Biology subjects

Nijman, V.

Publications and source records attributed to Nijman, V..

4 recordsLinked to original sources

bioRxiv2026

Abundance, diversity and activity of endogenous retroviruses in the slow loris.

Endogenous retroviruses (ERVs) constitute a significant fraction of vertebrate genomes and serve as genomic records of past retroviral infections, while also influencing host biology through regulatory co-option and, in some cases, ongoing retrotransposition. Despite extensive examination of ERVs in haplorrhine primates, equivalent analyses in strepsirrhines remain absent, leaving a substantial gap in our understanding of ERV diversity and evolutionary dynamics across the primate order. Here, we present the first comprehensive characterisation of ERVs in a strepsirrhine primate, identifying 15 Loris Endogenous Retrovirus (LERV) families encompassing 34 subfamilies and over 6,000 insertions in the Nycticebus coucang reference genome. Phylogenetic analyses resolved LERVs into three retroviral genera: betaretroviruses (LERV1-4), type-D betaretroviruses (LERV5-9), and gammaretroviruses (LERV10-15). LERV2a shows multiple hallmarks of recent or potentially ongoing retrotransposition, including a median insertion age of zero, a high proportion of identical LTR pairs, dN/dS ratios comparable to the active retrovirus HTLV, and insertional polymorphism between two conspecific genomes. Comparative genomic screening across Lorisidae revealed that LERV subfamily distribution broadly mirrors estimated insertion ages, with progressively fewer subfamilies detected in more distantly related species. These findings establish a detailed foundation for understanding retroviral evolution in Strepsirrhini and reveal that ongoing retroviral activity is not restricted to haplorrhine primates.

genomics↗

bioRxiv2025

Novel Endogenous Retrovirus in the Slow Loris

Endogenous retroviruses (ERVs) are the result of an exogenous infectious retrovirus becoming integrated within the host genome through infection of germline cells. The majority of ERV research has been conducted on humans and other great apes and research of them within other primates can provide unique insights. Screening the genome of two endangered slow lorises Nycticebus bengalensis and N. coucang with a previously identified LTR, a novel ERV was identified within their genomes with varying levels of completeness and numerous solo LTRs. Phylogenetic analysis of the genes of this ERV indicates that it is a betaretrovirus most closely related to HERV-K. Despite being closely related to HERV-K, the ERV does not appear to be within humans and is only found in Asian lorises and absent in all other primates. Due to the staggering similarity of viral insertions of this ERV between the two species of slow lorises, indicates that the current N. coucang genome may actually be a hybrid of the two species or a N. bengalensis from a different population as the reference genome. This study highlights that studying ERVs in more distant primates provides information about the genomes and evolution of these species as well as viral evolution.

genomics↗

bioRxiv2022

Multi-lingual multi-platform investigations of online trade in jaguar parts

We conducted research to understand online trade in jaguar parts and develop tools of utility for jaguars and other species. Our research took place to identify potential trade across 31 online platforms in Spanish, Portuguese, English, Dutch, French, Chinese, and Vietnamese. We identified 230 posts from between 2009 and 2019. We screened the images of animal parts shown in search results to verify if from jaguar; 71 posts on 12 different platforms in four languages were accompanied by images identified as definitely jaguar, including a total of 125 jaguar parts (50.7% posts in Spanish, 25.4% Portuguese, 22.5% Chinese and 1.4% French). Search effort varied among languages due to staff availability. Standardizing for effort across languages by dividing number of posts advertising jaguars by search time and number individual searches completed via term/platform combinations, the adjusted rankings of posts were: Portuguese #1, Chinese 2 (time) & 3 (searches), Spanish 3 & 4; French 5 & 4; English 5 & 2, and Dutch 6. Teeth were most common; 156 posts offered at least 367 apparent teeth. From these, 95 teeth were assessed as definitely jaguar; 71 jaguar teeth could be linked to a location, with the majority of the 71 offered for sale from Mexico, China, Bolivia, and Brazil (26.8, 25.4, 16.9, and 12.7% respectively). Ranking of number of teeth was Mexico (19), China (18), Bolivia (12), Brazil (9), Peru/Ecuador (most accurate probable location) (8), Venezuela (3), Guadeloupe (1), and Uruguay (1). The second most traded item, skins and derivative items were only identified from Latin America: Brazil (7), was followed by Peru (6), Bolivia (3), Mexico (2 and 1 skin piece), and Nicaragua and Venezuela (1 each). Whether by number of posts or pieces, the ranking of parts was teeth, skins/pieces of skins, heads, and bodies. Our research presents a snapshot of online jaguar trade and methods that may have utility for many species now traded online. Our research took place within a longer-term project to assist law enforcement in host countries to better identify potential illegal trade online, with research findings informing hubs in Latin America for building such capacity.

ecology↗

bioRxiv2019

Faecal DNA to the rescue: Shotgun sequencing of non-invasive samples reveals two subspecies of Southeast Asian primates to be Critically Endangered species

A significant number of Southeast Asian mammal species described in the 19th and 20th century were subsequently synonymized and are now considered subspecies. Many are affected by rapid habitat loss and there is thus an urgent need to re-assess the conservation status based on species boundaries established with molecular data. However, such data are lacking for many populations and subspecies. We document via a literature survey and empirical study how shotgun sequencing of faecal DNA is a still underutilized but powerful tool for accelerating such evaluations. We obtain 11 mitochondrial genomes for three subspecies in the langur genus Presbytis through shotgun sequencing of faecal DNA (P. femoralis femoralis, P. f. percura, P. siamensis cf. cana). The genomes support the resurrection of all three subspecies to species based on multiple species delimitation algorithms (PTP, ABGD, Objective Clustering) applied to a dataset covering 40 species and 43 subspecies of Asian colobines. For two of the newly recognized species (P. femoralis, P. percura), the results lead to an immediate change in the IUCN status to Critically Endangered due to small population estimates and fragmented habitat. We conclude that faecal DNA should be more widely used for clarifying species boundaries in endangered mammals.

zoology↗