Molecular Phylogenetics and Evolution

Understanding how dispersal and vicariance shape species distributions is a central goal in biogeography, yet the role of islands as sources of continental diversity remains poorly resolved. While multiple dispersal routes from the Eurasian continent to the Japanese Archipelago have been proposed, back dispersal from islands to the mainland is rarely documented, particularly in primary freshwater taxa constrained by marine barriers. Here, we investigated the population genetic structure and phylogeographic history of the Japanese stone loach Barbatula oreas, distributed in Hokkaido and Sakhalin, using mtDNA, nDNA, and genome-wide SNP data. We identified two differentiated Northern and Southern lineages within Hokkaido that diverged during the Pleistocene, indicating that geological events such as paleo-catchment reorganization, mountain uplift, and volcanic activity have shaped the present population structure. Ancestral area reconstruction based on mtDNA phylogeny identified Hokkaido as the origin of B. oreas and revealed dispersal from Hokkaido to Sakhalin, indicating back dispersal from islands toward the mainland. This pattern contrasts with the prevailing hypothesis of southward colonization from the continent via Sakhalin to Hokkaido. Additionally, low genetic differentiation between Hokkaido and Sakhalin suggested genetic exchange across the strait, consistent with paleo-catchment reconstruction indicating past catchment connectivity between the regions. These results highlight the combined roles of geological dynamics and sea-level fluctuations in shaping genetic structure, challenge the conventional continent-to-island dispersal paradigm. Moreover, our study demonstrates that island systems can act as biodiversity sources--not merely sinks--and provides a rare empirical example of back dispersal in primary freshwater species.

Polytypic species with large ranges may harbor unrecognized diversity because taxonomy ranks populations differing subtly in plumage as subspecies. The Ruddy Foliage-gleaner (Clibanornis rubiginosus) exemplifies this problem. It ranges from Mexico to Brazil, with 15 subspecies, and forms a non-monophyletic complex with two congeners, yet its songs had not been compared. We measured ten spectral and temporal variables on 104 recordings covering 14 of 15 subspecies. Bayesian linear mixed models showed three song groups: eight subspecies west of the Andes share a single-note song, whereas Amazonian and Guianan populations add a short introductory note and sing longer, lower-pitched songs. Within this group, watkinsorum sings the lowest-pitched and longest song and is phylogenetically closer to C. cinnamomeigula than to its Amazonian neighbors. The third group is C. cinnamomeigula alone, a white-eyed taxon in an otherwise dark-eyed group. Its high-pitched, vibrato song resembles none other in the genus. One-note and two-note songs differ in kind without intermediates, and every two-note taxon sequenced to date falls in one clade, so C. rubiginosus is paraphyletic. We recognize four species, C. rubiginosus sensu stricto, C. cinnamomeigula, C. watkinsorum, and C. obscurus. This raises Clibanornis from five species to eight and divides its only polytypic species.

Zingiberales includes eight morphologically distinctive families, but its family-level backbone has remained unstable, especially around Musaceae, Heliconiaceae, Lowiaceae, and Strelitziaceae. We analysed 1566 low-copy nuclear genes from 52 samples, representing all eight families and Pontederia crassipes as outgroup. Concatenated maximum likelihood and multispecies coalescent analyses recovered the same backbone: ((Zingiberaceae, Costaceae), (Cannaceae, Marantaceae)) is sister to (Musaceae, (Heliconiaceae, (Lowiaceae, Strelitziaceae))). Penalized-likelihood dating placed the sampled crown group in the Late Cretaceous, with several deep family-level divergences occurring on short internodes. Analysis of 1248 rerooted gene trees showed that conflict is concentrated on these deep branches and in several shallow clades. HyDe tests of empirical and simulated matrices, each including 62,475 triples, did not support widespread ancient hybridization among the major family-level lineages after filtering against the simulated null model. The nuclear data recover a stable Zingiberales backbone, and the long-standing instability of several deep nodes is best explained by rapid early divergence and extensive incomplete lineage sorting.

Arcellidae is a family of testate amoebae within Arcellinida (Amoebozoa), comprising three recognized genera: Arcella, Galeripora, and Antarcella. Although species in the family have been studied for nearly two centuries, many historically described taxa and major morphological groups remain unsampled at the molecular level. Here, we provide a comprehensive review of Arcellidae and generate new cytochrome c oxidase subunit I (COI) sequences for arcellid species from Canadian peatlands, focusing on tall-shelled Arcella historically classified in section Altae sensu Deflandre. COI phylogenetic analyses recover a strongly supported monophyletic clade corresponding to North American representatives of Altae, providing the first molecular corroboration of this morphologically defined group. Within this clade, we redescribe Arcella leidyana based on modern material from Eeyou Istchee (Quebec). We further describe Galeripora purdoni sp. nov. from a calcareous fen in eastern Ontario, representing a novel terrestrial lineage within the genus, and redescribe Galeripora artocrea, which we transfer to Arcella based on congruent molecular and morphological evidence. Phylogenomic analyses of Arcellidae isolates from the Protist 10,000 Genomes Project reveal an additional deep lineage basal to Arcella and Galeripora. Together, these results highlight hidden diversity and demonstrate the importance of integrative approaches for resolving arcellid systematics and refining its classification.

Understanding the relative roles of vicariance and dispersal in shaping diversity and distribution patterns is central to historical biogeography. In this study, we investigate the historical biogeography of the ancient centipede genus Digitipes Attems, 1930 from South and Southeast Asia. First, we determined the phylogenetic position of the genus Digitipes within the Order Scolopendromorpha (n=414) by assembling primary and published sequences (n=30) for two mtDNA markers (COI, 16S) and one nuclear marker (28S) using Maximum Likelihood and Bayesian inference. We further used single-locus and multi-locus coalescent-based species delimitation methods to identify putative species within the genus Digitipes. We then used three fossil calibrations to estimate divergence times in a Bayesian framework, and used the resulting time-calibrated phylogeny for biogeographic analysis in a likelihood framework (BioGeoBEARS). The genus Digitipes was monophyletic with strong support, with SEA lineages nested within the Indian clade and sister to the D. barnabasi species complex from the Western Ghats. D. pruthii, the Eastern Ghats species, was nested with the Western Ghats species clade. A single-locus mPTP-based species-delimitation method suggested the presence of 24 putative species, far exceeding the number of morphologically described species, indicating an underestimation of species diversity. Divergence time estimates suggest that Digitipes began diversifying around 126 mya (100-159 mya), affirming its Gondwanan origin. Time-stratified ancestral area reconstruction suggested that early vicariance, followed by jump dispersal and range expansion, shaped the distribution of the genus Digitipes in South and Southeast Asia. There was one dispersal event from India to Southeast Asia, following a transient land connection between them, around 50 mya, supporting the Out-of-India hypothesis. Additionally, three jump dispersal events and five range expansions explained diversification within peninsular India. Particularly, D. pruthii originated from a jump dispersal event from the Central Western Ghats to the Eastern Ghats around 37 mya. Our results highlight the importance of an integrative taxonomic framework to delineate hidden diversity and to obtain robust species hypotheses for testing biogeographic hypotheses.

The global study of freshwater clams in the genus Corbicula is frequently confounded by invasive androgenetic lineages that experience mitochondrial DNA capture and clonal propagation. In contrast, the endemic Corbicula of Sulawesi's ancient lakes reproduce sexually, offering a uniquely reliable system for mitochondrial population genetics. This study provides the first population-genetic framework for two endemic species, Corbicula possoensis (Lake Poso) and C. linduensis (Lake Lindu), using the cytochrome c oxidase subunit I (COI) marker. We analysed 90 newly generated COI sequences from C. possoensis (six stations) and C. linduensis (three stations), integrated with reference sequences from GenBank, to assess genetic diversity, population structure, and phylogeographic patterns. Hierarchical AMOVA revealed deep divergence between the two lakes ({Phi}_CT = 0.607), consistent with prolonged independent isolation rather than a single shared vicariance event, as the two species do not form a sister pair in the phylogeny. Within Lake Poso, C. possoensis exhibited exceptionally high genetic diversity (24 haplotypes; h = 0.876; {pi} = 0.016) and pronounced micro-geographic structuring into three phylogeographic zones (North: Tentena and Siuri; East: Tando Nceppo and Busogo Beach; Southwest: Bancea and Pendolo), each characterised by distinct haplogroups. Remarkably, the maximum divergence between zones (K2P = 2.33%) approached the interspecific distance between C. possoensis and C. linduensis (K2P = 2.42%), indicating that within-lake mitochondrial divergence has reached near-interspecific levels. Conversely, C. linduensis displayed near-panmixia and extreme genetic depauperation (3 haplotypes; h = 0.246; {pi} = 0.0004), indicating long-term demographic stasis within a restricted habitat. The deep phylogeographic zonation in C. possoensis suggests that its discrete populations should be treated as separate Management Units (MUs) in conservation planning to preserve locally adapted gene complexes, whereas the severely depauperate gene pool of C. linduensis renders it critically vulnerable to environmental disturbance and invasive species, warranting urgent IUCN Red List assessment. To validate these mitochondrial boundaries and inform future conservation strategies, multi-marker and genome-wide reassessments are strongly recommended.

Rapid radiations, where species quickly diversify with little to no change in the genetic composition of the taxa, provide unique opportunities to understand the processes underlying lineage divergence, especially when the newly formed species come into contact. This study examines three parapatrically distributed taxa of the Andean Diglossa carbonaria superspecies that differ strikingly in plumage and have been classified as an example of rapid lineage divergence. Using RADSeq data, we characterized the geographic structuring of genetic variation and investigated the possibility of introgressive hybridization at the contact zones between D. humeralis atterima and D. b. brunneiventris in northern Peru and between D. b. brunneiventris and D. carbonaria in Bolivia. We found weak genetic differentiation between D. humeralis atterima and D. b. brunneiventris and low, but diagnosable, differentiation between D. b. brunneiventris and D. carbonaria. At the contact zone between D. humeralis atterima and D. b. brunneiventris, the lack of genetic differentiation did not allow us to determine if hybridization was occurring between the taxa. In contrast, clustering analyses, diagnostic allele identification, and PCA analyses showed geographic patterns consistent with introgressive hybridization at the contact zone between D. b. brunneiventris and D. carbonaria, a geographic region where birds that are intermediate in plumage have been observed. Finally, we found a genetic break within the distribution of D. b. brunneiventris. The genetic divergence across this [~]450 km wide break is greater than that found between D. humeralis atterima and D. b. brunneiventris. Our results add to previous work documenting weak genetic differentiation between taxa that have striking plumage differences, and in showing that plumage color may be a poor phylogenetic marker. Lay SummaryO_LIWe studied three closely related avian taxa in Peru and Bolivia which have different plumages and adjacent ranges to examine how genetically distinct they are. C_LIO_LITo do this, we used RADseq data from 72 flowerpiercers sampled across their ranges to examine their population structure and to test whether the three taxa hybridize where their ranges meet. C_LIO_LIDespite their striking differences in plumage color, the three species showed few genetic differences. In one area where the ranges are adjacent, the groups were so similar that interbreeding could not be confirmed. In another, there was evidence of admixture, supported by observations of birds with intermediate plumage. C_LIO_LIFor these taxa, feather color may not reflect evolutionary relationships, and more extensive genetic sampling is needed to understand how these plumage differences evolved. C_LI

Resolving deep phylogenetic relationships requires integrating multiple lines of evidence, as distinct evolutionary forces shape signals from different genomic markers. Here, we investigate the systematics of the controversial APPD lineage (Anomiidae, Placunidae, Plicatulidae, and, by inference, Dimyidae) within Pectinida sensu lato using phylogenomic, comparative genomic, transcriptomic, proteomic, and morphological approaches. Our analyses consistently recover APPD as a monophyletic lineage sister to Limida and Pectinoidea, divergent at [~]428 Mya. With three novel high-quality genomes, extensive progressive chromosomal fusions demonstrate a reduction in chromosome number of the APPD lineage (6-13), compared with an ancestral 20 molluscan linkage groups (MLGs). Accompanied by extensive intrachromosomal gene-order scrambling, we identify one functional centromere in Placuna vitream flanked by two vestigial centromeric remnants on a single chromosome, providing a potential resource for investigating centromere inactivation and neocentromere formation. Mitochondrial genomes of APPD lineage exhibit unprecedented plasticity in translational decoding: Pododesmus employs the invertebrate mitochondrial code; Heteranomia employs +1 translational frameshifting to bypass in-frame TAG codons, whereas in Anomia, Enigmonia, Placuna, and Plicatulidae, TAA is reassigned to tyrosine and confirmed by proteomic evidence, which supports mitochondrial frameshifting in APPD lineage and defines a novel translation table for bivalves. Integrating phylogenetic distinctiveness, deep divergence, extreme karyotypic restructuring, unique mitochondrial features, and morphological diagnosability, we elevate the APPD lineage into Anomiida ord. nov. This revision resolves long-standing uncertainties for Pectinida sensu stricto and Limida, and establishes the APPD lineage as a valuable system for investigating chromosome fusion, centromere evolution, codon reassignment, and translational recoding. ClassificationBiological Sciences; Evolution SIGNIFICANCE STATEMENTWe have re-examined a controversial group of marine bivalves (Anomiidae, Placunidae, Plicatulidae, and Dimyidae). Our integrative approach shows that these animals split from scallops and their relatives more than 428 million years ago and have undergone drastic chromosomal fusions that reduced their chromosome number from 20 to as few as 6. Additionally, some species evolved unusual ways of reading their mitochondrial genetic code, either reassigning the stop codon to tyrosine or using +1 translational frameshifting to skip stop signals. The combination of deep evolutionary time and genomic divergence warrants recognizing them as a new order, Anomiida ord. nov. This work, as a case study, demonstrates how chromosome fusion and genetic code variation contribute to invertebrate diversity.

The Hesperiine genus Atrytonopsis Godman, 1900, occurs broadly across the American Southwest. Atrytonopsis margarita (Skinner, 1913) and Atrytonopsis python (W. H. Edwards, 1882) have look-alike appearances, concurrent flights, and geographic distributions which converge in New Mexico. Their similar wing markings and intertwined taxonomic history has made it challenging to fully understand the identity and occurrence of each. Burns (2015) revealed differences in genitalia, clarifying that they are distinct species. Genomic DNA analysis of more than 100 specimens now illuminates their genetic uniqueness, phylogenetic relationship, field identification challenges and details of their geographic distributions.

Understanding the evolutionary history of species within a geographic context is key to historical biogeography, as it reveals how geological and climatic changes shaped biodiversity. This is especially important in ecologically significant regions like the Amazon and Orinoco basins. Together, they host the worlds greatest freshwater fish diversity ([~]3,500 species), sharing a common but not yet fully understood evolutionary history. The gilded catfish (Brachyplatystoma rousseauxii), an ancient species widely distributed as a metapopulation in Neotropics, is an important model for studying past connectivity, divergence, and historical processes shaping fish diversity between these basins. This study analyzed the genetic structure, connectivity routes, and demographic history of B. rousseauxii using nuclear (microsatellite and ddRADseq) and mitochondrial DNA. Population structure analyses and coalescent models indicate that B. rousseauxii populations from the Orinoco and Amazon basins are genetically distinct, with no evidence of current gene flow. However, our results support the occurrence of a possible secondary contact event after the divergence, with the Boa Vista population retaining the genetic signal of this process. The ancestral population split occurred at the Rupununi Portal around 2.54 Ma (ddRAD) or 1.31 Ma (mtDNA). Then, the species colonized the Branco and Orinoco Rivers [~]1.90 Ma (ddRAD) or 0.6 Ma (mtDNA), rapidly expanding in the Orinoco (>1.3 or >0.29 Ma), while colonization of the Amazon from the Branco River was more recent ([≤]1.0 or [≤]0.15 Ma). Population expansion signal was detected in the Orinoco ([~]0.20 Ma), whereas the Amazon remained stable. Our findings suggest that the rise of the Vaupes Arch in the Late Miocene does not explain the observed genetic divergence. Likewise, the Casiquiare Canal and Japura-Guaviare headwaters are not connectivity routes between basins. Instead, the Rupununi Portal, including the recent capture of the Branco River by the Negro River, was the last point of connection and played a key role in shaping B. rousseauxiis distribution. These findings provide insights into Neotropical fish biogeography and the historical configuration of the Orinoco and Amazon basins.

Sexual conflict has been hypothesized as a driver of speciation, though its effects are likely heterogeneous across phylogenies and between sexes. The semi-aquatic bug, which inhabits water surfaces across diverse aquatic environments, has long served as a model for studying sexual conflict. While previous studies have focused on rapid antagonistic coevolution and the genetic basis of sexually antagonistic traits, the macroevolutionary consequences of asymmetrical sexual conflict--particularly male-dominated grasping traits versus female resistance--remain largely unexplored. Within the subgenus Pseudovelia, males exhibit pronounced phenotypic diversification in grasping structures, whereas females show modest, clade-specific resistance traits, suggesting male-biased asymmetric conflict. This system presents a valuable opportunity to examine how sexual conflict influences diversification and asymmetrical trait evolution across lineages. Using 204 individuals, representing over half of the subgenus's species diversity, we reconstructed a time-calibrated phylogeny, quantified diversification rates, assessed sexual conflict intensity across clades, and analyzed correlations between sexual trait evolution and diversification. Our results reveal extensive phylogenetic conflict, particularly within the East Asian clade, driven by introgression and incomplete lineage sorting (ILS). Furthermore, we observe significant phylogenetic heterogeneity in both phenotypic evolution and diversification rates. Notably, a male "trait package" enhancing grasping ability likely drives rapid diversification in the recently radiated "South China" lineage. In contrast, grasping traits involving abdominal segment VIII are associated with lower conflict intensity, facilitating greater evolutionary flexibility in female resistance and resulting in lineage-specific counter-adaptations. These findings highlight the heterogeneous dynamics of asymmetrical sexual conflict in shaping diversification and speciation.

Species-level delimitation within the genus Trichomycterus remains one of the main systematic challenges within the Trichomycterinae, particularly in lineages characterised by conservative external morphology, high apparent intraspecific variation, and historical diagnostic criteria based primarily on body proportions, colouration and a few meristic characters. In central Chile, Trichomycterus areolatus has traditionally been interpreted as a widely distributed and morphologically variable species, whilst T. maculatus, originally described from "Santiago du Chili", has remained subordinate to this broad conception without a modern phylogenetic reassessment. Here we reassess the specific boundaries of T. areolatus sensu lato using an integrative approach that combines complete mitogenomes, estimates of genetic divergence and comparative morphology of the cephalic laterosensory system associated with the neurocranium. Phylogenetic analyses reveal T. areolatus sensu lato to be non-monophyletic and identify a deeply divergent lineage, geographically coherent and attributable to T. maculatus. This lineage differs from restricted T. areolatus by extensive mitochondrial divergence, comparable to that observed between recognised species of Trichomycterinae, and by discrete characters of the cephalic lateral line system, primarily related to the continuity of the supraorbital canal and the arrangement of the associated pores. The congruence between mitogenomic, nuclear and morphological evidence supports the revalidation of Trichomycterus maculatus Valenciennes, 1846, and calls for a more restricted geographic circumscription of T. areolatus. These results demonstrate that the diversity of Trichomycterinae in central Chile has been underestimated, modify previous interpretation of the distribution of the species involved, and highlight the value of integrating mitogenomics and neurocranial/laterosensory characters into the taxonomy of morphologically conservative siluriform lineages.

Ledebouria, a geophytic herb native genus to Africa and represented by a few species in the Arabian Peninsula, Madagascar, India and Sri Lanka. For a long time Indian species were named as L. revoluta until recent molecular work clarified African L. revoluta is distinct from Indian and Sri Lankan species. Hence the name L. hyacinthina was resurrected. However, there is no clear molecular or morphological clarification of the different morphotypes and karyotypes observed in various accessions from peninsular India. Since plastid DNA sequence markers failed to detect diversity, we used the high density, low copy number marker set, the Angiosperms353, for phylogenomic analysis of eight accessions and analysed with the same markers from the global dataset from published work. Our analysis shows L. hyderabadensis is a distinct species, whereas other widely distributed Indian accessions under the other name L. hyacinthina are young lineages representing incipient species. Our results indicate that Ledebouria has not diversified enough at the molecular sequence level for the marker set used. The same is also true of the chloroplast sequences.

Sinia rhodoleuca, the sole species of the monotypic genus Sinia (Ochnaceae), was previously transferred to Sauvagesia based mainly on morphological similarities. However, its phylogenetic position has remained unresolved because molecular data for the species were unavailable. Here, we generated genomic data for Sinia rhodoleuca and reconstructed its phylogenetic position within Sauvagesieae. Our phylogenomic analyses consistently recovered Sinia rhodoleuca as sister to Indosinia, whereas the Neotropical Sauvagesia formed a distantly related lineage, rendering Sauvagesia broadly circumscribed non-monophyletic. Comparative morphological evidence further supports the close relationship between Sinia and Indosinia, particularly in their closely parallel secondary veins, lacerate stipules, and prominent petaloid staminodes, while differences in floral characters support their recognition as distinct genera. We therefore reinstate Sinia as a distinct genus and provide a revised taxonomic treatment of Sinia rhodoleuca. Our study demonstrates how phylogenomic evidence can resolve long-standing taxonomic uncertainties and reveal evolutionary relationships obscured by morphological similarity.

Polyploid parthenogenetic organisms are distributed nonrandomly with respect to their diploid sexual relatives, and this pattern has been well documented in plants. Comparable cases are rare in animals, and their origin has been reconstructed in only a few taxa. Separating general eco-evolutionary processes from taxonomic idiosyncrasy therefore requires further animal examples of independent origin. Here we studied the flightless weevil Catapionus nebulosus species group, in which polyploid females were reported by early karyological work. We surveyed the group across its Japanese range to reconstruct its phylogenomic background from mitochondrial DNA and genome-wide SNPs. The sex ratio shifted sharply toward females in northern Japan. The all-female lineage had a single origin, carried a signal of hybridization between two divergent sexual lineages, and experienced rapid expansion in range and population size. The lineage was polyploid, and unmated females reared in isolation produced fertile female offspring. The effective population size, as estimated by the larval density and genetic diversity of the sexual populations, both declined toward the northern margin of their distribution range, already south of the co-occurrence zone with the parthenogenetic lineage. Mate limitation offers the most plausible explanation for the northward spread of the parthenogen. This species group adds an animal example of polyploid parthenogenesis and offers a system for testing why such lineages persist beyond the range of their sexual relatives.

Mitochondrial loci were for long considered as markers of choice to reconstruct phylogenies. The development of high-throughput sequencing over the past two decades fostered the sequencing of mitogenomes, allowing further macroevolutionary questions to be tested. Several biological traits of birds (e.g. body mass, migration distances) have been related to mitochondrial substitution rates. Environmental parameters in ectothermics vertebrates, and potentially in endotherms, have been further suggested to impact substitution rates for specific taxa or loci. Yet, the relative importance of biological traits versus bioclimatic variables is unknown because the former were not systematically controlled for in studies that underlined the effect of the bioclimatic variables. To assess the importance of bioclimatic variables on selection regimes, we analysed the thirteen mitochondrial protein-coding genes for 176 Piciformes (toucans, honeyguides, woodpeckers), a clade with homogeneous life-history traits that can be found in diverse bioclimatic environments. Our analyses highlighted a negative relationship between temperature annual range and the non synonymous to synonymous substitutions ratio. The higher purifying selection in temperate environments may be a result of the strong constraints on maintaining an optimal metabolism in broader climatic variations. Our results further highlight that care should be taken when applying general mitochondrial clocks to estimate divergence times among avian lineages distributed in different climatic conditions.

True lemmings (genus Lemmus) underwent substantial range shifts during the Late Pleistocene and the Pleistocene-Holocene transition, but the impact of these events on present-day diversity remains poorly understood. Here, we used whole-genome sequencing data from modern and ancient samples across the Palearctic range to address this knowledge gap. Reconstruction of autosomal phylogeny revealed that Palearctic true lemmings exhibit relatively shallow genetic structure, contrasting with the deep divergence inferred from mitochondrial genomes. Genetic variation largely follows an isolation-by-distance pattern, and no elevated nuclear divergence was detected between the major mitochondrial lineages. Window-based phylogenetic analyses identified several peripheral populations with high concordance factors, including Norway and Amur lemmings. The high degree of phylogenetic concordance along the genome in these populations is likely a consequence of postglacial bottlenecks and isolation, as indicated by reduced heterozygosity and the presence of runs of homozygosity in them. Overall, our results indicate that the modern genomic structure of Palearctic lemmings was shaped primarily by range fragmentation and population isolation following the broad distribution of the genus during the Last Glacial Maximum. Thus, the current genetic structure appears to represent only a fraction of the Late Pleistocene true lemming diversity. This is illustrated by a genetically distinct ancient specimen ([~]40 ka BP) from the Indigirka River basin that does not cluster with any modern lineage. From a taxonomic perspective, these findings do not support strong species-level differentiation among the major Palearctic lineages and highlight the discrepancy between mitochondrial and nuclear patterns of diversity within the genus.

The evolution of multicellularity has long been linked to reproductive strategies. A long-standing debate concerns whether multicellular organisms are primarily stabilized by small single-cell propagules that minimize genetic heterogeneity or by larger multicellular and multinucleate propagules that may improve developmental success and survival of individuals. the Xanthophyceae provides an excellent model for investigating these questions, exhibiting transitions between unicellular to multicellular filamentous and coenocytic forms together with diverse reproductive modes, including single-cell zoospores and autospores, and multinucleate monospores and akinetes. However, a robust phylogenetic framework and systematic analyses of character evolution have remained lacking in this lineage. Here, we present a phylogenomic framework based on a nuclear dataset of 680 genes from 18 species, including 17 newly generated transcriptomes. Nuclear phylogenies robustly resolve all sampled inter-ordinal and inter-familial relationships with full concordance between concatenation and coalescent analyses, while plastid (141 genes) and mitochondrial (31 genes) datasets from 33 species recover identical topologies. Based on these results, we establish one new order (Pseudopleurochloridales), emend one order (Heterococcales), and propose five new families. Ancestral character reconstruction indicates at least four independent transitions from unicellular ancestors to simple multicellularity. Bayesian analyses of multicellularity and reproductive characters show that these transitions were consistently accompanied by shifts from multiple autospore-type propagules toward single monospore- and akinete-type propagules, whereas reversions to unicellularity were associated with the reappearance of autospore-based reproduction. These results provide a phylogenomic framework for understanding multicellular evolution in Xanthophyceae and shed light on the relationship between reproductive modes and the emergence of simple multicellularity.

Hybridization and introgression are thought to play key roles in the formation of biodiversity. However, detecting gene flow between species and understanding reticulation patterns remain challenging, especially in species-rich lineages with complex evolutionary histories. Adiantum is a large fern genus, and ecological studies in Amazonia have found that species identification is often difficult due to morphological similarity and overlapping characteristics among species. Although several hybrids have been described in tropical America, comprehensive studies investigating genetic exchanges in this genus are still lacking. We used chloroplast and nuclear phylogenomic data to examine evolutionary relationships among tropical American Adiantum species. By combining traditional phylogenetic analyses with advanced bioinformatic methods such as HybSeq-based target capture, reference-guided phasing (HybPhaser), and network-based analyses, we found widespread reticulate evolution involving both recent and ancient hybridization events. These were especially common among those species that have been difficult to delineate morphologically. Our findings indicate that reticulate evolution has played an important role in shaping the diversity of neotropical Adiantum, especially within the tetraphyllum lineage. Such widespread hybridization has no doubt contributed to morphological ambiguity and taxonomic challenges. Our integrated analytical approach provides a first attempt at untangling the reticulate evolutionary history in this group, and future studies with additional sampling can be expected to clarify the evolutionary processes further.

BackgroundThe tribal classification of scarab dung beetles (Coleoptera: Scarabaeinae) is currently largely incomplete due to the lack of robust phylogenetic evidence supporting the assignment of many Afro-Eurasian and American genera to tribes. MethodsWe used ultraconserved elements (UCEs) to infer phylogenetic relationships across most Afro-Eurasian dung beetle lineages, including 25 of the 27 extant genera currently incertae sedis. ResultsWe recovered full support for the monophyly of previously recognised tribes and for several phylogenetically and morphologically clearly delimited new tribal-level clades, allowing us to propose a complete tribal classification for all Afro-Eurasian dung beetle genera. Thirteen new tribes are described and diagnosed: Aphengoecini trib. nov., Bohepilissini trib. nov., Catharsiini trib. nov., Chalconotini trib. nov., Circelliini trib. nov., Dwesasilvasedini trib. nov., Haroldiini trib. nov., Heliocoprini trib. nov., Janssensantini trib. nov., Macroderini trib. nov., Nesovinsoniini trib. nov., Pycnopanelini trib. nov. and Tanzanolini trib. nov. The tribe Coprini sensu novo is redefined as comprising three subtribes: Coprina, Onychothecina subtrib. nov. and Pedariina subtrib. nov. The tribe Odontolomini is downranked to a subtribe of Endroedyolini sensu novo, becoming Endroedyolini Odontolomina stat. nov. The tribe Onthophagini sensu novo is redefined and divided into three subtribes: Helictopleurina stat. nov., Oniticellina stat. nov. and Onthophagina; the remaining former subtribes of Oniticellini (Attavicinina, Drepanocerina and Liatongina) are synonymised with Oniticellina; the subtribe Alloscelina of Onthophagini is synonymised with Onthophagina (syn. nov.). The tribe Panelini stat. rev. and sensu novo, comprising the single genus Panelus, is revalidated and redefined. Updated morphological diagnoses of Elassocanthonini, Gymnopleurini, Onitini and Scarabaeini are provided. The genus Phaedotrogus is synonymised with Haroldius (Haroldiini) (syn. nov.). An identification key to all Afro-Eurasian dung beetle tribes is provided. DiscussionOur results establish a robust phylogenetic framework and revised tribal classification for Afro-Eurasian Scarabaeinae dung beetles, providing a foundation for future taxonomic, comparative and macroevolutionary research.