Generation lengths of the world's birds and their implications for extinction risk

Frequent Hybridisation Between Parapatric Lekking Bird-of-Paradise Species

Hybridisation is known to occur between a wide range of taxa, including species for which strong sexual selection has led to markedly different sexual phenotypes and lek-mating behaviours. To what extent occasional hybridisation can overcome the reproductive barriers in such systems and, for example, lead to the establishment of hybrid zones is poorly known. In this study, we address this question by focusing on one of the most well-known avian radiations in which sexual selection has resulted in an extraordinary assemblage of phenotypic diversity and lek-mating behaviours: the birds-of-paradise (Paradisaeidae). We quantify the genome-wide distribution of introgression and find multiple signals of recent and historical gene flow between and within two genera of birds-of-paradise, Astrapia and Paradigalla. In addition, we present the first empirical genomic indication of a putative hybrid zone between two lekking bird-of-paradise species that differ substantially in their sexually selected traits and behaviours. Our findings are consistent with the idea that behavioural and phenotypic traits may constitute weaker pre- and post-zygotic barriers to gene flow than generally thought in lek-mating species.

Seasonally migratory songbirds have different historic population size characteristics than resident relatives

Modern genomic methods enable estimation of a lineage's long-term effective population sizes back to its origins. This ability allows unprecedented opportunities to determine how the adoption of a major life-history trait affects lineages' populations relative to those without the trait. We used this novel approach to study the population effects of the life-history trait of seasonal migration across evolutionary time. Seasonal migration is a common life-history strategy, but its effects on long-term population sizes relative to lineages that don't migrate are largely unknown. Using whole-genome data, we estimated effective population sizes over millions of years in closely related seasonally migratory and resident lineages in a group of songbirds. Our main predictions were borne out: Seasonal migration is associated with larger effective population sizes (Ne), greater long-term variation in Ne, and a greater degree of initial population growth than among resident lineages. Initial growth periods were remarkably long (0.63-4.29 Myr), paralleling the expansion and adaptation phases of taxon cycles, a framework of lineage expansion and eventual contraction over time encompassing biogeography and evolutionary ecology. Heterogeneity among lineages is noteworthy, despite geographic proximity (including overlap) and close relatedness. Seasonal migration imbues these lineages with fundamentally different population size attributes through evolutionary time compared to closely related resident lineages.

Different traits shape winners and losers in urban bird assemblages across seasons

Urbanisation is a major driver of global biodiversity decline, profoundly affecting animal communities. While most studies on bird communities have primarily focused on the breeding season, we aimed to identify species responses and their associated traits by adopting a stratified design and using a multi-season approach considering a gradient from highly urbanised city centres to the urban-rural fringe across six Italian cities. We found that bird assemblages exhibited different responses to urbanisation according to season. Winners (i.e. species positively affected by urbanisation) were characterised by traits such as colonial nesting, high productivity and longevity. In winter, these species displayed generalist foraging strategies and solitary behaviour. Losers (i.e. species negatively affected by urbanisation) tended to be insectivorous, ground-nesting and short-distance migratory species. Interestingly, intra-specific variations emerged, with wintering populations of some species exploiting highly urbanised areas despite not breeding there. Urban adapters, although not strictly winners, displayed resilience by navigating a range of urban conditions, effectively exploiting intermediate levels of urbanisation. This study provides novel insights into the complex ecological dynamics occurring within the urban matrix in different seasons. Our findings emphasise the importance of adopting a multi-season approach in research and urban planning to better understand species responses and develop more effective, sustainable strategies for biodiversity conservation in urban environments.

Adaptations to marine environments and the evolution of slow-paced life histories in endotherms

All organisms face a certain risk of dying before reproducing, putting strong pressure on individuals to reproduce as early as possible. Despite this, some organisms delay maturity, defer reproduction, and age slowly. The evolution of such slow-paced life is classically attributed to allometric effects and reduced extrinsic mortality, but might also result from the invasion of challenging environments requiring adaptations that boost adult survival yet impose substantial energetic and developmental costs. Here, we reveal that the invasion of marine environments by endotherms may have triggered adaptive shifts towards slow life histories, particularly in pelagic lineages. Such life history convergences may have been facilitated by the slow-paced nature of their non-marine ancestors, and were associated with adaptations for enhanced energy acquisition and storage, enabling a long reproductive lifespan at the expense of extended development. Ancestral traits and lifestyle changes might thus have been important in shaping the evolution of slow life histories.

Plio-Pleistocene Climatic Fluctuations and Divergence With Gene Flow Drive Continent-Wide Diversification in an African Bird

Diversification mechanisms in Sub-Saharan Africa have long attracted research interest, with varying support for either allopatric or parapatric models of speciation. However, studies have seldom been performed across the entire continent, a scale which could elucidate the relative importance of allopatric and parapatric models of divergence. To shed light on continental-scale patterns of African biogeography and diversification, we investigated the historical demography of a bird with a continent-wide distribution in Sub-Saharan Africa, the Yellow-Rumped Tinkerbird, Pogoniulus bilineatus. We sampled populations from across the continent and, using genomic data, assessed genetic diversity, structure, and differentiation, reconstructed the phylogeny, and performed alternative demographic model selection between neighbouring clade pairs. We uncovered substantial genetic structure and differentiation patterns which corroborated the phylogenetic topology. Structure was chiefly influenced by the arid corridor, a postulated biogeographical barrier in Sub-Saharan Africa. Moreover, peak genetic diversities coincided with postulated refugial areas while demographic reconstructions between genetic lineages supported allopatric models consistent with the Pleistocene Forest Refuge hypothesis. However, within lineages, divergence with gene flow was supported. Continent-wide patterns of diversification involve an integration of both allopatric and parapatric mechanisms, with a role for both periods of divergence in isolation and across ecological gradients. Furthermore, our study emphasises the importance of the arid corridor as a primary biogeographical feature across which diversification occurs, yet one that has hitherto received scant attention regarding its importance in avian diversification in Sub-Saharan Africa.

Mixed Outcomes in Recombination Rates After Domestication: Revisiting Theory and Data

The process of domestication has altered many phenotypes. Selection on these phenotypes has long been hypothesised to indirectly select for increases in the genome-wide recombination rate. This hypothesis is potentially consistent with theory on the evolution of the recombination rate, but empirical support has been unclear. We review relevant theory, lab-based experiments, and data comparing recombination rates in wild progenitors and their domesticated counterparts. We utilise population sequencing data and a deep learning method to infer genome-wide recombination rates for new comparisons of chicken/red junglefowl, sheep/mouflon, and goat/bezoar. We find evidence of increased recombination in domesticated goats compared to bezoars but more mixed results in chicken and generally decreased recombination in domesticated sheep compared to mouflon. Our results add to a growing body of literature in plants and animals that finds no consistent evidence of an increase in genome-wide recombination with domestication.

Ecophysical constraints on avian adaptation and diversification

The evolution of morphological diversity is ultimately governed by physical laws and ecological contexts, which together impose a range of ecophysical constraints. Substantial progress has been made in identifying how these constraints shape the form and function of producers (plants), but similar knowledge is lacking for consumers, in part because the requisite data have not been available at sufficient scale for animals. Using morphometric measurements for all birds, we demonstrate that observed variation is restricted-both for beak shape and body shape-to triangular regions of morphospace with clearly defined boundaries and vertices (corners). By combining morphometric data with information on ecological and behavioral functions, we provide evidence that the extent of avian morphospace reflects a trade-off between three fundamental physical tasks for feeding (crush, engulf, and reach) that characterize resource acquisition and processing by the beak and three physical tasks (fly, swim, and walk) that characterize avian lifestyles or locomotion. Phylogenetic analyses suggest that trajectories of morphological evolution trend toward the vertices, with lineages evolving from a core of functional generalists toward more specialized physical tasks. We further propose that expansion beyond the current boundaries of morphospace is constrained by the shorter evolutionary lifespan of functional specialists, although patterns of speciation rate and current extinction risk provide only weak support for this hypothesis. Overall, we show that the structure of avian morphospace follows relatively simple rules defined by ecophysical constraints and trade-offs, shedding light on the processes shaping modern animal diversity and responses to environmental change.

Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction

Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.

Association of poultry vaccination with interspecies transmission and molecular evolution of H5 subtype avian influenza virus

The effectiveness of poultry vaccination in preventing the transmission of highly pathogenic avian influenza viruses (AIVs) has been debated, and its impact on wild birds remains uncertain. Here, we reconstruct the movements of H5 subtype AIV lineages among vaccinated poultry, unvaccinated poultry, and wild birds, worldwide, from 1996 to 2023. We find that there is a time lag in viral transmission among different host populations and that movements from wild birds to unvaccinated poultry were more frequent than those from wild birds to vaccinated poultry. Furthermore, our findings suggest that the HA (hemagglutinin) gene of the AIV lineage that circulated predominately in Chinese poultry experienced greater nonsynonymous divergence and adaptive fixation than other lineages. Our results indicate that the epidemiological, ecological, and evolutionary consequences of widespread AIV vaccination in poultry may be linked in complex ways and that much work is needed to better understand how such interventions may affect AIV transmission to, within, and from wild birds.

North American avian species that migrate in flocks show greater long-term non-breeding range shift rates

BACKGROUND

Many species are exhibiting range shifts associated with anthropogenic change. For migratory species, colonisation of new areas can require novel migratory programmes that facilitate navigation between independently-shifting seasonal ranges. Therefore, in some cases range-shifts may be limited by the capacity for novel migratory programmes to be transferred between generations, which can be genetically and socially mediated.

METHODS

Here we used 50 years of North American Breeding Bird Survey and Audubon Christmas Bird Count data to test the prediction that breeding and/or non-breeding range-shifts are more prevalent among flocking migrants, which possess a capacity for rapid social transmission of novel migration routes.

RESULTS

Across 122 North American bird species, social migration was a significant positive predictor for the magnitude of non-breeding centre of abundance (COA) shift within our study region (conterminous United States and Southern Canada). Across a subset of 81 species where age-structured flocking was determined, migrating in mixed-age flocks produced the greatest shifts and solo migrants the lowest. Flocking was not a significant predictor of breeding COA shifts, which were better explained by absolute population trends and migration distance.

CONCLUSIONS

Our results suggest that social grouping may play an important role in facilitating non-breeding distributional responses to climate change in migratory species. We highlight the need to gain a better understanding of migratory programme inheritance, and how this influences spatiotemporal population dynamics under environmental change.

Scaling up to understand disease risk: distinct roles of host functional traits in shaping infection risk of avian malaria across different scales

Understanding the impacts of diversity on pathogen transmission is essential for public health and biological conservation. However, how the outcome and mechanisms of the diversity-disease relationship vary across biological scales in natural systems remains elusive. In addition, although the role of host functional traits has long been established in disease ecology, its integration into the diversity-disease relationship largely falls behind. By examining avian haemosporidians of 1101 birds from 86 species, we investigated how host functional traits and diversity may shape infection risk across individual and community levels. We found that host traits affect individual-level infection risk but fail to scale up the effect to the community level when testing community-weighted means. Moreover, functional divergence reduced community-level infection risk, indicating the dilution effect of functional diversity. Host richness also showed dilution effect at the community level, but not individual level for one parasite genus, suggesting that the dilution mechanism results from the aggregation of non-competent hosts into richer communities. These results demonstrate that the outcome and mechanism of diversity-disease relationship depend on biological scale, and aggregating observations may cause biased evidence and misattributed mechanisms. Overall, our work suppports the integration of trait-based ecology to further understand the diversity-disease relationship across biological scales.

Sperm as a speciation phenotype in promiscuous songbirds

Sperm morphology varies considerably among species. Sperm traits may contribute to speciation if they diverge fast in allopatry and cause conspecific sperm precedence upon secondary contact. However, their role in driving prezygotic isolation has been poorly investigated. Here we test the hypothesis that, early in the speciation process, female promiscuity promotes a reduction in overlap in sperm length distributions among songbird populations. We assembled a data set of 20 pairs of populations with known sperm length distributions, a published estimate of divergence time, and an index of female promiscuity derived from extrapair paternity rates or relative testis size. We found that sperm length distributions diverged more rapidly in more promiscuous species. Faster divergence between sperm length distributions was caused by the lower variance in the trait in more promiscuous species, and not by faster divergence of the mean sperm lengths. The reduced variance is presumably due to stronger stabilizing selection on sperm length mediated by sperm competition. If divergent sperm length optima in allopatry causes conspecific sperm precedence in sympatry, which remains to be shown empirically, female promiscuity may promote prezygotic isolation, and rapid speciation in songbirds.

Spread of yellow-bill-color alleles favored by selection in the long-tailed finch hybrid system

Carotenoid pigments produce the yellow and red colors of birds and other vertebrates. Despite their importance in social signaling and sexual selection, our understanding of how carotenoid ornamentation evolves in nature remains limited. Here, we examine the long-tailed finch Poephila acuticauda, an Australian songbird with a yellow-billed western subspecies acuticauda and a red-billed eastern subspecies hecki, which hybridize where their ranges overlap. We found that yellow bills can be explained by the loss of C(4)-oxidation, thus preventing yellow dietary carotenoids from being converted to red. Combining linked-read genomic sequencing and reflectance spectrophotometry measurements of bill color collected from wild-sampled finches and laboratory crosses, we identify four loci that together explain 53% of variance in this trait. The two loci of largest effect contain the genes CYP2J19, an essential enzyme for producing red carotenoids, and TTC39B, an enhancer of carotenoid metabolism. A paucity of protein-coding changes and an enrichment of associated upstream variants suggest that the loss of C(4)-oxidation results from cis-regulatory evolution. Evolutionary genealogy reconstruction indicates that the red-billed phenotype is ancestral and that yellow alleles at CYP2J19 and TTC39B first arose and fixed in acuticauda approximately 100 kya. Yellow alleles subsequently introgressed into hecki less than 5 kya. Across all color loci, acuticauda-derived variants show evidence of selective sweeps, implying that yellow bill coloration has been favored by natural selection. Our study illustrates how evolutionary transitions between yellow and red coloration can be achieved by successive selective events acting on regulatory changes at a few interacting genes.

Biological traits and biome features mediate responses of terrestrial bird demography to droughts

Changing drought regimes are a rising threat to biodiversity, yet their impacts on wildlife vary greatly. Acknowledging the factors associated with these consequences brings novel insights into species vulnerability resulting from extreme climatic events and facilitates effective mitigation of climate change risks. Based on 319 observations from 29 peer-reviewed studies on birds-a well-monitored taxonomic group-we extract the responses of demographic metrics to droughts for 204 species across eight terrestrial biomes to examine the consequences of droughts. According to relevant studies, we chose the factors potentially moderating bird demography under droughts and compiled the data for these factors from published datasets. A meta-analysis is performed to determine the drought effect on bird demography at individual and population levels, accounting for the influence of species traits, timescale and severity of droughts, as well as biome features. The results show that droughts have an overall negative effect on bird demography, and the effect is mediated by different factors at each level. For individuals exposed to droughts, declines in demographic rates are found to be related to narrower extents of occurrence of species, and a significant overall reduction in demographic rates is identified for individuals residing in deserts and xeric shrublands. At the population level, declines in abundance or reproductive performance are generally identified for invertivores, frugivores, nectarivores and omnivores; short-lived species with small clutch sizes also show greater susceptibilities under the impacts of droughts. Our findings additionally suggest that the demographic vulnerability of bird individuals and populations could be affected by the duration and magnitude of drought episodes. Although our results are subject to publication bias, these conclusions advance the assessment of vulnerability to extreme climatic events that used to be based on equally weighted species traits and support bird conservation by prioritizing the declining populations of species with drought-susceptible traits.

Prioritizing Conservation Areas for the Hyacinth Macaw (Anodorhynchus hyacinthinus) in Brazil From Low-Coverage Genomic Data

Estimates of current genetic diversity and population connectivity are especially important for endangered species that are subject to illegal harvesting and trafficking. Genetic monitoring can also ensure that management units are sustaining viable populations, while estimating genetic structure and population dynamics can influence genetic rescue efforts and reintroduction from captive breeding and confiscated animals. The Hyacinth Macaw (Anodorhynchus hyacinthinus) is a charismatic endangered species with a fragmented (allopatric) distribution. Using low coverage genomes, we aimed to investigate the dynamics across the remaining three large disjunct populations of Hyacinth Macaws in Brazil to inform conservation strategies. We obtained low coverage DNA data for 54 individuals from seven sampling sites. Our results showed that Hyacinth Macaws have four genetically structured clusters with relatively high levels of diversity. The Pantanal biome had two genetically distinct populations, with no obvious physical barriers that might explain this differentiation. We detected signs of gene flow between populations, with some geographical regions being more connected than others. Estimates of effective population size in the past million years of the species' evolutionary history showed a decline trend with the lowest Ne in all populations reached within the last few thousand years. Our findings suggest that populations from the Pantanal biome are key to connecting sites across its distribution, and maintaining the integrity of this habitat is important for protecting the species. Given the genetic structure found, we also highlight the need of conserving all wild populations to ensure the protection of the species' evolutionary potential.

Gene Expression Shifts in Emperor Penguin Adaptation to the Extreme Antarctic Environment

Gene expression can accelerate ecological divergence by rapidly tweaking the response of an organism to novel environments, with more divergent environments exerting stronger selection and supposedly, requiring faster adaptive responses. Organisms adapted to extreme environments provide ideal systems to test this hypothesis, particularly when compared to related species with milder ecological niches. The Emperor penguin (Aptenodytes forsteri) is the only endothermic vertebrate breeding in the harsh Antarctic winter, in stark contrast with the less cold-adapted sister species, the King penguin (A. patagonicus). Assembling the first de novo transcriptomes and analysing multi-tissue (brain, kidney, liver, muscle, skin) RNA-Seq data from natural populations of both species, we quantified the shifts in tissue-enhanced genes, co-expression gene networks, and differentially expressed genes characterising Emperor penguin adaptation to the extreme Antarctic. Our analyses revealed the crucial role played by muscle and liver in temperature homeostasis, fasting, and whole-body energy metabolism (glucose/insulin regulation, lipid metabolism, fatty acid beta-oxidation, and blood coagulation). Repatterning at the regulatory level appears as more important in the brain of the Emperor penguin, showing the lowest signature of differential gene expression, but the largest co-expression gene network shift. Nevertheless, over-expressed genes related to mTOR signalling in the brain and the liver support their central role in cold and fasting responses. Besides contributing to understanding the genetics underlying complex traits, like body energy reservoir management, our results provide a first insight into the role of gene expression in adaptation to one of the most extreme environmental conditions endured by an endotherm.

The global loss of avian functional and phylogenetic diversity from anthropogenic extinctions

Humans have been driving a global erosion of species richness for millennia, but the consequences of past extinctions for other dimensions of biodiversity-functional and phylogenetic diversity-are poorly understood. In this work, we show that, since the Late Pleistocene, the extinction of 610 bird species has caused a disproportionate loss of the global avian functional space along with ~3 billion years of unique evolutionary history. For island endemics, proportional losses have been even greater. Projected future extinctions of more than 1000 species over the next two centuries will incur further substantial reductions in functional and phylogenetic diversity. These results highlight the severe consequences of the ongoing biodiversity crisis and the urgent need to identify the ecological functions being lost through extinction.

Chromosome-level genome provides insights into evolution and diving adaptability in the vulnerable common pochard (Aythya ferina)

The common pochard (Aythya ferina) is a freshwater diving duck found in the Palearctic region that has been classified as vulnerable by the IUCN due to continuous and rapid population declines across their distribution. To gain a better understanding of its genetic mechanism of adaptive evolution, we successfully sequenced and assembled the first high-quality chromosome-level genome of A. ferina using Illumina, Nanopore and Hi-C sequencing technologies. A total assembly length of 1,130.78 Mbp was obtained, with over 98.81% (1,117.37Mbp) of sequence anchored to 35 pseudo-chromosomes. We predicted 17,232 protein-coding genes, 95.9% of which were functionally annotated. We identified 339 expanded and 937 contracted gene families in the genome of A. ferina, and detected 95 genes that have been positively selected. The significantly enriched Gene Ontology and enriched pathways were related to energy metabolism, immune, nervous, and sensory systems, suggests that these factors likely played an important role in its evolution. Importantly, we recovered signatures of positive selection on genes related to vasoconstriction that may be associated with thermoregulatory adaptations of A. ferina for underwater diving. Overall, the high-quality genome assembly and annotation in this study provides valuable genomic resources for ecological and evolutionary studies, as well as toward the conservation of A. ferina.

Characterization and distribution of de novo mutations in the zebra finch

Germline de novo mutations (DNMs) provide the raw material for evolution. The DNM rate varies considerably between species, sexes and chromosomes. Here, we identify DNMs in the zebra finch (Taeniopygia guttata) across 16 parent-offspring trios using two genome assemblies of different quality. Using an independent genotyping assay, we validate 82% of the 150 candidate DNMs. DNM rates are consistent between both assemblies, with estimates of 6.14 × 10-9 and 6.36 × 10-9 per site per generation. We observe a strong paternal bias in DNM rates (male-to-female ratio ɑ ≈ 4), but this bias is in transition mutations only, leading to a transition-to-transversion ratio of 3.18 and 3.57. Finally, we find that DNMs tend to be randomly distributed across chromosomes, not associated with recombination hotspots or genic regions. However, the sex chromosome chrZ shows a roughly fourfold increased DNM rate compared to autosomes, which is more than the expected increase due to chrZ spending two-thirds of its time in males. Overall, our results further enhance our understanding of DNMs in passerine songbirds.

Global Avian Functional Diversity Depends on the World's Most Widespread and Distinct Birds

The relationship between global trait distinctiveness and geographic range size is an emerging pattern of interest in macroecology. Early observations suggested that the relationship was positive, implying that globally widespread species hold the rarest combinations of traits. Here, we formally describe and test the relationship in the world's birds and consider its implications for global functional diversity and redundancy. We demonstrate that the relationship is best described as triangular with a positive upper boundary, with its linear model significance lost when including phylogenetic effects. The triangular relationship is formed by groups of phylogenetically related widespread species with moderate and high trait distinctiveness. Decomposing the relationship further using quantile regression highlights the unique traits of these widespread birds. Overall, the triangular relationship emphasises that while not all widespread species have rare trait combinations, those that do should not be overlooked in conservation efforts, regardless of their current threat status.

Ongoing introgression of a secondary sexual plumage trait in a stable avian hybrid zone

Hybrid zones are dynamic systems where natural selection, sexual selection, and other evolutionary forces can act on reshuffled combinations of distinct genomes. The movement of hybrid zones, individual traits, or both are of particular interest for understanding the interplay between selective processes. In a hybrid zone involving two lek-breeding birds, secondary sexual plumage traits of Manacus vitellinus, including bright yellow collar and olive belly color, have introgressed ~50 km asymmetrically across the genomic center of the zone into populations more genetically similar to Manacus candei. Males with yellow collars are preferred by females and are more aggressive than parental M. candei, suggesting that sexual selection was responsible for the introgression of male traits. We assessed the spatial and temporal dynamics of this hybrid zone using historical (1989-1994) and contemporary (2017-2020) transect samples to survey both morphological and genetic variation. Genome-wide single nucleotide polymorphism data and several male phenotypic traits show that the genomic center of the zone has remained spatially stable, whereas the olive belly color of male M. vitellinus has continued to introgress over this time period. Our data suggest that sexual selection can continue to shape phenotypes dynamically, independent of a stable genomic transition between species.

Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole-Genome Sequence Data

Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long-tailed duck (Clangula hyemalis) and velvet scoter (Melanitta fusca) were once important quarry sea duck species in NW Europe, but recent declines resulted in their reclassification as vulnerable on the IUCN Red List. We sequenced and assembled genomes for both species and resequenced 15 individuals of each. Using analyses based on site frequency spectra and sequential Markovian coalescence, we found C. hyemalis to show more historical demographic stability, whereas M. fusca was affected particularly by the Last (Weichselian) Glaciation. This likely reflects C. hyemalis breeding continuously across the Arctic, with cycles of glaciation primarily shifting breeding areas south or north without major population declines, whereas the more restricted southern range of M. fusca would lead to significant range contraction during glaciations. Both species showed evidence of declines over the past thousands of years, potentially reflecting anthropogenic pressures with the recent decline indicating an accelerated process. Analysis of runs of homozygosity (ROH) showed low but nontrivial inbreeding, with F ROH from 0.012 to 0.063 in C. hyemalis and ranging from 0 to 0.047 in M. fusca. Lengths of ROH suggested that this was due to ongoing background inbreeding rather than recent declines. Overall, despite demographically important declines, this has not yet led to strong inbreeding and genetic erosion, and the most pressing conservation concern may be the risk of density-dependent (Allee) effects. We recommend monitoring of inbreeding using ROH analysis as a cost-efficient method to track future developments to support effective conservation of these species.

Genetic diversity of a recovering European roller (Coracias garrulus) population from Serbia

The European Roller (Coracias garrulus), a long-distance migratory bird, faced a considerable decline in breeding pairs throughout Europe at the end of the 20th century. Due to conservation efforts and the installation of nesting boxes, the population of the European Roller in Serbia has made a remarkable recovery. Here, we used the variability of nucleotide sequences of the mitochondrial DNA (mtDNA) control region and 10 microsatellite loci to assess the genetic diversity and structuring, phylogeographic patterns and demographic history of this species using 224 individuals from Serbia. Our results showed moderate level of genetic diversity (HO = 0.392) and a slightly elevated level of inbreeding and homozygosity (FIS = 0.393). Genetic structuring based on microsatellite data indicated three genetic clusters, but without a clear spatial pattern. High haplotype diversity (Hd = 0.987) of the mtDNA control region sequences was detected, and neutrality tests indicated a recent demographic expansion. The phylogeographic analysis, which also included previously published sequences of the mtDNA control region, supported the subdivision into two distinct European and Asian haplogroups (ΦST = 0.712). However, the results of our study showed that a larger number of haplotypes sampled in Serbia are clustered in the Asian haplogroup as compared to previous studies, indicating a historically continuous distribution of this species and possibly a wider distribution of the subspecies Coracias garrulus semenovwi. Our results suggest that the European Roller population in Serbia is genetically stable, with no evidence of recent bottlenecks, and emphasize the importance of artificial nest boxes for promoting and maintaining population dynamics of European Rollers.

Genome and life-history evolution link bird diversification to the end-Cretaceous mass extinction

Complex patterns of genome evolution associated with the end-Cretaceous [Cretaceous-Paleogene (K-Pg)] mass extinction limit our understanding of the early evolutionary history of modern birds. Here, we analyzed patterns of avian molecular evolution and identified distinct macroevolutionary regimes across exons, introns, untranslated regions, and mitochondrial genomes. Bird clades originating near the K-Pg boundary exhibited numerous shifts in the mode of molecular evolution, suggesting a burst of genomic heterogeneity at this point in Earth's history. These inferred shifts in substitution patterns were closely related to evolutionary shifts in developmental mode, adult body mass, and patterns of metabolic scaling. Our results suggest that the end-Cretaceous mass extinction triggered integrated patterns of evolution across avian genomes, physiology, and life history near the dawn of the modern bird radiation.

Recent secondary contact, genome-wide admixture, and asymmetric introgression of neo-sex chromosomes between two Pacific island bird species

Secondary contact between closely related taxa represents a "moment of truth" for speciation-an opportunity to test the efficacy of reproductive isolation that evolved in allopatry and to identify the genetic, behavioral, and/or ecological barriers that separate species in sympatry. Sex chromosomes are known to rapidly accumulate differences between species, an effect that may be exacerbated for neo-sex chromosomes that are transitioning from autosomal to sex-specific inheritance. Here we report that, in the Solomon Islands, two closely related bird species in the honeyeater family-Myzomela cardinalis and Myzomela tristrami-carry neo-sex chromosomes and have come into recent secondary contact after ~1.1 my of geographic isolation. Hybrids of the two species were first observed in sympatry ~100 years ago. To determine the genetic consequences of hybridization, we use population genomic analyses of individuals sampled in allopatry and in sympatry to characterize gene flow in the contact zone. Using genome-wide estimates of diversity, differentiation, and divergence, we find that the degree and direction of introgression varies dramatically across the genome. For sympatric birds, autosomal introgression is bidirectional, with phenotypic hybrids and phenotypic parentals of both species showing admixed ancestry. In other regions of the genome, however, the story is different. While introgression on the Z/neo-Z-linked sequence is limited, introgression of W/neo-W regions and mitochondrial sequence (mtDNA) is highly asymmetric, moving only from the invading M. cardinalis to the resident M. tristrami. The recent hybridization between these species has thus enabled gene flow in some genomic regions but the interaction of admixture, asymmetric mate choice, and/or natural selection has led to the variation in the amount and direction of gene flow at sex-linked regions of the genome.

Whole-genome analysis reveals the diversification of Galapagos rail (Aves: Rallidae) and confirms the success of goat eradication programs

Similar to other insular birds around the world, the Galapagos rail (Laterallus spilonota Gould, 1841) exhibits reduced flight capacity following its colonization of the archipelago ~1.2 mya. Despite their short evolutionary history, rails have colonized seven different islands spanning the entire width of the archipelago. Galapagos rails were once common on islands with sufficiently high altitudes to support shrubs in humid habitats. After humans introduced goats, this habitat was severely reduced due to overgrazing. Habitat loss devastated some rail populations, with less than 50 individuals surviving, rendering the genetic diversity of Galapagos rail a pressing conservation concern. Additionally, one enigma is the reappearance of rails on the island of Pinta after they were considered extirpated. Our approach was to investigate the evolutionary history and geographic distribution of Galapagos rails as well as examine the genome-wide effects of historical population bottlenecks using 39 whole genomes across different island populations. We recovered an early divergence of rail ancestors leading to the isolated populations on Pinta and a second clade comprising the rest of the islands, historically forming a single landmass. Subsequently, the separation of the landmass ~900 kya may have led to the isolation of the Isabela population with more panmictic populations found on Santa Cruz and Santiago islands. We found that rails genomes contain long runs of homozygosity (>2 Mb) that could be related to the introduction of goats. Finally, our findings show that the modern eradication of goats was critical to avoiding episodes of inbreeding in most populations.

Unraveling the genomic landscape of Campylorhynchus wrens along western Ecuador's precipitation gradient: Insights into hybridization, isolation by distance, and isolation by the environment

Environmental gradients have the potential to influence genetic differentiation among populations ultimately leading to allopatric speciation. However, environmental gradients can also facilitate hybridization between closely related taxa. We investigated a putative hybrid zone in western Ecuador, involving two polytypic wren species (Aves: Troglodytidae), Campylorhynchus zonatus and C. fasciatus. Our study addressed two primary questions: (1) Is there evidence of population structure and genetic admixture between these taxa in western Ecuador? and (2) What are the relative contributions of isolation by distance and isolation by the environment to the observed genetic differentiation along the environmental gradient in this region? We analyzed 4409 single-nucleotide polymorphisms (SNPs) from 112 blood samples sequenced using ddRadSeq and a de novo assembly. The optimum number of genetic clusters ranged from 2 to 4, aligning with geographic origins, known phylogenetics, and physical or ecological constraints. We observed notable transitions in admixture proportions along the environmental gradient in western Ecuador between C. z. brevirostris and the northern and southern genetic clusters of C. f. pallescens. Genetic differentiation between the two C. f. pallescens populations could be attributed to an unreported potential physical barrier in central western Ecuador, where the proximity of the Andes to the coastline restricts lowland habitats, limiting dispersal and gene flow, especially among dry-habitat specialists. The observed admixture in C. f. pallescens suggests that this subspecies may be a hybrid between C. z. brevirostris and C. fasciatus, with varying degrees of admixture in western Ecuador and northwestern Peru. We found evidence of isolation by distance, while isolation by the environment was less pronounced but still significant for annual mean precipitation and precipitation seasonality. This study enhances our understanding of avian population genomics in tropical regions.

Role-reversed polyandry is associated with faster fast-Z in shorebirds

In birds, males are homogametic and carry two copies of the Z chromosome ('ZZ'), while females are heterogametic and exhibit a 'ZW' genotype. The Z chromosome evolves at a faster rate than similarly sized autosomes, a phenomenon termed 'fast-Z evolution'. This is thought to be caused by two independent processes-greater Z chromosome genetic drift owing to a reduced effective population size, and stronger Z chromosome positive selection owing to the exposure of partially recessive alleles to selection. Here, we investigate the relative contributions of these processes by considering the effect of role-reversed polyandry on fast-Z in shorebirds, a paraphyletic group of wading birds that exhibit unusually diverse mating systems. We find stronger fast-Z effects under role-reversed polyandry, which is consistent with particularly strong selection on polyandrous females driving the fixation of recessive beneficial alleles. This result contrasts with previous research in birds, which has tended to implicate a primary role of genetic drift in driving fast-Z variation. We suggest that this discrepancy can be interpreted in two ways-stronger sexual selection acting on polyandrous females overwhelms an otherwise central role of genetic drift, and/or sexual antagonism is also contributing significantly to fast-Z and is exacerbated in sexually dimorphic species.

Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae)

The family Melampittidae is endemic to New Guinea and consists of two monotypic genera: Melampitta lugubris (Lesser Melampitta) and Megalampitta gigantea (Greater Melampitta). Both Melampitta species have scattered and disconnected distributions across New Guinea in the central mountain range and in some of the outlying ranges. While M. lugubris is common and found in most montane regions of the island, M. gigantaea is elusive and known from only six localities in isolated pockets on New Guinea with very specific habitats of limestone and sinkholes. In this project, we apply museomics to determine the population structure and demographic history of these two species. We re-sequenced the genomes of all seven known M. gigantaea samples housed in museum collections as well as 24 M. lugubris samples from across its distribution. By comparing population structure between the two species, we investigate to what extent habitat dependence, such as in M. gigantaea, may affect population connectivity. Phylogenetic and population genomic analyses, as well as acoustic variation revealed that M. gigantaea consists of a single population in contrast to M. lugubris that shows much stronger population structure across the island. We suggest a recent collapse of M. gigantaea into its fragmented habitats as an explanation to its unexpected low diversity and lack of population structure. The deep genetic divergences between the M. lugubris populations on the Vogelkop region, in the western central range and the eastern central range, respectively, suggests that these three populations should be elevated to full species level. This work sheds new light on the mechanisms that have shaped the intriguing distribution of the two species within this family and is a prime example of the importance of museum collections for genomic studies of poorly known and rare species.

Evolution and genetic architecture of sex-limited polymorphism in cuckoos

Sex-limited polymorphism has evolved in many species including our own. Yet, we lack a detailed understanding of the underlying genetic variation and evolutionary processes at work. The brood parasitic common cuckoo (Cuculus canorus) is a prime example of female-limited color polymorphism, where adult males are monochromatic gray and females exhibit either gray or rufous plumage. This polymorphism has been hypothesized to be governed by negative frequency-dependent selection whereby the rarer female morph is protected against harassment by males or from mobbing by parasitized host species. Here, we show that female plumage dichromatism maps to the female-restricted genome. We further demonstrate that, consistent with balancing selection, ancestry of the rufous phenotype is shared with the likewise female dichromatic sister species, the oriental cuckoo (Cuculus optatus). This study shows that sex-specific polymorphism in trait variation can be resolved by genetic variation residing on a sex-limited chromosome and be maintained across species boundaries.

Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary

The "Amazon tipping point" is a global change scenario resulting in replacement of upland terra-firme forests by large-scale "savannization" of mostly southern and eastern Amazon. Reduced rainfall accompanying the Last Glacial Maximum (LGM) has been proposed to have acted as such a tipping point in the past, with the prediction that terra-firme inhabiting species should have experienced reductions in population size as drier habitats expanded. Here, we use whole-genomes of an Amazonian endemic organism (Scale-backed antbirds - Willisornis spp.) sampled from nine populations across the region to test this historical demography scenario. Populations from southeastern Amazonia and close to the Amazon-Cerrado ecotone exhibited a wide range of demographic patterns, while most of those from northern and western Amazonia experienced uniform expansions between 400 kya and 80-60 kya, with gradual declines toward 20 kya. Southeastern populations of Willisornis were the last to diversify and showed smaller heterozygosity and higher runs of homozygosity values than western and northern populations. These patterns support historical population declines throughout the Amazon that affected more strongly lineages in the southern and eastern areas, where historical "tipping point" conditions existed due to the widespread replacement of humid forest by drier and open vegetation during the LGM.

A slow-fast trait continuum at the whole community level in relation to land-use intensification

Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a 'slow-fast' axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that 'slow' and 'fast' strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification.

Ecological filtering shapes the impacts of agricultural deforestation on biodiversity

The biodiversity impacts of agricultural deforestation vary widely across regions. Previous efforts to explain this variation have focused exclusively on the landscape features and management regimes of agricultural systems, neglecting the potentially critical role of ecological filtering in shaping deforestation tolerance of extant species assemblages at large geographical scales via selection for functional traits. Here we provide a large-scale test of this role using a global database of species abundance ratios between matched agricultural and native forest sites that comprises 71 avian assemblages reported in 44 primary studies, and a companion database of 10 functional traits for all 2,647 species involved. Using meta-analytic, phylogenetic and multivariate methods, we show that beyond agricultural features, filtering by the extent of natural environmental variability and the severity of historical anthropogenic deforestation shapes the varying deforestation impacts across species assemblages. For assemblages under greater environmental variability-proxied by drier and more seasonal climates under a greater disturbance regime-and longer deforestation histories, filtering has attenuated the negative impacts of current deforestation by selecting for functional traits linked to stronger deforestation tolerance. Our study provides a previously largely missing piece of knowledge in understanding and managing the biodiversity consequences of deforestation by agricultural deforestation.

Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil

Investigating the impact of landscape features on patterns of genetic variation is crucial to understand spatially dependent evolutionary processes. Here, we assess the population genomic variation of two bird species (Conopophaga cearae and Sclerurus cearensis) through the Caatinga moist forest enclaves in northeastern Brazil. To infer the evolutionary dynamics of bird populations through the Late Quaternary, we used genome-wide polymorphism data obtained from double-digestion restriction-site-associated DNA sequencing (ddRADseq), and integrated population structure analyses, historical demography models, paleodistribution modeling, and landscape genetics analyses. We found the population differentiation among enclaves to be significantly related to the geographic distance and historical resistance across the rugged landscape. The climate changes at the end of the Pleistocene to the Holocene likely triggered synchronic population decline in all enclaves for both species. Our findings revealed that both geographic distance and historical connectivity through highlands are important factors that can explain the current patterns of genetic variation. Our results further suggest that levels of population differentiation and connectivity cannot be explained purely on the basis of contemporary environmental conditions. By combining historical demographic analyses and niche modeling predictions in a historical framework, we provide strong evidence that climate fluctuations of the Quaternary promoted population differentiation and a high degree of temporal synchrony among population size changes in both species.

Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird

Combating the current biodiversity crisis requires the accurate documentation of population responses to human-induced ecological change. However, our ability to pinpoint population responses to human activities is often limited to the analysis of populations studied well after the fact. Museum collections preserve a record of population responses to anthropogenic change that can provide critical baseline data on patterns of genetic diversity, connectivity, and population structure prior to the onset of human perturbation. Here, we leverage a spatially replicated time series of specimens to document population genomic responses to the destruction of nearly 90% of coastal habitats occupied by the Savannah sparrow (Passerculus sandwichensis) in California. We sequenced 219 sparrows collected from 1889 to 2017 across the state of California using an exome capture approach. Spatial-temporal analyses of genetic diversity found that the amount of habitat lost was not predictive of genetic diversity loss. Sparrow populations from southern California historically exhibited lower levels of genetic diversity and experienced the most significant temporal declines in genetic diversity. Despite experiencing the greatest levels of habitat loss, we found that genetic diversity in the San Francisco Bay area remained relatively high. This was potentially related to an observed increase in gene flow into the Bay Area from other populations. While gene flow may have minimized genetic diversity declines, we also found that immigration from inland freshwater-adapted populations into tidal marsh populations led to the erosion of divergence at loci associated with tidal marsh adaptation. Shifting patterns of gene flow through time in response to habitat loss may thus contribute to negative fitness consequences and outbreeding depression. Together, our results underscore the importance of tracing the genomic trajectories of multiple populations over time to address issues of fundamental conservation concern.

Assessing the global vulnerability of dryland birds to heatwaves

As global average surface temperature increases, extreme climatic events such as heatwaves are becoming more frequent and intense, which can drive biodiversity responses such as rapid population declines and/or shifts in species distributions and even local extirpations. However, the impacts of extreme climatic events are largely ignored in conservation plans. Birds are known to be susceptible to heatwaves, especially in dryland ecosystems. Understanding which birds are most vulnerable to heatwaves, and where these birds occur, can offer a scientific basis for adaptive management and conservation. We assessed the relative vulnerability of 1196 dryland bird species to heatwaves using a trait-based approach. Among them, 888 bird species are estimated to be vulnerable to heatwaves (170 highly vulnerable, eight extremely vulnerable), of which ~91% are currently considered non-threatened by the IUCN, which suggests that many species will likely become newly threatened with intensifying climate change. We identified the top three hotspot areas of heatwave-vulnerable species in Australia (208 species), Southern Africa (125 species) and Eastern Africa (99 species). Populations of vulnerable species recorded in the Living Planet Database were found to be declining significantly faster than those of non-vulnerable species (p = .048) after heatwaves occurred. In contrast, no significant difference in population trends between vulnerable and non-vulnerable species was detected when no heatwave occurred (p = .34). This suggests that our vulnerability framework correctly identified vulnerable species and that heatwaves are already impacting the population trends of these species. Our findings will help prioritize heatwave-vulnerable birds in dryland ecosystems in risk mitigation and adaptation management as the frequency of heatwaves accelerates in the coming decades.

African savanna raptors show evidence of widespread population collapse and a growing dependence on protected areas

The conversion of natural habitats to farmland is a major cause of biodiversity loss and poses the greatest extinction risk to birds worldwide. Tropical raptors are of particular concern, being relatively slow-breeding apex predators and scavengers, whose disappearance can trigger extensive cascading effects. Many of Africa's raptors are at considerable risk from habitat conversion, prey-base depletion and persecution, driven principally by human population expansion. Here we describe multiregional trends among 42 African raptor species, 88% of which have declined over a ca. 20-40-yr period, with 69% exceeding the International Union for Conservation of Nature criteria classifying species at risk of extinction. Large raptors had experienced significantly steeper declines than smaller species, and this disparity was more pronounced on unprotected land. Declines were greater in West Africa than elsewhere, and more than twice as severe outside of protected areas (PAs) than within. Worryingly, species suffering the steepest declines had become significantly more dependent on PAs, demonstrating the importance of expanding conservation areas to cover 30% of land by 2030-a key target agreed at the UN Convention on Biological Diversity COP15. Our findings also highlight the significance of a recent African-led proposal to strengthen PA management-initiatives considered fundamental to safeguarding global biodiversity, ecosystem functioning and climate resilience.

Protected area coverage of vulnerable regions to conserve functional diversity of birds

Global-change drivers are increasing the rates of species extinction worldwide, posing a serious threat to ecosystem functioning. Preserving the functional diversity of species is currently a priority to mitigate abrupt biodiversity loss in the coming decades. Therefore, understanding what factors better predict functional diversity loss in bird assemblages at a global scale and how existing protected areas cover the most vulnerable regions is of key importance for conservation. We examined the environmental factors associated with the risk of functional diversity loss under 3 scenarios of bird species extinction based on species distribution range size, generation length, and International Union for the Conservation of Nature conservation status. Then, we identified regions that deserve special conservation focus. We also assessed how efficiently extant terrestrial protected areas preserve particularly vulnerable bird assemblages based on predicted scenarios of extinction risk. The vulnerability of bird functional diversity increased as net primary productivity, land-use diversity, mean annual temperature, and elevation decreased. Low values for these environmental factors were associated with a higher risk of functional diversity loss worldwide through two mechanisms: one independent of species richness that affects assemblages with low levels of niche packing and high functional dissimilarity among species, and the other that affects assemblages with low species richness and high rates of extinction. Existing protected areas ineffectively safeguarded regions with a high risk of losing functional diversity in the next decades. The global predictors and the underlying mechanisms of functional vulnerability in bird assemblages we identified can inform strategies aimed at preserving bird-driven ecological functions worldwide.

Prioritizing the reassessment of data-deficient species on the IUCN Red List

Despite being central to the implementation of conservation policies, the usefulness of the International Union for Conservation of Nature (IUCN) Red List of Threatened Species is hampered by the 14% of species classified as data-deficient (DD) because information to evaluate these species' extinction risk was lacking when they were last assessed or because assessors did not appropriately account for uncertainty. Robust methods are needed to identify which DD species are more likely to be reclassified in one of the data-sufficient IUCN Red List categories. We devised a reproducible method to help red-list assessors prioritize reassessment of DD species and tested it with 6887 DD species of mammals, reptiles, amphibians, fishes, and Odonata (dragonflies and damselflies). For each DD species in these groups, we calculated its probability of being classified in a data-sufficient category if reassessed today from covariates measuring available knowledge (e.g., number of occurrence records or published articles available), knowledge proxies (e.g., remoteness of the range), and species characteristics (e.g., nocturnality); calculated change in such probability since last assessment from the increase in available knowledge (e.g., new occurrence records); and determined whether the species might qualify as threatened based on recent rate of habitat loss determined from global land-cover maps. We identified 1907 species with a probability of being reassessed in a data-sufficient category of >0.5; 624 species for which this probability increased by >0.25 since last assessment; and 77 species that could be reassessed as near threatened or threatened based on habitat loss. Combining these 3 elements, our results provided a list of species likely to be data-sufficient such that the comprehensiveness and representativeness of the IUCN Red List can be improved.

Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change

The Arctic is experiencing the fastest rates of global warming, leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidence of recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins (Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F. a. naumanni and the temperate, smaller-sized subspecies F. a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F. a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations. Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.

GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes

Ultraconserved elements (UCEs) are the most conserved regions among the genomes of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial. Here, using an increased number of sequenced genomes with high taxonomic coverage, we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird genomes, respectively. Our results show that these UCEs are functionally constrained and that their adjacent genes are prone to widespread expression with low expression diversity across tissues. Functional enrichment of mammalian and avian UCEs shows different trends indicating that UCEs may contribute to adaptive evolution of taxa. Focusing on lineage-specific accelerated evolution, we discover that the proportion of fast-evolving UCEs in nine mammalian and 10 avian test lineages range from 0.19% to 13.2%. Notably, up to 62.1% of fast-evolving UCEs in test lineages are much more likely to result from GC-biased gene conversion (gBGC). A single cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression of Nova1 and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between gBGC and selection shaped lineage-specific substitution patterns, even in the most constrained regulatory elements. In summary, our results show that gBGC played an important role in facilitating lineage-specific accelerated evolution of UCEs, and further support the idea that a combination of multiple evolutionary forces shapes adaptive evolution.

Generation time and seasonal migration explain variation in spatial population synchrony across European bird species

Spatial population synchrony is common among populations of the same species and is an important predictor of extinction risk. Despite the potential consequences for metapopulation persistence, we still largely lack understanding of what makes one species more likely to be synchronized than another given the same environmental conditions. Generally, environmental conditions in a shared environment or a species' sensitivity to the environment can explain the extent of synchrony. Populations that are closer together experience more similar fluctuations in their environments than those populations that are further apart and are therefore more synchronized. The relative importance of environmental and demographic stochasticity for population dynamics is strongly linked to species' life-history traits, such as pace of life, which may impact population synchrony. For populations that migrate, there may be multiple environmental conditions at different locations driving synchrony. However, the importance of life history and migration tactics in determining patterns of spatial population synchrony have rarely been explored empirically. We therefore hypothesize that increasing generation time, a proxy for pace of life, would decrease spatial population synchrony and that migrants would be less synchronized than resident species. We used population abundance data on breeding birds from four countries to investigate patterns of spatial population synchrony in growth rate and abundance. We calculated the mean spatial population synchrony between log-transformed population growth rates or log-transformed abundances for each species and country separately. We investigated differences in synchrony across generation times in resident (n = 67), short-distance migrant (n = 86) and long-distance migrant (n = 39) bird species. Species with shorter generation times were more synchronized than species with longer generation times. Short-distance migrants were more synchronized than long-distance migrants and resident birds. Our results provide novel empirical links between spatial population synchrony and species traits known to be of key importance for population dynamics, generation time and migration tactics. We show how these different mechanisms can be combined to understand species-specific causes of spatial population synchrony. Understanding these specific drivers of spatial population synchrony is important in the face of increasingly severe threats to biodiversity and could be key for successful future conservation outcomes.

Megafaunal extinctions, not climate change, may explain Holocene genetic diversity declines in Numenius shorebirds

Understanding the relative contributions of historical and anthropogenic factors to declines in genetic diversity is important for informing conservation action. Using genome-wide DNA of fresh and historic specimens, including that of two species widely thought to be extinct, we investigated fluctuations in genetic diversity and present the first complete phylogenomic tree for all nine species of the threatened shorebird genus Numenius, known as whimbrels and curlews. Most species faced sharp declines in effective population size, a proxy for genetic diversity, soon after the Last Glacial Maximum (around 20,000 years ago). These declines occurred prior to the Anthropocene and in spite of an increase in the breeding area predicted by environmental niche modeling, suggesting that they were not caused by climatic or recent anthropogenic factors. Crucially, these genetic diversity declines coincide with mass extinctions of mammalian megafauna in the Northern Hemisphere. Among other factors, the demise of ecosystem-engineering megafauna which maintained open habitats may have been detrimental for grassland and tundra-breeding Numenius shorebirds. Our work suggests that the impact of historical factors such as megafaunal extinction may have had wider repercussions on present-day population dynamics of open habitat biota than previously appreciated.

The Relevance of Time in Biological Scaling

Various phenotypic traits relate to the size of a living system in regular but often disproportionate (allometric) ways. These "biological scaling" relationships have been studied by biologists for over a century, but their causes remain hotly debated. Here, I focus on the patterns and possible causes of the body-mass scaling of the rates/durations of various biological processes and life-history events, i.e., the "pace of life". Many biologists have regarded the rate of metabolism or energy use as the master driver of the "pace of life" and its scaling with body size. Although this "energy perspective" has provided valuable insight, here I argue that a "time perspective" may be equally or even more important. I evaluate various major ways that time may be relevant in biological scaling, including as (1) an independent "fourth dimension" in biological dimensional analyses, (2) a universal "biological clock" that synchronizes various biological rates/durations, (3) a scaling method that uses various biological time periods (allochrony) as scaling metrics, rather than various measures of physical size (allometry), as traditionally performed, (4) an ultimate body-size-related constraint on the rates/timing of biological processes/events that is set by the inevitability of death, and (5) a geological "deep time" approach for viewing the evolution of biological scaling patterns. Although previously proposed universal four-dimensional space-time and "biological clock" views of biological scaling are problematic, novel approaches using allochronic analyses and time perspectives based on size-related rates of individual mortality and species origination/extinction may provide new valuable insights.

Using GPS tracking to monitor the breeding performance of a low-density raptor improves accuracy, and reduces long-term financial and carbon costs

Traditionally, demographic monitoring of birds has been undertaken by intensive monitoring of nesting sites. However, this is challenging for low-density species, whereby the effort and costs involved in locating and monitoring remote sites can be prohibitive or even bias research findings. We show that Global Positioning System (GPS) tracking can overcome these challenges for a low-density raptor. Field monitoring of martial eagles Polemaetus bellicosus from 2013 to 2021 showed consistently poor breeding performance, with a mean productivity of 0.22 (±0.04) fledged young/pair/year. Using GPS tracking data to infer breeding performance gave a significantly higher productivity of 0.46 (±0.10) fledged young/pair/year. Breeding rate and success were also underestimated by field monitoring. These differences were likely due to logistical constraints of field monitoring, particularly relating to finding alternative nests. Comparing costs between approaches, we estimated that GPS monitoring was financially cheaper than field monitoring per sample after 10 years. Carbon costs per sample were lower for GPS-based approaches than field monitoring from the second year, and over a 10-year period GPS monitoring produced considerable savings (200% less carbon). We recommend that despite high initial costs, for long-term demographic monitoring of low-density species, or where logistical constraints make traditional field monitoring inaccurate, remote monitoring options should be considered.

Local colonisations and extinctions of European birds are poorly explained by changes in climate suitability

Climate change has been associated with both latitudinal and elevational shifts in species' ranges. The extent, however, to which climate change has driven recent range shifts alongside other putative drivers remains uncertain. Here, we use the changing distributions of 378 European breeding bird species over 30 years to explore the putative drivers of recent range dynamics, considering the effects of climate, land cover, other environmental variables, and species' traits on the probability of local colonisation and extinction. On average, species shifted their ranges by 2.4 km/year. These shifts, however, were significantly different from expectations due to changing climate and land cover. We found that local colonisation and extinction events were influenced primarily by initial climate conditions and by species' range traits. By contrast, changes in climate suitability over the period were less important. This highlights the limitations of using only climate and land cover when projecting future changes in species' ranges and emphasises the need for integrative, multi-predictor approaches for more robust forecasting.

Consequences of cross-season demographic correlations for population viability

Demographic correlations are pervasive in wildlife populations and can represent important secondary drivers of population growth. Empirical evidence suggests that correlations are in general positive for long-lived species, but little is known about the degree of variation among spatially segregated populations of the same species in relation to environmental conditions. We assessed the relative importance of two cross-season correlations in survival and productivity, for three Atlantic puffin (Fratercula arctica) populations with contrasting population trajectories and non-overlapping year-round distributions. The two correlations reflected either a relationship between adult survival prior to breeding on productivity, or a relationship between productivity and adult survival the subsequent year. Demographic rates and their correlations were estimated with an integrated population model, and their respective contributions to variation in population growth were calculated using a transient-life table response experiment. For all three populations, demographic correlations were positive at both time lags, although their strength differed. Given the different year-round distributions of these populations, this variation in the strength population-level demographic correlations points to environmental conditions as an important driver of demographic variation through life-history constraints. Consequently, the contributions of variances and correlations in demographic rates to population growth rates differed among puffin populations, which has implications for-particularly small-populations' viability under environmental change as positive correlations tend to reduce the stochastic population growth rate.

Humanity's diverse predatory niche and its ecological consequences

Although humans have long been predators with enduring nutritive and cultural relationships with their prey, seldom have conservation ecologists considered the divergent predatory behavior of contemporary, industrialized humans. Recognizing that the number, strength and diversity of predator-prey relationships can profoundly influence biodiversity, here we analyze humanity's modern day predatory interactions with vertebrates and estimate their ecological consequences. Analysing IUCN 'use and trade' data for ~47,000 species, we show that fishers, hunters and other animal collectors prey on more than a third (~15,000 species) of Earth's vertebrates. Assessed over equivalent ranges, humans exploit up to 300 times more species than comparable non-human predators. Exploitation for the pet trade, medicine, and other uses now affects almost as many species as those targeted for food consumption, and almost 40% of exploited species are threatened by human use. Trait space analyses show that birds and mammals threatened by exploitation occupy a disproportionally large and unique region of ecological trait space, now at risk of loss. These patterns suggest far more species are subject to human-imposed ecological (e.g., landscapes of fear) and evolutionary (e.g., harvest selection) processes than previously considered. Moreover, continued overexploitation will likely bear profound consequences for biodiversity and ecosystem function.

The evolution of early-life telomere length, pace-of-life and telomere-chromosome length dynamics in birds

Telomeres, the short DNA sequences that protect chromosome ends, are an ancient molecular structure, which is highly conserved across most eukaryotes. Species differ in their telomere lengths, but the causes of this variation are not well understood. Here, we demonstrate that mean early-life telomere length is an evolutionary labile trait across 57 bird species (representing 35 families in 12 orders) with the greatest trait diversity found among passerines. Among these species, telomeres are significantly shorter in fast-lived than in slow-lived species, suggesting that telomere length may have evolved to mediate trade-offs between physiological requirements underlying the diversity of pace-of-life strategies in birds. This association was attenuated when excluding studies that may include interstitial telomeres in the estimation of mean telomere length. Curiously, within some species, larger individual chromosome size predicts longer telomere lengths on that chromosome, leading to the hypothesis that telomere length also covaries with chromosome length across species. We show that longer mean chromosome length or genome size tends to be associated with longer mean early-life telomere length (measured across all chromosomes) within a phylogenetic framework constituting up to 31 bird species. These associations were strengthened when excluding highly influential outliers. However, sensitivity analyses suggested that they were susceptible to sample size effects and not robust to the exclusion of studies that may include interstitial telomeres. Combined, our analyses generalize patterns previously found within a few species and provide potential adaptive explanations for the 10-fold variation in telomere lengths observed among birds.

Quantifying the impacts of predation by Great Black-backed Gulls Larus marinus on an Atlantic Puffin Fratercula arctica population: Implications for conservation management and impact assessments

The management of predator-prey conflicts can be a key aspect of species conservation. For management approaches to be effective, a robust understanding of the predator-prey relationship is needed, particularly when both predator and prey are species of conservation concern. On the Isle of May, Firth of Forth, Scotland, numbers of breeding Great Black-backed Gulls Larus marinus, a generalist predator, have been increasing since the 1980s, which has led to increasing numbers of sympatrically breeding Atlantic Puffins Fratercula arctica being predated during the breeding season. This may have consequences for species management on the Isle of May and impact assessments of offshore windfarms in the wider Firth of Forth area. We used population viability analysis to quantify under what predation pressure the Atlantic Puffin population may decline and become locally extinct over a three-generation period. The predation level empirically estimated in 2017 (1120 Puffins per year) was not sufficient to drive a decline in the Puffin population. Rather, an increase to approximately 3000 Puffins per year would be required to cause a population decline, and >4000 to drive the population to quasi-extinction within 66 years. We discuss the likelihood of such a scenario being reached on the Isle of May, and we recommend that where predator-prey conflicts occur, predation-driven mortality should be regularly quantified to inform conservation management and population viability analyses associated with impact assessments.