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Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions 1 – 3 . Here we address these issues by analysing the genomes of 363 bird species 4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous–Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies. Using intergenic regions and coalescent methods to analyse the genomes of 363 bird species, the authors present a well-supported tree confirming that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary.

The fish order Syngnathiformes has been referred to as a collection of misfit fishes, comprising commercially important fish such as red mullets as well as the highly diverse seahorses, pipefishes, and seadragons—the well-known family Syngnathidae, with their unique adaptations including male pregnancy. Another ornate member of this order is the species mandarinfish. No less than two types of chromatophores have been discovered in the spectacularly colored mandarinfish: the cyanophore (producing blue color) and the dichromatic cyano-erythrophore (producing blue and red). The phylogenetic position of mandarinfish in Syngnathiformes, and their promise of additional genetic discoveries beyond the chromatophores, made mandarinfish an appealing target for whole-genome sequencing. We used linked sequences to create synthetic long reads, producing a highly contiguous genome assembly for the mandarinfish. The genome assembly comprises 483 Mbp (longest scaffold 29 Mbp), has an N50 of 12 Mbp, and an L50 of 14 scaffolds. The assembly completeness is also high, with 92.6% complete, 4.4% fragmented, and 2.9% missing out of 4584 BUSCO genes found in ray-finned fishes. Outside the family Syngnathidae, the mandarinfish represents one of the most contiguous syngnathiform genome assemblies to date. The mandarinfish genomic resource will likely serve as a high-quality outgroup to syngnathid fish, and furthermore for research on the genomic underpinnings of the evolution of novel pigmentation.

Long-read sequencing offers a great improvement in the assembly of complex genomic regions, such as the major histocompatibility complex (MHC) region, which can contain both tandemly duplicated MHC genes (paralogs) and high repeat content. The MHC genes have expanded in passerine birds, resulting in numerous MHC paralogs, with relatively high sequence similarity, making the assembly of the MHC region challenging even with long-read sequencing. In addition, MHC genes show rather high sequence divergence between alleles, making diploid-aware assemblers incorrectly classify haplotypes from the same locus as sequences originating from different genomic regions. Consequently, the number of MHC paralogs can easily be over- or underestimated in long-read assemblies. We therefore set out to verify the MHC diversity in an original and a haplotype-purged long-read assembly of one great reed warbler Acrocephalus arundinaceus individual (the focal individual) by using Illumina MiSeq amplicon sequencing. Single exons, representing MHC class I (MHC-I) and class IIB (MHC-IIB) alleles, were sequenced in the focal individual and mapped to the annotated MHC alleles in the original long-read genome assembly. Eighty-four percent of the annotated MHC-I alleles in the original long-read genome assembly were detected using 55% of the amplicon alleles and likewise, 78% of the annotated MHC-IIB alleles were detected using 61% of the amplicon alleles, indicating an incomplete annotation of MHC genes. In the haploid genome assembly, each MHC-IIB gene should be represented by one allele. The parental origin of the MHC-IIB amplicon alleles in the focal individual was determined by sequencing MHC-IIB in its parents. Two of five larger scaffolds, containing 6–19 MHC-IIB paralogs, had a maternal and paternal origin, respectively, as well as a high nucleotide similarity, which suggests that these scaffolds had been incorrectly assigned as belonging to different loci in the genome rather than as alternate haplotypes of the same locus. Therefore, the number of MHC-IIB paralogs was overestimated in the haploid genome assembly. Based on our findings we propose amplicon sequencing as a suitable complement to long-read sequencing for independent validation of the number of paralogs in general and for haplotype inference in multigene families in particular.

The biotas of the Galápagos Islands are one of the best studied island systems and have provided a broad model for insular species’ origins and evolution. Nevertheless, some locally endemic taxa, such as the Galápagos Rail Laterallus spilonota, remain poorly characterized. Owing to its elusive behavior, cryptic plumage, and restricted distribution, the Galápagos Rail is one of the least studied endemic vertebrates of the Galapagos Islands. To date, there is no genetic data for this species, leaving its origins, relationships to other taxa, and levels of genetic diversity uncharacterized. This lack of information is critical given the adverse fate of island rail species around the world in the recent past. Here, we examine the genetics of Galápagos Rails using a combination of mitogenome de novo assembly with multilocus nuclear and mitochondrial sequencing from both modern and historical samples. We show that the Galápagos Rail is part of the “American black rail clade”, sister to the Black Rail L. jamaicensis, with a colonization of Galápagos dated to 1.2 million years ago. A separate analysis of one nuclear and two mitochondrial markers in the larger population samples demonstrates a shallow population structure across the islands, possibly due to elevated island connectivity. Additionally, birds from the island Pinta possessed the lowest levels of genetic diversity, possibly reflecting past population bottlenecks associated with overgrazing of their habitat by invasive goats. The modern and historical data presented here highlight the low genetic diversity in this endemic rail species and provide useful information to guide conservation efforts.

We studied long-term trends and the yearly variation in mean spring passage time in 36 passerine bird species trapped at Ottenby Bird Observatory in south-eastern Sweden. Between the years 1952-2002, data were available for 22-45 years depending on species. Most long-distance migrant species passed progressively earlier over the study period (range: 2.5 days earlier to 0.7 days later per 10 years, with an average of 0.9 days earlier per 10 years). The annual variation in timing of migration in most species, regardless of migration distance, correlated negatively with the winter index of the North Atlantic Oscillation (NAO), a large-scale climate phenomenon influencing the climate in the North Atlantic region. Birds passed earlier after mild and humid winters, corresponding to the high phase of the NAO. This corroborates the pattern found at a nearby migration site with a comparable dataset (Helgoland, 600 km WSW of Ottenby). However, short/medium-distance migrant species at Ottenby, in contrast to the situation at Helgoland, have shown no general trend of earlier passage in recent years. This was probably a consequence of the shorter study period at Ottenby, which included only the last 22-32 years (41 years at Helgoland), when the NAO showed no significant trend. At the species-specific level, the long-term trends in passage time were similar at the two sites, and there was some congruence to the extent that a given species was affected by NAO. Long-distance migrants wintering south and south-east of the breeding grounds showed some of the strongest changes in long-term trends (passing progressively earlier) at Ottenby, and for some of these species passage time varied negatively with NAO. Obviously, and contrary to previous suggestions, variations in NAO also influence birds migrating through eastern Europe, although the direct or indirect mechanisms through which this is achieved are unknown.

Larks (Alaudidae) constitute one of the avian families best adapted to xeric environments, having colonized a wide suite of open habitats including deserts. Although their highest diversity is in Africa, larks occur on all nonpolar continents. We tested whether larks exhibit exceptional and/or correlated shifts in the tempos of speciation and ecological trait diversification in the face of open ecological space. We employed a near-complete phylogeny and a morphological dataset including several recently recognized species. We found homogeneity in diversification dynamics across the family and evidence for a diversity-dependent slowdown in cladogenesis, which indicates that Alaudidae may approach their ‘ecological limit’. We did not observe an early burst in phenotypic diversification, as would be expected in a ‘classic’ adaptive radiation. Our findings suggest that the morphology of larks shows a high level of evolutionary conservatism and overall lack of ecomorphological convergence: ecological variables (diet and habitat)—which by contrast display a higher lability—explain little of shape/size variation except beak shape. Both adaptation to aridity and dietary transitions have evolved independently in multiple lineages across subfamilies. This study supports the idea that continental radiations in open habitats may reach an equilibrium faster than those in tropical forests, due to differences in ecological opportunities.

Neo-sex chromosomes often originate from sex chromosome–autosome fusions and constitute an important basis for the study of gene degeneration and expression in a sex chromosomal context. Neo-sex chromosomes are known from many animal and plant lineages, but have not been reported in birds, a group in which genome organization seems particularly stable. Following indications of sex linkage and unexpected sex-biased gene expression in warblers (Sylvioidea; Passeriformes), we have conducted an extensive marker analysis targeting 31 orthologues of loci on zebra finch chromosome 4a in five species, representative of independent branches of Passerida. We identified a region of sex linkage covering approximately the first half (10 Mb) of chromosome 4a, and associated to both Z and W chromosomes, in three Sylvioidea passerine species. Linkage analysis in an extended pedigree of one species additionally confirmed the association between this part of chromosome 4a and the Z chromosome. Markers located between 10 and 21 Mb of chromosome 4a showed no signs of sex linkage, suggesting that only half of the chromosome was involved in this transition. No sex linkage was observed in non-Sylvioidea passerines, indicating that the neo-sex chromosome arose at the base of the Sylvioidea branch of the avian phylogeny, at 47.4–37.6 millions years ago (MYA), substantially later than the ancestral sex chromosomes (150 MYA). We hypothesize that the gene content of chromosome 4a might be relevant in its transition to a sex chromosome, based on the presence of genes (for example, the androgen receptor ) that could offer a selective advantage when associated to Z-linked sex determination loci.

Several bird species have advanced the timing of their spring migration in response to recent climate change. European short-distance migrants, wintering in temperate areas, have been assumed to be more affected by change in the European climate than long-distance migrants wintering in the tropics. However, we show that long-distance migrants have advanced their spring arrival in Scandinavia more than short-distance migrants. By analyzing a long-term data set from southern Italy, we show that long-distance migrants also pass through the Mediterranean region earlier. We argue that this may reflect a climate-driven evolutionary change in the timing of spring migration.

Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.

Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.