Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species

Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur

Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive potential of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam's famous Ha Long Bay and with less than 100 living individuals one of the most threatened primates in the world. Using high-coverage whole genome data of four wild individuals, we revealed the Cat Ba langur as sister species to its conspecifics of the northern limestone langur clade and found no evidence for extensive secondary gene flow after their initial separation. Compared to other primates and mammals, the Cat Ba langur showed low levels of genetic diversity, long runs of homozygosity, high levels of inbreeding and an excess of deleterious mutations in homozygous state. On the other hand, genetic diversity has been maintained in protein-coding genes and on the gene-rich human chromosome 19 ortholog, suggesting that the Cat Ba langur retained most of its adaptive potential. The Cat Ba langur also exhibits several unique non-synonymous variants that are related to calcium and sodium metabolism, which may have improved adaptation to high calcium intake and saltwater consumption.

Disseminating "hidden" scientific collections: the medium and large-sized terrestrial mammals at the Museo di Anatomia Comparata "Giovanni Battista Grassi", Roma, Italy

The dissemination of specimen data in scientific collections is a crucial step in making them available to the scientific community. However, even today, especially in some countries, little or nothing is known about the contents of the naturalistic collections of some museums. This is regrettable, especially in cases where the collections include historic specimens and endangered species. The Museum of Comparative Anatomy "Giovanni Battista Grassi", situated in Rome, Italy, houses historical anatomical and didactic collections, with specimens gathered from 1600s and almost worldwide. The collection holds 444 specimens of medium and large-sized terrestrial mammals, comprising 25 fossils, 40 skins, 186 skulls, 70 skeletons and 123 anatomical pieces, representing 63% of recent mammal orders, mainly from localities of Africa and Europe. A list of this material, indexed by the orders and families, is provided, as well as comments on the conservation status of the species. Remarkable data are summarised, including new data on a hippopotamus specimen from an extinct population and the record of three rhinoceros species from 1600s. Besides comparative anatomical studies, the Museum of Comparative Anatomy of Sapienza University emerges as a source of important material for biodiversity genomics.

Phylogenomic analyses provide insights into primate evolution

Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.

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

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.

Masturbation in a male Phayre's langur, Trachypithecus phayrei

Masturbation is a common auto-sexual behaviour in humans but is not explicitly known in a major portion of non-human primates. We report the first masturbatory behaviour in a male Phayre's langur, Trachypithecus phayrei, observed in a semi-evergreen forest in northeastern Bangladesh. Like other Asian colobines, the multi-male-multi-female groups of the Phayre's langur suggest a multilevel social organization and a complex hierarchy among males. The lack of sexual opportunity could result in masturbation and sperm competition among males. However, sperm competition is reported to be low in such non-seasonal breeders. Hence, we suggest an adequate characterization of the socio-sexual behaviour and reproductive strategies of this globally endangered primate in order to demonstrate the causes, cost and consequences of masturbation. We also urge further scientific exploration into masturbation among primates due to its evolutionary and conservational significance.

Evolutionary history of Sundaland shrews (Eulipotyphla: Soricidae: Crocidura) with a focus on Borneo

The hyperdiverse shrew genus Crocidura is one of few small mammal genera distributed across Sundaland and all of its boundaries. This represents a rare opportunity to study the geological history of this region through the evolutionary history of these shrews. We generate a phylogeny of all recognized species of Sundaland Crocidura and show that most speciation events took place during the Pleistocene, prior to the inundation of the Sunda Shelf around 400 000 years ago. We find east–west differentiation within two separate lineages on Borneo, and that the current taxonomy of its two endemic species does not reflect evolutionary history, but ecophenotypic variation of plastic traits related to elevation. Sulawesi shrews are monophyletic, with a single notable exception: the black-footed shrew (C. nigripes). We show that the black-footed shrew diverged from its relatives on Borneo recently, suggesting a human-assisted breach of Wallace’s line. Overall, the number of Crocidura species, especially on Borneo, probably remains an underestimate.