Low phylogeographic diversity in the calcified green macroalga <i>Halimeda macroloba</i> (Bryopsidales) in Southeast Asia

Understanding the genetic diversity and distribution patterns of seaweeds species is crucial for evaluating key regions of high genetic diversity. Identifying hotspots of high intraspecific diversity is an important step for developing conservation strategies. Grateloupia is a diverse genus of Rhodophyta, many of which are resource of numerous useful bioactive compounds; therefore, the genus is valuable target for conservation. The aim of this study is to examine the genetic diversity and population structure of two Grateloupia species, Grateloupia asiatica and Grateloupia jejuensis, with the understanding of the phylogeography of the Korean genetic diversity hotspot for two species. Plastid rbcL gene sequences of 134 specimens of G. asiatica and 112 specimens of G. jejuensis collected from the Korean coast were analyzed. We evaluated the number of haplotypes, genetic diversity (haplotype and nucleotide diversity), and haplotype networks of two species. Historical demographic was inferred by calculating neutrality tests and genetic differentiation was estimated using the fixation index, FST. Our results show that both species are generally similar in geographical distribution patterns, that is, relatively homogeneous with few haplotypes derived from the most frequent haplotype. The east coast of Korea is identified as a 'hotspot' with the highest genetic diversity for both species, whereas Jeju Island is identified as a 'cold spot' with the lowest genetic diversity for G. jejuensis. Analyses across most distribution ranges of the two species in Korea reveal low genetic and haplotype diversities, which could indicate that these two Grateloupia species have either experienced a historical lack of diversity or a recent reduction in diversity due to high gene flow. The low genetic diversity values found in the present study raise considerable concern about the conservation status of these two Grateloupia species and highlight the need to locate further hotspots of genetic diversity to strengthen their resilience against further decline.

In order to provide baseline information for the genetic resources, genetic variation in wild and cultured Pinctada fucata martensii from southern Korea and Japan was studied using nucleotide sequence analysis of 379 base pairs (bp) in the mitochondrial cytochrome oxidase subunit I gene (COI). The study included three hatchery stocks from Korea (Tongyeong) and Japan (Mie and Tsushima) and one wild stock from Korea (Geoje). A total of 3 haplotypes were identified in hatchery stocks of 78 individuals, of which 63 individuals shared 1 haplotype. Overall, nucleotide diversity (π) was low, ranging from 0.000 to 0.002, and haplotype diversity (h) ranged from 0.000 to 0.541. Considerably low haplotype and nucleotide diversities in hatchery stock indicated that low effective population size and consecutive selective breeding of P. fucata martensii could be responsible for the reduction in genetic variation. The wild stock exhibited low haplotype diversity (0.507 ± 0.039) with two shared haplotypes. The results of the present study with first record of wild pearl oyster in Korea support the possibility that the transplanted pearl oyster for overwintering experiments could have survived in winter. In order to enhance and/or maintain genetic diversity in the hatchery stock, further research should be directed toward genetic monitoring and evaluation of the hatchery and wild pearl oysters.

Members of the mangrove genus Rhizophora represent the most commonly occurring and highly valued species in the Indo-West Pacific region. However, to date, few studies have been directed towards the understanding of their genetic variation. The levels and patterns of genetic variation at chloroplast and nuclear gene regions were studied in R. apiculata, R. mucronata, and R. stylosa sampled from Southeast Asia and Japan. All three species were characterized by low intraspecific genetic variation and a deficiency of heterozygotes in populations within the region, consistent with findings in studies on other mangrove species. Rhizophora mucronata and R. stylosa were also found to be more closely related than any of them with R. apiculata. During the Last Glacial Maximum, sea levels dropped to 120 m below the current levels, exposing part of the Sunda Shelf that became a barrier that limited gene flow between marine species living in the Pacific and Indian Oceans. Today, the Malay Peninsula is thought to still serve as a barrier to gene flow between populations occurring on its coasts. The pattern of genetic differentiation of R. apiculata supports the hypothesis of the land barrier effect of the Malay Peninsula, but such patterns were not found in R. mucronata and R. stylosa. Our findings suggest that R. apiculata, R. mucronata, and R. stylosa have different demographic histories despite being closely related and having sympatric distributions today. Furthermore, all three species appear to have high levels of inbreeding due to limited pollen and propagule dispersal, and that both these factors contributed to population differentiation.

BackgroundHepatitis A virus (HAV) infection is one of the major causes of acute viral hepatitis. HAV genotypes and its genetic diversity is rarely investigated in our region as well as worldwide.AimsThe aims of the present study were to determine the HAV genotypes and its risk factors and to investigate the genetic diversity of the HAV isolates in the West Bank, Palestine.Study designA cohort of 161 clinically and laboratory-confirmed HAV (IgM-positive) cases and 170 apparently healthy controls from all the districts of the West Bank, Palestine during the period of 2014 to 2016 were tested for HAV infection using IgM antibodies, RT-PCR and sequence analysis of the VP3/VP1 junction region of the HAV genome. Phylogenetic analysis, genetic diversity and haplotypes analysis were used to characterize the VP3/VP1 sequences.ResultsAll the 34 sequences of the HAV were found to be of HAV-IB sub-genotype. The phylogenetic analysis showed four main clusters with cluster III exclusively consisting of 18 Palestinian isolates (18/23-78%), but with weak bootstrap values. A high haplotype diversity (Hd) and low nucleotide diversity (π) were observed. Cluster III showed high number of haplotypes (h = 8), but low haplotype (gene) diversity (Hd = 0.69). A total of 28 active haplotypes with some consisting of more than one sequence were observed using haplotype network analysis. The Palestinian haplotypes are characterized by closely related viral haplotypes with one SNV away from each other which ran parallel to cluster III in the phylogenetic tree. A smaller Palestinian haplotype (4 isolates) was three SNVs away from the major haplotype cluster (n = 10) and closer to others haplotypes from Iran, Spain, and South Africa. Young age, low level of parent’s education, infrequent hand washing before meals, and drinking of un-treated water were considered the major HAV risk factors in the present study.ConclusionHaplotype network analysis revealed haplotype variation among the HAV Palestinian sequences despite low genetic variation and nucleotide diversity. In addition, this study reconfirmed that age and parent’s level of education as HAV risk factors, while hand washing and treating drinking water as protective factors.

This study has a specific goal in mind: Genetic Variation Study Within Populations of Coptodon zilliii, Oreochromis aureus, and Oreochromis niloticus, and analysed the partial Cytb gene sequence of mtDNA to determine genetic diversity among these species in the Khaur Abdallah and Shatt Al-Arab in the south of Iraq, where the mitochondrial cytochrome b gene was used.DNA was isolated from 40 specimens of the three species collected from two different sites and examined. The gene size for Coptodon zilliii,Oreochromis aureus, and Oreochromis niloticus was (439, 326 & 473 bp long (amplified Cytb gene)), respectively. The study found that two haplotypes in Khaur Abdallah and one in the Shatt-Al-Arab river in Coptodon zilliii populations, while was found one haplotype in Khaur Abdallah and one in the Shatt-Al-Arab in both Oreochromis aureus, and Oreochromisniloticus populations by using Software DnaSP v5.1. In each of the species Oreochromis aureus and Oreochromis niloticus, the research identified two types of unique haplotypes, one in Khaur Abdallah and the other in Shatt-Al-Arab. However, three haplotype patterns for Coptodon zilliii populations were discovered: one in the Shatt al-Arab River and two in Khaur Abdallah. Low nucleotide (π) and haplotype diversity (Hd) values were found in both Oreochromisaureus and Oreochromis niloticus populations in the Shatt Al-Arab river and Khaur Abdallah, indicating low genetic variation among populations for both species in the two regions. However, there was no diversity within the Oreochromis aureus population in both Shatt Al-Arab and Khaur Abdallah. The population of Oreochromis niloticus has the same indication. Three haplotypes for Coptodon zilliii indicate to genetic variance across populations in the Shatt Al-Arab riverand Khaur Abdallah regions, although no variety within the Coptodon zilliii species was found in the Shatt Al-Arab river. In the Khaur Abdallah district, there was little genetic diversity among them.

Background. One of the most mysterious phenomenon related to biological invasions is the so-called “genetic paradox”. It is supposed that invasive species population starts from a small number of individuals and thus should possess low genetic variation, and then what mechanisms provide it successive distribution instead of lower survivorship in front of native species is not clear. It has been shown that there are several scenarios of invasion that may help to overcome this paradox. Here, we investigate genetic variation within and between the invasive populations of land snail in Leningrad region aimed to test the various probable invasion scenarios. Materials and methods. Samples were collected in Leningrad region in May-October 2014 at both shores of the Gulf of Finland with maximal distance between the sites in 80 km and stored in 96% ethanol. As a molecular marker to study genetic variation a sequence of DNA fragment of mitochondrial cytochrome oxidase 1 was used. Results. We revealed abnormally low haplotype and nucleotide diversity in the snail populations under study. Therewith four haplotypes uncovered among 47 specimens from the territory of approximately 100 km2 were unique for Leningrad area. Phylogenetic analysis showed one sample from Denmark in the same cluster with samples from Leningrad region. This indirectly point on colonization route from Central Europe through Denmark, but this assumption should be confirmed by enlarge sampling. Conclusions. The data obtained suggest the ‘bridgehead’ model of the land snail invasion in Leningrad region. In favor of this evidence that all haplotypes recovered in Leningrad area were unique, differing from the closest haplotype from Denmark by several mutations. This fact together with extremely low haplotype and nucleotide diversity most likely points that snails first accumulated at a small territory during a rather long period. Neutrality test are in accordance with balancing selection.

BackgroundPlasmodium knowlesi is a simian malaria parasite that has been reported to cause malaria in humans in Southeast Asia. This parasite invades the erythrocytes of humans and of its natural host, the macaque Macaca fascicularis, via interaction between the Duffy binding protein region II (PkDBPαRII) and the Duffy antigen receptor on the host erythrocytes. In contrast, the P. knowlesi gamma protein region II (PkγRII) is not involved in the invasion of P. knowlesi into humans. PkγRII, however, mediates the invasion of P. knowlesi into the erythrocytes of M. mulata, a non-natural host of P. knowlesi via a hitherto unknown receptor. The haplotypes of PkDBPαRII in P. knowlesi isolates from Peninsular Malaysia and North Borneo have been shown to be genetically distinct and geographically clustered. Also, the PkDBPαRII was observed to be undergoing purifying (negative) selection. The present study aimed to determine whether similar phenomena occur in PkγRII.MethodsBlood samples from 78 knowlesi malaria patients were used. Forty-eight of the samples were from Peninsular Malaysia, and 30 were from Malaysia Borneo. The genomic DNA of the samples was extracted and used as template for the PCR amplification of the PkγRII. The PCR product was cloned and sequenced. The sequences obtained were analysed for genetic diversity and natural selection using MEGA6 and DnaSP (version 5.10.00) programmes. Genetic differentiation between the PkγRII of Peninsular Malaysia and North Borneo isolates was estimated using the Wright’s FST fixation index in DnaSP (version 5.10.00). Haplotype analysis was carried out using the Median-Joining approach in NETWORK (version 4.6.1.3).ResultsA total of 78 PkγRII sequences was obtained. Comparative analysis showed that the PkγRII have similar range of haplotype (Hd) and nucleotide diversity (π) with that of PkDBPαRII. Other similarities between PkγRII and PkDBPαRII include undergoing purifying (negative) selection, geographical clustering of haplotypes, and high inter-population genetic differentiation (FST index). The main differences between PkγRII and PkDBPαRII include length polymorphism and no departure from neutrality (as measured by Tajima’s D statistics) in the PkγRII.ConclusionDespite the biological difference between PkγRII and PkDBPαRII, both generally have similar genetic diversity level, natural selection, geographical haplotype clustering and inter-population genetic differentiation index.

The rapid spread of HBV has resulted in the emergence of new variants. These viral genotypes and variants, in addition to carcinogenic risk, can be key predictors of therapy response and outcomes. As a result, a better knowledge of these emerging HBV traits will aid in the development of a treatment for HBV infection. However, many Sub-Saharan African nations, including Kenya, have insufficient molecular data on HBV strains circulating locally. This study conducted a population-genetics analysis to evaluate the genetic diversity of HBV among Kenyan blood donors. In addition, within the same cohort, the incidence and features of immune-associated escape mutations and stop-codons in Hepatitis B surface antigen (HBsAg) were determined. In September 2015 to October 2016, 194 serum samples were obtained from HBsAg-positive blood donors residing in eleven different Kenyan counties: Kisumu, Machakos, Uasin Gishu, Nairobi, Nakuru, Embu, Garissa, Kisii, Mombasa, Nyeri, and Turkana. For the HBV surface (S) gene, HBV DNA was isolated, amplified, and sequenced. The sequences obtained were utilized to investigate the genetic and haplotype diversity within the S genes. Among the blood donors, 74.74% were male, and the overall mean age was 25.36 years. HBV genotype A1 (88.14%) was the most common, followed by genotype D (10.82%), genotype C (0.52%), and HBV genotype E (0.52%). The phylogenetic analysis revealed twelve major clades, with cluster III comprising solely of 68 blood donor isolates (68/194-35.05%). A high haplotype diversity (Hd = 0.94) and low nucleotide diversity (π = 0.02) were observed. Kisumu county had high number of haplotypes (22), but low haplotype (gene) diversity (Hd = 0.90). Generally, a total of 90 haplotypes with some consisting of more than one sequence were observed. The gene exhibited negative values for Tajima's D (-2.04, p<0.05) and Fu's Fs (-88.84). Several mutations were found in 139 isolates, either within or outside the Major Hydrophilic Area (MHR). There were 29 mutations found, with 37.9% of them situated inside the "a" determinant. The most common mutations in this research were T143M and K122R. Escape mutations linked to diagnostic failure, vaccination and immunoglobulin treatment evasion were also discovered. Also, one stop-codon, W163STP, inside the MHR, was found in one sample from genotype A. In Kenya, HBV/A1 is still the most common genotype. Despite limited genetic and nucleotide diversity, haplotype network analysis revealed haplotype variance among HBV genotypes from Kenyan blood donors. The virological properties of immune escape, which may be the source of viral replication endurance, were discovered in the viral strains studied and included immune-escape mutations and stop-codon. The discovery of HBsAg mutations in MHR in all isolates highlighted the need of monitoring MHR mutations in Kenya.

Populations of anadromous European smelt (Osmerus eperlanus L.) are declining across its range with mitigation efforts for this ecologically important species hindered by a lack of demographic information. Here, mitochondrial DNA (mtDNA) and microsatellite analyses were used to describe historical and recurrent demographics for the species across a large part of its range. mtDNA revealed a shallow phylogeographic structure indicating a cohesive ancestral population, low overall haplotype and nucleotide diversities. However, microsatellites revealed unexpectedly high genetic structuring (FST = 0.15; p < 0.0001), including (i) isolation by distance effects over various scales, (ii) separation between Baltic and Atlantic samples and (iii) the highest interpopulation divergence and the lowest intrapopulation variation among UK sites. The results indicate that despite considerable dispersal potential, there is strong structuring among rivers, which should be recognised as separate management units. Furthermore, individual clustering analyses revealed further population separation within waterways and the need to resolve isolating mechanisms. Overall levels of genetic variation were found to be lower than those reported for other osmerids, with evidence suggesting that a considerable portion of ancestral variation has been eroded. As such, low genetic variation may limit resilience to environmental change. Proactive management strategies are discussed, with the prioritisation of UK populations recommended.

In 1911 and 1917, the first commercial plantings of African oil palm (Elaeis guineensis Jacq.) were made in Indonesia and Malaysia in Southeast Asia. In less than 15 years, basal stem rot (BSR) was reported in Malaysia. It took nearly another seven decades to identify the main causal agent of BSR as the fungus, Ganoderma boninense. Since then, research efforts have focused on understanding G. boninense disease epidemiology, biology, and etiology, but limited progress was made to characterize pathogen genetic diversity, spatial structure, pathogenicity, and virulence. This study describes pathogen variability, gene flow, population differentiation, and genetic structure of G. boninense in Sarawak (Malaysia), Peninsular Malaysia, and Sumatra (Indonesia) inferred by 16 highly polymorphic cDNA-SSR (simple sequence repeat) markers. Marker-inferred genotypic diversity indicated a high level of pathogen variability among individuals within a population and among different populations. This genetic variability is clearly the result of outcrossing between basidiospores to produce recombinant genotypes. Although our results indicated high gene flow among the populations, there was no significant genetic differentiation among G. boninense populations on a regional scale. It suggested that G. boninense genetic makeup is similar across a wide region. Furthermore, our results revealed the existence of three admixed genetic clusters of G. boninense associated with BSR-diseased oil palms sampled throughout Sarawak, Peninsular Malaysia, and Sumatra. We postulate that the population structure is likely a reflection of the high genetic variability of G. boninense populations. This, in turn, could be explained by highly successful outcrossing between basidiospores of G. boninense from Southeast Asia and introduced genetic sources from various regions of the world, as well as regional adaptation of various pathogen genotypes to different palm hosts. Pathogen variability and population structure could be employed to deduce the epidemiology of G. boninense, as well as the implications of plantation cultural practices on BSR disease control in different regions.

A detailed investigation was carried out to determine the genetic structure and haplotype diversity of Malaysian horseshoe crab (Tachypleus gigas [Muller, 1785]) distributed along the west coast of Peninsular Malaysia. Mitochondrial DNA (AT rich region = 369 bp) analysis showed that T. gigas had 13 haplotypes along the Malaysian west coast of which 4 were unique to Selangor samples while 3 were unique to Johor sample and 1 each were unique to other two stations respectively. Highest haplotype diversity (h) was observed among the Selangor samples (0.873±0.071) followed by Langkawi, Johor and Kedah samples with 0.833±0.222, 0.752±0.066 and 0.733±0.155 values, respectively. Over all haplotype diversity of T. gigas in west coast of Malaysia was observed to be 0.797±0.129. Pair wise haplotype frequency (FST) value were statistically significant (p<0.05) for all the groups except for Langkawi/Kedah samples indicating higher gene flow (Lower haplotype diversity) among these two populations. Average nucleotide diversity (π) was higher in Selangor samples (0.0083±0.001) followed by Johor (0.0063±0.0011) and it was almost similar in Langkawi (0.0045±0.0012) and Kedah (0.0040±0.0008) samples which indicated higher polymorphic sites in Selangor and Johor samples while it was lower in Langkawi and Kedah samples. In addition phylogenetic analysis clearly clustered T. gigas samples from T. tridentatus samples indicating good phylogenetic signals in mtDNA AT rich region. Overall, findings from this study have important implications for proper management and conservation of this living fossil along the west coast of Peninsular Malaysia.

Species spread in a new environment is often associated with founders' effect, and reduced effective population size and genetic diversity. However, reduced genetic diversity does not necessarily translate to low establishment and spread potential. Paracoccus marginatus Williams and Granara de Willink is a polyphagous pest that has invaded 4 continents in around 34 years. It was first detected in the Northern Territory, Australia in July 2023. Following this, we collected 45 specimens from 20 suburbs across 3 regions. Using mitochondrial cytochrome oxidase I and nuclear ribosomal RNA genes (18S and 28S), we examined molecular diagnostics robustness, genetic diversity, haplotype network, and demographics (Tajima D) of the recently detected Australian population. We compared our samples with publicly available sequences deposited on GenBank. All 3 genes were suitable for molecular diagnosis with a 100% identity score. For all 3 genes, we found low nucleotide diversity, haplotype diversity, and negative Tajima D in the newly detected P. marginatus population, suggesting a recent single founder event by a few individuals. Comparing our study's sequences with global sequences showed low haplotype diversity, nucleotide diversity, and Tajima's D, suggesting that despite low genetic diversity at the 3 genes, P. marginatus has successfully invaded South America, Africa, Asia, and Oceania. Our study highlights the role of demographic and life history traits in the species' invasion success. We provide a baseline dataset from the first detection of P. marginatus in Australia. Further analysis of the spread can provide insights into invasive species' adaptation in a novel environment.

In the 18 months between the early summer of 1940 and the winter of 1941 the Imperial Japanese Army (hereinafter the IJA) spent time in close observation of new developments. The power vacuum generated in the British, French, and Dutch colonies of South East Asia by the German conquest of Western Europe in the spring of 1940 suddenly gave rise to the possibility of a war against the British, French, and Dutch as a way of seizing control over the rich natural resources under their dominion. Since its formation, the IJA’s organization and planning had continued, with its principal focus being upon Siberia and China. However, spurred on by these new developments, in 1940–41 the IJA’s focus suddenly switched southwards. In pursuing the ultimate objective of the Dutch East Indies, the advancing IJA had two obstacles to break through: In the east, the defeat of US military forces in the Philippines and the Western Pacific and the support offered thereto by the US Pacific Fleet stationed in Pearl Harbor. In the west, the Japanese forces aimed at the subjugation of the British forces stationed in Hong Kong, the Malay Peninsula, Singapore, and Burma. While the Imperial Japanese Navy (IJN) was to be principally responsible for winning the war against the Americans in the Pacific, it was to be the land battles against the British in South East Asia which the IJA troops were chiefly to deal with. According to Japanese strategic planning, the order of the invasion was to be as follows: (1) the occupation of Hong Kong, (2) the seizure of the Malay Peninsula and Singapore, (3) the exclusion of the British forces from Burma, with the Malay Peninsula and Singapore being the most important targets. Whilst leaving the overall discussion on the overall strategic planning for the IJN and IJA to Professor Kiyoshi Ikeda’s chapter in the second volume of the present series,1 this essay outlines the IJA’s war preparations against Britain on a tactical and operational level, focusing on its invasion plan for the Malay Peninsula and Singapore.

The Malayan tapir (Tapirus indicus) is an endangered species in Southeast Asia (SEA). Over the years, there has only been a few reports on its population genetic structure and evolutionary history in SEA. In particular, while the captive Malayan tapir population in Thailand has received fairly more research in recent years, there has not been any wide-scale population genetic study in the Malay Peninsula since the last decade. In this study, we report on the genetic diversity and attempt to make inferences on the phylogeography of the Malayan tapir in the Malay Peninsula, using the mitochondrial DNA control region, including also data from previous studies. We identified 12 novel haplotypes and two distinct Malayan tapir clades with a divergence time of 14.6 million years ago (mya) in the Peninsular Malaysia (i.e. southern Malay Peninsula) samples, as opposed to only one clade found in the Thai (i.e. Thailand western border and northern Malay Peninsula) captive individuals, with an almost two-fold higher nucleotide diversity compared to the latter. The co-occurrence of the two lineages in southern Malay Peninsula suggested past historical events of population isolation, migration and admixture as a result of episodic glacial periods and paleoenvironmental changes in SEA. Only one haplotype shared between the populations of the two regions suggested further gene flow restriction at the narrow corridor of the Malay Peninsula as of present day.

The genetic structure of selected five finfish populations, namely, almaco jack (Seriola rivoliana), sailfin grouper (Mycteroperca olfax), stalkeye scorpionfish (Pontinus strigatus), wahoo (Acanthocybium solandri) and yellowfin tuna (Thunnus albacares) in the Galapagos Islands, was studied using mitochondrial DNA cytochrome b (797 bp) and D-loop (426 bp). The results of the present study showed that (1) almaco jack, yellowfin tuna and wahoo had high haplotype diversities and numerous singleton haplotypes and spread over extensive ranges, as expected in pelagic fishes, while only Galapagos yellowfin tuna from D-loop dataset showed population expansion (P < 0.05); (2) sailfin grouper cyt b had low haplotype and nucleotide diversities, confirming the concern from previous study that the fish was overfished in waters off the Galapagos Islands. It further supports the need to effectively manage sailfin grouper; (3) Stalkeye scorpionfish cyt b had also low haplotype and nucleotide diversities, but with significant negative Fu’s Fs, (P < 0.01), indicating genetic hitchhiking and overall reduction of genetic variation, supporting the need to monitor stalkeye scorpionfish; and (4) no genetic differentiation was found between Galapagos and Western Pacific yellowfin tuna (P = 0.9). The singleton haplotypes specific to the Galapagos yellowfin tuna population might indicate reproductive isolated units or founders. The results provide an insight into the genetic structure of finfish populations, which can be used to draw an effective management plan for ensuring their long-term sustainability in the Galapagos Islands.