Tablizo, F. | bioRxiv Science

bioRxiv2025

Genomic Analysis Reveals Recent Population Decline and Exceptionally Low Genome-Wide Heterozygosity of the Critically Endangered Philippine Eagle, Pithecophaga jefferyi (Aves: Accipitridae)

The Philippine Eagle (Pithecophaga jefferyi), is one of the rarest eagles in the world and is the national bird of the Philippines. It is listed by the International Union for Conservation of Nature (IUCN) as a critically endangered raptor and has been the subject of an intensive captive breeding program which started more than 30 years ago to ensure the survival and conservation of the species. To infer the genetic diversity and demographic history of the Philippine Eagle, we sequenced and analyzed the genomes of 35 individuals under the captive breeding program of the Philippine Eagle Foundation. Phylogenetic analysis of the draft reference sequence generated in this study placed P. jefferyi within the subfamily Circaetinae of Accipitridae. Demographic history reconstruction from genome-wide variants revealed two historical bottlenecks, as well as an ongoing population decline which was found to predate documented deforestation in the Philippines. This observation suggests that unobserved natural or anthropogenic factors might have severely affected the Philippine Eagle population long before habitat fragmentation. Genome-wide heterozygosity estimates placed the Philippine Eagle as having one of the lowest genome-wide heterozygosity levels measured among raptors. This highlights the precarious genetic state of the Philippine Eagle, as critically low heterozygosity raises risks of inbreeding depression, reduced reproductive success, and increased vulnerability to diseases, climate change, and habitat loss. The genomic resources generated in this study can therefore guide conservation strategies such as breeding program design, genetic monitoring, and other efforts to diversify existing populations to ensure both demographic stability and genetic resilience of the Philippine Eagle. Subject AreasPhilippine Eagle, Genomics, Genome-wide heterozygosity, Demographic History, Conservation, Biodiversity, Bioinformatics

genomics↗

bioRxiv2025

Gut microbial communities of velvet worm Euperipatoides rowelli (Onychophora) across deadwood microhabitats in southeastern Australia.

This study investigated the gut microbial community of the velvet worm Euperipatoides rowelli, a saproxylic invertebrate residing in deadwood microhabitats within historical refugia in the Tallaganda forest, New South Wales, Australia. The eucalyptus-dominated temperate forest is marked by unique topography, hydrology, and historical influences from Pleistocene glacial cycles. We described patterns in gut microbial community structure and composition across eight sites. The velvet worms were unfed for two weeks prior to dissection to lessen the influence of transient prey-associated microorganisms. Amplicon sequencing of the V4-V5 region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform, with positive and negative controls integrated to assess contamination and ensure data quality. Alpha and beta diversity metrics demonstrated minimal overall variation among sites, suggesting broadly similar community structure. However, a closer look at individual taxa revealed contrasting patterns. Proteobacteria dominated the gut microbiome, with genus A37b (Rickettsia) forming part of the core microbiome in 50% of individuals; its presence varied among sites. In contrast, Spiroplasma displayed substantial site-specific variation in relative abundance. These findings suggest that, while overall diversity remained relatively stable, particular taxa displayed heterogenous distributions across historical refugia. Collectively, our findings suggest that gut microbiomes of velvet worms are shaped more by environmental filtering within deadwood microhabitats than by host geographic differences, reflecting a combination of stochastic and niche-driven assembly processes. Impact StatementWe present the first characterization of the gut microbiome in the saproxylic velvet worm Euperipatoides rowelli from temperate Australian forests. Despite marked host genetic divergence, microbial communities showed minimal spatial structuring, suggesting substantial environmental filtering within deadwood microhabitats. The limited variation and transient taxa may indicate microbial associations are more likely environmentally acquired rather than host-specific. These findings broaden our understanding of the microbiome assembly in underexplored invertebrates and underscore the influence of ecological context over site-based spatial differentiation in shaping gut microbial communities.

microbiology↗