Molecular delineation of the Y-borne Sry gene in the Formosan pangolin (Manis pentadactyla pentadactyla) and its phylogenetic implications for Pholidota in extant mammals

Pangolin Genomes Offer Key Insights and Resources for the World's Most Trafficked Wild Mammals

Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (∼43x-77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.

The brain of the tree pangolin (Manis tricuspis). VII. The amygdaloid body

Here, we describe the cytoarchitecture and chemoarchitecture of the amygdaloid body of the tree pangolin. Our definition of the amygdaloid body includes the pallial portions of the amygdala, and the centromedial group that is a derivative of the subpallium and part of the extended amygdala. The remainder of the extended amygdala is not described herein. Within the amygdaloid body of the tree pangolin, we identified the basolateral group (composed of the lateral, basal, and accessory basal amygdaloid nuclei), the superficial, or cortical nuclei (the anterior and posterior cortical nuclei, the periamygdaloid cortex, and nuclei of the olfactory tract), the centromedial group (the central amygdaloid nucleus and the medial nuclear cluster), and other amygdaloid nuclei (the anterior amygdaloid area, the amygdalohippocampal area, the intramedullary group, and intercalated islands). The location within and relative to each other within the amygdaloid body and the internal subdivisions of these groups were very similar to that reported in other mammalian species, with no clearly derived features specific to the tree pangolin. The only variation was the lack of an insular appearance of the intercalated islands, which in the tree pangolin were observed as a continuous band of neurons located dorsomedial to the basolateral group similar in appearance to and almost continuous with the intramedullary group. In carnivores, the closest relatives of the pangolins, and laboratory rats, a similar appearance of portions of the intercalated islands has been noted.

Development and characterization of 20 polymorphic microsatellite markers for the white-bellied pangolin Phataginus tricuspis (Mammalia, Pholidota)

Pangolins, or scaly anteaters, have recently been flagshiped as one of the most illegally traded mammals, and as a corollary, as potential intermediate hosts at the origin of the COVID-19 pandemic. In order to improve the traceability of their trade, we developed 20 polymorphic microsatellite loci for the white-bellied pangolin (Phataginus tricuspis), the species most frequently found on African bushmeat markets. We genotyped 24 white-bellied pangolins from the Douala market, Cameroon, originating from the Ebo forest c. 75 km north-east of Douala. The number of alleles per locus ranged from 4 to 12 (mean = 6.95), and mean observed and expected heterozygosities were 0.592 (0.208-0.875) and 0.671 (0.469-0.836), respectively. Genetic diversity was higher than that cross-estimated from microsatellite loci developed for other species of pangolins. Two loci deviated from Hardy-Weinberg equilibrium and two loci showed linkage disequilibrium. Genetic variance (PCoA) was increased with the addition of 13 pangolins of unknown origin, possibly suggesting that the Douala market is fed from differentiated source populations of white-bellied pangolins. Each of the 37 individuals had a unique multilocus genotype. The unbiased probability of identity (uPI) and the probability of identity among siblings (PIsibs) were both very low (uPI = 8.443 e-21; PIsibs = 1.011 e-07). Only five microsatellite loci were needed to reach the conservative value of PIsibs < 0.01, overall indicating a powerful discriminating power of our combined loci. These 20 newly developed microsatellite loci might prove useful in tracing the local-to-global trade of the white-bellied pangolin, and will hopefully contribute to the DNA-assisted implementation of future conservation strategies at reasonable costs.

The brain of the tree pangolin (Manis tricuspis). VI. The brainstem and cerebellum

The brainstem (midbrain, pons, and medulla oblongata) and cerebellum (diencephalic prosomere 1 through to rhombomere 11) play central roles in the processing of sensorimotor information, autonomic activity, levels of awareness and the control of functions external to the conscious cognitive world of mammals. As such, comparative analyses of these structures, especially the understanding of specializations or reductions of structures with functions that have been elucidated in commonly studied mammalian species, can provide crucial information for our understanding of the behavior of less commonly studied species, like pangolins. In the broadest sense, the nuclear complexes and subdivisions of nuclear complexes, the topographical arrangement, the neuronal chemistry, and fiber pathways of the tree pangolin conform to that typically observed across more commonly studied mammalian species. Despite this, variations in regions associated with the locus coeruleus complex, auditory system, and motor, neuromodulatory and autonomic systems involved in feeding, were observed in the current study. While we have previously detailed the unusual locus coeruleus complex of the tree pangolin, the superior olivary nuclear complex of the auditory system, while not exhibiting additional nuclei or having an altered organization, this nuclear complex, particularly the lateral superior olivary nucleus and nucleus of the trapezoid body, shows architectonic refinement. The cephalic decussation of the pyramidal tract, an enlarged hypoglossal nucleus, an additional subdivision of the serotonergic raphe obscurus nucleus, and the expansion of the superior salivatory nucleus, all indicate neuronal specializations related to the myrmecophagous diet of the pangolins.

The brain of the tree pangolin (Manis tricuspis). V. The diencephalon and hypothalamus

The diencephalon (dorsal thalamus, ventral thalamus, and epithalamus) and the hypothalamus, play central roles in the processing of the majority of neural information within the central nervous system. Given the interactions of the diencephalon and hypothalamus with virtually all portions of the central nervous system, the comparative analysis of these regions lend key insights into potential neural, evolutionary, and behavioral specializations in different species. Here, we continue our analysis of the brain of the tree pangolin by providing a comprehensive description of the organization of the diencephalon and hypothalamus using a range of standard and immunohistochemical staining methods. In general, the diencephalon and hypothalamus of the tree pangolin follow the organization typically observed across mammals. No unusual structural configurations of the ventral thalamus, epithalamus, or hypothalamus were noted. Within the dorsal thalamus, the vast majority of typically identified nuclear groups and component nuclei were observed. The visual portion of the tree pangolin dorsal thalamus appears to be organized in a manner not dissimilar to that seen in most nonprimate and noncarnivore mammals, and lacks certain features that are present in the closely related carnivores. Within the ventral medial geniculate nucleus, a modular organization, revealed with parvalbumin neuropil immunostaining, is suggestive of specialized auditory processing in the tree pangolin. In addition, a potential absence of hypothalamic cholinergic neurons is suggestive of unusual patterns of sleep. These observations are discussed in an evolutionary and functional framework regarding the phylogeny and life history of the pangolins.

The brain of the tree pangolin (Manis tricuspis). IV. The hippocampal formation

Employing a range of standard and immunohistochemical stains we provide a description of the hippocampal formation in the brain of the tree pangolin. For the most part, the architecture, chemical neuroanatomy, and topological relationships of the component parts of the hippocampal formation of the tree pangolin were consistent with that observed in other mammalian species. Within the hippocampus proper fields CA1, 3, and 4 could be identified with certainty, while CA2 was tentatively identified as a small transitional zone between the CA1 and CA3 fields. Within the dentate gyrus evidence for adult hippocampal neurogenesis at a rate comparable to other mammals was observed. The subicular complex and entorhinal cortex also exhibited divisions typically observed in other mammalian species. In contrast to many other mammals, an architecturally and neurochemically distinct CA4 field was observed, supporting Lorente de Nó's proposed CA4 field, at least in some mammalian species. In addition, up to seven laminae were evident in the dentate gyrus. Calretinin immunostaining revealed the three sublamina of the molecular layer, while immunostaining for vesicular glutamate transporter 2 and neurofilament H indicate that the granule cell layer was composed of two sublamina. The similarities and differences observed in the tree pangolin indicate that the hippocampal formation is an anatomically and neurochemically conserved neural unit in mammalian evolution, but minor changes may relate to specific life history features and habits of species.

Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification

Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp). We used a time-calibrated, Bayesian inference phylogenetic framework and conducted character-based, genetic and phylogenetic delineation of species hypotheses within African common pangolins. We identified six geographic lineages partitioned into western Africa, Ghana, the Dahomey Gap, western central Africa, Gabon and central Africa, all diverging during the Middle to Late Pleistocene. MtDNA (cytochrome b + control region) was the sole locus to provide diagnostic characters for each of the six lineages. Tree-based Bayesian delimitation methods using single- and multilocus approaches gave high support for 'species' level recognition of the six African common pangolin lineages. Although the diversification of African common pangolins occurred during Pleistocene cyclical glaciations, causative correlation with traditional rainforest refugia and riverine barriers in Africa was not straightforward. We conclude on the existence of six cryptic lineages within African common pangolins, which might be of major relevance for future conservation strategies. The high discriminative power of the mtDNA markers used in this study should allow an efficient molecular tracing of the regional origin of African common pangolin seizures.

Genomic analyses of the Formosan harvest mouse (Micromys minutus) and comparisons to the brown Norway rat (Rattus norvegicus) and the house mouse (Mus musculus)

The harvest mouse, Micromys minutus (MMIN), has a very wide range of distribution (from the British Isles across the Euroasian continent to Japan and Taiwan). We studied an isolated population of MMIN in Taiwan, which is at the southeastern margin of the species' geographic distribution, and compared its genetic complement with those of the same species previously reported from other geographic locations and with two model rodent species, the house mouse (Mus musculus) and the brown Norway rat (Rattus norvegicus). The diploid number (2N) of MMIN was 68, consistent with that reported for other populations. However, variations were noted in the fundamental number (FN) and the shape and banding patterns of the individual chromosomes among populations. The FN of MMIN was estimated to be 72, including 2 bi-armed autosomes, 31 one-armed autosomes, and one pair of one-armed sex chromosomes. Here, we propose the first ideogram for MMIN. C-banding, Ag-NOR, and the locations of 18S rRNA gene sequences (MMIN chromosomes no. 10, 14, 19, 29, 31, 33, and X) mapped by fluorescence in situ hybridization (FISH) are also reported. Additionally, we compared the 18S rDNA sequences and performed cross-species X chromosome painting (FISH) for M. minutus, M. musculus, and R. norvegicus. The results indicate that both genetic elements are rather conserved across species. Thus, implications for the phylogenetic position of Micromys were limited.

Use of a cytogenetic whole-genome comparison to resolve phylogenetic relationships among three species: implications for mammalian systematics and conservation biology

The objective was to apply a novel modification of a genome-wide, comparative cytogenetic technique (comparative genomic hybridization, comparative genomic hybridization (CGH)), to study species belonging to the myrmecophagous (ant/termite eating) mammalian orders/superorders (Pholidota, Tubulidentata, Carnivora, and Xenarthra), as a model for other applications in mammalian systematics and conservation biology. In this study, CGH was applied to high-quality metaphase spreads of pangolin (Pholidota), using probes of sloth and canine (Xenarthra and Carnivora, respectively) genomic DNA labeled with different fluorophores, thereby facilitating analysis of the visible color spectrum on pangolin karyotypes. Our results posited that pholidotes are closer to carnivores than to xenarthrans, which confirmed the current consensus that myrmecophagy in these mammalian lineages was more likely because of homoplasy (convergent evolution) than being an ancestral character. Since the modified CGH technique used is genome-wide, has chromosome-level resolution, and does not need full genome sequencing, it has considerable potential in systematics and other fields.