systematics have obscured the roles of polyploidy, hybridization, and repetitive element dynamics in forming exceptionally large genomes. Here, we address this issue by developing a custom target-capture probe set (288 nuclear orthologs), integrating time-calibrated multispecies coalescent analysis and biogeographic modelling with nuclear DNA content estimates, cytotype inference and repeatome profiles to better understand the evolution of the group. We recovered a well-resolved backbone, consistent with a Paleocene split of Psilotaceae into two genera, and an Oligocene crown diversification of Tmesipteris into two strongly supported lineages (Pacific and Tasman clades). Diversification seems to coincide with the emergence of island habitats across Zealandia and New Caledonia, consistent with long-distance dispersal, founder events, and life-form shifts. Nuclear and plastid discordance is for the most part concentrated within the Pacific clade, indicative of potential recurrent hybridization and/or incomplete lineage sorting (ILS). Genome analyses reveal multiple independent whole-genome multiplications, producing several octoploid lineages and intraspecific cytotype diversity. Repetitive DNA content is exceptionally high, with clade-specific dynamics of transposable elements and satellite DNA. We confirm the taxonomic independence of T. oblanceolata from T. truncata, and identify two putative nothotaxa in the Pacific clade, plus a distinct Fijian taxon closely allied to T. alticola, which could represent an undescribed species. Altogether, these findings point to whole-genome multiplication, hybridization, inter-island dispersal, and repetitive DNA accumulation as primary drivers of diversification and genome gigantism in Tmesipteris.