The Eurasian lynx (Lynx lynx) exhibits geographic variability and phylogenetic intraspecific relationships. Previous morphological studies have suggested the existence of multiple lynx subspecies, but recent genetic research has questioned this classification, particularly in Central Asia. In this study, we aimed to analyse the geographic and genetic variation in Central Asian lynx populations, particularly the Turkestan lynx and Altai lynx populations, using morphometric data and mtDNA sequences to contribute to their taxonomic classification. The comparative analysis of morphometric data revealed limited clinal variability between lynx samples from the Altai and Tien Shan regions. By examining mtDNA fragments (control region and cytochrome b) obtained from Kazakhstani lynx populations, two subspecies were identified: L. l. isabellinus (represented by a unique haplotype of the South clade, H46) and L. l. wrangeli (represented by haplotypes H36, H45, and H47 of the East clade). L. l. isabellinus was recognized only in Tien Shan Mountain, while Altai lynx was likely identical to L. l. wrangeli and found in northern Kazakhstan, Altai Mountain, Saur and Tarbagatai Mountains, and Tien Shan Mountain. The morphological and mtDNA evidence presented in this study, although limited in sample size and number of genetic markers, renders the differentiation of the two subspecies challenging. Further sampling and compilation of whole-genome sequencing data are necessary to confirm whether the proposed subspecies warrant taxonomic standing.
Dromedary camels are a domestic species characterized by various adaptive traits. Limited efforts have been employed toward identifying genetic regions and haplotypes under selection that might be related to such adaptations. These genetic elements are considered valuable sources that should be conserved to maintain the dromedaries' adaptability. Here, we have analyzed whole genome sequences of 40 dromedary camels from different Arabian Peninsula populations to assess their genetic relationship and define regions with signatures of selection. Genetic distinction based on geography was observed, classifying the populations into four groups: (1) North and Central, (2) West, (3) Southwest, and (4) Southeast, with substantial levels of genetic admixture. Using the de-correlated composite of multiple signal approach, which combines four intra-population analyses (Tajima's D index, nucleotide diversity, integrated haplotype score, and number of segregating sites by length), a total of 36 candidate regions harboring 87 genes were identified to be under positive selection. These regions overlapped with 185 haplotype blocks encompassing 1 340 haplotypes, of which 30 (∼2%) were found to be approaching fixation. The defined candidate genes are associated with different biological processes related to the dromedaries' adaptive physiologies, including neurological pathways, musculoskeletal development, fertility, fat distribution, immunity, visual development, and kidney physiology. The results of this study highlight opportunities for further investigations at the whole-genome level to enhance our understanding of the evolutionary pressures shaping the dromedary genome.
Despite is known to have widespread distribution and the most active species of the family Chlorocyphidae, the molecular data of Rhinocypha fenestrella (Rambur, 1842) are relatively scarce. The present study is the first that examined the genetic diversity and phylogeographic pattern of the peacock jewel-damselfly R. fenestrella by sequencing the cytochrome C oxidase I (cox1) and 16S rRNA gene regions from 147 individuals representing eight populations in Malaysia. A total of 26 and 10 unique haplotypes were revealed by the cox1 and 16S rRNA genes, respectively, and 32 haplotypes were recovered by the concatenated sequences of cox1+16S. Analyses indicated that haplotype AB2 was the most frequent and the most widespread haplotype in Malaysia while haplotype AB1 was suggested as the common ancestor haplotype of the R. fenestrella that may arose from the Negeri Sembilan as discovered from cox1+16S haplotype network analysis. Overall haplotype and nucleotide diversities of the concatenated sequences were Hd = 0.8937 and Pi = 0.0028, respectively, with great genetic differentiation (FST = 0.6387) and low gene flow (Nm = 0.14). Population from Pahang presented the highest genetic diversity (Hd = 0.8889, Pi = 0.0022, Nh = 9), whereas Kedah population demonstrated the lowest diversity (Hd = 0.2842, Pi = 0.0003, Nh = 4). The concatenated sequences of cox1+16S showed genetic divergence ranging from 0.09% to 0.97%, whereas the genetic divergence for cox1 and 16S rRNA genes were 0.16% to 1.63% and 0.01% to 0.75% respectively. This study provides for the first-time insights on the intraspecific genetic diversity, phylogeographic pattern and ancestral haplotype of Rhinocypha fenestrella. The understanding of molecular data especially phylogeographic pattern can enhance the knowledge about insect origin, their diversity, and capability to disperse in particular environments.
Nicobari pig is reared by Nicobarese, a native tribal population of Andaman and Nicobar Islands. Nicobari pig has maintained its genetic identity due to geographical isolation. This communication is the first report on maternal inheritance of Nicobari pigs. DNA polymorphism data showed seven haplotypes. D-loop sequence information and mitogenome analysis were able to earmark Nicobari pigs to Asian clade. The domestication process of pigs and its expansion pattern help to understand human migration pattern. Based on this hypothesis, this communication elucidates the probable origin of Nicobarese. Earlier studies indicated that Nicobarese had genetic affinities to races distributed in China, Malaysia and Thailand. Our data on maternal inheritance of Nicobari pig correlates with the data on migration of Nicobarese. Moreover, we could establish a novel connection of Nicobarese with people of Northeastern parts of India, Philippines and Vietnam through phylogenetic signal and geographical provenance of Nicobari pig. We further concluded that migration of Nicobarese happened during Western route of migration (WRM) ∼4000 years before present. Therefore, we propose one wave hypothesis of peopling of Nicobar based on our study and existence of Ausrtroasiatic language, Mon-Khmer in these islands.
Killer cell immunoglobulin-like receptors (KIR) genotype and haplotype frequencies have been reported to vary distinctly between populations, which in turn contributes to variation in the alloreactivity of natural killer (NK) cells. Utilizing the diverse KIR genes to identify suitable transplant donors would prove challenging in multi-ethnic countries, even more in resource-limited countries where KIR genotyping has not been established. In this study, we determined the KIR genotypes from 124 unrelated Malaysians consisting of the Malays, Chinese, Indians, and aboriginal people through polymerase chain reaction sequence-specific primer (PCR-SSP) genotyping and employing an expectation-maximization (EM) algorithm to assign haplotypes based on pre-established reference haplotypes. A total of 27 distinct KIR haplotypes were discerned with higher frequencies of haplotype A (55.2%) than haplotype B (44.8%). The most frequent haplotypes were cA01:tA01 (55.2%), cB01:tB01 (18.1%), and cB02:tA01 (13.3%), while the least frequent haplotypes were cB03:tB01 (1.2%), cB04:tB03 (0.4%), and cB03:tA01 (0.4%). Several haplotypes were identified to be unique to a specific ethnic group. The genotype with the highest frequency was genotype AB (71.8%), followed by AA (19.4%), and BB (8.9%). The Indians exhibited the lowest genotype AA but the highest genotype BB, whereas genotype BB was absent in the aboriginal people. Despite the limitations, the genotype and haplotypes in the Malaysian population were successfully highlighted. The identification of ethnic-specific KIR genotypes and haplotypes provides the first step to utilizing KIR in identifying suitable transplant donors to further improve the transplant outcome in the Malaysian population.
Type 1 diabetes (T1D) is a complex autoimmune disorder that is highly prevalent globally. The interactions between genetic and environmental factors may trigger T1D in susceptible individuals. HLA genes play a significant role in T1D pathogenesis, and specific haplotypes are associated with an increased risk of developing the disease. Identifying risk haplotypes can greatly improve the genetic scoring for early diagnosis of T1D in difficult to rank subgroups. This study employed next-generation sequencing to evaluate the association between HLA class II alleles, haplotypes, and amino acids and T1D, by recruiting 95 children with T1D and 150 controls in the Kuwaiti population. Significant associations were identified for alleles at the HLA-DRB1, HLA-DQA1, and HLA-DQB1 loci, including DRB1*03:01:01, DQA1*05:01:01, and DQB1*02:01:01, which conferred high risk, and DRB1*11:04:01, DQA1*05:05:01, and DQB1*03:01:01, which were protective. The DRB1*03:01:01~DQA1*05:01:01~DQB1*02:01:01 haplotype was most strongly associated with the risk of developing T1D, while DRB1*11:04-DQA1*05:05-DQB1*03:01 was the only haplotype that rendered protection against T1D. We also identified 66 amino acid positions across the HLA-DRB1, HLA-DQA1, and HLA-DQB1 genes that were significantly associated with T1D, including novel associations. These results validate and extend our knowledge on the associations between HLA genes and T1D in Kuwaiti children. The identified risk alleles, haplotypes, and amino acid variations may influence disease development through effects on HLA structure and function and may allow early intervention via population-based screening efforts.
The widespread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continuously impacts our economic and public health. The potential of emerging variants to increase transmissibility and evade vaccine-induced immunity lets us put more effort to research on viral mutations and explore the pathogenic haplotypes. In this study, we characterized the haplotype and sub-haplotype diversity of SARS-CoV-2 global variants in January-March and the areas with low and high COVID19 vaccination rates in May 2021 by analyzing viral proteome of complete genome sequences published. Phylogenetic tree analysis of the proteomes of SARS-CoV-2 variants with Neighbor-Joining and Maximum Parsimony methods indicated that haplotype 2 variant with nsp12 P323L and Spike D614G was dominant (98.81%), including new sub-haplotypes 2A_1 to 2A_3, 2B_1 to 2B_3, and 2C_1 to 2C_2 emerged post-one-year COVID-19 outbreak. In addition, the profiling of sub-haplotypes indicated that sub-haplotype 2A_1 with the mutations at N501Y, A570D, D614G, P681H, T716I, S982A, and D118H in Spike was over 58% in May 2021 in the high partly vaccinated rate group (US, Canada, and Germany). Meanwhile, the new haplotype 2C_3 bearing the mutations at EFR156-158del, T19R, A222V, L452R, T478K, and D614G in Spike occupied over 54.8% in May 2021 in the low partly vaccinated rate group (India, Malaysia, Taiwan, and Vietnam). Sub-haplotypes 2A_1 and 2C_3 had a meaningful alternation of ACE2-specific recognition site, neutralization epitopes, and furin cleavage site in SARS-CoV-2 Spike protein. The results discovered the haplotype diversity and new sub-haplotypes of SARS-CoV-2 variants post one-year pandemic in January-March 2021, showing the profiles of sub-haplotypes in the groups with low and high partly vaccinated rates in May 2021. The study reports the emergence of new SARS-CoV-2 sub-haplotypes during ongoing pandemic and vaccination in early 2021, which might help inform the response to vaccination strategies.
The Apolipoprotein E ε4 (APOE ε4) haplotype is the strongest genetic risk factor for late-onset Alzheimer's disease (AD). The Translocase of Outer Mitochondrial Membrane-40 (TOMM40) gene maintains cellular bioenergetics, which is disrupted in AD. TOMM40 rs2075650 ('650) G versus A carriage is consistently related to neural and cognitive outcomes, but it is unclear if and how it interacts with APOE. We examined 21 orthogonal neural networks among 8,222 middle-aged to aged participants in the UK Biobank cohort. ANOVA and multiple linear regression tested main effects and interactions with APOE and TOMM40 '650 genotypes, and if age and sex acted as moderators. APOE ε4 was associated with less strength in multiple networks, while '650 G versus A carriage was related to more language comprehension network strength. In APOE ε4 carriers, '650 G-carriage led to less network strength with increasing age, while in non-G-carriers this was only seen in women but not men. TOMM40 may shift what happens to network activity in aging APOE ε4 carriers depending on sex.
The true mahseer (Tor spp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. In this study, we sequenced and assembled 11 complete mahseer mitogenomes collected from Java of Indonesia, Pahang and Terengganu of Peninsular Malaysia as well as Sarawak of East Malaysia. The mitogenome evolutionary relationships among closely related Tor spp. samples were investigated based on maximum likelihood phylogenetic tree construction. Compared to the commonly used COX1 gene fragment, the complete COX1, Cytb, ND2, ND4 and ND5 genes appear to be better phylogenetic markers for genetic differentiation at the population level. In addition, a total of six population-specific mitolineage haplotypes were identified among the mahseer samples analyzed, which this offers hints towards its taxonomical landscape.
Cytochrome P450 enzymes play a central role in the phase I biotransformation process of a wide range of compounds, including xenobiotics, drugs, hormones and vitamins. It is noteworthy that these enzymes are highly polymorphic and, depending on the genetic makeup, an individual may have impaired enzymatic activity. Therefore, the identification of genetic variants in these genes could facilitate the implementation of pharmacogenetic studies and genetic predisposition to multifactorial diseases. We have established the frequencies of CYP2B6 (rs3745274; rs2279343) and CYP3A4 (rs2740574) alleles and genotypes in 209 healthy Malian subjects using TaqMan drug metabolism genotyping assays for allelic discrimination. Allele frequencies were 37% for CYP2B6 rs3745274; 38% for CYP2B6 rs2279343; and 75% for CYP3A4 rs2740574 respectively. Overall, the frequencies observed in Mali are statistically comparable to those reported across Africa except North Africa. The major haplotypes in CYP2B6 rs3745274 and CYP2B6 rs2279343 were represented by GA (60.24%) followed by TG (35.36%). We noted a strong linkage disequilibrium between CYP2B6 rs3745274 and CYP2B6 rs2279343 with D' = 0.91 and r2 = 0.9. The frequencies of the genotypic combinations were 43.5% (GT/AG), 37.3% (GG/AA) and 11.5% (TT/GG) in the combination of CYP2B6-rs3745274 and CYP2B6-rs2279343; 26.8% (GT/CC), 25.4%, (GT/CT), 17.2% and GG/CT in the combination CYP2B6-rs3745274-CYP3A4-rs2740574; 26.8% (AG/CC), 23.9% (AA/CC), 19.1% (AG/CT), and 11% (AA/CT) in the combination CYP2B6-rs2279343-CYP3A4-rs2740574, respectively. The most common triple genotype was GT/AG/CC with 24.9%, followed by GG/AA/CC with 23.9%, GT/AG/CT with 16.7%, and GG/AA/CT with 10%. Our results provide new insights into the distribution of these pharmacogenetically relevant genes in the Malian population. Moreover, these data will be useful for studies of individual genetic variability to drugs and genetic predisposition to diseases.
The present study aimed to examine the genetic diversity of human malaria parasites (i.e., P. falciparum, P. vivax and P. knowlesi) in Malaysia and southern Thailand targeting the 19-kDa C-terminal region of Merozoite Surface Protein-1 (MSP-119). This region is essential for the recognition and invasion of erythrocytes and it is considered one of the leading candidates for asexual blood stage vaccines. However, the genetic data of MSP-119 among human malaria parasites in Malaysia is limited and there is also a need to update the current sequence diversity of this gene region among the Thailand isolates. In this study, genomic DNA was extracted from 384 microscopy-positive blood samples collected from patients who attended the hospitals or clinics in Malaysia and malaria clinics in Thailand from the year 2008 to 2016. The MSP-119 was amplified using PCR followed by bidirectional sequencing. DNA sequences identified in the present study were subjected to Median-joining network analysis with sequences of MSP-119 obtained from GenBank. DNA sequence analysis revealed that PfMSP-119 of Malaysian and Thailand isolates was not genetically conserved as high number of haplotypes were detected and positive selection was prevalent in PfMSP-119, hence questioning its suitability to be used as a vaccine candidate. A novel haplotype (Q/TNG/L) was also detected in Thailand P. falciparum isolate. In contrast, PvMSP-119 was highly conserved, however for the first time, a non-synonymous substitution (A1657S) was reported among Malaysian isolates. As for PkMSP-119, the presence of purifying selection and low nucleotide diversity indicated that it might be a potential vaccine target for P. knowlesi.
DNA profiling of X-chromosomal short tandem repeats (X-STR) has exceptional value in criminal investigations, especially for complex kinship and incest cases. In this study, Investigator® Argus X-12 Quality Sensor (QS) kits were successfully used to characterize 12 X-STR loci in 199 unrelated healthy Kedayan individuals living in Sabah and Sarawak, Malaysia. The LG1 haplogroup (DXS8378 - DXS10135 - DXS10148) has the largest HD (0.9799) as compared with all other closely linked haplotype groups examined (LG2; DXS7132-DXS10074-DXS10079, LG3; DXS10103-DXS10101-HPRTB and LG4; DXS10134-DXS7423-DXS10146). Data from statistical analysis showed that high combined of PDM, PDF, MEC_Krüger, MEC_Kishida, MEC_Desmarais, and MEC_Desmarais_duo values (0.999999994405922, 0.99999999999999, 0.999990463834938, 0.999999975914808, 0.999999975985006, and 0.999996491927194, respectively) in the Kedayan. In a two-dimensional scaling (MDS) plot and dendrogram constructed using allele frequencies at the 12 X-STR loci, Kedayan appear to be most closely related to their other Austronesian populations including the Malays and Filipinos as compared with other reference population groups. Findings from the present study thus demonstrate high genetic variability across the 12 tested X-STR loci and can be used for population studies and forensic applications.
Benthic species, though ecologically important, are vulnerable to genetic loss and population size reduction due to impacts from fishing trawls. An assessment of genetic diversity and population structure is therefore needed to assist in a resource management program. To address this issue, the two-spined yellowtail stargazer (Uranoscopus cognatus) was collected within selected locations in the Indo-West Pacific (IWP). The partial mitochondrial DNA cytochrome c oxidase subunit 1 and the nuclear DNA recombination activating gene 1 were sequenced. Genetic diversity analyses revealed that the populations were moderately to highly diversified (haplotype diversity, H = 0.490-0.900, nucleotide diversity, π = 0.0010-0.0034) except sampling station (ST) 1 and 14. The low diversity level, however was apparent only in the matrilineal marker (H = 0.118-0.216; π = 0.0004-0.0008), possibly due to stochastic factors or anthropogenic stressors. Population structure analyses revealed a retention of ancestral polymorphism that was likely due to incomplete lineage sorting in U. cognatus, and prolonged vicariance by the Indo-Pacific Barrier has partitioned them into separate stock units. Population segregation was also shown by the phenotypic divergence in allopatric populations, regarding the premaxillary protrusion, which is possibly associated with the mechanism for upper jaw movement in biomechanical feeding approaches. The moderate genetic diversity estimated for each region, in addition to past population expansion events, indicated that U. cognatus within the IWP was still healthy and abundant (except in ST1 and 14), and two stock units were identified to be subjected to a specific resource management program.
The Plasmodium knowlesi apical membrane antigen-1 (PkAMA-1) plays an important role in the invasion of the parasite into its host erythrocyte, and it has been regarded as a potential vaccine candidate against human knowlesi malaria. This study investigates genetic diversity and natural selection of the full length PkAMA-1 of P. knowlesi clinical isolates from Peninsular Malaysia. Blood samples were collected from P. knowlesi malaria patients from Peninsular Malaysia. The PkAMA-1 gene was amplified from DNA samples using PCR, cloned into a plasmid vector and sequenced. Results showed that nucleotide diversity of the full length PkAMA-1 from Peninsular Malaysia isolates (π: 0.006) was almost similar to that of Sarawak (π: 0.005) and Sabah (π: 0.004) isolates reported in other studies. Deeper analysis revealed Domain I (π: 0.007) in the PkAMA-1 had the highest diversity as compared to Domain II (π: 0.004) and Domain III (π: 0.003). Z-test indicated negative (purifying) selection of the gene. Combined alignment analysis at the amino acid level for the Peninsular Malaysia and Sarawak PkAMA-1 sequences revealed 34 polymorphic sites. Thirty-one of these sites were dimorphic, and 3 were trimorphic. The amino acid sequences could be categorised into 31 haplotypes. In the haplotype network, PkAMA-1 from Peninsular Malaysia and Sarawak were separated into two groups.
Heritability of major depressive disorder (MDD) is between 36 and 44%, suggesting that up to nearly half of the phenotypic variability is attributable to genes. A number of genetic polymorphisms have been shown to predispose certain individuals to depression. Of particular interest are the polymorphisms of the vitamin D receptor (VDR) gene. Although the VDR gene has been well characterized and a vast number of polymorphisms have been identified, the association between BsmI (rs1544410), ApaI (rs7975232) and TaqI (rs731236) single-nucleotide polymorphisms (SNPs), together with their haplotypes, and MDD risk have yet to be established. We conducted a matched case-control study with a total of 600 participants comprising 300 major depressive disorder (MDD) cases and 300 controls matched by age, gender and ethnicity in a 1:1 ratio, in four public hospitals in Kuala Lumpur and Selangor. Three adjacent SNPs of the VDR gene-BsmI (rs1544410), ApaI (rs7975232) and TaqI (rs731236)-were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Odds ratios and 95% confidence intervals (CIs) were obtained from conditional logistic regression using Stata 16. Linkage disequilibrium and haplotype association with MDD were analyzed using the online SNPStats program. None of the genotypes of the three SNPs was significantly associated with risk of developing MDD after adjusting for confounding factors. However, the TAC (BAt) haplotype was associated with increased odds of MDD (adjusted OR = 2.17, 95% CI = 1.30-3.61, p = 0.003) using CCT (baT) as reference haplotype. The findings suggest that the BsmI-ApaI-TaqI TAC (BAt) haplotype of the VDR gene increases susceptibility to MDD.
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
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.
Malaria parasites in the phylum Apicomplexa (Order: Haemosporida) infect diverse vertebrates and invertebrate hosts. At least seven genera of haemosporidian parasites have been described to exclusively infect bats. Most of these parasites remain enigmatic with a poorly known host range. Here, we investigated 271 bats belonging to 21 species and seven families from six provinces of Thailand. Overall, 124 out of 271 bats (45.8%) were positive for haemosporidian parasites, while none had Plasmodium, based on microscopic examination of blood smears and PCR amplification. We obtained 19 distinct cytochrome b (cytb) nucleotide haplotypes of Hepatocystis from seven bat species (families: Craseonycteridae, Hipposideridae, Pteropodidae, and Rhinolophidae). Nycteria was found in four bat species (Craseonycteridae, Emballonuridae, Megadermatidae, and Pteropodidae) and Polychromophilus in two species (Emballonuridae, Vespertilionidae). Phylogenetic analysis inferred from cytb sequences placed Hepatocystis into 2 different clades. Most Hepatocystis infections were found in insectivorous bats and clustered together with a sequence from Hipposideros larvatus in Cambodia (in subclade 1a). A single sequence of Hepatocystis obtained from a frugivorous bat, Cynopterus brachyotis, was placed in the same clade with Hepatocystis from the same bat species previously reported in Malaysia (clade 2). Nycteria in these Thai bats were clearly separated from the African isolates previously reported in bats in the family Rhinolophidae. Polychromophilus murinus from Myotis siligorensis was placed in a distinct clade (clade 2) from Polychromophilus melanipherus isolated from Taphozous melanopogon (clade 1). These results confirmed that at least two distinct species of Polychromophilus are found in Thailand. Collectively, Hepatocystis presented no host specificity. Although Megaderma spasma seemed to be infected by only Nycteria, its respective parasite does not show specificity to only a single bat host. Polychromophilus murinus and P. melanipherus seem to infect a narrower host range or are somehow restricted to bats in the families Vespertilionidae and Emballonuridae, respectively.
Village chicken production, a traditional, small-scale, and extensive backyard poultry industry, has been profitable for local farmers in Myanmar. However, there is scanty information available concerning the infection of these chickens with avian pathogens, including haemoprotozoan parasites. In the present study, we provide the first report of microscopic detection and molecular identification of Leucocytozoon and Plasmodium parasites from seven different areas of Myanmar. Leucocytozoon gametocytes were detected in 17.6% (81/461) of the blood smears from village chickens. The nested polymerase chain reaction (PCR) for targeting Leucocytozoon mitochondrial cytochrome b (cyt b) genes had a 17.6% positive rate. Although the positive rate of nested PCR targeting Plasmodium/Haemoproteus cyt b was 34.3%, the PCR protocol was observed to possibly amplify DNA of a certain species of Leucocytozoon. There were no obvious clinical signs in the infected birds. Statistical analysis of the microscopic detection and PCR detection rates using the age and sex of birds as internal factors revealed that the statistical significances differed according to the study area. The sequencing of 32 PCR products obtained from each study area revealed infection by Leucocytozoon caulleryi in three birds, Leucocytozoon sabrazesi in two birds, Leucocytozoon schoutedeni in two birds, Leucocytozoon sp. in eighteen birds, and Plasmodium juxtanucleare in seven birds; however, Haemoproteus infection was not detected. While L. sabrazesi was detected in chickens from the central region of Myanmar, the other haemosporidians were detected in those from different areas. In the haplotype analysis, we detected 17 haemosporidian cyt b haplotypes, including two for L. caulleryi, one for L. sabrazesi, two for L. schoutedeni, nine for Leucocytozoon sp., and three for P. juxtanucleare. Phylogenetic analysis of the cyt b haplotypes revealed a considerably close genetic relationship among chicken haemosporidians detected in Myanmar, Thailand, and Malaysia. These results indicate that well-recognized widespread species of chicken Leucocytozoon and Plasmodium are distributed nationwide in Myanmar, providing new insights into the ecosystem and control strategies of haemosporidian parasites in domesticated chickens in Myanmar.
Ectodysplasin A1 receptor (EDAR) is a TNF receptor family member with roles in the development and growth of hair, teeth and glands. A derived allele of EDAR, single-nucleotide variant rs3827760, encodes EDAR:p.(Val370Ala), a receptor with more potent signalling effects than the ancestral EDAR370Val. This allele of rs3827760 is at very high frequency in modern East Asian and Native American populations as a result of ancient positive selection and has been associated with straighter, thicker hair fibres, alteration of tooth and ear shape, reduced chin protrusion and increased fingertip sweat gland density. Here we report the characterisation of another SNV in EDAR, rs146567337, encoding EDAR:p.(Ser380Arg). The derived allele of this SNV is at its highest global frequency, of up to 5%, in populations of southern China, Vietnam, the Philippines, Malaysia and Indonesia. Using haplotype analyses, we find that the rs3827760 and rs146567337 SNVs arose on distinct haplotypes and that rs146567337 does not show the same signs of positive selection as rs3827760. From functional studies in cultured cells, we find that EDAR:p.(Ser380Arg) displays increased EDAR signalling output, at a similar level to that of EDAR:p.(Val370Ala). The existence of a second SNV with partly overlapping geographic distribution, the same in vitro functional effect and similar evolutionary age as the derived allele of rs3827760, but of independent origin and not exhibiting the same signs of strong selection, suggests a northern focus of positive selection on EDAR function in East Asia.