M. Thomas P. Gilbert’s research while affiliated with Globe Institute of Technology and other places

Loss of genetic diversity threatens a species' adaptive potential and long-term resilience. Predicted to be extinct by 2038, the orange-bellied parrot (Neophema chrysogaster) is a Critically Endangered migratory bird threatened by numerous viral, bacterial and fungal diseases. The species has undergone multiple population crashes, reaching a low of three wild-born females and 13 males in 2016 and is now represented by only a single wild population and individuals in the captive breeding program. Here we used our high-quality long-read reference genome, and contemporary and historical resequenced genomes from as early as 1829, to track the long-term genomic erosion and immunogenetic diversity decline in this species. 62% of genomic diversity was lost between historical (mean autosomal heterozygosity = 0.00149 ± 0.000699 SD) and contemporary (0.00057 ± 0.000026) parrots. A greater number and length of runs of homozygosity in contemporary samples was also observed. A temporal reduction of the number of alleles at Toll-like receptor genes was found (historical average alleles = 5.78 ± 2.73; contemporary = 3.89 ± 2.10), potentially exacerbating disease susceptibility in the contemporary population. Of particular concern is the new threat of avian influenza strain (HPAI) to Australia. We discuss the conservation implications of our findings and propose that hybridization and synthetic biology may be required to address the catastrophic loss of genetic diversity that has occurred this species in order to prevent extinction.

The recently extirpated Zanzibar leopard was the only known African leopard ( Panthera pardus spp.) population restricted exclusively to a major island habitat. Although its demise was driven through habitat change and conflict with humans, given its role as a keystone species for the Zanzibar Archipelago, its successful potential reintroduction might offer a means for helping preserve the natural biodiversity of its former habitat. Whether this is feasible, however, would be contingent on both whether closely related source populations can be identified on mainland Africa, and whether the Zanzibar form exhibited any special adaptations that might need to be considered when choosing such a source. In light of these questions, we genomically profiled two of the six known historic specimens, to explore whether they represent a realistic candidate for de‐extirpation through reintroduction. Our analyses indicate that despite its geographical separation, the Zanzibar leopard shared a close genetic relationship with mainland East African individuals. Furthermore, although its uniqueness as an island population was emphasised by genomic signatures of high inbreeding and increased mutation load, the latter similar to the level of the critically endangered Amur leopard ( P. p. orientalis ), we find no evidence of functionally significant genetic diversity unique to Zanzibar. We therefore conclude that should attempts to restore leopards to Zanzibar be considered, then mainland East African leopards would provide a suitable gene pool.

Now extinct, the aurochs (Bos primigenius) was a keystone species in prehistoric Eurasian and North African ecosystems, and the progenitor of cattle (Bos taurus), domesticates that have provided people with food and labour for millennia¹. Here we analysed 38 ancient genomes and found 4 distinct population ancestries in the aurochs—European, Southwest Asian, North Asian and South Asian—each of which has dynamic trajectories that have responded to changes in climate and human influence. Similarly to Homo heidelbergensis, aurochsen first entered Europe around 650 thousand years ago², but early populations left only trace ancestry, with both North Asian and European B. primigenius genomes coalescing during the most recent glaciation. North Asian and European populations then appear separated until mixing after the climate amelioration of the early Holocene. European aurochsen endured the more severe bottleneck during the Last Glacial Maximum, retreating to southern refugia before recolonizing from Iberia. Domestication involved the capture of a small number of individuals from the Southwest Asian aurochs population, followed by early and pervasive male-mediated admixture involving each ancestral strain of aurochs after domestic stocks dispersed beyond their cradle of origin.

The potential of ancient DNA analyses to provide independent sources of information about events in the historical record remains to be demonstrated. Here we apply palaeogenomic analysis to human remains excavated from a medieval well at the ruins of Sverresborg Castle in central Norway. In Sverris Saga, the Old Norse saga of King Sverre Sigurdsson, one passage details a 1197-CE raid on the castle and mentions a dead man thrown into the well. Radiocarbon dating supports that these are that individual’s remains. We sequenced the Well-man’s nuclear genome to 3.4× and compared it to Scandinavian populations, revealing he was closely related to inhabitants of southern Norway. This was surprising because King Sverre’s defeated army was assumed to be recruited from parts of central Norway, whereas the raiders were from the south. The findings also indicate that the unique genetic drift seen in present-day southern Norwegians already existed 800 years ago.

Gray wolves (Canis lupus) in Asia encompass most of the species' global genetic diversity and many endangered populations. However, a clear understanding of the evolutionary history of wolves from many parts of Asia, especially southern regions, is lacking. We used 98 whole genomes of wolves sampled across Eurasia to better resolve their evolutionary history by investigating phylogenetic and gene flow histories across the genome, and to characterize their demographic history and genetic diversity. The strongest barriers to gene flow coincided with boundaries separating the three major extant wolf lineages - Indian, Tibetan, and Holarctic. Wolves in the central Asian mountain ranges belonged to the Holarctic lineage, and despite their geographic adjacency only shared minimal ancestry with the Tibetan lineage. In contrast, wolves from eastern Asia share population-wide ancestry with the Tibetan lineage, which may reflect an unsampled lineage similar, but not exactly to, the modern-day Tibetan lineage. Wolves from southwestern Asia also share population-wide ancestry with the Indian lineage, likely due to old (>6kya) admixture events. Long-term historical declines over the last 100,000 years, geographic isolation, and recent inbreeding have resulted in the Indian and Tibetan wolves having some of the lowest levels of genetic diversity and highest realized genetic loads. In contrast, adjacent populations exhibit some of the highest genetic diversity, due in part to admixture along contact zones. Our study illustrates how using multiple approaches that consider heterogenous signals across the genome can more fully resolve the historical and contemporary processes that have led to present-day species' diversity.

Feralisation, the process by which domesticated organisms revert to a wild state, is a widespread phenomenon across various species. Successfully adapting to a new environment with different access to food, shelter, and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 draft genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed distinct taxonomic and functional profiles between the two groups. While taxonomic enrichment was balanced, microbial functional capacities were significantly enriched in feral cats. These functional enhancements, particularly in amino acid and lipid degradation, correspond to feral cats' dietary reliance on crude protein and fat. Additionally, functional differences were consistent with behavioural contrasts, such as the more aggressive and elusive behaviour measured in feral cats compared to the docile behaviour of domestic cats. Finally, the observed enrichment in short-chain fatty acid, neurotransmitter, and vitamin B12 production in feral cats aligns with improved cognitive function and potentially contributes to their heightened aggression and elusiveness. Our findings suggest that microbiome shifts may play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, supporting the adaptive success of feral cats in the wild.

The decline in bee diversity, largely driven by habitat loss, climate change and invasive species, is well‐documented. Within this context, the genus Megachile Latreille, 1802 (Hymenoptera: Megachilidae), a diverse group of solitary leafcutter bees, lacks comprehensive species‐level conservation and taxonomic assessments, potentially concealing population declines and extinctions. Megachile pruina is one of Bermuda's three bee species and possibly the last native bee on the island. Formerly distributed widely across the island, it is now restricted to a small 11.5 ha area within the Castle Harbour Islands Nature Reserve. Classified as ‘Vulnerable’ under the Bermuda Protected Species Act, its taxonomic and conservation status remains uncertain, particularly its evolutionary relationships with populations in the United States. Here, we analyse nuclear genomes and mitochondrial genomes to reveal that Bermuda's M. pruina population is genetically distinct from mainland US populations and show no close association with any sampled US population, suggesting that Bermuda's represent a unique evolutionary lineage. Our genetic diversity assessment shows lower genetic diversity in Bermuda's population compared with the United States, highlighting a higher level of vulnerability than originally thought. We recommend maintaining its current protection status and advocate for the pressing need of expanding ecological and biological studies to facilitate appropriate conservation and monitoring measures.

We present a genome assembly from an individual male Alexandrinus eques , formerly Psittacula eques (the Mauritius Parakeet; Chordata; Aves; Psittaciformes; Psittacidae). The genome sequence is 1203.8 megabases in span. Most of the assembly is scaffolded into 35 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.