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Despite the escalating biodiversity crisis, many species remain unknown to science and may even disappear unnoticed. This is particularly true for many island populations. We illustrate the problem of detecting overlooked species and its consequences by exploring a rare and geographically restricted migratory songbird. We find that this consists of two-hence even rarer-species: the Japanese endemic Ijima's Leaf Warbler Phylloscopus ijimae from the Izu Islands and the Tokara Leaf Warbler from the Tokara Islands. We describe the latter as a new cryptic species, ie one that is morphologically highly similar to, but genetically distinct from, a known species. The genetic divergence is revealed by analyses of nuclear genome-wide and mitochondrial DNA and supported by differences in vocalizations, while the morphological differences are minimal. We evaluate key conservation genomic indicators, showing that both species show low levels of genetic diversity and signs of a decrease of effective population size. Our genome-wide analysis revealed short runs of homozygosity and a low estimated deleterious load, suggesting limited recent inbreeding and possible purging of harmful alleles-indicators of genetic recovery after past demographic fluctuations. Ijima's Leaf Warbler is already classified as Vulnerable as well as a "Natural Monument" in Japan, and we propose that the Tokara Leaf Warbler should retain this status, with continued focused monitoring. Our study not only highlights the importance of integrating genomics with taxonomy for uncovering cryptic avian diversity but also provides a critical foundation for future conservation efforts.

Understanding how biodiversity is formed and maintained, is a key topic in both ecology and conservation biology. Both ecological and evolutionary processes jointly shape community assembly and maintain biodiversity, often through complex interactions. This study aims to examine how ecological and evolutionary processes jointly shape the global and regional distribution patterns of diversity in the avian family Paridae, focusing on assembly and species pairwise levels. We integrated phylogenetic information, environmental variables (net primary productivity and environmental heterogeneity), and species traits (plumage, song, and morphometrics). We applied structural equation modeling to evaluate how these evolutionary and ecological factors integratively influence the parids diversity. We also used the Bayesian generalized linear mixed model MCMCglmm to assess how these factors affect range overlap between species pairs and, ultimately, patterns of sympatry. The result shows that diversity patterns in Paridae are shaped by both ecological and evolutionary drivers, with mechanisms differing regionally. Patterns of sympatry largely reflect secondary contact, with a pronounced tendency for sympatry among close relatives, and no evidence of character displacement. In Eastern Eurasia, particularly in the diversity center of the Sino-Himalayan mountains, speciation rate is constrained, and richness pattern is strongly influenced by environmental factors and plumage color diversity, possibly due to the relatively saturated ecological niches resulting from a long evolutionary history. In contrast, in the Western region, centered on Europe, where ecological niche space is thought to remain more available, rapid speciation plays a greater role in generating the richness pattern. Here, variation in plumage and morphometric traits further promote species coexistence and diversity. Our findings underscore the need to integrate evolutionary history, contemporary ecological dynamics, and phenotypic traits to understand the mechanisms that shape global diversity patterns of parids. Regional differences in assembly processes, niche saturation in areas with long evolutionary history versus speciation-driven richness in niche-available regions highlight the complex interplay of ecology and evolution in maintaining such the diversity.

Geographic barriers and geological historical events may play pivotal roles in driving allopatric divergence among closely related species. Here, we investigate the genomic divergence patterns and ecological niche separation of the Willow Tit Poecile montanus and the Marsh Tit P. palustris species groups in China, and their ecological niche separation across East Asia. Through comprehensive genomic sequencing, population genomic analysis, and integration of public occurrence data, we unveil striking parallels in the geographic divergence patterns between these two species groups. Notably, both species exhibit multiple divergent lineages in China, with similar spatial distributions of gene flow barriers. Furthermore, our analysis reveals unique evolutionary histories in the southwestern clades of both species groups, highlighting the intricate interplay between historical distribution dynamics, ecological preferences, and genetic divergence. Our study significantly enhances our understanding of the processes underlying the diversification of closely related widespread species within the framework of shared geographical constraints, and stresses the need for a taxonomic revision.

The Bar-tailed Lark Ammomanes cinctura is a polytypic bird species with a wide distribution. One of its three subspecies, A. c. arenicolor, has previously been found to show deep mitochondrial divergence between its geographically most distant populations, from Morocco and Saudi Arabia, respectively. We applied an integrative approach using genome-wide single nucleotide polymorphisms (SNPs), mitochondrial DNA (mtDNA), morphological and bioacoustic data to investigate the evolutionary divergence within A. cinctura. We confirmed the existence of two distinct mitochondrial clades: one including samples from Morocco and Cape Verde Islands and the other including samples from Saudi Arabia and Iran. We estimated that these lineages diverged 2.14 million years ago (Mya). In contrast, we recovered shallow divergence in the nuclear SNPs (estimated split time: 0.08 Mya) between the samples from Cape Verde–Morocco versus Saudi Arabia–Iran, and population structure analyses favored a single genetic cluster. Analyses of museum specimens confirmed earlier statements that the eastern subspecies, A. c. zarudnyi, has slightly longer wing and tail than the two others, and that the three subspecies are slightly divergent in plumage. Finally, our analyses of vocalisations suggested that some geographical differences might exist, but the commonest song type is found across the range. The reasons for the considerably deeper divergence in mitochondrial DNA relative to that of nuclear SNPs are unresolved and will require more comprehensive sampling to elucidate.

Universally recognized scientific names for organisms are necessary for accurate and efficient communication. Incongruence in taxonomic treatments results in situations where one name is used for different entities or one entity is known by different names, with negative consequences for conservation, science, trade, legislation, law enforcement, and education, leading to discord among stakeholders and confusion among users. Within the ornithological community taxonomic incongruence among four widely adopted global bird checklists has led to calls for the development of a single unified global avian taxonomy or checklist. Here we introduce AviList, a comprehensive, collaborative and evolving effort towards developing a unified global avian taxonomy, spearheaded by representatives of most current global checklists and many major regional authorities, and supported by the International Ornithologists' Union (IOU), BirdLife International and the Cornell Lab of Ornithology. AviList version 2025, the first version, was officially launched on 11 June 2025 and is available online as a comprehensive, searchable public-access database. It recognizes 11,131 bird species in 2376 genera, 252 families and 46 orders. This global effort has resolved over 1000 species-level taxonomic incongruences among existing checklists. With AviList's launch, the IOC World Bird List and the Clements Checklist of Birds of the World have ceased any independent taxonomic updates, while BirdLife International is in the process of total alignment, leading to a harmonization in the classification underpinning a number of major bird projects, including eBird, Macaulay Library, Merlin Bird ID and the IUCN Red List. Adoption of AviList will improve inter-operability across global biodiversity, molecular, ecological and spatial databases (e.g. GBIF). Strong governance of AviList will ensure it is a "living" document that is regularly updated by a global community of bird taxonomists as new scientific advances are made, with positive impacts for conservation, academia and human society. It is hoped that AviList will support and encourage taxonomic science by identifying areas where further research is most needed, and that it will provide a blueprint for taxonomic authorities in other organismic groups endeavoring to achieve taxonomic harmonization.

Background: Museomics utilizes historical genetic data from museum specimens to inform threatened species conservation. The Yellow-breasted Bunting (Emberiza aureola) and the Jankowski's Bunting (E. jankowskii), categorized as Critically Endangered or Endangered, respectively, have experienced population declines since the 1970s-1980s. Comparing genetic diversity changes before and after declines is crucial for refining conservation strategies.

Results: We de novo assembled genomes for both species and resequenced 29 E. aureola (16 historical pre-decline specimens from the 1930s to the 1950s) and 18 E. jankowskii (4 historical pre-decline specimens from the 1950s to the 1960s), with 45 individuals from six least-concern Emberiza species for comparison. Genetic diversity remained stable in both endangered species from the pre-decline to post-decline periods, with their overall genetic diversity levels being comparable to those of their least-concern congeners. While historically, both had large effective population sizes, E. jankowskii showed a gradual decline over 1000 generations, whereas E. aureola remained stable. Both modern populations of E. aureola and E. jankowskii exhibited a higher proportion of long runs of homozygosity (ROH) compared to their historical counterparts, indicating an increased impact of inbreeding following population declines.

Conclusions: Despite severe population declines, both species retained high genetic diversity but experienced increased inbreeding. E. jankowskii faces ongoing effective population size decline. These insights guide targeted conservation strategies, highlighting the value of museomics in understanding demographic and genetic histories.

BackgroundResolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene-Pleistocene boundary.ResultsHere we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees. Topology tests show a large degree of gene tree-species tree discordance but only 40-54% of intronic gene trees and 36-75% of exonic genic trees can be explained by incomplete lineage sorting and gene tree estimation errors. Estimated branch lengths for three successive internal branches in the inferred species trees suggest the existence of an empirical anomaly zone. The most common topology recovered for species in this anomaly zone was not similar to any coalescent or concatenated inference phylogenies, suggesting presence of anomalous gene trees. However, this interpretation is complicated by the presence of gene flow because extensive introgression was detected among these species. When exploring tree topology distributions, introgression, and regional variation in recombination rate, we find that many autosomal regions contain signatures of introgression and thus may mislead phylogenetic inference. Conversely, the phylogenetic signal is concentrated to regions with low-recombination rate, such as the Z chromosome, which are also more resistant to interspecific introgression.ConclusionsCollectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.

Animals that colonize islands often undergo significant evolutionary changes in comparison with their continental counterparts as a response to specific island conditions. The pace of such changes can be relatively fast, which poses challenges in the evaluation of the taxonomic status of island taxa. The Japanese and Manchurian Bush Warbler species complex (Horornis diphone-canturians), which breeds in East Asia and the Japanese Archipelago, is such an avian example. This species complex exhibits significant morphological differentiation between different taxa, and the taxonomic status and phylogenetic relationships within the complex are debated. Here, we updated the taxonomy of this species complex and shed insight on its evolutionary history using multi-locus phylogeographic and acoustic analyses. Our results support the conventional treatment of the two continental taxa borealis and canturians as subspecies of H. canturians, contrary to some recent proposals that they are affiliated to H. diphone. We also document a reduction in body size, that is dwarfism, and vocal divergence in the nominate subspecies H. d. diphone, which is endemic to the remote and isolated Ogasawara Islands. These changes may have happened following colonization of these islands, which was estimated to have taken place approximately 0.2 million years ago. Although H. d. diphone is clearly distinctive and deserves recognition as an evolutionarily significant unit, H. d. diphone and other H. diphone samples were not reciprocally monophyletic. Because of this lack of reciprocal monophyly and a relatively recent divergence time, we advocate maintaining its current subspecies status. We also detected reduced genetic diversity, measured as heterozygosity, in H. d. diphone. We suggest that conservation efforts in the Ogasawara Islands should prioritize the protection of this endemic subspecies. Collectively, our findings suggest that the separation between the populations on the East Asian continent and the Japanese Archipelago, followed by colonization of remote oceanic islands through long-distance dispersal, underlie rapid phenotypic and genetic diversification of the Horornis diphone-canturians species complex.

Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of 4 Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and similar to 39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which-in combination-support the following tree topology: ([{E. godlewskii, E. cia}, E. cioides], E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.

The fundamental value of universal nomenclatural systems in biology is that they enable unambiguous scientific communication. However, the stability of these systems is threatened by recent discussions asking for a fairer nomenclature, raising the possibility of bulk revision processes for "inappropriate" names. It is evident that such proposals come from very deep feelings, but we show how they can irreparably damage the foundation of biological communication and, in turn, the sciences that depend on it. There are four essential consequences of objective codes of nomenclature: universality, stability, neutrality, and transculturality. These codes provide fair and impartial guides to the principles governing biological nomenclature and allow unambiguous universal communication in biology. Accordingly, no subjective proposals should be allowed to undermine them.