Molecular Phylogenetic Relationships and Unveiling Novel Genetic Diversity among Slow and Pygmy Lorises, including Resurrection of Xanthonycticebus intermedius

Abstract

Genetic analysis of historical museum collections presents an opportunity to clarify the evolutionary history of understudied primate groups, improve taxonomic inferences, and inform conservation efforts. Among the most understudied primate groups, slow and pygmy lorises (genera Nycticebus and Xanthonycticebus) are nocturnal strepsirrhines found in South and Southeast Asia. Previous molecular studies have supported five species, but studies using morphological data suggest the existence of at least nine species. We sequenced four mitochondrial loci, CO1, cytb, d-loop, and ND4, for a total of 3324 aligned characters per sample from 41 historical museum specimens for the most comprehensive geographic coverage to date for these genera. We then combined these sequences with a larger dataset composed of samples collected in Vietnam as well as previously published sequences (total sample size N = 62). We inferred phylogenetic relationships using Bayesian inference and maximum likelihood methods based on data from each locus and on concatenated sequences. We also inferred divergence dates for the most recent common ancestors of major lineages using a BEAST analysis. Consistent with previous studies, we found support for Xanthonycticebus pygmaeus as a basal taxon to the others in the group. We also confirmed the separation between lineages of X. pygmaeus from northern Vietnam/Laos/China and southern Vietnam/Cambodia and included a taxonomic revision recognizing a second taxon of pygmy loris, X. intermedius. Our results found support for multiple reciprocally monophyletic taxa within Borneo and possibly Java. The study will help inform conservation management of these trade-targeted animals as part of a genetic reference database for determining the taxonomic unit and provenance of slow and pygmy lorises confiscated from illegal wildlife trade activities.

Not one, but multiple radiations underlie the biodiversity of Madagascar’s endangered lemurs

“…5 However, most studies to date have suffered from poor species-level sampling, and several new species have been identified in recent years, making lorisiform taxonomy and diversification a subject of continuing discussion. 8,45,46 Our macroevolutionary rate analyses (Fig. 2A, Figs.…”

Conservation museomics

“…There are examples of collections-based research being used to inform conservation actions, planning, or policies, such as determining the historical distributions of living and extinct species to inform protected area planning and monitoring (Arengo et al, 2018), resolving taxonomic issues to inform species assessments and wildlife trade management (Blair et al, 2023;Penna et al, 2024), and assessing anthropogenic impacts on genetic diversity and species extinctions (as reviewed in Benham & Bowie [2023] and Jensen et al [2022]). However, collection-derived DNA in general has been underutilized for conservation (Jensen et al, 2022); as such, there is not yet a standardized framework with best practices to inform conservation decisions based on DNA derived from natural history collections.…”

“…There are examples of collections‐based research being used to inform conservation actions, planning, or policies, such as determining the historical distributions of living and extinct species to inform protected area planning and monitoring (Arengo et al., 2018), resolving taxonomic issues to inform species assessments and wildlife trade management (Blair et al., 2023; Penna et al., 2024), and assessing anthropogenic impacts on genetic diversity and species extinctions (as reviewed in Benham & Bowie [2023] and Jensen et al. [2022]).…”

Slowly Making Sense: A Review of the Two-Step Venom System within Slow (Nycticebus spp.) and Pygmy Lorises (Xanthonycticebus spp.)

“…The slow and pygmy lorises (Primates, Strepsirrhini, Lorisinae) (hereon referred to collectively as slow lorises) are nocturnal primates with at least ten species in two genera distributed across southeast Asia ( Nycticebus bengalensis Lacépède 1800, N. bancanus Lyon, 1906, N. borneanus Lyon, 1906, N. kayan Munds, Nekaris and Ford 2013, N. menagensis Lydekker 1893, N. coucang Boddaert 1785, N. hilleri Stone and Rehn, 1902, N. javanicus Geoffroy Saint-Hilaire 1812, Xanthonyticebus pygameus Bonhote, 1907 and X. intermedius Dao Van Tien, 1960) [ 50 , 51 , 52 , 53 ]. Several morphological traits characterise slow lorises, partly linked to their dedicated tree dwelling nature and specialised diet of exudates [ 54 ].…”

“…The slow and pygmy lorises (Primates, Strepsirrhini, Lorisinae) (hereon referred to collectively as slow lorises) are nocturnal primates with at least ten species in two genera distributed across southeast Asia (Nycticebus bengalensis Lacépède 1800, N. [50][51][52][53]. Several morphological traits characterise slow lorises, partly linked to their dedicated tree dwelling nature and specialised diet of exudates [54].…”