Pangolin Genomes Offer Key Insights and Resources for the World’s Most Trafficked Wild Mammals
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PROVIDER: S-EPMC10551234 | biostudies-literature | 2023 Oct
REPOSITORIES: biostudies-literature
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Project description:BackgroundRaillietina species belong to the family Davaineidae, which parasitizes in a wide variety of mammals and birds, causing stunted growth, lethargy, emaciation, and digestive tract obstruction. However, only a limited number of Raillietina species have been identified in wild animals.MethodsWe analyzed and annotated the complete mitochondrial (mt) genome of a worm from the intestine of a wild pangolin using Illumina sequencing of whole genomic DNA.ResultsThese findings showed the presence of two mtDNA sequences in Raillietina sp., designated as mt1 and mt2, with the lengths of 14,331 bp and 14,341 bp, respectively. Both the mts genomes of Raillietina sp. comprised 36 genes, containing 12 protein-coding genes (PCGs), 2 ribosomal RNAs, and 22 transfer RNAs. Gene arrangements of both mt genomes of Raillietina sp. were similar to those of most flatworms, except for taeniids, which shift positions between tRNAL1 and tRNAS2 genes. Twenty of 22 tRNA secondary structures of Raillietina sp. had a typical cloverleaf structure similar to Raillietina tetragona. Sequence differences between the mt1 and mt2 genomes were 4.4%, and this difference arises from the mtDNA heteroplasmic mutations. Moreover, heteroplasmic mtDNA mutations were detected in PCGs, tRNAs, rRNAs, NCRs, and intergenes, but the highest proportion of heteroplasmy of 79.0% was detected in PCGs, indicating the occurrence of mtDNA heteroplasmy in Raillietina sp. To our knowledge, this is the first report of mtDNA heteroplasmy in tapeworm parasites. Phylogenetic analyses of 18S rRNA, ITS2, and 12 PCG sequences demonstrated that the worm was clustered with other Raillietina species in the Davaneidae family.ConclusionsWe found a novel Raillietina species in wild pangolin with the existence of mitochondrial DNA heteroplasmy. Thus, these findings provide insights into the heterogeneity of the mt genome in parasitic cestodes, and mt genome data contributes to the understanding of pangolin-parasitic cestodes in terms of their molecular biology, epidemiology, diagnosis, and taxonomy.
| S-EPMC9195439 | biostudies-literature
Project description:BackgroundEffective conservation management of highly mobile species depends upon detailed knowledge of movements of individuals across their range; yet, data are rarely available at appropriate spatiotemporal scales. Flying-foxes (Pteropus spp.) are large bats that forage by night on floral resources and rest by day in arboreal roosts that may contain colonies of many thousands of individuals. They are the largest mammals capable of powered flight, and are highly mobile, which makes them key seed and pollen dispersers in forest ecosystems. However, their mobility also facilitates transmission of zoonotic diseases and brings them in conflict with humans, and so they require a precarious balancing of conservation and management concerns throughout their Old World range. Here, we analyze the Australia-wide movements of 201 satellite-tracked individuals, providing unprecedented detail on the inter-roost movements of three flying-fox species: Pteropus alecto, P. poliocephalus, and P. scapulatus across jurisdictions over up to 5 years.ResultsIndividuals were estimated to travel long distances annually among a network of 755 roosts (P. alecto, 1427-1887 km; P. poliocephalus, 2268-2564 km; and P. scapulatus, 3782-6073 km), but with little uniformity among their directions of travel. This indicates that flying-fox populations are composed of extremely mobile individuals that move nomadically and at species-specific rates. Individuals of all three species exhibited very low fidelity to roosts locally, resulting in very high estimated daily colony turnover rates (P. alecto, 11.9 ± 1.3%; P. poliocephalus, 17.5 ± 1.3%; and P. scapulatus, 36.4 ± 6.5%). This indicates that flying-fox roosts form nodes in a vast continental network of highly dynamic "staging posts" through which extremely mobile individuals travel far and wide across their species ranges.ConclusionsThe extreme inter-roost mobility reported here demonstrates the extent of the ecological linkages that nomadic flying-foxes provide across Australia's contemporary fragmented landscape, with profound implications for the ecosystem services and zoonotic dynamics of flying-fox populations. In addition, the extreme mobility means that impacts from local management actions can readily reverberate across jurisdictions throughout the species ranges; therefore, local management actions need to be assessed with reference to actions elsewhere and hence require national coordination. These findings underscore the need for sound understanding of animal movement dynamics to support evidence-based, transboundary conservation and management policy, tailored to the unique movement ecologies of species.
| S-EPMC7440933 | biostudies-literature
Project description:African pangolins are hunted for their meat and for use in local traditional medicine, as well as for their scales, which are trafficked internationally, especially to growing Asian markets. Pangolin's population genetic structure can be used to trace the geographic origins of trafficked scales, but substantial sampling gaps across pangolins' ranges hinder these efforts. In this study, we documented population structure and dynamics in the two species of African pangolin, the white-bellied pangolin (Phataginus tricuspis) and the giant pangolin (Smutsia gigantea) in the underexplored Republic of Congo. Using the mitochondrial control region and two nuclear markers (beta-fibrinogen and titin), we identified high genetic diversity in both species. We document a distinct mitochondrial lineage of the white-bellied pangolin, which was most likely shaped by river barriers together with dynamics of forest refugia related to the climatic shifts during the Pleistocene. We detected population growth in the white-bellied pangolin coinciding with a dry period during the Pleistocene, suggesting some ability for this typically forest-dwelling species to persist under diverse environmental conditions. Using landscape genetics, we found all but one of the pangolins we sampled at bush meat markets originated locally. A single individual appeared to have been imported to Congo from Cameroon. These findings significantly contribute to our understanding of pangolin population biology and local trade dynamics. In addition, our data from a previously unstudied part of pangolins' ranges will help us to better understand international wildlife trafficking patterns and to target conservation and protection strategies for these highly vulnerable species.
| S-EPMC11437027 | biostudies-literature
Project description:The botanical family Cucurbitaceae includes a variety of fruit crops with global or local economic importance. How their genomes evolve and the genetic basis of diversity remain largely unexplored. In this study, we sequence the genome of the wax gourd (Benincasa hispida), which bears giant fruit up to 80 cm in length and weighing over 20 kg. Comparative analyses of six cucurbit genomes reveal that the wax gourd genome represents the most ancestral karyotype, with the predicted ancestral genome having 15 proto-chromosomes. We also resequence 146 lines of diverse germplasm and build a variation map consisting of 16 million variations. Combining population genetics and linkage mapping, we identify a number of regions/genes potentially selected during domestication and improvement, some of which likely contribute to the large fruit size in wax gourds. Our analyses of these data help to understand genome evolution and function in cucurbits.
| S-EPMC6856369 | biostudies-literature
Project description:Terrestrial mammals are experiencing a massive collapse in their population sizes and geographical ranges around the world, but many of the drivers, patterns and consequences of this decline remain poorly understood. Here we provide an analysis showing that bushmeat hunting for mostly food and medicinal products is driving a global crisis whereby 301 terrestrial mammal species are threatened with extinction. Nearly all of these threatened species occur in developing countries where major coexisting threats include deforestation, agricultural expansion, human encroachment and competition with livestock. The unrelenting decline of mammals suggests many vital ecological and socio-economic services that these species provide will be lost, potentially changing ecosystems irrevocably. We discuss options and current obstacles to achieving effective conservation, alongside consequences of failure to stem such anthropogenic mammalian extirpation. We propose a multi-pronged conservation strategy to help save threatened mammals from immediate extinction and avoid a collapse of food security for hundreds of millions of people.
| S-EPMC5098989 | biostudies-literature
Project description:Pangolins, unique mammals with scales over most of their body, no teeth, poor vision, and an acute olfactory system, comprise the only placental order (Pholidota) without a whole-genome map. To investigate pangolin biology and evolution, we developed genome assemblies of the Malayan (Manis javanica) and Chinese (M. pentadactyla) pangolins. Strikingly, we found that interferon epsilon (IFNE), exclusively expressed in epithelial cells and important in skin and mucosal immunity, is pseudogenized in all African and Asian pangolin species that we examined, perhaps impacting resistance to infection. We propose that scale development was an innovation that provided protection against injuries or stress and reduced pangolin vulnerability to infection. Further evidence of specialized adaptations was evident from positively selected genes involving immunity-related pathways, inflammation, energy storage and metabolism, muscular and nervous systems, and scale/hair development. Olfactory receptor gene families are significantly expanded in pangolins, reflecting their well-developed olfaction system. This study provides insights into mammalian adaptation and functional diversification, new research tools and questions, and perhaps a new natural IFNE-deficient animal model for studying mammalian immunity.
| S-EPMC5052048 | biostudies-literature
Project description:While most mammals show birth hour peaks at times of the 24-h cycle when they are less active, there are exceptions to this general pattern. Such exceptions have been little explored, but may clarify evolutionary reasons for the diel timing of births. We investigated intraspecific variation in birth hour in wild blue monkeys Cercopithecus mitis stuhlmanni, a diurnal primate, to identify factors that differentiated daytime versus nighttime births. Behavioral and life history data from 14 groups over 14 years revealed that 4% of 484 births occurred during the day. Probability of daytime birth varied with mother's age, peaking at 15.7 years. Births whose annual timing deviated most from the population's peak birth months were 5 times more likely to occur during daytime than those that deviated less. There was no evidence that mother's rank or infant sex influenced birth hour, and mixed evidence that daytime births were more probable in larger groups. Survivorship did not differ significantly for infants born during the day versus night. Prime-aged mothers may be able to handle the consequences of an unusual birth hour more successfully than mothers with less experience or those weakened by age. Daytime birth may be more advantageous in the off-season because nights are colder at that time of year. These findings are consistent with hypotheses relating birth hour to the risk of losing social protection in group-living animals, but are not consistent with those emphasizing risk of conspecific harassment. Patterns of within-species variation can help in evaluating evolutionary hypotheses for non-random birth hour.
| S-EPMC9616064 | biostudies-literature
Project description:Area of Habitat (AOH) is "the habitat available to a species, that is, habitat within its range". It complements a geographic range map for a species by showing potential occupancy and reducing commission errors. AOH maps are produced by subtracting areas considered unsuitable for the species from their range map, using information on each species' associations with habitat and elevation. We present AOH maps for 5,481 terrestrial mammal and 10,651 terrestrial bird species (including 1,816 migratory bird species for which we present separate maps for the resident, breeding and non-breeding areas). Our maps have a resolution of 100 m. On average, AOH covered 66 ± 28% of the range maps for mammals and 64 ± 27% for birds. The AOH maps were validated independently, following a novel two-step methodology: a modelling approach to identify outliers and a species-level approach based on point localities. We used AOH maps to produce global maps of the species richness of mammals, birds, globally threatened mammals and globally threatened birds.
| S-EPMC9719530 | biostudies-literature
Project description:BackgroundThe cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood.ResultsHere, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species.ConclusionIn summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding.
| S-EPMC6862822 | biostudies-literature
Project description:Across multiple taxa, population structure and dynamics depend on effective signalling between individuals. Among mammals, chemical communication is arguably the most important sense, underpinning mate choice, parental care, territoriality and even disease transmission. There is a growing body of evidence that odours signal genetic information that may confer considerable benefits including inbreeding avoidance and nepotism. To date, however, there has been no clear evidence that odours encode population-level information in wild mammals. Here we demonstrate for the first time the existence of 'odour dialects' in genetically distinct mammalian subpopulations across a large geographical scale. We found that otters, Lutra lutra, from across the United Kingdom possess sex and biogeography-specific odours. Subpopulations with the most distinctive odour profiles are also the most genetically diverse but not the most genetically differentiated. Furthermore, geographic distance between individuals does not explain regional odour differences, refuting other potential explanations such as group odour sharing behaviour. Differences in the language of odours between subpopulations have the potential to affect individual interactions, which could impact reproduction and gene-flow.
| S-EPMC5648788 | biostudies-literature