Endangered Species

Freshwater ecosystems are highly biodiverse1 and important for livelihoods and economic development2, but are under substantial stress3. To date, comprehensive global assessments of extinction risk have not included any speciose groups primarily living in freshwaters. Consequently, data from predominantly terrestrial tetrapods4,5 are used to guide environmental policy6 and conservation prioritization7, whereas recent proposals for target setting in freshwaters use abiotic factors8-13. However, there is evidence14-17 that such data are insufficient to represent the needs of freshwater species and achieve biodiversity goals18,19. Here we present the results of a multi-taxon global freshwater fauna assessment for The IUCN Red List of Threatened Species covering 23,496 decapod crustaceans, fishes and odonates, finding that one-quarter are threatened with extinction. Prevalent threats include pollution, dams and water extraction, agriculture and invasive species, with overharvesting also driving extinctions. We also examined the degree of surrogacy of both threatened tetrapods and freshwater abiotic factors (water stress and nitrogen) for threatened freshwater species. Threatened tetrapods are good surrogates when prioritizing sites to maximize rarity-weighted richness, but poorer when prioritizing based on the most range-restricted species. However, they are much better surrogates than abiotic factors, which perform worse than random. Thus, although global priority regions identified for tetrapod conservation are broadly reflective of those for freshwater faunas, given differences in key threats and habitats, meeting the needs of tetrapods cannot be assumed sufficient to conserve freshwater species at local scales.

Threatened species are by definition species that are in need of assistance. In the absence of suitable conservation interventions, they are likely to disappear soon1. There is limited understanding of how and where conservation interventions are applied globally, or how well they work2,3. Here, using information from the International Union for Conservation of Nature Red List and other global databases, we find that for species at risk from three of the biggest drivers of biodiversity loss-habitat loss, overexploitation for international trade and invasive species4-many appear to lack the appropriate types of conservation interventions. Indeed, although there has been substantial recent expansion of the protected area network, we still find that 91% of threatened species have insufficient representation of their habitats within protected areas. Conservation interventions are not implemented uniformly across different taxa and regions and, even when present, have infrequently led to substantial improvements in the status of species. For 58% of the world's threatened terrestrial species, we find conservation interventions to be notably insufficient or absent. We cannot determine whether such species are truly neglected, or whether efforts to recover them are not included in major conservation databases. If they are indeed neglected, the outlook for many of the world's threatened species is grim without more and better targeted action.

The aye-aye (Daubentonia madagascariensis) is the only extant member of the Daubentoniidae primate family. Although several reference genomes exist for this endangered strepsirrhine primate, the predominant usage of short-read sequencing has resulted in limited assembly contiguity and completeness, and no protein-coding gene annotations have yet been released. Here, we present a novel, fully annotated, chromosome-level hybrid de novo assembly for the species based on a combination of Oxford Nanopore Technologies long reads and Illumina short reads and scaffolded using genome-wide chromatin interaction data-a community resource that will improve future conservation efforts as well as primate comparative analyses.

Conservation management of endangered species increasingly relies on genomic approaches to understand how long-term small population sizes affect the fitness of extant individuals. However, despite the growing investment in genomic resources by conservation programmes, the impact that sequencing methods have on the ability to detect inbreeding-related phenomena has been largely overlooked. Here, we compare the use of whole-genome and reduced-representation sequencing approaches in 148 individuals of the critically endangered parrot, the kākāpō (Strigops habroptilus), to assess inbreeding and its effects on female reproductive success. We explore how sequencing choice influences the identification of long stretches of homozygosity across the genome (runs of homozygosity, ROH), and compare the conservation implications of the results produced by each method. Both whole-genome and reduced-representation sequencing approaches provided comparable estimates of genome-wide inbreeding (FROH) and revealed consistent effects on egg hatching success, suggesting that reduced-representation sequencing is capable of detecting inbreeding depression in wild populations under certain conditions. Whole-genome sequencing enabled chromosome-level inbreeding analyses, which revealed no strong evidence of chromosome-specific effects beyond the genome-wide signal. These results suggest that inbreeding depression in kākāpō reflects small effects across many chromosomes rather than strong effects on only a few, and that the primary benefit of whole-genome sequencing lies in improving the precision of genome-wide inbreeding estimates rather than identifying chromosome-specific effects. Our findings highlight the distinct benefits of each sequencing approach in conservation, particularly within the context of resource limitations.