Uncovering the magnitude of African pangolin poaching with extensive nanopore DNA genotyping of seized scales

Trade in pangolins is illegal, and yet tons of their scales and products are seized at various ports. These large seizures are challenging to process and comprehensively genotype for upstream provenance tracing and species identification for prosecution. We implemented a scalable DNA barcoding pipeline in which rapid DNA extraction and MinION sequencing were used to genotype a substantial proportion of pangolin scales subsampled from 2 record shipments seized in Singapore in 2019 (37.5 t). We used reference sequences to match the scales to phylogeographical regions of origin. In total, we identified 2346 cytochrome b (cytb) barcodes of white-bellied (Phataginus tricuspis) (from 1091 scales), black-bellied (Phataginus tetradactyla) (227 scales), and giant (Smutsia gigantea) (1028 scales) pangolins. Haplotype diversity was higher for P. tricuspis scales (121 haplotypes, 66 novel) than that for P. tetradactyla (22 haplotypes, 15 novel) and S. gigantea (25 haplotypes, 21 novel) scales. Of the novel haplotypes, 74.2% were likely from western and west-central Africa, suggesting potential resurgence of poaching and newly exploited populations in these regions. Our results illustrate the utility of extensively subsampling large seizures and outline an efficient molecular approach for rapid genetic screening that should be accessible to most forensic laboratories and enforcement agencies.

Distribution patterns, carbon sources and niche partitioning in cave shrimps (Atyidae: Typhlatya)

Cave shrimps of the Typhlatya genus are common and widespread in fresh, brackish and marine groundwater throughout the Yucatan Peninsula (Mexico). These species are ideal models to test niche partitioning within sympatric species in oligotrophic systems. Nevertheless, their food sources remain unidentified, and despite their frequency and functional importance, distribution and abundance patterns of these species within caves have not been fully recognized. Here, we describe the abundance of three Typhlatya species in different temporal and spatial scales, investigate changes in water conditions, and potential sources of carbon as an indication of food origin. Species composition and abundance varied markedly in space and time revealing patterns that differed from one system to another and in relation to environmental parameters. Isotope analysis showed that each species reflects a particular δ¹³C and Δ¹⁴C fingerprint, suggesting they feed in different proportions from the available carbon sources. Overall, our findings suggest a niche partitioning of habitat and feeding sources amongst the three Typhlatya species investigated, where environmental characteristics and physiological differences could play an important role governing their distribution patterns.

New distribution records of subterranean crustaceans from cenotes in Yucatan (Mexico)

New records of 14 stygobiont crustacean species pertaining to six Malacostraca orders from 32 cenotes are presented, with their associated caves of the state of Yucatan, Mexico, together with an individual account for each species. Species composition of most of the investigated cenotes is examined for the first time. A thermosbaenacean and two amphipod species were not formally recorded to the cenote ecosystems of the state of Yucatan prior to our research. Distribution data of a cirolanid isopod previously known only from its type locality is also provided. Barcodes of mitochondrial cytochrome c oxidase subunit I for the reported peracarid species previously lacking this information have been included in present study as tools for species identification and a baseline of further molecular genetic analyses.

Explaining diversity patterns in dark waters – a study of aquatic caves in Yucatán, Mexico

In the tropics, limestone caves in karstic areas are known for their unique biodiversity. However, many caves remain unstudied and little is known about underlying gradients that determine diversity and biomass in aquatic microhabitats. Here, we sampled zooplankton and benthos in a set of 12 aquatic caves, locally called closed cenotes in Yucatán, Mexico. Our aim was to explain diversity patterns and differences in biomass with particular attention for correlations between bat colony characteristics and other biota. Compared with caves that support photosynthesis, diversity was low with an average of four planktonic and two benthic species in these dark caves. Undetectable phosphorus concentrations in the water suggest this nutrient is limiting. Several associations hint at a potential link between bat abundance and functional guild composition, water quality and aquatic biota. As such, more bats were linked to higher nitrate concentrations. Yet this was not translated to higher invertebrate biomass, probably since phosphorus is limiting. Overall, the trends found in this survey suggest that bats could be important as fertilizers of the caves although mechanistic links that mediate the flux of nutrients need to be confirmed experimentally.

How is the anchialine fauna distributed within a cave? A study of the Ox Bel Ha System, Yucatan Peninsula, Mexico

A study describing the diversity and distribution pattern of the stygobitic fauna in the Ox Bel Ha anchialine cave system adjacent to the Caribbean coast of the Yucatan Peninsula, Mexico is presented. A total of 15 species of crustaceans were collected in three surveys at four points situated along a 10.2 km transect perpendicular to the coast line. A freshwater mass dominated throughout the transect with a halocline that appeared progressively deeper, from 10 to 18 m, with increasing distance from the coast. All the recorded species, except for one, occurred throughout the transect with no defined pattern. Abundance and species richness did not vary significantly with distance from the coast, whereas diversity (H’) peaked in the second sampling site at 3.17 km from the coast. As expected, most of the organisms occurred only in the freshwater layer, except for the remipede Xibalbanustulumensis (Yager, 1987) that was found always at or below the halocline, and five other species that were found above and below the halocline. In the horizontal scale, species composition and occurrence mixed without a defined pattern, both, for sampling dates and sites. The results show that the analyzed fauna is distributed throughout the 10.2 km transect without showing any defined horizontal zonation pointing to a high connectivity among all sections. Due to the high connectivity within the caves in the area, it is expected that significant variation in species composition and distribution will be found at a larger regional scale.

High genetic diversity and absence of founder effects in a worldwide aquatic invader

The introduced oriental shrimp Palaemon macrodactylus has recently become widespread in temperate estuaries worldwide. However, this recent worldwide spread outside of its native range arises after a previous introduction to the US Pacific coast, where it was restricted for more than 30 years. Using a phylogeographic approach, the present work investigates the genetic history of the invasion of this decapod worldwide. Japan acted as the main native source area for worldwide introduced populations, but other native areas (likely South Korea and China) may act as source populations as well. The recently introduced European and NW Atlantic populations result from colonization from both Japan and an unknown area of the native range, although colonization from the NE Pacific could not be ruled out. Most introduced populations had higher haplotypic diversity than most native populations. P. macrodactylus has a strong potential to become one of the most widespread introduced species and may become the dominant estuarine shrimp in Europe. The ecological and economic consequences of this invasion remain to be thoroughly evaluated.

Phylogeography of the sponge Suberites diversicolor in Indonesia: insights into the evolution of marine lake populations

The existence of multiple independently derived populations in landlocked marine lakes provides an opportunity for fundamental research into the role of isolation in population divergence and speciation in marine taxa. Marine lakes are landlocked water bodies that maintain a marine character through narrow submarine connections to the sea and could be regarded as the marine equivalents of terrestrial islands. The sponge Suberites diversicolor (Porifera: Demospongiae: Suberitidae) is typical of marine lake habitats in the Indo-Australian Archipelago. Four molecular markers (two mitochondrial and two nuclear) were employed to study genetic structure of populations within and between marine lakes in Indonesia and three coastal locations in Indonesia, Singapore and Australia. Within populations of S. diversicolor two strongly divergent lineages (A & B) (COI: p = 0.4% and ITS: p = 7.3%) were found, that may constitute cryptic species. Lineage A only occurred in Kakaban lake (East Kalimantan), while lineage B was present in all sampled populations. Within lineage B, we found low levels of genetic diversity in lakes, though there was spatial genetic population structuring. The Australian population is genetically differentiated from the Indonesian populations. Within Indonesia we did not record an East-West barrier, which has frequently been reported for other marine invertebrates. Kakaban lake is the largest and most isolated marine lake in Indonesia and contains the highest genetic diversity with genetic variants not observed elsewhere. Kakaban lake may be an area where multiple putative refugia populations have come into secondary contact, resulting in high levels of genetic diversity and a high number of endemic species.