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.