The DNA-binding protein PRDM9 has a critical role in specifying meiotic recombination hotspots in mice and apes, but appears to be absent from other vertebrate species, including birds. To study the evolution and determinants of recombination in species lacking PRDM9, we inferred fine-scale genetic maps from population resequencing data for two bird species, the zebra finch Taeniopygia guttata and the long-tailed finch Poephila acuticauda. We find that both species have hotspots, which are enriched near functional genomic elements. Unlike in mice and apes, the two species share most hotspots, with conservation seemingly extending over tens of millions of years. These observations suggest that in the absence of PRDM9, recombination targets functional features that both enable access to the genome and constrain its evolution.

Speciation generally involves a three-step process--range expansion, range fragmentation and the development of reproductive isolation between spatially separated populations. Speciation relies on cycling through these three steps and each may limit the rate at which new species form. We estimate phylogenetic relationships among all Himalayan songbirds to ask whether the development of reproductive isolation and ecological competition, both factors that limit range expansions, set an ultimate limit on speciation. Based on a phylogeny for all 358 species distributed along the eastern elevational gradient, here we show that body size and shape differences evolved early in the radiation, with the elevational band occupied by a species evolving later. These results are consistent with competition for niche space limiting species accumulation. Even the elevation dimension seems to be approaching ecological saturation, because the closest relatives both inside the assemblage and elsewhere in the Himalayas are on average separated by more than five million years, which is longer than it generally takes for reproductive isolation to be completed; also, elevational distributions are well explained by resource availability, notably the abundance of arthropods, and not by differences in diversification rates in different elevational zones. Our results imply that speciation rate is ultimately set by niche filling (that is, ecological competition for resources), rather than by the rate of acquisition of reproductive isolation.

The DNA-binding protein PRDM9 has a critical role in specifying meiotic recombination hotspots in mice and apes, but appears to be absent from other vertebrate species, including birds. To study the evolution and determinants of recombination in species lacking PRDM9, we inferred fine-scale genetic maps from population resequencing data for two bird species, the zebra finch Taeniopygia guttata and the long-tailed finch Poephila acuticauda. We find that both species have hotspots, which are enriched near functional genomic elements. Unlike in mice and apes, the two species share most hotspots, with conservation seemingly extending over tens of millions of years. These observations suggest that in the absence of PRDM9, recombination targets functional features that both enable access to the genome and constrain its evolution.Meiotic recombination is a ubiquitous and fundamental genetic process that shapes variation in populations, yet our understanding of its underlying mechanisms is based on a handful of model organisms, scattered throughout the tree of life. One pattern shared among most sexually reproducing species is that meiotic recombination tends to occur in short segments of 100s to 1000s of base pairs, termed "recombination hotspots" (1). In apes and mice, the location of hotspots is largely determined by PRDM9, a zinc-finger protein that binds to specific motifs in the genome during meiotic prophase and generates H3K4me3 marks, eventually leading to double-strand breaks (DSBs) and both crossover and non-crossover + to whom correspondence should be addressed. * co-first authors [2][3][4][5]. In mammals, the zinc-finger domain of PRDM9 evolves quickly, with evidence of positive selection on residues in contact with DNA (2, 6), and as a result, there is rapid turnover of hotspot locations across species, subspecies, and populations (7-10). Europe PMC Funders GroupAlthough PRDM9 plays a pivotal role in controlling recombination localization in mice and apes, many species lacking PRDM9 nonetheless have hotspots (6). An artificial example is provided by mice knockouts for PRDM9. Despite being sterile, they make similar numbers of DSBs as wild-type mice, and their recombination hotspots appear to default to residual H3K4me3 mark locations, notably at promoters (10). A natural but puzzling example is provided by canids, which carry premature stop codons in PRDM9 yet are able to recombine and remain fertile (11,12). Like in mouse PRDM9 knockouts, in dogs and in other species without PRDM9 such as the yeast Saccharomyces cerevisae and the plant Arabidopsis thaliana, hotspots tend to occur at promoters or other regions with promoter-like features (11, 13,14). In yet other taxa without PRDM9, including Drosophila species (15), honeybees (16), and Caenorhabditis elegans (17), short, intense recombination hotspots appear to be absent altogether.To further explore how the absence of PRDM9 shapes the fine-scale recombination landscape and impacts its evolution, we turn to birds, because an analysis of the chick...

The primary explanation for the latitudinal gradient in species diversity must lie in why species fail to expand ranges across different climatic regimes. Theories of species gradients based in niche conservatism assume that whole clades are confined to particular climatic regimes because the traits they share limit adaptation to alternative regimes. We assess these theories in an analysis of the twofold decline in bird species richness along the Himalayas from the southeast to the northwest. The presence of fewer species in the northwest is entirely due to a steep decline in the number of forest species; species occupying more open habitats show a reversed gradient. Forest species numbers are exceptionally high at midelevations (1,000-2,000 m) in the southeast, which experience a warm, wet climate not present in the northwest, and a high proportion of these species fail to expand their range to the northwest. Despite this, many species do have populations or close relatives that straddle different climatic regimes along altitudinal gradients and/or the regional gradient, implying that climate-based niche conservatism per se does not strongly constrain range limits. We argue that climate- and competition-mediated resource distributions are important in setting northerly range limits and show that one measure of forest resources (foliage density) is lower in the northwest.

Across hybrid zones, the sex chromosomes are often more strongly differentiated than the autosomes. This is regularly attributed to the greater frequency of reproductive incompatibilities accumulating on sex chromosomes and their exposure in the heterogametic sex. Working within an avian hybrid zone, we explore the possibility that chromosome inversions differentially accumulate on the Z chromosome compared to the autosomes and thereby contribute to Z chromosome differentiation. We analyse the northern Australian hybrid zone between two subspecies of the long-tailed finch (Poephila acuticauda), first described based on differences in bill colour, using reduced-representation genomic sequencing for 293 individuals over a 1,530-km transect. Autosomal differentiation between subspecies is minimal. In contrast, 75% of the Z chromosome is highly differentiated and shows a steep genomic cline, which is displaced 350 km to the west of the cline in bill colour. Differentiation is associated with two or more putative chromosomal inversions, each predominating in one subspecies. If inversions reduce recombination between hybrid incompatibilities, they are selectively favoured and should therefore accumulate in hybrid zones. We argue that this predisposes inversions to differentially accumulate on the Z chromosome. One genomic region affecting bill colour is on the Z, but the main candidates are on chromosome 8. This and the displacement of the bill colour and Z chromosome cline centres suggest that bill colour has not strongly contributed to inversion accumulation. Based on cline width, however, the Z chromosome and bill colour both contribute to reproductive isolation established between this pair of subspecies.

Chromosomal inversions evolve frequently but the reasons for this remain unclear. We used cytological descriptions of 411 species of passerine birds to identify large pericentric inversion differences between species, based on the position of the centromere. Within 81 small clades comprising 284 of the species, we found 319 differences on the 9 largest autosomes combined, 56 on the Z chromosome, and 55 on the W chromosome. We also identified inversions present within 32 species. Using a new fossil-calibrated phylogeny, we examined the phylogenetic, demographic and genomic context in which these inversions have evolved. The number of inversion differences between closely related species is consistently predicted by whether the ranges of species overlap, even when time is controlled for as far as is possible. Fixation rates vary across the autosomes, but inversions are more likely to be fixed on the Z chromosome than the average autosome. Variable mutagenic input alone (estimated by chromosome size, map length, GC content or repeat density) cannot explain the differences between chromosomes in the number of inversions fixed. Together, these results support a model in which inversions increase because of their effects on recombination suppression in the face of hybridization. Other factors associated with hybridization may also contribute, including the possibility that inversions contain incompatibility alleles, making taxa less likely to collapse following secondary contact.

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Within regions, differences in the number of species among clades must be explained by clade age, net diversification rate, or immigration. We examine these alternatives by assessing historical causes of the low diversity of a bird parvorder in the Himalayas (the core Corvoidea, 57 species present), relative to its more species rich sister clade (the Passerida, ∼400 species present), which together comprise the oscine passerines within this region. The core Corvoidea contain ecologically diverse species spanning a large range of body sizes and elevations. Despite this diversity, on the basis of ecological, morphological, and phylogenetic information, we infer that the best explanation for the low number of species within the Himalayan core Corvoidea is one in which ecology limits diversification and/or immigration. Within the core Corvoidea, body size is correlated with elevation: large species are found at high elevations, and small species at lower elevations. This contrasts with the presence of many small‐bodied species spanning all elevations in the Passerida and many large bodied species at low elevations in the other orders of birds (the nonpasserines). Cladogenetic events leading to ecological differences between species in body size and shape mostly occurred millions of years ago, and the rate of evolutionary change has declined toward the present. Elevational distributions have been evolutionarily more labile, but are also associated with ancient cladogenetic events. We suggest the core Corvoidea occupy a restricted volume of ecological space in competition with other bird species, and this has limited in situ diversification and/or immigration.