Molecular Phylogenetics and Evolution

Speciation can be a slow process for long-lived organisms with large populations due to persistent incomplete lineage sorting, while hybridisation can further obscure species boundaries through admixture. In eucalypts, there is tremendous morphological and environmental variation with almost a thousand described species, subspecies, and hybrid taxa falling into multiple subgenera and intermediate sections. Multilocus molecular studies have generated concatenated species trees supporting deeper divergence between the Corymbia + Blakella + Angophora clade with the rest of eucalypts. However, the proportion of gene trees that recover the concatenated tree topology, including the taxonomic relationships among individual subgenera and sections, remains underappreciated. In this study, we assessed the predictive power of current eucalypt taxonomy - represented as a concatenated tree - in explaining topological variation across gene trees. To do this, we first extracted 1,187 BUSCO loci from short-read data of 701 samples representing roughly 500 described species using CAPTUS. We then inferred individual gene trees and a concatenated species tree using IQ-TREE2. Finally, we calculated the concordance factors for every described subgenus and section on the concatenated tree, and developed a taxonomic consistency test that tracks the taxonomic placement of each sample across gene trees. We show that, even though most taxonomic groups are monophyletic on the concatenated tree with 100% bootstrap support, several groups exhibit very low concordance, indicating that most gene trees do not recover their relationships as represented by the concatenated tree. These results highlight important considerations for current eucalypt taxonomic classification and provide a phylogenomic inference pipeline that can be applied not only to future eucalypt studies, but also to other evolutionarily complex groups of taxa.

Aim To investigate how repeated historical connections between continental islands and the mainland have shaped the phylogeographic structure and genetic diversity of populations, using the widespread water strider Aquarius paludum as a model. Location Japan Taxon Water strider Aquarius paludum (Insecta: Hemiptera: Gerridae) Methods We analysed mitochondrial (COI and COII) and nuclear (ITS1) DNA sequences from populations across the Japanese archipelago and the Eurasian continent. Phylogenetic and population genetic analyses were used to reconstruct phylogeographic structure and infer demographic history. Results Western Japanese populations exhibited nucleotide diversity comparable to that of continental populations despite their insular distribution. Bayesian phylogenetic analyses identified two major mitochondrial haplogroups (A and B) that frequently co-occurred across the Japanese archipelago. Haplogroup A, which is rare on the Eurasian continent, occurred at high frequency in Japan and showed pronounced isolation by distance, whereas haplogroup B showed only weak but significant isolation by distance and was significantly more frequent in populations closer to the coast. These contrasting spatial patterns within species indicate distinct demographic histories for the two mitochondrial lineages. Main conclusion Repeated colonization from the Eurasian continent and the long-term coexistence of mitochondrial lineages with different demographic histories have shaped the pattern of genetic diversity of A. paludum in the Japanese archipelago. Our findings exemplify how continental islands can accumulate genetic diversity through lineage accumulation and secondary contact, which produces an intraspecific phylogeographic pattern comparable to those observed during an early phase of the taxon cycle between species.

Kashmir voles (Hyperacrius) are poorly studied fossorial arvicolines of the southern Himalayan slopes, with two species recognized. We sequenced Cytb from voles collected in northern Pakistan and combined these data with existing GenBank sequences, yielding 194 tips spanning nearly all arvicoline genera. We analyzed five data sets with maximum likelihood and compared external measurements among species using principal component and linear discriminant analyses. We recovered five well-supported clades of Hyperacrius separated by ~12-14% p-distance, which we treat as distinct species. We recognize clade 1 as H. wynnei, and populations referred to H. w. traubi are genetically indistinguishable from H. w. wynnei. We recognize H. zygomaticus, new rank (clade 2), and tentatively allocate clade 5 to H. brachelix. Clades 3 and 4 likely represent undescribed species. Morphometric analyses of external measurements clearly distinguish H. wynnei but not clades 3 and 4 (overall classification accuracy 70.3%). Phylogenetic analyses including nuclear genes placed Hyperacrius as sister to a clade containing Microtini, Arvicola, Lagurini, Dinaromys, and Ellobiusini, whereas mitochondrial analyses weakly allied it with Ellobiusini. Its traditional placement in Clethrionomyini is thus unsupported, although its exact position remains unresolved. Alticola is nonmonophyletic, with A. macrotis sequences nested within Clethrionomys, likely reflecting mitochondrial capture.

Premise of the study: Doryopteris J.Sm. is a genus of dry-adapted ferns found widely across the southern hemisphere and the tropics. In the Hawaiian Islands, the genus is represented by four endemic species and one putative hybrid. Two of the endemic species (D. decora and D. decipiens) are widespread across all major islands, while two (D. angelica and D. takeuchii) are federally and state-listed endangered single-island endemics.We aimed to resolve the evolutionary relationships and biogeographic history of Hawaiian Doryopteris. Methods: We used a target-capture approach and the GoFlag 408 flagellate land plant probe set to sequence more than 400 nuclear loci for 40 Hawaiian and 29 non-Hawaiian individuals in Doryopteris and the related genera Lytoneuron and Ormopteris. After processing the sequences into alignments and single nucleotide polymorphism sites, we performed phylogenetic inference and population-level principal component analyses. Key results: We infer that Hawaiian Doryopteris are monophyletic and are nested within the pantropical species D. concolor. Within Hawai'i, clades and clusters of individuals correspond to geographical, geological, and climatological factors, more so than species identifications, with a few exceptions. We posit that Hawaiian Doryopteris represents an incipient radiation at the very earliest stages of divergence, and that budding speciation has led to non-monophyly of several taxa. Conclusions Our inference using genome-wide sequencing data sheds light on the complex evolutionary history of Hawaiian Doryopteris. Overall, the phylogeny of Hawaiian Doryopteris shows strong links with geographical, geological, and climatological processes and little with morphological evolution.

Abstract Habitat configuration influences population connectivity and, consequently, genetic structure. River networks provide heterogeneous, hierarchically arranged environments that shift drastically from upstream to downstream. We compared congeneric species across Ephemeroptera, Plecoptera, and Trichoptera, emphasizing longitudinal replacement (upstream to downstream) and the rarely studied wet rock (hygropetric) habitats. We surveyed six rivers on the Muroto Peninsula, Japan, qualitatively sampling aquatic insects at 63 sites. Cluster analysis based on the environmental data classified surveyed sites into four clusters. We analyzed a total of 10 species from four genera that exhibit longitudinal replacement patterns within genera. Genetic analyses based on the mitochondrial cytochrome c oxidase subunit I region revealed that upstream species showed higher genetic diversity than downstream species. In contrast, species adapted to hygropetric exhibited the lowest genetic differentiation among all habitat types. A novel contribution of this study is the inclusion of hygropetric species. The surprisingly low differentiation in hygropetric species suggests high connectivity, similar to lentic species. By comparing congeneric taxa across orders within environmentally similar rivers, we reduce phylogenetic and environmental confounds, strengthening inference that habitat configuration and dispersal traits jointly shape genetic structure. These findings provide a new perspective on riverine spatial ecology and underscore the importance of microhabitat-aware comparisons for evolutionary inference.

The Asparagaceae is an economically and ecologically important angiosperm (monocot) clade, containing iconic garden plants such as asparagus, hyacinth and agave, and arid-adapted keystone species like Joshua tree and dragon blood tree. The approximately 2,500 species in the family are spread across seven subfamilies: Agavoideae, Aphyllanthoideae, Asparagoideae, Brodiaeoideae, Lomandroideae, Nolinoideae and Scilloideae. Relationships among the seven subfamilies are generally unresolved and the sources of gene tree-species tree discordance are largely unknown. Investigating the biology underlying such discordance requires a robust sampling of both taxa and molecular markers, due to the extremely short branches that form the backbone of the Asparagaceae phylogeny. Using targeted sequencing of 1,726 low-copy nuclear genes, and a nearly complete sampling of genera, we interrogate relationships among all seven Asparagaceae subfamilies and investigate the underlying sources of discordance across the phylogeny. Analyses using different phylogenomic approaches (multispecies coalescence vs. nuclear gene supermatrix vs. chloroplast gene supermatrix) each revealed extensive discordance across the Asparagaceae backbone, which may be associated with rapid lineage diversifications that occurred in Africa shortly following the origin of the family ~49 Ma. Specifically, we found that two branches, representing ancestors of Aphyllanthoideae and Nolinoideae, may be responsible for much of the backbone discordance. The placement of Aphyllanthoideae, represented by one extant taxon (Aphyllanthes monspeliensis), is controversial with discordant topologies across many studies. However, multispecies coalescence-based analyses from this study strongly support a sister relationship between Aphyllanthoideae and a larger Agavoideae + Scilloideae + Brodiaeoideae clade. According to gene tree quartet frequencies and ABBA-BABA tests, we cannot reject incomplete lineage sorting (ILS) as the main source of discordance for the placement of Aphyllanthoideae; our results leave open the possibility of an ancient reticulation involving an ancestor of Aphyllanthoideae and an extinct basal Asparagaceae lineage. Regarding Nolinoideae, we found that conflicting support for two possible bifurcating clades (Asparagoideae + Nolinoideae vs. Asparagoideae + Lomandroideae) was associated with skewed support for alternative gene tree topologies, suggesting that phenomena other than ILS may explain the observed discordance. A quartet-based ABBA-BABA analysis, used to test for signatures of introgression, revealed a putative ancient hybridization event between two divergent, ancestral lineages which may have contributed to the origin of the Nolinoideae clade in Africa ~45 Ma. In sum, this study elucidates the long-troublesome backbone of the Asparagaceae phylogeny and advances our understanding of the evolutionary and biogeographical origins of all extant subfamilies. More broadly, this study expands our understanding of the various sources of gene tree discordance that may arise from natural processes associated with rapid lineage radiations across the tree of life.

Hydractiniidae is a diverse family of colonial hydrozoans exhibiting substantial variation in colony organization, reproduction and life-cycle strategies, including species with and without a medusa stage. Several hydractiniids are also established model organisms, yet species boundaries and distributions remain incompletely resolved, limiting comparisons of reproductive and developmental traits across taxa. Here, we combine morphological and molecular data to reassess hydractiniid diversity, species identities, and life-cycle variation in material from the North Atlantic and Arctic Ocean. We integrate detailed observations of colonies and reproductive structures with DNA barcoding and mitochondrial genomes to evaluate species boundaries and provide molecular support for taxonomic identifications. Our results confirm 10 species in the study area, occurring from shallow waters to 2600 m depth and from coastal fjords to deep-sea hydrothermal vents. We further show that some historical species identifications and distribution records require reassessment. We establish a new genus for Arctic hydractiniid species (Bonneviactinia gen. nov.) and reassign two species to Schuchertinia. Mapping reproductive strategies onto the phylogeny reveals a broad pattern of increasing retention of medusa characters, from fixed sporosacs through reduced and fixed medusoids and non-liberated eumedusoids to fully developed, free-swimming feeding medusae, suggesting a progressive evolutionary trajectory in life-cycle complexity across Hydractiniidae. Furthermore, we clarify the identity of Podocoryna carnea and, through rearing experiments from polyp stage to medusae, characterize its morphological variation and developmental stages. By linking morphologically documented specimens and vouchers to genetic data, we establish reference resources that will facilitate future taxonomic, phylogenetic and biodiversity studies, including molecular surveys of marine communities. Together, these results demonstrate the value of integrative taxonomy for resolving hydractiniid diversity and provide a comparative foundation for investigating the evolution of reproductive strategies and life-cycle complexity in Medusozoa.

The origin of multicellular animals from unicellular ancestors remains a major evolutionary question. To address this transition, a reconstruction of the nature of the last unicellular ancestor of animals (LUAA) is key, and requires broad sampling of extant unicellular relatives, which together with animals form the clade Holozoa. Environmental surveys suggest that unicellular Holozoa diversity extends beyond the five groups with characterized members (Choanoflagellatea, Ichthyosporea, Filasterea, Corallochytrea, and Atreyea). However, the extent of the environmental diversity within and outside these groups remains unclear. To fill this gap, we here systematically re-evaluated Holozoa diversity using environmental 18S rDNA sequences compiled from updated datasets, including long-read metabarcoding surveys. We report nine uncharacterized lineages inside Holozoa (seven newly identified here), provisionally placed outside the described groups. We also uncovered a previously unreported diverse lineage deeper inside Opisthokonta, separate from Holozoa and Fungi. In addition, we identified 21 uncharacterized lineages within Choanoflagellatea and Ichthyosporea (eleven newly reported here). We used short-read metabarcoding datasets to characterize the environmental and geographical distributions of these lineages. Many are globally distributed and some can reach relative abundances comparable to those of the described groups, while others are restricted to specific environments. Our findings reveal substantial uncharacterized diversity missing from the cultured taxa used in comparative studies of animal origins. By placing this diversity in a phylogenetic and environmental context, our study will guide the targeted isolation efforts needed to broaden the taxon sampling available to reconstruct LUAA and unravel the unicellular-to-multicellular transition that gave rise to animals.

Self-fertilization results in reduction of heterozygosity over time, accelerated by small population sizes, restricted ranges, and fragmented habitats. Yet some species maintain heterozygosity despite these factors. One is Corallorhiza bentleyi, a threatened, mycoheterotrophic, self-pollinating orchid restricted to Virginia and West Virginia, USA. Reduced representation sequencing was employed across five of the ~12 known localities of C. bentleyi, including representatives of sister species C. involuta from Mexico, to quantify patterns of population structure and genomic diversity. Surveys of C. bentleyi revealed a predominance of the cleistogamous (closed-flowered) growth form. Differentiation was observed between the two species but with weak population structure in C. bentleyi. Surprisingly, excess heterozygosity and negative inbreeding were recovered in both species, counter to expectations. Analyses provided evidence against bioinformatic artifacts (collapsed paralogs), small-sample bias (Robertson effect), and accumulation of mutations along chromosomes due to low recombination associated with selfing (Meselson effect) as explanations for excess heterozygosity. Demographic analyses favored a model of post-glacial divergence among C. bentleyi and C. involuta lacking bottlenecks. Finally, simulations under alternative selection scenarios favored models of overdominance vs. those of negative frequency dependent selection. It was concluded that overdominance, namely selection against selfed homozygotes, is the most likely explanation for elevated heterozygosity in C. bentleyi. Conservation concerns are discussed in light of these findings and the threats of extinction for one of the most vulnerable orchid species in North America.

Asian Passifloraceae occupy a distinctive evolutionary and ecological position within the family despite their relatively low species diversity compared with the Neotropics. Many Asian representatives are highly localized, small and often ephemeral climbers that persist seasonally through rhizomes, tuberous stems or dormant seeds, while considerable morphological plasticity may obscure species limits and evolutionary relationships. Xishuangbanna, southwestern China, lies at the convergence of Southeast Asian, Indian-Himalayan and southern Chinese floristic elements and represents an important regional centre of Passifloraceae diversity, with two species of Adenia and five species of Passiflora, including the recently described P. xishuangbannaensis and P. menghaiensis. We investigate the evolutionary relationships, plastome evolution and population genomics of these taxa using complete plastome assemblies, a concatenated dataset of 68 selected plastid protein-coding genes, 356 reconstructed nuclear Coding Sequences (CDS), and Genotyping-By-Sequencing (GBS) across the known wild distribution of P. xishuangbannaensis. Plastid, concatenated nuclear and nuclear coalescent phylogenies were strongly incongruent and differed from published classifications based on morphology and earlier phylogenies (ITS, ncpGS, ctyGS, ndhF and trnL-F). Gene-tree discordance and phylogenetic-network inference indicated widespread incomplete lineage sorting together with introgression. The two statistically best-supported network models placed P. menghaiensis, which showed high genetic similarity to the Indian P. napalensis, as a sister lineage involved in independent reticulation events associated with P. altebilobata, P. xishuangbannaensis and P. sumatrana. A pronounced biogeographic pattern was evident within Passiflora supersection Disemma, particularly in the P. siamica-P. cochinchinensis lineage across the Hua Line, whereas relationships among other Asian Passiflora blurred this boundary. This pattern suggests that diversification and reticulation within the Asian lineage may have overlapped temporally with the development of the biogeographic divide represented by the Hua Line. The concentration of early-diverging lineages around Xishuangbanna and the eastern Himalayan-Indian region further points to this area as an important centre in the early diversification of Asian Passiflora. Within this context, the highly localized P. xishuangbannaensis may represent either a relictual of an early Asian lineage or the surviving product of an ancient reticulate complex, contrasting with lineages such as P. siamica that subsequently expanded farther across Southeast Asia. Comparative plastome analyses revealed extensive structural and gene-content evolution within subgenus Decaloba, including pseudogenization, gene and intron losses, and repeated Inverted-Repeat (IR) expansions and contractions; substantial plastome modification also characterized supersection Disemma. Passiflora sumatrana exhibited a particularly distinctive IR expansion extending into the accD-pafII region, potentially characterizing this lineage. Adenia plastomes were generally more structurally conservative, although A. penangiana displayed an IR-boundary contraction involving the rps19-rpl2 region. Mitochondrial CDS and non-coding regions provided the best-resolved phylogenetic signal and revealed strong discordance with the chloroplast phylogeny, consistent with maternal mitochondrial inheritance and variable plastid transmission, potentially involving paternal or biparental inheritance and heteroplasmy. GBS analyses of P. xishuangbannaensis using complementary distant-reference, de novo and closely related-reference approaches showed that mapping to P. organensis provided the clearest SNP distribution and population resolution. ADMIXTURE, PCA and FST analyses revealed two strongly geographically structured populations with additional substructure and substantial differentiation (FST = 0.112). Linkage disequilibrium based demographic reconstruction using GONE2 indicated declining effective population size (Ne) toward the present in both populations, with a particularly abrupt recent decline in Pop1 and a more gradual decline in Pop2. Few candidate Self-Incompatibility (SI) genes could be confidently reconstructed, including limited recovery of highly variable docking regions. However, the intracellular region of an S-locus Receptor Kinases (SRK) contained a distinctive non-synonymous substitution predicted to alter protein configuration without major disruption of overall folding, potentially contributing to compatibility differences between populations. Together, these results reveal a complex evolutionary history combining historical dispersal, incomplete lineage sorting, reticulation, morphological plasticity, plastome structural evolution and strong population differentiation. The narrow distributions and recent demographic decline of these newly recognized Xishuangbanna taxa emphasize their conservation importance, while broader Asian taxon sampling and deeper genomic sequencing will be essential to resolve the evolutionary history of this discreet and poorly known Passifloraceae radiation.

Rapid diversification can generate regional biodiversity through ancestral polymorphism, admixture, and ecological differentiation, while leaving complex genomic signals. We analysed whole-genome variation in 325 butterflies, including 166 individuals of the Papilio bianor species complex and six outgroup species, to reconstruct lineage relationships and demographic history. Nuclear genomic analyses recovered three major clades corresponding to the recognized species and placed the island lineage as sister to continental P. bianor. Analyses of 18,635 autosomal window trees revealed extensive genealogical discordance, with incomplete lineage sorting predominating among continental lineages and the strongest introgression signals involving island related ancestry. Demographic modelling supported early island continental divergence followed by continental diversification and ancient admixture. The best fitting fastsimcoal2 model inferred an admixed origin of the Eastern China lineage, while BPP analyses supported ancient island-related introgression into the Eastern China ancestor, Western Himalaya and southwestern Thailand. Peripheral populations exhibited pronounced genetic differentiation and distinct demographic histories; Western Himalaya additionally showed mitochondrial affinity with Yaeyama despite its placement within the Himalayan nuclear lineage. Together, these findings suggest that introgression among deeply differentiated ancestral populations and incomplete lineage sorting during rapid divergence jointly shaped lineage diversity in the P. bianor complex. This study provides an empirical framework for investigating how lineage diversity emerges rapidly during the early stages of speciation, particularly in groups with deep ancestral population structure.

Gene flow between diverging species can reshuffle genomic variation and greatly influence the speciation process, sometimes reinforcing, sometimes eroding species boundaries. However, the effect of ecological and historical processes on the patterns of introgression remains poorly understood. Here, we focus on the evolutionary history of Heliconius besckei, a geographically restricted butterfly endemic to the Brazilian Atlantic Forest, together with the mimetic H. melpomene nanna, the sympatric non-mimetic H. ethilla narcaea, and its closely related H. numata robigus. Using whole-genome sequencing, genome-wide tests of introgression, demographic modelling and palaeoclimatic species distribution models, we tested the extent and timing of interspecific gene flow in relation to mimicry, ecological context, and changes in geographic overlap. Despite strong genomic differentiation among the four focal Heliconius species, we detected widespread signatures of interspecific gene flow, greatly influenced by geographical overlap. Demographic models including post-divergence gene flow were better supported than strict-isolation models. In addition, genome-wide introgression analyses showed more numerous and larger candidate introgressed regions between H. besckei and H. ethilla narcaea, consistent with recurrent opportunities for exchange between these currently sympatric species. Species distribution models further recovered repeated expansions of suitable habitat for H. besckei during cold periods, providing a potential geographic context for secondary contact within the Atlantic Forest. Together, our results reveal recurrent gene flow occurring under different temporal, geographic, and potentially selective contexts, and show that the evolutionary history of a geographically restricted lineage can be shaped by repeated genetic exchange while substantial species differentiation is maintained.

The Fusarium oxysporum species complex (FOSC) comprises numerous plant pathogens infecting crops such as tomato, lettuce, melon, and banana. Despite its economic and ecological importance and decades of research, the species names linked to different phylogenetic lineages within this species complex remain largely controversial. Earlier taxonomic frameworks relied on a limited number of marker genes, variable taxon sampling and inconsistent species definitions, leading to a fragmented and unstable taxonomy. To address these challenges, we here analysed nearly 2,500 conserved marker genes from 660 genomes, including genome assemblies from 22 ex-type strains that were sequenced using long-read sequencing technology, representing nearly half of the 51 currently described species within FOSC. Maximum likelihood- and coalescence-based analyses of the full phylogenomic data matrix as well as subsets yielded a robust phylogeny of FOSC, which was furthermore corroborated by whole genome comparisons. Many previously described species are redundant, while two novel lineages remain undescribed. Direct comparisons to traditional marker gene-based approaches demonstrate their inadequacy for species delimitation in FOSC. We show that our phylogenomic framework can guide the detection of novel marker genes able to distinguish the major lineages within FOSC, which will be essential for taxon delineation and classification in future studies. Thus, our phylogenomic analyses provide a stable cornerstone for revising FOSC taxonomy and offers a critical resource for the broader research community.

Aquaporin-10 (AQP10) is an aquaglyceroporin that transports small, uncharged molecules, such as water and glycerol. In some species, such as mice and cattle, the AQP10 gene (Aqp10) is pseudogenized. In rodents, pseudogenization of Aqp10 is limited to the Myomorpha suborder, while Aqp10 remains intact in other rodent lineages. The order Cetartiodactyla encompasses diverse species, including Suina, Tylopoda, Ruminantia, and Whippomorpha. The distribution of intact Aqp10 across the entire Cetartiodactyla and analyses estimating the timing of Aqp10 pseudogenization have not been sufficiently investigated. In this study, we identified species within Cetartiodactyla that retain intact Aqp10 and analyzed the detailed patterns of pseudogenization to elucidate the specifics of pseudogenization within this order. We collected Aqp10 loci by BLAST and synteny analyses of publicly available genome databases of 51 cetartiodactyl species from 17 families. Dot plot and alignment analyses revealed that seudogenization of Aqp10 occurred in 42 Cetartiodactyla species, including the Camelidae, warthog (Suidae), Antilocapridae, okapi (Giraffidae), Cervidae, Bovidae, Hippopotamidae, and Cetacea. In contrast, nine species retained an intact Aqp10: pig and babirusa (Suidae), peccary (Tayassuidae), mouse deeres (Tragulidae), giraffes (Giraffidae), and musk deers (Moschidae). The timing of pseudogenization was estimated by comparing patterns of exon deletions, frameshifts, and nonsense mutations in Aqp10 pseudogenes. RT-PCR analysis of cattle and sheep tissues revealed that these species express Aqp3 and Aqp7 in their intestines, but not Aqp10. Collectively, these findings indicate that Aqp10 pseudogenization occurred independently in multiple cetartiodactyl lineages and provide new insights into the evolutionary history of Aqp10 loss within this order.

The allorecognition system of the hydroid Hydractinia symbiolongicarpus plays an essential role in mediating self vs. non-self recognition among cnidarian colonies, analogous to the role of the major histocompatibility complex (MHC) in bilaterian immune systems. Both complexes have contiguous stretches of similar, highly duplicated genes, suggesting a homologous relationship. Protein structural prediction methods such as AlphaFold2 also indicate structural similarity between the proteins encoded within the Hydractinia ARC and the MHC. We have determined the structure of the ARC in the related hydrozoan Podocoryna americana to determine the degree of conservation of the cnidarian allorecognition complex. Protein structural prediction methods have revealed a number of candidate allorecognition proteins that form a long contiguous complex. Phylogenies suggest homology between cnidarian allorecognition genes, as well as syntenic conservation of this gene complex across hydrozoans. Ongoing comparative genomic analyses across bilaterian species aim to clarify the relationship between the ARC and the MHC, thereby informing our understanding of the evolutionary origins of bilaterian adaptive immunity.

The palaeogeographic history of the Neotropics has inspired multiple diversification models, emphasizing either the Andes or Amazonia as primary drivers of biodiversity. However, the extensive Pebas wetland system that covered western Amazonia during the Miocene has gained attention as a potential barrier to dispersal and diversification. This system may have contributed to the modern diversity imbalance between the Andes and Amazonia, known as the Gentry pattern. Most evidence for this hypothesis comes from isolated case studies and fossils. Here, we conduct a meta-analysis including 1,361 species of Neotropical butterflies to evaluate the role of the Pebas wetland on the dynamics of dispersal and diversification. We found that Andean- and Amazonian-centred clades show complementary but temporarily distinct biogeographic patterns. High Andean diversity reflects an Andean origin, with early occupancy and diversification occurring within the Andes, followed by post-Pebas dispersal into Amazonia. By contrast, Amazonian-centred clades, reflect an Amazonian origin, with an early diversification in Amazonia and subsequent post-Pebas colonization of the Andes. While several clades show little evidence of Pebas influence, our study suggests that the Pebas wetland did not uniformly restrict diversification, but rather selectively constrained dispersal between the Andes and Amazonia, preventing simultaneous diversification in both regions and thereby creating a diversity imbalance that characterizes the modern Neotropic.

Habitat fragmentation and destruction in old-growth forests represents a primary threat to specialist species, frequently resulting in the erosion of genetic diversity. The Hermit Beetle, Osmoderma barnabita, is a protected relic of primeval forests and an obligate saproxylic specialist whose larval development depends exclusively on the wood-mould of hollow trees. This study provides the first high-resolution, genome-wide assessment of O. barnabita across seven Polish forest complexes using double-digestion Restriction-site Associated DNA sequencing data from 49 individuals. Following rigorous quality control and reference bias assessment, we evaluate contemporary population structure. To distinguish between evolutionary processes, we isolated 2,920 putatively adaptive outliers from the neutral background, evaluating both neutral and adaptive genomic signals. The analyses revealed four distinct genetic clusters, confirming that the Polish metapopulation is severely subdivided. Crucially, the westernmost population in the Lower Silesian Forest emerged as the most divergent evolutionary unit (FST up to 0.360), suggesting potential hybrid origin or long-term isolation. We observed a striking linear correlation (R2=0.986) between neutral diversity and adaptive potential, indicating that genetic drift in small and isolated forest fragments is actively depleting the variation required for long-term persistence of this species. Our findings demonstrate significant gene flow restriction across all sites, suggesting that current conservation frameworks fail to encompass these highly differentiated lineages. To mitigate this genetic vulnerability, we recommend reclassifying these clusters as independent Management Units and Evolutionary Significant Units. Maintaining forest continuity and protecting local micro-habitats are essential to prevent further isolation and preserve the genomic integrity of this saproxylic flagship species.

Lineages that have undergone little apparent evolutionary change over long geological intervals are often described as "living fossils", with iconic examples including the coelacanth, tuatara, and Ginkgo. However, studies of morphological and molecular data have produced mixed evidence regarding whether living fossils have evolved more slowly than their relatives. We tested for reduced evolutionary rates using a sister-pairs approach, analysing a comprehensive set of morphological and molecular data for 45 living-fossil lineages and their close relatives across the Tree of Life. Living-fossil lineages showed substantially reduced rates of morphological evolution, whereas evidence for reduced molecular rates was weaker. To test whether this pattern could be explained by species poverty, we also analysed other depauperate lineages (species-poor clades contrasted with species-rich sister clades) and found a weak tendency towards reduced molecular rates but without a corresponding slowdown in morphological evolution. Our study reveals that the living-fossil concept captures a quantifiable pattern of prolonged morphological conservatism, but also suggests that living fossils lack other shared biological or life-history characteristics that might unite them as a group.

Eusociality, characterized by overlapping generations, cooperative brood care, and reproductive division of labour, has arisen independently across diverse, phylogenetically distant insect orders, including Hymenoptera (ants, bees, and wasps), Blattodea (termites), and Coleoptera (weevils). While multiple studies have investigated the molecular evolution of sociality from solitary ancestors in Hymenoptera and Blattodea, so far little is known about the evolutionary signatures of social evolution in Coleoptera. Weevils (Curculionidae) provide an ideal system for addressing this question, as they cover the full spectrum of social complexity from parental care, through several origins of facultative eusociality to the only obligately eusocial beetle, Austroplatypus incompertus. We generated genome assemblies for A. incompertus and two facultatively eusocial weevil species, Xylosandrus germanus and Xyleborinus saxesenii, which together with 18 publicly available weevil genomes span two independent evolutionary origins of sociality. Our analyses reveal a genome-wide relaxation of purifying selection with increasing social complexity, which is most pronounced in A. incompertus. We find a significant excess of convergent gene family contractions in lineages where sociality evolved, and no evidence of elevated positive selection. These findings indicate that the molecular mechanisms of social evolution in weevils are primarily characterised by relaxed selection and gene loss, rather than adaptive innovation and gene family expansions. These observations are consistent with sheltering and reduced effective population size playing an important role, a pattern not previously observed in other clades.

Geographic isolation is a major driver of lineage divergence. However, strong ecological selection can promote reproductive isolation despite opportunities for gene flow in geographically continuous landscapes such as mountains. Here, we test whether ecological divergence across elevational gradients can promote speciation within a single mountain range. Integrating phylogenomic (ddRAD), morphological, and bioacoustic data, we test predictions of elevation-mediated parapatric speciation in Platymantis (Lahatnanguri) ground-dwelling frogs on Mindanao Island, Philippines. Phylogenomic analyses recovered an endemic radiation across neighboring mountain ranges and revealed a hierarchical pattern of diversification among three monophyletic lineages, with deeper divergence separating the mountain lineages Highland 1 and Highland 2 and more recent divergence occurring within a single mountain range. This topology identified a morphologically and acoustically distinct low-elevation lineage (<1,400 m a.s.l.) as closely related to the high-elevation Highland 1 lineage (>1,400 m a.s.l.), providing a natural test of divergence along an elevational gradient. The parapatric Lowland and Highland 1 lineages appear to have diverged relatively recently, as reflected in their shallow genome-wide differentiation, yet exhibit pronounced morphological and acoustic divergence. Population genomic analyses further recover discrete genomic clusters and no evidence of contemporary hybridization between the parapatric lineages, indicating independent evolutionary trajectories despite geographic continuity. Together, these findings are consistent with parapatric speciation along an elevational gradient and demonstrate how substantial phenotypic and reproductive-isolation divergence can accumulate despite limited genome-wide differentiation. More broadly, our results indicate that the exceptional biodiversity of oceanic archipelagos may arise not only from diversification among islands (and among mountains within islands) but also from lineage divergence along elevational gradients within mountains themselves. These empirical results support the biological plausibility of parapatric speciation within single mountain systems and highlight an underrecognized mechanism contributing to biodiversity in topographically complex oceanic archipelagos.