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We describe the discovery of a previously unknown population of Melodious Lark Mirafra cheniana from northern Tanzania and southern Kenya, some 2000 km north of what was previously thought to be its northern limit in central Zimbabwe. The identification of this population as M. cheniana is based primarily on analyses of mitochondrial DNA and song. We also clarify relationships within this genus by sequencing material of White-tailed Lark Mirafra albicauda for the first time; although its relationships with other species in the group remain unclear, our analyses clearly show it to be different from M. cheniana in the newly discovered population. The discovery of a population of M. cheniana in East Africa conforms to a known pattern for closely related lark species to have disjunct distributions in southern and eastern Africa.

Biological specimens in natural history collections constitute a massive repository of genetic information. Many specimens have been collected in areas in which they no longer exist or in areas where present-day collecting is not possible. There are also specimens in collections representing populations or species that have gone extinct. Furthermore, species or populations may have been sampled throughout an extensive time period, which is particularly valuable for studies of genetic change through time. With the advent of high-throughput sequencing, natural history museum resources have become accessible for genomic research. Consequently, these unique resources are increasingly being used across many fields of natural history. In this paper, we summarize our experiences of resequencing hundreds of genomes from historical avian museum specimens. We publish the protocols we have used and discuss the entire workflow from sampling and laboratory procedures, to the bioinformatic processing of historical specimen data.

Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satDNA causes problems during the assembly of genomes, and therefore it is still difficult to study it in detail in nonmodel organisms as well as across broad evolutionary timescales. Here, we combined the use of short- and long-read data to explore the diversity and evolution of satDNA between individuals of the same species and between genera of birds spanning similar to 40 millions of years of bird evolution using birds-of-paradise (Paradisaeidae) and crow (Corvus) species. These avian species highlighted the presence of a GC-rich Corvoidea satellitome composed of 61 satellite families and provided a set of candidate satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satDNA of crow species rapidly diverged between closely related species while the satDNA appeared more similar between birds-of-paradise species belonging to different genera.

Aim: The species diversity and endemism of tropical biotas are major contributors to global biodiversity, but the factors underlying the formation of these systems remain poorly understood. Location: The world's largest tropical island, New Guinea. Time period: Miocene to present. Major taxa studied: Passerine birds. Methods: We first generated a species-level phylogeny of all native breeding passerine birds to analyse spatial and elevational patterns of species richness, species age and phylogenetic diversity. Second, we used an existing dataset on bill morphology to analyse spatial and elevational patterns of functional diversity. Results: The youngest New Guinean species are principally distributed in the lowlands and outlying mountain ranges, with the lowlands also maintaining the majority of non-endemic species. In contrast, many species occurring in the central mountain range are phylogenetically distinct, range-restricted, endemic lineages. Centres of accumulation for the oldest species are in montane forest, with these taxa having evolved unique bill forms in comparison to the remaining New Guinean species. For the morphological generalists, attaining a highland distribution does not necessarily represent the end to dispersal and diversification, because a number of new species have formed in the outlying mountain ranges, following recent colonization from the central range. Main conclusions: We conclude that a general model of tropical montane diversification is that lineages commonly colonize the lowlands, shifting their ranges upslope through time to become range-restricted montane forest endemics, attaining novel functional adaptations to these environments.

Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the “black-and-white wagtails”, a group of five species in the songbird genusMotacilla: one species, the White Wagtail (M. alba), shows wide intra-specific plumage variation, while the four others form two pairs of very similar-looking species (African Pied WagtailM. aguimp+ Mekong WagtailM. samveasnaeand Japanese WagtailM. grandis+ White-browed WagtailM. maderaspatensis, respectively). However, the two species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the phylogenetic relationships within this group, with a special emphasis on characterizing the extent of gene tree heterogeneity and its underlying causes. We first used multispecies coalescent methods to generate a “complete evidence” phylogenetic hypothesis based on genome-wide variants, while accounting for incomplete lineage sorting and introgression. We then investigated the variation in phylogenetic signal across the genome, to quantify the extent of discordance across genomic regions, and test its underlying causes. We found that wagtail genomes are mosaics of regions supporting variable genealogies, because of ILS and inter-specific introgression. The most common topology across the genome, supportingM. albaandM. aguimpas sister species, appears to be influenced by ancient introgression. Additionally, we inferred another ancient introgression event, betweenM. albaandM. grandis. By combining results from multiple analyses, we propose a phylogenetic network for the black-and-white wagtails that confirms that similar phenotypes evolved in non-sister lineages, supporting parallel plumage evolution. Furthermore, the inferred reticulations do not connect species with similar plumage coloration, suggesting that introgression does not underlie parallel plumage evolution in this group. Our results demonstrate the importance of investigation of genome-wide patterns of gene tree heterogeneity to help understanding the mechanisms underlying phenotypic evolution.

The Asian and Australo-Papuan faunas meet and intermix across the islands of Wallacea. Untangling the origins and relationships of the species inhabiting these archipelagos is an ongoing project that has lasted for well over a century. In recent years, molecular phylogenetic studies have made considerable progress in clarifying the affinities of enigmatic Wallacean taxa, but taxonomic riddles remain, even in groups as well studied as birds. Such is the case with Sulawesi Thrush Cataponera turdoides, a scarce and elusive montane songbird whose taxonomic placement has remained controversial since its description. To determine the evolutionary relationships of this monotypic genus, we obtained a museum specimen and employed whole-genome resequencing to generate a multi-locus dataset. Phylogenetic analyses were performed using UCEs, and individual mitochondrial and nuclear genes. We show that Cataponera is a true thrush of the large and geographically widespread genus Turdus. It belongs to a clade predominantly composed of migratory Palearctic species, but has no close relatives within that group. Sulawesi Thrush is one of only two members of the genus Turdus known to have crossed Wallace's Line to form resident populations.

Mountain biotas have considerable conservation and research importance, but the formation of montane communities remains incompletely understood. Study of Indo-Pacific island faunas has inspired two main hypotheses for the generation of montane diversity. The first posits that montane populations arise via direct colonization from other mountain areas, while the second invokes recruitment from adjacent lowland populations. We sought to reconcile these apparently conflicting hypotheses by asking whether a species’ ancestral geographic origin determines its mode of mountain colonization. To this end, island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recovered the phylogenetic relationships of the region’s montane species, and used this information to reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also performed genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal Palearctic climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. The patterns and processes revealed for this group are compatible with taxon cycles, a hypothesized process of lowland lineage expansion followed by montane relictualization. Collectively, our analyses explain much of the distributional variation within a complex biological system, and provide a synthesis of two seemingly discordant hypotheses for montane community formation.

Habitat fragmentation is a major extinction driver. Despite dramatically increasing fragmentation across the globe, its specific impacts on population connectivity across species with differing life histories remain difficult to characterize, let alone quantify. Here, we investigate patterns of population connectivity in six songbird species from Singapore, a highly fragmented tropical rainforest island. Using massive panels of genome‐wide single nucleotide polymorphisms across dozens of samples per species, we examined population genetic diversity, inbreeding, gene flow and connectivity among species along a spectrum of ecological specificities. We found a higher resilience to habitat fragmentation in edge‐tolerant and forest‐canopy species as compared to forest‐dependent understorey insectivores. The latter exhibited levels of genetic diversity up to three times lower in Singapore than in populations from contiguous forest elsewhere. Using dense genomic and geographic sampling, we identified individual barriers such as reservoirs that effectively minimize gene flow in sensitive understorey birds, revealing that terrestrial forest species may exhibit levels of sensitivity to fragmentation far greater than previously expected. This study provides a blueprint for conservation genomics at small scales with a view to identifying preferred locations for habitat corridors, flagging candidate populations for restocking with translocated individuals and improving the design of future reserves.

We used museomics to reconstruct the mitochondrial genome from two individuals of the Moroccan, endemic and extinct trout, Salmo pallaryi. We further obtained partial data from 21 nuclear genes previously used for trout phylogenetic analyses. Phylogenetic analyses including publicly available data from the mitochondrial control region and the cytochrome b gene, and the 21 nuclear genes place S. pallaryi among other North African trouts. Mitochondrial DNA places S. pallaryi close to Salmo macrostigma within a single North African clade. Although the nuclear coverage of the genome was low, both specimens were independently positioned as sisters to one of two distantly related North African clades, viz. the Atlas clade with the Dades trout, Salmo multipunctatus as sister. Phylogenetic discordance between mitochondrial DNA and nuclear DNA phylogenies is briefly discussed. As several specimens that were extracted failed to produce DNA of sufficient quality, we discuss potential reasons for that. We suggest that museum specimens in poor physical condition may be better for DNA extraction compared to better-preserved ones, possibly related to the innovation of formalin as a fixative before ethanol storage in the early 20

Tropical islands are renowned as natural laboratories for evolutionary study. Lineage radiations across tropical archipelagos are ideal systems for investigating how colonization, speciation, and extinction processes shape biodiversity patterns. The expansion of the island thrush across the Indo-Pacific represents one of the largest yet most perplexing island radiations of any songbird species. The island thrush exhibits a complex mosaic of pronounced plumage variation across its range, and is arguably the world’s most polytypic bird. It is a sedentary species largely restricted to mountain forests, yet it has colonized a vast island region spanning a quarter of the globe. We conducted comprehensive sampling of island thrush populations and obtained genome-wide SNP data, which we used to reconstruct its phylogeny, population structure, gene flow, and demographic history. The island thrush evolved from migratory Palearctic ancestors and radiated explosively across the Indo-Pacific during the Pleistocene, with numerous instances of gene flow between populations. Its bewildering plumage variation masks a biogeographically intuitive stepping stone colonization path from the Philippines through the Greater Sundas, Wallacea and New Guinea to Polynesia. The island thrush’s success in colonizing Indo-Pacific mountains can be understood in light of its ancestral mobility and adaptation to cool climates; however, shifts in elevational range, degree of plumage variation and apparent dispersal rates in the eastern part of its range raise further intriguing questions about its biology.

A taxonomic classification that accurately captures evolutionary history is essential for conservation. Genomics provides powerful tools for delimiting species and understanding their evolutionary relationships. This allows for a more accurate and detailed view on conservation status compared with other, traditionally used, methods. However, from a practical and ethical perspective, gathering sufficient samples for endangered taxa may be difficult. Here, we use museum specimens to trace the evolutionary history and species boundaries in an Asian oriole clade. The endangered silver oriole has long been recognized as a distinct species based on its unique coloration, but a recent study suggested that it might be nested within the maroon oriole-species complex. To evaluate species designation, population connectivity, and the corresponding conservation implications, we assembled a de novo genome and used whole-genome resequencing of historical specimens. Our results show that the silver orioles form a monophyletic lineage within the maroon oriole complex and that maroon and silver forms continued to interbreed after initial divergence, but do not show signs of recent gene flow. Using a genome scan, we identified genes that may form the basis for color divergence and act as reproductive barriers. Taken together, our results confirm the species status of the silver oriole and highlight that taxonomic revision of the maroon forms is urgently needed. Our study demonstrates how genomics and Natural History Collections (NHC) can be utilized to shed light on the taxonomy and evolutionary history of natural populations and how such insights can directly benefit conservation practitioners when assessing wild populations.

We re‐evaluated the taxonomy of the Striated Prinia Prinia crinigera–Brown Prinia P. polychroa complex using molecular, morphological and vocal analyses. The extensive seasonal, sexual, age‐related, geographical and taxon‐specific variation in this complex has never before been adequately studied. As no previous genetic or vocal analyses have focused on this group, misinterpretation of taxonomic signals from limited conventional morphological study alone was likely. Using mitochondrial and nuclear DNA, we found that P. crinigera sensu lato (s.l.) comprises two non‐sister groups of taxa (Himalayan crinigera and Chinese striata groups) that differ substantially morphologically and vocally and that are broadly sympatric in Yunnan Province, China. Prinia polychroa cooki (Myanmar) and P. p. rocki (southern Vietnam) are each morphologically, vocally and genetically distinct. Thai, Cambodian and Laotian populations formerly ascribed to P. p. cooki are morphologically and vocally most similar to and most closely related to Javan P. p. polychroa, and require a new name, proposed here. Prinia p. bangsi of Yunnan is part of the crinigera group rather than of P. polychroa, and hence there is no evidence for sympatry between P. polychroa s.l. and P. crinigera s.l., nor of the occurrence of P. polychroa in mainland China or Taiwan. We recommend the recognition of five species in the complex, with the following suggestions for new English names: Himalayan Prinia P. crinigera sensu stricto (s.s.; with subspecies striatula, crinigera, yunnanensis and bangsi); Chinese Prinia P. striata (subspecies catharia, parumstriata and striata); Burmese Prinia P. cooki (monotypic); Annam Prinia P. rocki (monotypic) and Deignan's Prinia P. polychroa s.s. (subspecies Javan polychroa and the new Southeast Asian taxon). This study underlines the importance of using multiple datasets for the elucidation of diversity of cryptic bird species and their evolutionary history and biogeography.

Old World orioles (Oriolidae) are medium-sized passerine birds confined largely to forested areas of Africa, Eurasia and Australasia. We present a new complete molecular (mtDNA) subspecies level phylogeny of the Oriolidae including all 113 taxa (35 species) together with a backbone phylogeny of 19 taxa from the main Oriolus clades based on (i) 21 nuclear genes, (ii) whole mito-genomes, and (iii) genome-wide ultraconserved elements. We use this phylogeny to assess systematic relationships and the biogeographical history of this avian family. Furthermore, we use morphological measurements to investigate the relationship between size and shape axes and upstream or back-colonization of this extensive island region from Asia. We show that several subspecies or groups of subspecies may warrant species rank and we find a continental example of two morphologically distinct species (O. mellianus/O. traillii) being genetically (mtDNA) very similar. Biogeographically, we confirm previous findings that members of the Oriolidae originated in Australo-Papua. Dispersal out of this area took place around 15 Mya to southeast Asia and Africa, and from Africa to the Palearctic followed by recolonization of the Indonesian and Philippine island region during the Plio-Pleistocene. Recolonisation of the Indonesian and Philippine islands coincided with an increase in body size, which may have facilitated the ability to co-exist with other congenerics.

AIM: The taxon cycle concept provides a geographically explicit and testable set of hypotheses for exploring the evolutionary processes underlying the distribution of species in space and time. Here, we test taxon cycle predictions within a large avian island radiation, the core Campephagidae and explicitly integrate the concepts of ‘supertramps’, ‘great speciators’ and relictualization. LOCATION: The Indo‐Pacific, Australia, Asia and Africa. TAXON: Corvoid passerine birds. METHODS: We constructed a new time‐calibrated molecular phylogeny of the core Campephagidae (cuckooshrikes, cicadabirds and trillers) using Bayesian phylogenetic methods. Ancestral range estimation methods and diversification rate analyses were used to explore the dispersal and diversification history of the group. We used an extensive dataset on wing morphology and range distributions to test for correlations between evolutionary age of species and dispersal capacity, diversification and distribution, while accounting for phylogenetic non‐independence. RESULTS: The core Campephagidae represents an ecologically homogeneous radiation distributed across the Indo‐Pacific, Australia, Southeast Asia and Africa. Its members represent a continuum of dispersal abilities; some species are widespread and undifferentiated (‘supertramps’) or show strong differentiation of local populations (‘great speciators’), and a few are endemic to single islands (relicts). We show that older species relative to younger species inhabit fewer and larger islands at higher elevations. The level of intraspecific variation measured as the number of subspecies also decreases with species age, and is highest in ‘great speciators’ with intermediate levels of dispersal abilities (as per hand‐wing index). MAIN CONCLUSIONS: Based on trait correlations with species age, we infer phases of range expansion and contraction over millions of years (taxon cycles), within a single monophyletic group of birds. These observations demonstrate reconciliation of the concepts of ‘supertramps’, ‘great speciators’ and relictual palaeoendemics within the temporal stages of the taxon cycle.

Species represent an important unit for the study of diversity, but may not always be delimited consistently across regions and clades. Many of these taxonomic inconsistencies are due to the variab...

A taxonomic classification that accurately captures evolutionary history is essential for conservation. Genomics provides powerful tools for delimiting species and understanding their evolutionary relationships. This allows for a more accurate and detailed view on conservation status compared with other, traditionally used, methods. However, from a practical and ethical perspective, gathering sufficient samples for endangered taxa may be difficult. Here, we use museum specimens to trace the evolutionary history and species boundaries in an Asian oriole clade. The endangered silver oriole has long been recognized as a distinct species based on its unique coloration, but a recent study suggested that it might be nested within the maroon oriole-species complex. To evaluate species designation, population connectivity, and the corresponding conservation implications, we assembled a de novo genome and used whole-genome resequencing of historical specimens. Our results show that the silver orioles form a monophyletic lineage within the maroon oriole complex and that maroon and silver forms continued to interbreed after initial divergence, but do not show signs of recent gene flow. Using a genome scan, we identified genes that may form the basis for color divergence and act as reproductive barriers. Taken together, our results confirm the species status of the silver oriole and highlight that taxonomic revision of the maroon forms is urgently needed. Our study demonstrates how genomics and Natural History Collections (NHC) can be utilized to shed light on the taxonomy and evolutionary history of natural populations and how such insights can directly benefit conservation practitioners when assessing wild populations.

Mountain regions contain extraordinary biodiversity. The environmental heterogeneity and glacial cycles often accelerate speciation and adaptation of montane species, but how these processes influence the genomic differentiation of these species is largely unknown. Using a novel chromosome-level genome and population genomic comparisons, we study allopatric divergence and selection in an iconic bird living in a tropical mountain region in New Guinea, Archbold's bowerbird ( Amblyornis papuensis ). Our results show that the two populations inhabiting the eastern and western Central Range became isolated ca 11 800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is probably associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between the eastern and western Central Range probably drive adaptive divergence between them.

We review Irestedt et al.’s (2017) neotypification of the senior species name superba Pennant, 1781 in the bird-of-paradise genus Lophorina in response to Elliott et al. (2020) who challenged the resultant shift in name from the small isolate in New Guinea’s Vogelkop to the widespread species in the island’s central cordillera. In nine male plumage traits which differentiate the two species, six of which had been identified as novel by Irestedt et al., we show that the only two figures of the perished male holotype of superba match the central cordillera species more closely than the Vogelkop. We find as well that not only was the trading of bird-of-paradise skins from the central cordillera to coastal ports in the Vogelkop feasible before European contact, but application of superba to the central cordillera species also promotes nomenclatural stability: the name has been used overwhelmingly at species rank for that widespread form throughout post-19th century media. Re-assessment of Irestedt et al.’s point-by-point justification of neotypification under Article 75.3 of the ICZN (1999) Code establishes, furthermore, that their case meets the requirements of every condition specified in the article; the neotypification is thus valid. Elliott et al.’s alternative to fix superba to the Vogelkop isolate by type locality restriction is not Code-compliant, nor is their evidence for interpreting J.R. Forster as the author of the name. In conclusion, we lay out the correct nomenclature for the taxa of Lophorina under the Code.

Bird-mediated seed dispersal is crucial for the regeneration and viability of ecosystems, often resulting in complex mutualistic species networks. Yet, how this mutualism drives the evolution of seed dispersing birds is still poorly understood. In the present study we combine whole genome re-sequencing analyses and morphometric data to assess the evolutionary processes that shaped the diversification of the Eurasian nutcracker (Nucifraga), a seed disperser known for its mutualism with pines (Pinus). Our results show that the divergence and phylogeographic patterns of nutcrackers resemble those of other non-mutualistic passerine birds and suggest that their early diversification was shaped by similar biogeographic and climatic processes. The limited variation in foraging traits indicates that local adaptation to pines likely played a minor role. Our study shows that close mutualistic relationships between bird and plant species might not necessarily act as a primary driver of evolution and diversification in resource-specialized birds.

The presence of two undescribed cisticola warblers in the marshes of the Kilombero floodplain in central Tanzania has been known since the 1980s and these putative new species have been illustrated in field guides on African birds, although with no formal name. Here we name both species, based on two museum specimens collected in 1961 and recently detected in a museum collection. We use these specimens to provide formal descriptions of each form and, using DNA sequence data extracted from these specimens, we place them in a broad phylogenetic framework for the genus Cisticola. The phylogenetic placement indicates that one of the new species is nested within a group of plain-backed duetting cisticolas and the other within the streak-backed marsh cisticolas. We use our own and public recordings to characterize the vocal repertoire of each of these new species and compare song characteristics with other members of their respective clades. Dating of nodes in the molecular phylogeny suggests that both cisticolas endemic to the Kilombero became isolated and diverged from their sister-species between 2.5 and 3.5 million years ago, long after the formation of the Eastern Arc Mountains and the Malawi Rift. We propose that both species should be classified as globally endangered, owing to immense anthropogenic pressures on the floodplain, as documented in several publications and by a recent Ramsar Advisory Mission.

Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat‐rich and GC‐rich regions (genomic “dark matter”) limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long‐read, linked‐read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC‐rich microchromosomes and the repeat‐rich W chromosome. Telomere‐to‐telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.

We produced a high-quality de novo genome assembly of the red-legged partridge A. rufa , the first reference genome of its genus, by utilising novel 10× Chromium technology. The estimated genome size was 1.19 Gb with an overall genome heterozygosity of 0.0022; no runs of homozygosity were observed. In total, 21,589 protein coding genes were identified and assigned to 16,772 orthologs. Of these, 201 emerged as unique to Alectoris and were enriched for positive regulation of epithelial cell migration, viral genome integration and maturation. Using PSMC analysis, we inferred a major demographic decline commencing ~140,000 years ago, consistent with forest expansion and reduction of open habitats during the Eemian interglacial. Present-day populations exhibit the historically lowest genetic diversity . Besides implications for management and conservation, this genome also promises key insights into the physiology of these birds with a view to improving poultry husbandry practices.

Archipelagoes serve as important ‘natural laboratories’ which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a ‘great speciator’, comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major center of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.

The female-specific W chromosomes of most Neognathae birds are highly degenerated and gene-poor. Previous studies have demonstrated that the gene repertoires of the Neognathae bird W chromosomes, despite being in small numbers, are conserved across bird species, likely due to purifying selection maintaining the regulatory and dosage-sensitive genes. Here we report the discovery of DNA-based sequence duplications from the Z to the W chromosome in birds-of-paradise (Paradisaeidae, Passeriformes), through sequence transposition. The original transposition involved nine genes, but only two of them (ANXA1 and ALDH1A1) survived on the W chromosomes. Both ANXA1 and ALDH1A1 are predicted to be dosage-sensitive, and the expression of ANXA1 is restricted to ovaries in all the investigated birds. These analyses suggest the newly transposed gene onto the W chromosomes can be favored for their role in restoring dosage imbalance or through female-specific selection. After examining seven additional songbird genomes, we further identified five other transposed genes on the W chromosomes of Darwin&rsquo, s finches and one in the great tit, expanding the observation of the Z-to-W transpositions to a larger range of bird species, but not all transposed genes exhibit dosage-sensitivity or ovary-biased expression We demonstrate a new mechanism by which the highly degenerated W chromosomes of songbirds can acquire genes from the homologous Z chromosomes, but further functional investigations are needed to validate the evolutionary forces underlying the transpositions.

It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.

The babblers are a diverse group of passerine birds comprising 452 species. The group was long regarded as a “scrap basket” in taxonomic classification schemes. Although several studies have assessed the phylogenetic relationships for subsets of babblers during the past two decades, a comprehensive phylogeny of this group has been lacking. In this study, we used five mitochondrial and seven nuclear loci to generate a dated phylogeny for babblers. This phylogeny includes 402 species (ca. 89% of the overall clade) from 75 genera (97%) and all five currently recognized families, providing a robust basis for taxonomic revision. Our phylogeny supports seven major clades and reveals several non-monophyletic genera. Divergence time estimates indicate that the seven major clades diverged around the same time (18–20 million years ago, Ma) in the early Miocene. We use the phylogeny in a consistent way to propose a new taxonomy, with seven families and 64 genera of babblers, and a new linear sequence of names.

A new classification is proposed for the subfamily Fluvicolinae in the New World Flycatchers (Tyrannidae), based on the results of a previously published phylogeny including more than 90% of the species. In this classification we propose one new family level name (Ochthoecini) and one new generic name (Scotomyias). We also resurrect three genera (Heteroxolmis, Pyrope and Nengetus) and subsume five (Tumbezia, Lathrotriccus, Polioxolmis, Neoxolmis and Myiotheretes) into other genera to align the classification with the current understanding of phylogenetic relationships in Fluvicolinae.

The widespread Old World avian family Locustellidae ('grassbirds and allies') comprises 62 extant species in 11 genera. In the present study, we used one mitochondrial and, for most species, four nuclear loci to infer the phylogeny of this family. We analysed 59 species, including the five previously unsampled genera plus two genera that had not before been analysed in a densely sampled dataset. This study revealed extensive disagreement with current taxonomy; the genera Bradypterus, Locustella, Megalurus, Megalurulus and Schoenicola were all found to be non-monophyletic. Non-monophyly was particularly pronounced for Megalurus, which was widely scattered across the tree. Three of the five monotypic genera (Amphilais, Buettikoferella and Malia) were nested within other genera; one monotypic genus (Chaetornis) formed a clade with one of the two species of Schoenicola; whereas the position of the fifth monotypic genus (Elaphrornis) was unresolved. Robsonius was confirmed as sister to the other genera. We propose a phylogenetically informed revision of genus-level taxonomy, including one new generic name. Finally, we highlight several non-monophyletic species complexes and deep intra-species divergences that point to conflict in taxonomy and suggest an underestimation of current species diversity in this group.