The Japanese or Honshū wolf was one the most distinct gray wolf subspecies due to its small stature and endemicity to the islands of Honshū, Shikoku, and Kyūshū. Long revered as a guardian of farmers and travellers, it was persecuted from the 17th century following a rabies epidemic, which led to its extinction in the early 20th century. To better understand its evolutionary history, we sequenced the nuclear genome of a 19th century Honshū wolf specimen to an average depth of coverage of 3.7✕. We find Honshū wolves were closely related to a lineage of Siberian wolves that were previously believed to have gone extinct in the Late Pleistocene, thereby extending the survival of this ancient lineage until the early 20th century. We also detected significant gene flow between Japanese dogs and the Honshū wolf, corroborating previous reports on Honshū wolf dog interbreeding.
White-bellied swiftlets of the Collocalia esculenta complex constitute a radiation of colony-breeding swifts distributed throughout the tropical Indo-Pacific region. Resolution of their taxonomy is challenging due to their morphological uniformity. To analyze the evolutionary history of this complex, we combine new biometric measurements and results from plumage assessment of museum specimens with novel as well as previously published molecular data. Together, this body of information constitutes the largest systematic dataset for white-bellied swiftlets yet compiled, drawn from 809 individuals belonging to 32 taxa for which new molecular, biometric, and/or plumage data are presented. We propose changing the classification of white-bellied swiftlets, for which two species are currently recognized, to elevate eight regional forms to species level, and we also describe two new subspecies. The ten taxa we recommend recognizing at the species level are: Collocalia linchi (Java to Lombok, Sumatran hills), C. dodgei (montane Borneo), C. natalis (Christmas Island), C. affinis (Greater Sundas, including the Thai-Malay Peninsula and Andaman-Nicobar Islands), C. marginata (Philippines), C. isonota (Philippines), C. sumbawae (west Lesser Sundas), C. neglecta (east Lesser Sundas), C. esculenta (Sulawesi, Moluccas, New Guinea, Bismarck Archipelago, Solomon Islands), and C. uropygialis (Vanuatu, New Caledonia). Future molecular and morphological work is needed to resolve questions of speciation and population affinities in the Philippines, Christmas Island, Wallacea and central Melanesia, and to shed light on historic diversification and patterns of gene flow in the complex.
Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The analysis of molecular variance (AMOVA) analysis, pairwise F ST , and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.
The medically important mosquito, Aedes albopictus is native to Asia and has become a major health concern in most Asian countries including Malaysia. Being recognized as a dengue vector, a clearer understanding of how mosquito populations are geographically connected, may therefore represent a profound yet significant understanding of control strategies. There are no documented reports on the genetic structure of Ae. albopictus populations from different developed settlements inferred from microsatellite DNA markers in Malaysia, particularly in Penang Island (Northern Peninsular Malaysia). Here, we assessed the molecular population genetics of Ae. albopictus in terms of their allelic variation, genetic diversity and population structure. A total of 42 mosquitoes were sampled from Jelutong, Batu Maung and Balik Pulau which represented urban, suburban and rural areas in Penang Island respectively and analysed for polymorphism at six microsatellite loci. All of the microsatellite markers were successfully amplified and were polymorphic, showing low genetic structure among geographic populations (FST= 0.0362). It is supported with admixture individuals observed in STRUCTURE and FCA and this suggests that high gene flow has been experienced between populations. These findings implicate passive dispersal through human-aided transportation; as a factor shaping the genetic structure of Ae. albopictus populations in Penang Island.
The Malay people are an important ethnic composition in Southeast Asia, but their genetic make-up and population structure remain poorly studied. Here we conducted a genome-wide study of four geographical Malay populations: Peninsular Malaysian Malay (PMM), Singaporean Malay (SGM), Indonesian Malay (IDM) and Sri Lankan Malay (SLM). All the four Malay populations showed substantial admixture with multiple ancestries. We identified four major ancestral components in Malay populations: Austronesian (17%-62%), Proto-Malay (15%-31%), East Asian (4%-16%) and South Asian (3%-34%). Approximately 34% of the genetic makeup of SLM is of South Asian ancestry, resulting in its distinct genetic pattern compared with the other three Malay populations. Besides, substantial differentiation was observed between the Malay populations from the north and the south, and between those from the west and the east. In summary, this study revealed that the genetic identity of the Malays comprises a mixed entity of multiple ancestries represented by Austronesian, Proto-Malay, East Asian and South Asian, with most of the admixture events estimated to have occurred 175 to 1,500 years ago, which in turn suggests that geographical isolation and independent admixture have significantly shaped the genetic architectures and the diversity of the Malay populations.
Uncovering the hidden diversity and evolutionary history of arthropods of medico-veterinary importance could have significant implications for vector-borne disease control and epidemiological intervention. The buffalo fly Haematobia exigua is an obligate bloodsucking ectoparasite of livestock. As an initial step towards understanding its population structures and biogeographic patterns, we characterized partial cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) sequences of H. exigua from three distinct geographic regions in Southeast Asia. We detected two distinct mitochondrial haplogroups of H. exigua in our surveyed geographic regions. Haplogroup I is widespread in the Southeast Asian mainland whereas haplogroup II is generally restricted to the type population Java Island. Both haplogroups were detected co-occurring on Borneo Island. Additionally, both haplogroups have undergone contrasting evolutionary histories, with haplogroup I exhibited a high level of mitochondrial diversity indicating a population expansion during the Pleistocene era dating back to 98,000 years ago. However, haplogroup II presented a low level of mitochondrial diversity which argues against the hypothesis of recent demographic expansion.
The demersal brown banded bamboo shark Chiloscyllium punctatum is a major component of sharks landed in Malaysia. However, little is known about their population structure and the effect of high fishing pressure on these weak swimming sharks. Both mitochondrial DNA control region (1072 bp) and NADH dehydrogenase subunit 2 (1044 bp) were used to elucidate the genetic structure and connectivity of C. punctatum among five major areas within the Sundaland region. Our findings revealed (i) strong genetic structure with little present day mixing between the major areas, (ii) high intra-population genetic diversity with unique haplotypes, (iii) significant correlation between genetic differentiation and geographical distance coupled with detectable presence of fine scale geographical barriers (i.e. the South China Sea), (iv) historical directional gene flow from the east coast of Peninsular Malaysia towards the west coast and Borneo, and (v) no detectable genetic differentiation along the coastline of east Peninsular Malaysia. Genetic patterns inferred from the mitochondrial DNA loci were consistent with the strong coastal shelf association in this species, the presence of contemporary barriers shaped by benthic features, and limited current-driven egg dispersal. Fine scale population structure of C. punctatum highlights the need to improve genetic understanding for fishery management and conservation of other small-sized sharks.
The fall armyworm (FAW) Spodoptera frugiperda is thought to have undergone a rapid 'west-to-east' spread since 2016 when it was first identified in western Africa. Between 2018 and 2020, it was recorded from South Asia (SA), Southeast Asia (SEA), East Asia (EA), and Pacific/Australia (PA). Population genomic analyses enabled the understanding of pathways, population sources, and gene flow in this notorious agricultural pest species. Using neutral single nucleotide polymorphic (SNP) DNA markers, we detected genome introgression that suggested most populations in this study were overwhelmingly C- and R-strain hybrids (n = 252/262). SNP and mitochondrial DNA markers identified multiple introductions that were most parsimoniously explained by anthropogenic-assisted spread, i.e., associated with international trade of live/fresh plants and plant products, and involved 'bridgehead populations' in countries to enable successful pest establishment in neighbouring countries. Distinct population genomic signatures between Myanmar and China do not support the 'African origin spread' nor the 'Myanmar source population to China' hypotheses. Significant genetic differentiation between populations from different Australian states supported multiple pathways involving distinct SEA populations. Our study identified Asia as a biosecurity hotspot and a FAW genetic melting pot, and demonstrated the use of genome analysis to disentangle preventable human-assisted pest introductions from unpreventable natural pest spread.
The sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throughout the Indo-Pacific. Diverse colour variation is reported in both species. To reconstruct the phylogeny of the genus and assess gene flow across the Indo-Pacific we sequenced mitochondrial 16S rDNA, ATPase-6, and ATPase-8, and nuclear 28S rDNA and the Calpain-7 intron. Our analyses revealed that E. diadema formed a single trans-Indo-Pacific clade, but E. calamaris contained three discrete clades. One clade was endemic to the Red Sea and the Gulf of Oman. A second clade occurred from Malaysia in the West to Moorea in the East. A third clade of E. calamaris was distributed across the entire Indo-Pacific biogeographic region. A fossil calibrated phylogeny revealed that the ancestor of E. diadema diverged from the ancestor of E. calamaris ~ 16.8 million years ago (Ma), and that the ancestor of the trans-Indo-Pacific clade and Red Sea and Gulf of Oman clade split from the western and central Pacific clade ~ 9.8 Ma. Time since divergence and genetic distances suggested species level differentiation among clades of E. calamaris. Colour variation was extensive in E. calamaris, but not clade or locality specific. There was little colour polymorphism in E. diadema.
Lions are one of the world's most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions (Panthera leo spelaea), 12 historic lions (Panthera leo leo/Panthera leo melanochaita) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 y ago and that the 2 lineages likely did not hybridize following their divergence. Within modern lions, we found 2 main lineages that diverged ca. 70,000 y ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic diversity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute toward the understanding of the evolutionary history of lions and complement conservation efforts to protect the diversity of this vulnerable species.
The population genetic structure of Simulium tani was inferred from mitochondria-encoded sequences of cytochrome c oxidase subunits I (COI) and II (COII) along an elevational gradient in Cameron Highlands, Malaysia. A statistical parsimony network of 71 individuals revealed 71 haplotypes in the COI gene and 43 haplotypes in the COII gene; the concatenated sequences of the COI and COII genes revealed 71 haplotypes. High levels of genetic diversity but low levels of genetic differentiation were observed among populations of S. tani at five elevations. The degree of genetic diversity, however, was not in accordance with an altitudinal gradient, and a Mantel test indicated that elevation did not have a limiting effect on gene flow. No ancestral haplotype of S. tani was found among the populations. Pupae with unique structural characters at the highest elevation showed a tendency to form their own haplotype cluster, as revealed by the COII gene. Tajima's D, Fu's Fs, and mismatch distribution tests revealed population expansion of S. tani in Cameron Highlands. A strong correlation was found between nucleotide diversity and the levels of dissolved oxygen in the streams where S. tani was collected.
A phylogeographic study of an economically important freshwater fish, the striped snakehead, Channa striata in Sundaland was carried out using data from mtDNA ND5 gene target to elucidate genetic patterning. Templates obtained from a total of 280 individuals representing 24 sampling sites revealed 27 putative haplotypes. Three distinct genetic lineages were apparent; 1)northwest Peninsular Malaysia, 2)southern Peninsular, east Peninsular, Sumatra and SW (western Sarawak) and 3) central west Peninsular and Malaysian Borneo (except SW). Genetic structuring between lineages showed a significant signature of natural geographical barriers that have been acting as effective dividers between these populations. However, genetic propinquity between the SW and southern Peninsular and east Peninsular Malaysia populations was taken as evidence of ancient river connectivity between these regions during the Pleistocene epoch. Alternatively, close genetic relationship between central west Peninsular Malaysia and Malaysian Borneo populations implied anthropogenic activities. Further, haplotype sharing between the east Peninsular Malaysia and Sumatra populations revealed extraordinary migration ability of C. striata (>500 km) through ancient connectivity. These results provide interesting insights into the historical and contemporary landscape arrangement in shaping genetic patterns of freshwater species in Sundaland.
The coastal mosquito Aedes togoi occurs more or less continuously from subarctic to subtropic zones along the coasts of the Japanese islands and the East Asian mainland. It occurs also in tropical Southeast Asia and the North American Pacific coast, and the populations there are thought to have been introduced from Japan by ship. To test this hypothesis, the genetic divergence among geographic populations of A. togoi was studied using one mitochondrial and three nuclear gene sequences. We detected 71 mitochondrial haplotypes forming four lineages, with high nucleotide diversity around temperate Japan and declining towards peripheral ranges. The major lineage (L1) comprised 57 haplotypes from temperate and subarctic zones in Japan and Southeast Asia including southern China and Taiwan. Two other lineages were found from subtropical islands (L3) and a subarctic area (L4) of Japan. The Canadian population showed one unique haplotype (L2) diverged from the other lineages. In the combined nuclear gene tree, individuals with mitochondrial L4 haplotypes diverged from those with the other mitochondrial haplotypes L1-L3; although individuals with L1-L3 haplotypes showed shallow divergences in the nuclear gene sequences, individuals from Southeast Asia and Canada each formed a monophyletic group. Overall, the genetic composition of the Southeast Asian populations was closely related to that of temperate Japanese populations, suggesting recent gene flow between these regions. The Canadian population might have originated from anthropogenic introduction from somewhere in Asia, but the possibility that it could have spread across the Beringian land bridge cannot be ruled out.
Fin whales (Balaenoptera physalus) and blue whales (B. musculus) are the two largest species on Earth and are widely distributed across the world's oceans. Hybrids between these species appear to be relatively widespread and have been reported in both the North Atlantic and North Pacific; they are also relatively common, and have been proposed to occur once in every thousand fin whales. However, despite known hybridization, fin and blue whales are not sibling species. Rather, the closest living relative of fin whales are humpback whales (Megaptera novaeangliae). To improve the quality of fin whale data available for analysis, we assembled and annotated a fin whale nuclear genome using in-silico mate pair libraries and previously published short-read data. Using this assembly and genomic data from a humpback, blue, and bowhead whale, we investigated whether signatures of introgression between the fin and blue whale could be found. We find no signatures of contemporary admixture in the fin and blue whale genomes, although our analyses support ancestral gene flow between the species until 2.4-1.3 Ma. We propose the following explanations for our findings; i) fin/blue whale hybridization does not occur in the populations our samples originate from, ii) contemporary hybrids are a recent phenomenon and the genetic consequences have yet to become widespread across populations, or iii) fin/blue whale hybrids are under large negative selection, preventing them from backcrossing and contributing to the parental gene pools.
The complex climatic and geological history of Southeast Asia has shaped this region's high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have shaped the distribution of biota within this region, and whether such patterns show evidence of isolation within palaeodrainage basins. Our analyses revealed three major mitochondrial clades within A. panchax. The basal divergence of A. panchax mitochondrial lineages was approximately 3.5 Ma, whilst the subsequent divergence timings of these clades occurred early Pleistocene (~2.6 Ma), proceeding through the Pleistocene. Continuous phylogeographic analysis showed a clear west-east dispersal followed by rapid radiation across Southeast Asia. Individuals from Krabi, just north of the Isthmus of Kra, were more closely related to the Indian lineages, providing further evidence for a freshwater faunal disjunction at the Isthmus of Kra biogeographic barrier. Our results suggest that Sulawesi, across the Wallace Line, was colonised relatively recently (~30 ka). Nuclear DNA is less geographically structured, although Mantel tests indicated that nuclear genetic distances were correlated with geographic proximity. Overall, these results imply that recent gene flow, as opposed to historical isolation, has been the key factor determining patterns of nuclear genetic variation in A. panchax, however, some evidence of historical isolation is retained within the mitochondrial genome. Our study further validates the existence of a major biogeographic boundary at the Kra Isthmus, and also demonstrates the use of widely distributed fresh/brackishwater species in phylogeographic studies, and their ability to disperse across major marine barriers in relatively recent time periods.
Anopheles balabacensis, the primary vector of Plasmodium knowlesi in Sabah, Malaysia, is both zoophilic and anthropophilic, feeding on macaques as well as humans. It is the dominant Anopheles species found in Kudat Division where it is responsible for all the cases of P. knowlesi. However there is a paucity of basic biological and ecological information on this vector. We investigated the genetic variation of this species using the sequences of cox1 (1,383 bp) and cox2 (685 bp) to gain an insight into the population genetics and inter-population gene flow in Sabah. A total of 71 An. balabacensis were collected from seven districts constituting 14 subpopulations. A total of 17, 10 and 25 haplotypes were detected in the subpopulations respectively using the cox1, cox2 and the combined sequence. Some of the haplotypes were common among the subpopulations due to gene flow occurring between them. AMOVA showed that the genetic variation was high within subpopulations as compared to between subpopulations. Mantel test results showed that the variation between subpopulations was not due to the geographical distance between them. Furthermore, Tajima's D and Fu's Fs tests showed that An. balabacensis in Sabah is experiencing population expansion and growth. High gene flow between the subpopulations was indicated by the low genetic distance and high gene diversity in the cox1, cox2 and the combined sequence. However the population at Lipasu Lama appeared to be isolated possibly due to its higher altitude at 873 m above sea level.
Documenting the scale and intensity of fine-scale spatial genetic structure (FSGS), and the processes that shape it, is relevant to the sustainable management of genetic resources in timber tree species, particularly where logging or fragmentation might disrupt gene flow. In this study we assessed patterns of FSGS in three species of Dipterocarpaceae (Parashorea tomentella, Shorea leprosula and Shorea parvifolia) across four different tropical rain forests in Malaysia using nuclear microsatellite markers. Topographic heterogeneity varied across the sites. We hypothesised that forests with high topographic heterogeneity would display increased FSGS among the adult populations driven by habitat associations. This hypothesis was not supported for S. leprosula and S. parvifolia which displayed little variation in the intensity and scale of FSGS between sites despite substantial variation in topographic heterogeneity. Conversely, the intensity of FSGS for P. tomentella was greater at a more topographically heterogeneous than a homogeneous site, and a significant difference in the overall pattern of FSGS was detected between sites for this species. These results suggest that local patterns of FSGS may in some species be shaped by habitat heterogeneity in addition to limited gene flow by pollen and seed dispersal. Site factors can therefore contribute to the development of FSGS. Confirming consistency in species' FSGS amongst sites is an important step in managing timber tree genetic diversity as it provides confidence that species specific management recommendations based on species reproductive traits can be applied across a species' range. Forest managers should take into account the interaction between reproductive traits and site characteristics, its consequences for maintaining forest genetic resources and how this might influence natural regeneration across species if management is to be sustainable.
Weedy rice (Oryza spp.) is a major nuisance to rice farmers from all over the world. Although the emergence of weedy rice in East Malaysia on the island of Borneo is very recent, the threat to rice yield has reached an alarming stage. Using 47,027 genotyping-by-sequencing (GBS)-derived SNPs and candidate gene analysis of the plant architecture domestication gene TAC1, we assessed the genetic variations and evolutionary origin of weedy rice in East Malaysia. Our findings revealed two major evolutionary paths for genetically distinct weedy rice types. Whilst the cultivar-like weedy rice are very likely to be the weedy descendant of local coexisting cultivars, the wild-like weedy rice appeared to have arisen through two possible routes: (i) accidental introduction from Peninsular Malaysia weedy rice populations, and (ii) weedy descendants of coexisting cultivars. The outcome of our genetic analyses supports the notion that Sabah cultivars and Peninsular Malaysia weedy rice are the potential progenitors of Sabah weedy rice. Similar TAC1 haplotypes were shared between Malaysian cultivated and weedy rice populations, which further supported the findings of our GBS-SNP analyses. These different strains of weedy rice have convergently evolved shared traits, such as seeds shattering and open tillers. A comparison with our previous simple-sequence repeat-based population genetic analyses highlights the strength of genome-wide SNPs, including detection of admixtures and low-level introgression events. These findings could inform better strategic management for controlling the spread of weedy rice in the region.
The brown rat (Rattus norvegicus) is a relatively recent (<300 years) addition to the British fauna, but by association with negative impacts on public health, animal health and agriculture, it is regarded as one of the most important vertebrate pest species. Anticoagulant rodenticides were introduced for brown rat control in the 1950s and are widely used for rat control in the UK, but long-standing resistance has been linked to control failures in some regions. One thus far ignored aspect of resistance biology is the population structure of the brown rat. This paper investigates the role population structure has on the development of anticoagulant resistance. Using mitochondrial and microsatellite DNA, we examined 186 individuals (from 15 counties in England and one location in Wales near the Wales-England border) to investigate the population structure of rural brown rat populations. We also examined individual rats for variations of the VKORC1 gene previously associated with resistance to anticoagulant rodenticides. We show that the populations were structured to some degree, but that this was only apparent in the microsatellite data and not the mtDNA data. We discuss various reasons why this is the case. We show that the population as a whole appears not to be at equilibrium. The relative lack of diversity in the mtDNA sequences examined can be explained by founder effects and a subsequent spatial expansion of a species introduced to the UK relatively recently. We found there was a geographical distribution of resistance mutations, and relatively low rate of gene flow between populations, which has implications for the development and management of anticoagulant resistance.
Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails) along an elevational gradient in Borneo. Each taxon pair presents a different elevational range distribution across the island, yet results were uniform: little or no gene flow was detected in any pairwise comparisons. These results are congruent with an allopatric "species-pump" model for generation of species diversity and elevational parapatry of congeners on Borneo, rather than in situ generation of species by "ecological speciation" along an elevational gradient.