Journal of Heredity

Focal and intelligent passerine songbirds, corvids (Aves: Corvidae) have served as models for research on the genomics of hybridization and cognition. Clarks Nutcracker (Nucifraga columbiana), the sole North American member of its genus, is distributed in mountain forests from northern Mexico to northern British Columbia. A seed predator, N. columbiana is highly reliant on pine nuts from Pinus spp. conifers, which it both consumes directly from cones and caches for future use. Because cached seeds are often forgotten or abandoned, it is a major seed disperser for high elevation pines--in particular Whitebark Pine P. albicaulis. Previous studies of genetic variation in Clarks Nutcracker found range-wide panmixia and generally high levels of heterozygosity at a handful of nuclear and mitochondrial loci, potentially due to seasonal elevational movements and long term dispersal. An earlier genome assembly from low-coverage short read data was highly fragmented and has not to date been used as the basis for population-level resequencing. Here we report on the first chromosome-scale genome assembly for N. colombiana. We generated long-read sequencing and genome conformation mapping data from tissues sampled from a male N. columbiana individual in Wyoming, USA. These data were assembled into a highly contiguous and complete assembly, which showed strong chromosomal synteny with New Caledonian crow (Corvus moneduloides). This genome has relatively low heterozygosity compared to other Corvid genomes and to previous population-level heterozygosity estimates for the species. We also found evidence of a long-term decline in effective population size dating back to the Pleistocene, after accounting for a technical artifact common to demographic inference using the pairwise sequential Markovian coalescent. These findings raise concerns about the future viability of the species and its mutualist P. albicaulis; we hope the assembly will motivate further comparative and conservation genomics research.

The worlds largest and rarest eagle, the Philippine Eagle (Pithecophaga jefferyi), also known as the monkey-eating eagle, is the national bird of the Philippines. This raptor species is endemic to the Philippine archipelago, with populations on the islands of Luzon, Leyte, Samar, and Mindanao. It is critically endangered, with an average estimated population of 392 potentially breeding pairs or 784 mature individuals. In this paper, we describe a reference genome of the Philippine Eagle (Pithecophaga jefferyi) from a female juvenile from the province of Nueva Ecija on the island of Luzon. We generated a de novo genome assembly with high contiguity and completeness, comprising 178 contigs totaling 1.345 Gbp. The genome was sequenced at a coverage of 75.2x, and Benchmarking Universal Single-Copy Orthologs (BUSCO)/Compleasm analysis yielded a BUSCO score of 99.92% (aves_odb12), corresponding to 99.7% single-copy, 0.21% duplicated, and 0.08% fragmented genes. A consensus mitogenome sequence of 19,377 bp was also generated. The genome assembly included 23,847 putative genes, and our annotation estimated that 15.78% of the genome consisted of repetitive elements. Genome heterozygosity (H) was estimated to be 0.020%, in comparison to other birds with genome heterozygosity values ranging from 0.0103% to 0.923%. Whole-genome comparisons with publicly available genomes suggest that the Philippine eagle belongs to the snake-eagle subfamily (Circaetinae) rather than the harpy-eagle subfamily (Harpiinae). Pairwise sequentially Markovian coalescent (PSMC) analysis suggests that the effective population size was around 4,000 individuals from about 100 KYA to about 1 KYA. Finally, we constructed a minimum spanning network, which revealed that our mitogenome from the northern island of Luzon occupies a peripheral position, separated from the dominant haplotype cluster found in the southern island of Mindanao by multiple mutational steps, indicating substantial mitochondrial divergence.

Sturgeon and paddlefish represent some of the most early diverging branches of ray-finned fishes and have undergone at least one global and several lineage-specific whole genome duplication events. White sturgeon (Acipenser transmontanus), the largest freshwater fish in North America, have experienced at least two rounds of whole genome duplication, and may exhibit both di- and multi-valent meiotic segregation. Moreover, they exhibit contemporary ploidy variants due to spontaneous autopolyploidy, particularly in aquaculture. Nonetheless, as a species with several population segments that exhibit chronic recruitment failure, conservation aquaculture is an important part of their management. To facilitate the development of genetic tools to aid white sturgeon conservation, as well as a basis to understand how ploidy changes and variation historically and contemporarily shape the evolution of this species, we present a genome assembly for a white sturgeon from the Snake River, Idaho, USA. Analysis of sequence data used for assembly indicated a haploid genome size of approximately 1.5Gbp, implying tetraploidy (4N), while analysis of heterozygous k-mers from 21 to 41 bp suggest the genome reflects both 4N and 8N variants. The final genome assembly, scaffolded using linkage maps constructed from Fraser River and Snake River F1 families, contained 6.26Gbp in 832,145 scaffolds, consistent with published genome size estimates. Conserved ortholog completeness for this genome (90.5%; 22.8% single-copy and 67.7% duplicated) was similar to the putatively diploid sterlet sturgeon, and the largest linkage map-based scaffold was 55.2Gbp, though the N50 for this assembly was only 416Kbp, indicating the assembly remains fragmented. We demonstrate the utility of this assembly by identifying genomic regions significantly associated with sex. Genetic markers, designed for inclusion in an amplicon genotyping panel, predicted sex 96.6% and 81.5% correctly in females and males, respectively, providing a strong overall association ({square}2 p-value < 2.7x10-37) with some variation by geographic region. Article summaryFunctional polysomes (more than two chromosomes that pair in meiosis) are rare among vertebrates. White sturgeon, the largest freshwater fish in North America, are tetraploid and occasionally hexaploid. Several populations of this species are stagnant or declining, requiring aquaculture to bolster reproduction. We analyzed whole genomic data and assembled the genome of an individual from the unique Snake River, Idaho, population. Results indicate most genetic variants are consistent with tetraploidy, and the genome assembly, while fragmented, is largely complete. We demonstrate its utility by designing genetic markers for sex for use in conservation and commercial aquaculture.

Understanding how contemporary population declines affect the genomic diversity and structure of threatened species is important for effective conservation. The Eurasian curlew (Numenius arquata) is experiencing severe population declines across Europe, with Ireland among the most extreme, showing declines exceeding 90% over 40 years. Genomic data are increasingly incorporated into policy and used to assess conservation status by estimating genetic diversity, differentiation, inbreeding, effective population size, and adaptive divergence. Such data for curlew is scarce, and the population structure among northern and north-western European breeding populations remains unclear. To address this, we generated whole-genome resequencing data for 56 curlews across Ireland, Britain and Sweden. Irish and British populations showed minimal interpopulation differentiation, but both were substantially differentiated from Sweden. This was apparent from principal component analysis, and admixture and FST analyses. Measures of genetic diversity (nucleotide diversity, heterozygosity, Watterson's{theta} ) were similar across populations. A slightly elevated Tajima's D in Ireland, along with elevated FROH in Ireland and Britain relative to Sweden, may be the early genomic signs of recent population declines. We identified locally selected candidate genes. These had putative roles in metabolic processes, the immune response, and were potentially associated with distinct migratory behaviours and environmental conditions. We find a potential lag in genomic effects of decline being detectable following population contraction. We also show highly migratory species can exhibit differentiation in ecologically relevant traits, potentially driven by high site fidelity. These findings warrant consideration in translocation planning and broader conservation strategies.

We present a genome assembly from a female Cistugo seabrae (Seabras wing-gland bat; Chiroptera; Cistugidae). The genome sequence is 1.9 gigabases (Gb) in span. The majority of the assembly is scaffolded into 25 chromosomal pseudomolecules, with the XX chromosomes assembled. The assembly has a contig N50 of 51.9 Mb and a scaffold N50 of 91.4 Mb. Species taxonomyEukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Chiroptera; Yangochiroptera; Vespertilionoidea; Cistugidae; Cistugo; Cistugo seabrae Thomas, 1912 (Teeling et al., 2005; Bickham et al., 2004; Lack et al., 2010).

Tigriopus copepods are found in splash pools on all seven continents from the equator to Arctic and Antarctic regions. Given their geographic distribution, frequent exposure to extreme environmental conditions in the high intertidal zone, and strong signatures of local adaptation, these copepods have become models for exploring patterns of adaptation to stressful environments. However, most studies focus on a relatively small subset of Tigriopus species, and there are few genome resources representing the diversity of Tigriopus species and populations. Here, we combine long-read, Pacific Biosciences HiFi data with short-read, Illumina HiC and RNA-seq data to assemble and annotate a genome sequence representing a Tigriopus population from the coast of central Chile. Based on the level of divergence that we observed in mitochondrial genes, we also performed a comparison of morphological characteristics between individuals of this population and members of the T. angulatus complex. The haplotypes that we assembled (qhTigAngs1.1.hap1 & qhTigAngs1.1.hap2) are placed into 12 major scaffolds (N50 18-19 Mbp, L50 6-7), equivalent to the number of chromosomes in other Tigriopus species. BUSCO and k-mer analyses of each haplotype and BUSCO analyses of gene models are relatively complete (95-99%) with respect to gene and k-mer content. Analyses of mitochondrial data also suggest that the Chilean population of Tigriopus we sampled may represent a novel species that we call Tigriopus aff. angulatus. These genomic resources will help us understand the diversity and structure of Tigriopus species and populations as well as facilitate future comparisons of adaptation across parallel environmental gradients.

Understanding evolutionary processes is greatly facilitated by high-quality data on genetic variation. We report the development of a genomic toolkit for a recently bottlenecked, long-term studied species, the Seychelles warbler (Ptimerl dezil; Acrocephalus sechellensis). This toolkit comprises a reference genome assembled into 31 chromosomes, together with functional annotations and reference-panel-free imputation of whole-genome sequences from 1,935 individuals. The genomic data have been used to assign the sequenced individuals into a genetic pedigree. Individual genomic data are associated with a suite of phenotypic metadata, amassed from three decades of fieldwork in this closed, long-term monitored population. We compared sex and parentage assigned using the genomic data with the previously recorded sex and parentage metadata to identify and correct 41 sample DNA samples labelled with the wrong identity. This population resource enables a wide range of analyses, that include, but are not limited to phylogenetics, metabarcoding, recombination rates, linkage patterns, adaptation, heritability, demographic history, selection, and inbreeding estimates. We wish to encourage interest from researchers seeking to collaborate on future analyses and data collection. Overall, our methods demonstrate the potential of next generation sequencing and statistical tools to provide dense genomic datasets at large sample sizes for wild populations.

Genetics may help address the biodiversity crisis by providing information about genetic diversity and temporal changes in demography for species of interest. Advances in whole-genome sequencing create new opportunities for demographic analysis, even based on the two copies of a genome found in a single diploid individual. The Vertebrate Genomes Project (VGP) is generating high-quality, chromosome-level reference genomes across the full range of extant vertebrate species, with its first phase delivering assemblies spanning approximately 95% of vertebrate orders. Using 512 diploid VGP genomes, we quantified intra-species heterozygosity, runs of homozygosity (ROH), and inferred past effective population sizes (Ne) with the Pairwise Sequentially Markovian Coalescent (PSMC). Threatened species are more likely to exhibit lower heterozygosity and longer ROH, though there is large variation in both measures across all IUCN categories. Interestingly, PSMC suggests that estimated historical Ne several thousand generations ago is a better predictor of threatened status than the present day estimate. Co-analysing with life history traits, we found that marine species tend to have lower ROH content, while fossorial species show significantly higher inbreeding levels. Indeed, habitat and foraging strata are much stronger predictors of IUCN status than genetics, with estimated historical Ne providing a small but significant amount of additional information. Together, these results suggest that, while measures of genetic diversity are correlated with IUCN status, much of that correlation may derive from ecological factors such as habitat, with only a relatively small direct contribution. Nevertheless, reference genomes like those generated by the VGP can yield valuable information, like historical Ne, while facilitating population monitoring and management for species of interest.

The blue mussel species complex (Mytilus edulls) is of particular interest both as model species in population genetics and ecology, but also as an economic resource in many regions. Using 10X genomics pseudo-long reads, I assembled genomes of three closely related blue mussel lineages from the Mytllus species complex in the Northern hemisphere. Given the huge diversity within and between lineages in this complex, the objective was to produce affordable genomic resources for population and evolutionary genomic studies to broaden the coverage of this diverse species complex. I used transcriptome guided corrections and scaffolding on a chromosome scale genome of a close species to reduce the fragmentation of the genomes. The result is a set of partially fragmented genomes of equivalent completeness to already published genomes. Three new draft genomes are added to the fast increasing genomic resources of this complex for the Mediterranean M. galloprovlnclalls, the South-European M. edulls and the the North-European M. edulls.

Neotropical raptors are among the most threatened avian groups, facing increasing extinction risks due to habitat loss and human persecution. Despite their importance for ecosystem stability, basic data on their distribution, abundance, and genetic diversity remain scarce. To address these gaps, we assembled and annotated the complete mitochondrial genomes of eight high-priority raptor species from the Neotropics, including the endangered Chaco Eagle (Buteogallus coronatus), Harpy Eagle (Harpia harpyja), and Rufous-tailed Hawk (Buteo ventralis). Mitogenome sizes ranged from 17,848 to 20,449 bp, with consistent gene content, and a Control Region architecture common in Falconidae and Accipitridae. Phylogenetic analyses provided strong support for most relationships, highlighting the value of mitogenomic data for phylogeographic studies. We further designed in silico metabarcoding primers for environmental DNA applications. Primers targeting the 12S rRNA gene and a mini-barcode for the Harpy Eagles Control Region showed high resolution using short, conserved sequences ideal for combining degraded DNA with next-generation sequencing. These resources enable evolutionary research and non-invasive biodiversity monitoring in difficult-to-survey habitats. Overall, our study provides essential genetic tools for monitoring and protecting these ecologically vital yet threatened birds across the Americas.

Reconstructing the evolutionary dynamics of natural populations requires an understanding of the geographical distribution of nuclear and mitochondrial genetic diversity. The analysis of these two genetic markers frequently discloses discordant patterns (mito-nuclear discordance) that can arise simply as a consequence of their different effective population sizes (Ne). Species-specific sex-biased dispersal may contribute to the mito-nuclear discordance observed in natural populations. However, the relative contribution of genetic drift versus sex-biased dispersal in driving mito-nuclear discordance remains insufficiently evaluated. Here, we use forward genetic simulations to address this knowledge gap. Our findings support the baseline level of mito-nuclear discordance arising from distinct genomic Ne, but show that this inherent discordance is magnified by sex-biased dispersal patterns. We demonstrate that female-biased dispersal leads to a marked spatial mismatch between mitochondrial and nuclear diversity across the simulated populations, thereby reducing the spatial concordance between mitochondrial and nuclear markers. Conversely, male dispersal patterns appear to increase, although to a reduced degree, the intrinsic level of discordance between nuclear and mitochondrial geographical marker distribution. Our results highlight the importance of integrating the intrinsic characteristics of nuclear and mitochondrial genomes and the impact of sex-biased dispersal for accurately interpreting patterns of genetic diversity and reconstructing evolutionary histories.

Examples of convergent evolution, wherein distantly related organisms evolve similar traits, including behaviors, underscore the adaptive power of natural selection. In birds, obligate brood parasitism, and the associated loss of parental care behaviors, has evolved independently in seven different lineages, though little is known about the genetic basis of the complex suite of traits associated with this rare life history strategy. We generated genome assemblies for ten brood parasitic species plus eight species representatives of their parental/nesting outgroups. This includes nine long-read chromosome-level assemblies, with scaffold N50 sizes ranging from 38.1 to 72.6 MB, and gene representation completeness measures >97%. Leveraging this new catalog of avian genomes, we constructed clade-level alignments that reveal variation in chromosomal synteny, provide first-time or improved annotations of protein-coding and non-coding genes, and define cross-species ortholog reference sets. We also refine estimates for the timing of the seven independent origins of brood parasitism, ranging from recent events such as 1.6 to 4.5 million years ago in Molothrus cowbirds to much earlier origins over 30 million years ago in two of the three cuckoo lineages. These genomic resources lay the foundation for investigating the genetic and genomic underpinnings of brood parasitism, including the loss of parental care, shifts in mating systems, perhaps resulting in heightened sperm competition, elevated annual fecundity, improved spatial cognition related to nest-finding, and the diverse adaptations shaped by intense coevolution with host species.

The golden jackal (Canis aureus) is rapidly expanding its range in Europe, driven by climate and habitat changes, human influence, and changes in competition with wolves. Its ecological flexibility enables it to thrive in various habitats, including urban areas, raising concerns about its potential role in spreading zoonotic diseases. Jackals may act as reservoirs for pathogens such as Lyme disease and babesiosis, affecting wildlife, humans, and pets. Their close genetic relationship with domestic dogs also increases the risk of hybridization and host-jumping, complicating disease dynamics. To better understand their dispersal ability and host-pathogen dynamics, we present the first chromosome-level genome assembly of the golden jackal, generated using PacBio HiFi sequencing and reference-based scaffolding. The final assembly has a total length of 2.53 Gb in 325 scaffolds, with 98.41% of the sequence anchored to the expected 38+XY chromosomes. The assembly shows high contiguity, with scaffold and contig N50 values of 68.03 Mb and 56.64 Mb, respectively. Annotation revealed 26,084 protein-coding genes, and repetitive elements account for 40.58% of the total assembly. This high-quality reference genome provides an essential resource for studying the genetic basis of the golden jackals adaptation, ecological interactions, and potential as a zoonotic reservoir. It also supports efforts to monitor population expansion and its effects on ecosystems. By advancing our understanding of golden jackal genetics, this work enables future research on evolution, host-pathogen dynamics, and the broader consequences of wildlife dispersal in a rapidly changing environment.

The complete mitochondrial genome (mitogenome) of the tjaku{square}a, Liopholis kintorei was obtained using next-generation sequencing, making it the first recorded mitogenome of the genus Liopholis and the Tiliquini. The mitogenome is 16,844bp in length with a base composition of A (31.7%), T (24.4%), G (14.6%), and C (29.3%) and a G + C content of 43.9%. The genome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes (12S and 16S), and three non-coding fragments, consisting of the putative control region and two mitochondrially encoded heavy strand origin of replication region (OriH). The gene order is identical to that of typical skink mitogenomes. This genomic resource will provide valuable information for genetic studies of this genus and contribute to the growing collection of mitogenomes within the family Scincidae.

Haplotype-resolved (phased) genome assemblies are emerging as important assets for genomic studies of species with high heterozygosity, but remain lacking for key animal lineages. Here, we use PacBio HiFi and Omni-C technologies to assemble the first phased, annotated, chromosome-level genome for any annelid: the reef-building tubeworm Galeolaria caespitosa (Serpulidae). The assembly is 803.5 Mbp long (scaffold N50 = 76.5 Mbp) for haplotype 1 and 789.3 Mbp long (scaffold N50 = 75.4 Mbp) for haplotype 2, which are arranged into 11 pairs of chromosomes showing no sign of sex chromosomes. This compares with cytological analyses reporting 12-13 pairs in Galeolarias closest relatives, including species that are protandrous hermaphrodites. We combined long-read and short-read transcriptome sequencing to annotate both haplotypes, resulting in 43,191 predicted proteins for haplotype 1, 39,675 proteins for haplotype two, and 55.5% of proteins with at least one functional annotation. We also assembled a mitochondrial genome 23 Kbp long, annotating all genes typically found in mitochondrial DNA apart from those coding the 16S ribosomal subunit and the protein atp8 -- a short, fast-evolving mitochondrial gene missing in other metazoans. Comparing Galeolarias genome to those of three other annelids reveals limited collinearity despite 32.2% of shared orthologous gene clusters (4,248 of 13,174 clusters counted in Galeolaria), suggesting extensive chromosomal rearrangements among lineages. New high-quality annelid genomes may help resolve the genetic and evolutionary basis of this diversity.

Hybridization is widespread among marine fishes and can contribute to adaptation, diversification, and the generation of novel phenotypes. In clownfishes, only two wild hybrids Amphiprion leucokranos and A. thiellei have been described, yet those naturally occurring clownfish hybrids remain rarely documented. Both hybrids involve crosses with A. sandaracinos. During field surveys in the Philippines, we identified a previously undocumented clownfish individual with an unusual phenotype resembling both A. sandaracinos and A. perideraion. To characterize its origin, we combined genomic, mitochondrial, and phenotypic comparisons to previously described clownfish hybrid systems. Genome-wide PCA and admixture analyses supported mixed ancestry between A. sandaracinos and A. perideraion. Reconstruction of the mitochondrial genome placed the individual within the A. sandaracinos mitochondrial lineage. Together, these results support a hybrid origin and suggest predominant A. sandaracinos ancestry, consistent with a backcrossed descendant rather than a first-generation hybrid. Comparisons with the previously characterized hybrid A. leucokranos further revealed similarities in genomic composition and phenotype across independently derived clownfish hybrid systems. Our findings identify a previously undocumented natural clownfish hybrid and suggest that integrating genomic and field-based approaches may reveal additional cryptic hybrid systems and improve understanding of hybridization in clownfishes.

Seven species of marine turtles remain in a world currently threatened by anthropogenic activities and climate change, standing at the precipice of extinction. Urgent conservation endeavours are imperative to safeguard their survival and preserve the biodiversity of marine ecosystems. Yet, genetic studies on these turtles have leaned on restricted genetic markers, such as the mitochondrial control region. The markers could provide incomplete or biased estimations of genetic diversity and population structure, thereby limiting precise conservation strategies. Here, we have generated a de novo genome assembly and high-quality whole-genome population datasets from hawksbill turtles nesting and foraging in Singapore. This initiative aims to contribute to unbiased, fine-resolution genetic data on the species, conducting a comprehensive population genomic study. Our analysis results demonstrated a remarkable enhancement in genetic markers. While we identified five different haplotypes defined by five variants within 69 mitochondrial control region sequences, the analysis of 35 whole genome sequences uncovered approximately 12 million single nucleotide polymorphisms (SNPs). Within the Singapore hawksbill turtle population, our whole-genome analysis revealed a pronounced degree of inbreeding, with most samples sharing at least a first cousin relationship. Furthermore, within a multiple-paternity nest, we identified related parents. Additionally, our inference of demographic history underscored the impact of past climate change on the decreasing hawksbill turtle population. We believe this pioneering study will substantially enhance the field of conservation genetic study of marine turtles.

We assembled and annotated a chromosome-level reference genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (QV = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This reference genome, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

Ex-situ conservation is crucial for preserving endangered species by breeding to preserve genetic diversity and provide surplus for translocation, thereby supporting in-situ conservation and enhancing wild populations. Genomic tools can assist breeding strategies and ensure long-term success of ex-situ conservation efforts by assessing genetic introgression, determining genetic origin and status, and inferring genetic relatedness of potential founders. This study aims to develop a comprehensive genomic approach for assessing the genetic profiles of candidate founders for ex-situ breeding, with the goal of releasing surplus individuals while using the endangered Saker Falcons (Falco cherrug) as a study model. Genetic clustering of 31 captive sakers revealed both diverse origins, some matching wild Asian individuals (Mongolia), and a lineage (Group III) divergent from wild populations. Comparative analyses detected hybridisation signals in 61.3% of individuals, including three with gyrfalcon (F. rusticolus) introgression and Group IIIs pronounced divergence indicating past interbreeding with an unknown falcon species. All captive birds exhibited severe inbreeding (FROH = 0.352), far exceeding wild population levels (FROH = 0.131). Using the partial pedigree data of the captive sakers, we established a genetic relatedness threshold of 0.154 (95% CI: 0.096-0.211) to identify cases of related dyads (both full and half-siblings). At this threshold, 18.3% of captive dyads showed relatedness, with asymmetric genetic contributions between pairs, reflecting a functionally small breeding flock. To avoid risks from releasing admixed or inbred individuals, we recommend excluding introgressed birds, strategically pairing purebreds, and sourcing new founders from genetically validated wild sources, especially underrepresented Central Asian lineages. Applying this genomic framework, we demonstrate its role in safeguarding genetic integrity and preventing genetic erosion in conservation breeding programmes, thereby establishing a standard for genomic-led ex-situ conservation.

Tropical regions are biodiversity-rich, yet remain underrepresented in the availability of genomic resources, as is evident in the Western Ghats of India, a biodiversity hotspot with high endemism. Here, we present high-quality, de novo genome assemblies for seven birds, representing seven families distributed in the Western Ghats: Black-naped Monarch (Monarchidae: Hypothymis azurea), Indian Yellow Tit (Paridae: Machlolophus aplonotus), Brown-cheeked Fulvetta (Leiothrichidae: Alcippe poioicephala), Malabar Trogon (Trogonidae: Harpactes fasciatus), Blue-bearded Bee-eater (Meropidae: Nyctyornis athertoni), Malabar Whistling-Thrush (Muscicapidae: Myophonus horsfieldii), Orange-headed Thrush (Turdidae: Geokichla citrina). Using a hybrid Oxford Nanopore long reads - Illumina short reads approach, we assembled genomes with sizes ranging from 1.03 to 1.13 Gbp. All assemblies demonstrated high contiguity and completeness (BUSCO scores >97%, UCEs >4799). Repeat masking identified [~]10% of the genomes as interspersed repeats, and functional annotations yielded an average of 9,619 protein-coding genes per species. Comparative analysis showed our assemblies had significantly higher contiguity than the median of existing avian genomes on NCBI (Wilcoxson test, p = 0.00226). Our genome assemblies fill a key geographic and taxonomic gap in the genomic data and provide a foundational resource for evolutionary and ecological research in the Old-World tropics.