Project description:Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large interarea genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g., LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g., NKAIN3), or different loci in an identical gene (e.g., TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g., DDB1/DAK) or genetic convergence driven by admixture (e.g., MTHFD1 and RAD18), new mutations (e.g., STK11), or notably purifying selection (e.g., MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples.
Project description:Previous studies have shown that the world's largest reptile - the leatherback turtle Dermochelys coriacea - conducts flexible foraging migrations that can cover thousands of kilometres between nesting sites and distant foraging areas. The vast distances that may be travelled by migrating leatherback turtles have greatly complicated conservation efforts for this species worldwide. However, we demonstrate, using a combination of satellite telemetry and stable isotope analysis, that approximately half of the nesting leatherbacks from an important rookery in South Africa do not migrate to distant foraging areas, but rather, forage in the coastal waters of the nearby Mozambique Channel. Moreover, this coastal cohort appears to remain resident year-round in shallow waters (<50 m depth) in a relatively fixed area. Stable isotope analyses further indicate that the Mozambique Channel also hosts large numbers of loggerhead turtles Caretta caretta. The rare presence of a resident coastal aggregation of leatherback turtles not only presents a unique opportunity for conservation, but alongside the presence of loggerhead turtles and other endangered marine megafauna in the Mozambique Channel, highlights the importance of this area as a marine biodiversity hotspot.
Project description:The region with the highest marine biodiversity on our planet is known as the Coral Triangle or Indo-Australian Archipelago (IAA)1,2. Its enormous biodiversity has long attracted the interest of biologists; however, the detailed evolutionary history of the IAA biodiversity hotspot remains poorly understood3. Here we present a high-resolution reconstruction of the Cenozoic diversity history of the IAA by inferring speciation-extinction dynamics using a comprehensive fossil dataset. We found that the IAA has exhibited a unidirectional diversification trend since about 25 million years ago, following a roughly logistic increase until a diversity plateau beginning about 2.6 million years ago. The growth of diversity was primarily controlled by diversity dependency and habitat size, and also facilitated by the alleviation of thermal stress after 13.9 million years ago. Distinct net diversification peaks were recorded at about 25, 20, 16, 12 and 5 million years ago, which were probably related to major tectonic events in addition to climate transitions. Key biogeographic processes had far-reaching effects on the IAA diversity as shown by the long-term waning of the Tethyan descendants versus the waxing of cosmopolitan and IAA taxa. Finally, it seems that the absence of major extinctions and the Cenozoic cooling have been essential in making the IAA the richest marine biodiversity hotspot on Earth.
Project description:Understanding how biodiversity varies from place to place is a fundamental goal of ecology and an important tool for halting biodiversity loss. Parasitic wasps (Hymenoptera) are a diverse and functionally important animal group, but spatial variation in their diversity is poorly understood. We survey a community of parasitic wasps (Ichneumonidae: Pimplinae) using Malaise traps up a mountain in the Brazilian Atlantic Rainforest, and relate the catch to biotic and abiotic habitat characteristics. We find high species richness compared with previous similar studies, with abundance, richness, and diversity peaking at low to intermediate elevation. There is a marked change in community composition with elevation. Habitat factors strongly correlated with elevation also strongly predict changes in the pimpline community, including temperature as well as the density of bamboo, lianas, epiphytes, small trees, and herbs. These results identify several possible surrogates of pimpline communities in tropical forests, which could be used as a tool in conservation. They also contribute to the growing evidence for a typical latitudinal gradient in ichneumonid species richness, and suggest that low to medium elevations in tropical regions will sometimes conserve the greatest number of species locally, but to conserve maximal biodiversity, a wider range of elevations should also be targeted.
Project description:Indigenous chickens at the Swahili coast and other traditional migratory corridors in Kenya represent important populations that are inconclusively characterized. Using a comprehensive dataset of Kenyan indigenous chickens and additional mined data of chickens from 8 African and 5 Asian countries, we performed univariate and multivariate assessments to uncover the underlying phenotypic and morphometric variability. Kenyan indigenous chickens expressed differentiation of several qualitative and quantitative traits, both among different counties in the Swahili coast, and among coastal, western, and northern migratory corridors. There was a substantial population stratification of these chickens, particularly distinctive clustering of chickens from Marsabit, Lamu, and Kilifi counties. The pooled dataset further clarified a closer phenotypic and morphometric proximity of chickens within different geographical regions. We additionally revealed a preponderance of bantam and rumpless traits to hot and humid locales, and feathered shanks to cooler regions. Currently, most chicken breeding programs in developing countries rely on phenotypic and morphometric properties. Hence, the high chicken diversity and population stratification observed in our study, possibly shaped by natural and artificial selective pressures, reveal opportunities for complementary phenotypic and genotypic assessments to identify resources for effective breed improvement and conservation strategies of indigenous chickens in the tropics.
Project description:Understanding air pollution in East Asia is of great importance given its high population density and serious air pollution problems during winter. Here, we show that the day-to-day variability of East Asia air pollution, during the recent 21-year winters, is remotely influenced by the Madden-Julian Oscillation (MJO), a dominant mode of subseasonal variability in the tropics. In particular, the concentration of particulate matter with aerodynamic diameter less than 10 micron (PM10) becomes significantly high when the tropical convections are suppressed over the Indian Ocean (MJO phase 5-6), and becomes significantly low when those convections are enhanced (MJO phase 1-2). The station-averaged PM10 difference between these two MJO phases reaches up to 15% of daily PM10 variability, indicating that MJO is partly responsible for wintertime PM10 variability in East Asia. This finding helps to better understanding the wintertime PM10 variability in East Asia and monitoring high PM10 days.
Project description:Tropical deforestation and forest fragmentation are among the most important biodiversity conservation issues worldwide, yet local extinctions of millions of animal and plant populations stranded in unprotected forest remnants remain poorly explained. Here, we report unprecedented rates of local extinctions of medium to large-bodied mammals in one of the world's most important tropical biodiversity hotspots. We scrutinized 8,846 person-years of local knowledge to derive patch occupancy data for 18 mammal species within 196 forest patches across a 252,669-km(2) study region of the Brazilian Atlantic Forest. We uncovered a staggering rate of local extinctions in the mammal fauna, with only 767 from a possible 3,528 populations still persisting. On average, forest patches retained 3.9 out of 18 potential species occupancies, and geographic ranges had contracted to 0-14.4% of their former distributions, including five large-bodied species that had been extirpated at a regional scale. Forest fragments were highly accessible to hunters and exposed to edge effects and fires, thereby severely diminishing the predictive power of species-area relationships, with the power model explaining only ~9% of the variation in species richness per patch. Hence, conventional species-area curves provided over-optimistic estimates of species persistence in that most forest fragments had lost species at a much faster rate than predicted by habitat loss alone.
Project description:Interactions within lichen communities include, in addition to close mutualistic associations between the main partners of specific lichen symbioses, also more elusive relationships between members of a wider symbiotic community. Here, we analyze association patterns of cyanolichen symbionts in the tropical montane forests of Taita Hills, southern Kenya, which is part of the Eastern Afromontane biodiversity hotspot. The cyanolichen specimens analyzed represent 74 mycobiont taxa within the order Peltigerales (Ascomycota), associating with 115 different variants of the photobionts genus Nostoc (Cyanobacteria). Our analysis demonstrates wide sharing of photobionts and reveals the presence of several photobiont-mediated lichen guilds. Over half of all mycobionts share photobionts with other fungal species, often from different genera or even families, while some others are strict specialists and exclusively associate with a single photobiont variant. The most extensive symbiont network involves 24 different fungal species from five genera associating with 38 Nostoc photobionts. The Nostoc photobionts belong to two main groups, the Nephroma-type Nostoc and the Collema/Peltigera-type Nostoc, and nearly all mycobionts associate only with variants of one group. Among the mycobionts, species that produce cephalodia and those without symbiotic propagules tend to be most promiscuous in photobiont choice. The extent of photobiont sharing and the structure of interaction networks differ dramatically between the two major photobiont-mediated guilds, being both more prevalent and nested among Nephroma guild fungi and more compartmentalized among Peltigera guild fungi. This presumably reflects differences in the ecological characteristics and/or requirements of the two main groups of photobionts. The same two groups of Nostoc have previously been identified from many lichens in various lichen-rich ecosystems in different parts of the world, indicating that photobiont sharing between fungal species is an integral part of lichen ecology globally. In many cases, symbiotically dispersing lichens can facilitate the dispersal of sexually reproducing species, promoting establishment and adaptation into new and marginal habitats and thus driving evolutionary diversification.
Project description:Freshwater mussels are sensitive to habitat and water quality, revealing the fastest rates of human-mediated global extinction among aquatic animals. These animals are especially diverse in tropical Asia, the faunas of which are characterized by high levels of endemism. Here we describe four new species and four new subspecies of freshwater mussels from Myanmar. Leoparreysia whitteni sp. nov., the smallest representative of this genus, was discovered from the Ayeyarwady and Chindwin rivers. Radiatula myitthanensis sp. nov. and R. chindwinensis sp. nov. were recorded from the Chindwin Basin, and R. mouhoti haungthayawensis ssp. nov. has been discovered from the Haungthayaw River. Indochinella pugio has been revised with a description of three subspecies: I. pugio viridissima ssp. nov. from the Sittaung, Bilin and Bago rivers, I. pugio daweiensis ssp. nov. from the Dawei River, and I. pugio paradoxa ssp. nov. from the Haungthayaw River. Yaukthwa elongatula sp. nov., a peculiar species, conchologically resembling representatives of the genus Solenaia (Gonideinae) with ultra-elongated shell was found in the Chindwin Basin. Our records highlight that tropical Asia harbors numerous, but still overlooked local endemic lineages of freshwater bivalves, which may be on the brink of extinction due to the high anthropogenic and climate change impacts.
Project description:The promise of Indigenous and local knowledge (ILK) for conservation policy depends on how pervasively ILK is held among local people. In the Peruvian Amazon, we conducted a landscape-scale concordance analysis between (1) ILK for game, timber, and fish species collected by the largest representative ILK survey as yet undertaken in tropical forests, and (2) remotely sensed land cover as proxies for species habitat. From our survey among 4000 households in 235 communities, we find that concordant ILK is highly pervasive across gender, age, place of origin, and social status, irrespective of species and people's indigeneity. Resource users possess more concordant knowledge than nonusers for timber and fish, not game. Concordance between ILK for fish and remote sensing is associated with cooperative forest clearing in shifting cultivation-an informal community institution in which forest peoples engage with nature. Our findings point to the promise of ILK for large-scale tropical conservation.