Phylogeography and genetic diversity of East Asian Neolitsea sericea (Lauraceae) based on variations in chloroplast DNA sequences

Neolitsea sericea is an evergreen broad leaved tree in the warm-temperate regions of East Asia. This area is a hotspot for plant species richness and endemism caused by dynamic changes in land configuration during the Quaternary. However, the historical migration of such evergreen tree species is still poorly understood. In an attempt to reconstruct the phylogeographic history of N. sericea during the Quaternary, we identified the chloroplast DNA haplotypes of 287 individuals from 33 populations covering almost all of its geographic range. Analyses were based on sequence data from the trnL–F, psbC–trnS, and rps16 regions. Nine haplotypes were identified. The majority included ancestral types in the southwestern part of the main islands of Japan, with other region-specific haplotypes being found in populations on the Korean Peninsula, Taiwan (Isl. Lanyu), and elsewhere in Japan. A statistical parsimony network revealed two lineages derived from Japanese main islands. One was represented on the Korean Peninsula, the other on Isl. Lanyu. The current distribution of N. sericea has been shaped by colonization via land bridges. During the glacial periods, two primary, but separate migration routes were followed—from the southwestern part of the Japanese main islands to either the Korean Peninsula or Taiwan. In addition, we believe the Zhoushan populations were shaped by post-glacial processes through an ECS land bridge (East China Sea basin) from northern refugia that existed during the late Pleistocene.     

Genetic variation of Mytilus coruscus Gould (Bivalvia: Mytilidae) populations in the East China Sea inferred from mtDNA COI gene Sequence

In order to characterize the genetic relationship of six populations of Mytilus coruscus Gould in the East China Sea, a 681 bp region of mtDNA COI gene was sequenced and analyzed. Eighty four individuals in total were collected from three cultured populations and three wild populations from three localities of the coast of East China Sea. The sequences from these different populations identified 62 polymorphic sites, which included 41 singleton variable sites and 21 parsimony informative sites that defined 45 distinct haplotypes. Phylogenetic analysis showed that most haplotypes were highly interconnected with each other. Thirty seven of the 45 haplotypes were only found in their own populations, seven were found at two-four localities and only haplotype NO.2 was found in all six populations, indicating that most haplotypes were locally restricted. All haplotypes had shaped two similar branches, each including individuals from all six strains. The results of F_ST values indicated that the genetic distances between populations are not closely associated with their geographic distances.     

Chloroplast DNA variation and genetic structure of Miscanthus sinensis in southwest China

Miscanthus sinensis is a dominant perennial C4 grass with the potential to being a feedstock crop in North America, Europe, and China. Variation in chloroplast DNA sequence was used to obtain information regarding the genetic diversity and structure of populations of M. sinensis in southwest China. Chloroplast DNA, trnL-F and rpl20-rps12 sequences from seventy-five individuals representing 14 populations of M. sinensis were used to study the sequence variation. Seven haplotypes and 16 polymorphic sites (2.7%) were identified. Five substitutions, 6 indels, and 5 existing substitutions and indels sites, were detected through splicing these two gene segments. The genetic diversity within the studied populations (diversity of haploids, h = 0.561, nucleotide diversity, π = 0.00504) was low, this may be affected by the relatively larger effect of genetic drift on the chloroplast DNA, reflecting smaller effective populations than nuclear DNA. Genetic variance within the populations was higher than that between the populations, suggesting that higher gene flow may exist within these populations. The results of parsimony network in seven haplotypes indicated that H1 and H2 may be ancient haplotypes, which may help guide future research on the origin of M. sinensis. Our results provide information on the genetic diversity and structure of M. sinensis and may assist future studies on the phylogeography of M. sinensis.     

Variation of mitochondrial DNA in Far Eastern mullet pilengas, Liza haematocheilus Temminck and Schlegel, acclimatized in the Azov-Black Sea basin

This study continues the investigation of genetic variation in the populations of native and acclimatized in the Azov-Black Sea basin pilengas from the Sea of Japan. The previous comparison based on allozyme analysis was supplemented by analysis of restriction polymorphism of a mitochondrial DNA fragment containing the cytochrome b gene and the D-loop. Five out of fifteen tested endonucleases detected polymorphic sites. In the samples of native and acclimatized pilengas, five common haplotypes were found; ten and three “unique” haplotypes were detected in the Far Eastern and the Azov populations, respectively. The differences in haplotype distributions between these populations were highly significant (P < 0.001). The mtDNA variation was lower in the Azov than in the Far Eastern population (haplotype diversity μ respectively 6.35 ± 0.27 and 9.14 ± 0.55), which is in good agreement with the decrease in the number of polymorphic loci and the mean number of alleles per locus, found earlier for allozyme markers in this population. The reasons for these differences in the acclimatized population are discussed.     

Genetic diversity and population structure of Sepiella japonica (Mollusca: Cephalopoda: Decapoda) inferred by mitochondrial DNA (COI) variations

In order to describe the genetic diversity of five geographical populations of cuttlefish (Sepiella japonica) along with Chinese coast and determined their phylogenetic relationship, partial mitochondrial COI gene (681bp in length) was amplified from 96 individuals collected from these populations and sequenced. The 5 populations of cuttlefish inhabit Yellow Sea, East China Sea and South China Sea. Out of 22 polymorphic nucleotides identified, 8 were represented by a single sequence, 12 were parsimony informative, which defined 22 haplotypes. Haplotype and nucleotide diversity were low among populations. Of 22 haplotypes, 15 appeared only in a single population, 6 appeared in 2 or 3 populations and 1 was shared by all populations. The COI gene was monomorphic in Qingdao population. The haplotypes identified clustered into 2 clades, each covered individuals from 5 populations each. Pairwise F_ST were not proportional to the geographical distances. Among the 5 populations, relatively high level of genetic diversity was found in Ningde population which was recommended to be the best choice of germplasm resources for artificial releasing project.     

Phylogeography of Cycas revoluta Thunb. (Cycadaceae) on the Ryukyu Islands: very low genetic diversity and geographical structure

Variations in the chloroplast and mitochondrial DNA of Cycas revoluta Thunb. (Cycadaceae) were examined in 22 populations distributed across the Ryukyu Islands and southern Kyushu. Among the 14,130 bp of sequence examined, only one site mutation and one indel were polymorphic. The identified polymorphisms were located in the spacers between trnS (UGA) and trnfM (CAU) of the chloroplast DNA and between nad1 exon B and exon C of the mitochondrial DNA, respectively. Three haplotypes were identified from the Ryukyu Islands and southern Kyushu. The areas of distribution of the three haplotypes were highly geographically structured. The boundaries of two of the three haplotypes were demarcated by Okinoerabujima Island in the middle Ryukyus. The northern type and southern types lay north and south of the island, respectively. The third haplotype was almost sympatrically distributed with the southern type. The genetic variation within C. revoluta was estimated to be very low (h = 0.641, π = 0.00071) in comparison to its relative in Taiwan, C. taitungensis, which possesses 97 cpDNA haplotypes and 55 mtDNA haplotypes from two relic populations. A reasonable explanation for the low genetic diversity of the cycad on the Ryukyu Islands could be severe bottleneck effects, resulting from the submersion of low islands and the diminished landmass of islands in the interglacial age in the Quaternary period. The geographically restricted nature of the haplotypes could be attributed to vicariance resulting from the land configuration of the Ryukyu Islands, including changes in geography during the interglacial age in the Quaternary.     

Genetic Population Structure of Chum Salmon in the Pacific Rim Inferred from Mitochondrial DNA Sequence Variation

We examined the genetic population structure of chum salmon, Oncorhynchus keta, in the Pacific Rim using mitochondrial (mt) DNA analysis. Nucleotide sequence analysis of about 500 bp in the variable portion of the 5′ end of the mtDNA control region revealed 20 variable nucleotide sites, which defined 30 haplotypes of three genealogical clades (A, B, and C), in more than 2,100 individuals of 48 populations from Japan (16), Korea (1), Russia (10), and North America (21 from Alaska, British Columbia, and Washington). The observed haplotypes were mostly associated with geographic regions, in that clade A and C haplotypes characterized Asian populations and clade B haplotypes distinguished North American populations. The haplotype diversity was highest in the Japanese populations, suggesting a greater genetic variation in the populations of Japan than those of Russia and North America. The analysis of molecular variance and contingency χ² tests demonstrated strong structuring among the three geographic groups of populations and weak to moderate structuring within Japanese and North American populations. These results suggest that the observed geographic pattern might be influenced primarily by historic expansions or colonizations and secondarily by low or restricted gene flow between local groups within regions. In addition to the analysis of population structure, mtDNA data may be useful for constructing a baseline for stock identification of mixed populations of high seas chum salmon.     

High level of variation at Abies alba chloroplast microsatellite loci in Europe

Based on two polymorphic chloroplast microsatellites that had been previously identified and sequence characterized in the genus Abies, genetic variation was studied in a total of 714 individuals from 17 European silver fir (Abies alba Mill.) populations distributed all over the natural range. We found eight and 18 different length variants at each locus, respectively, which combined into 90 different haplotypes. Genetic distances between most populations were high and significant. There is also evidence for spatial organization of the distribution of haplotypes, as shown by permutation tests, which demonstrate that genetic distances increase with spatial distances. A large heterogeneity in levels of diversity across populations was observed. Furthermore, there is good congruence in the levels of allelic richness of the two loci across populations. The present organization of levels of allelic richness across the range of the species is likely to have been shaped by the distribution of refugia during the last glaciation and the subsequent recolonization processes.     

Geographic distribution and diversity of mitochondrial DNA haplotypes in South American sea lions (Otaria flavescens) and fur seals (Arctocephalus australis)

Genetic diversity and population structure of two species of South American pinnipeds, Otaria flavescens and Arctocephalus australis, from colonies located along the south-eastern coast of South America, were analysed using mitochondrial DNA haplotypes and compared with two populations of these species from the Pacific coast. A 445 base-pair segment, that included the tRNA-Glu gene (31 bp) and the adjacent cytochrome b gene (414 bp), was amplified using the polymerase chain reaction and sequenced directly. O. flavescens and A. australis showed six and seven haplotypes with 12 and 20 polymorphic sites, respectively. In the Atlantic Ocean there was an individual of A. australis that showed an haplotype that was highly divergent from the others. If this haplotype is excluded, the pattern of haplotype differentiation obtained for both species indicated a possible bottleneck that would have occurred 110,000 years ago, which also affected other pinnipeds. Colonies of the Atlantic and the Pacific did not share haplotypes. This result, based on a limited number of samples for the comparisons between oceans, suggests that populations from both oceans correspond to different evolutionarily significant units. O. flavescens on the Atlantic coast shows two clusters of breeding colonies in Uruguay and Patagonia, separated by a thousand kilometres. Colonies within clusters did not show significant differences in haplotype frequencies, but the difference between the clusters was significant, suggesting that they correspond to different conservation stocks.     

Molecular insights into the genetic and haplotype diversity among four populations of Catla catla from Madhya Pradesh revealed through mtDNA cyto b gene sequences

In the present investigation, the genetic structure of four populations of Catla catla, sequences of mitochondrial gene, cytochrome b (cyto b) from four populations were sequenced and analyzed. The sequences of mitochondrial regions revealed high haplotype diversity and low nucleotide diversity. The lowest 249 polymorphic sites and 0.00 parsimony informative sites were detected in populations of Fish Federation Pond (CCFFB) whereas highest 330 polymorphic sites and 56 parsimony informative sites were detected in populations of Narmada River (CCNRH) in the cyto b gene sequences in Catla catla populations. The twelve different haplotypes were detected among the four populations studied, lowest population specific haplotype as 2.00 was observed in Fish Federation Pond (CCFFB) and highest was in Population of Narmada River and Tighra reservoir. Sequencing of cyto b gene revealed 12 number of haplotypes (h) with haplotype (gene) diversity (Hd) 0.8736 and nucleotide diversity (π) 0.6474. These data clearly indicated that, feral/wild population showing highest values of polymorphisms, parsimony, haplotype diversity showing good, healthy habitat is lotic water (Narmada River) and lentic water body (Tighra reservoir). The results also concluded that the partial cyto b is polymorphic and can be a potential marker to determine ecological habitat based genetic differentiation among the populations.     

Sequence diversity of MHC class-II <Emphasis Type="BoldItalic">DRB</Emphasis> gene in gazelles (<Emphasis Type="BoldItalic">Gazella subgutturosa</Emphasis>) raised in Sanliurfa of Turkey

In this study, we aimed to assess the sequence diversity of major histocompatibility complex (MHC) class-II DRB gene at exon 2 in gazelles raised in Sanliurfa Province of Turkey. Twenty DNA samples isolated from gazelles (Gazella subgutturosa) were used for sequencing exon 2 of MHC class-II DRB gene. Target region was amplified by polymerase chain reaction (PCR) and their products were directly sequenced. Nine of these 20 samples yielded unambiguously readable sequences. Three of the nine samples were homozygotes and each showed different sequences. A 262-bp sequence obtained from the three homozygote samples were submitted to GenBank (accession numbers: KC309405, KC309406 and KC309407). Using an allele specific PCR, we detected 10 additional haplotypes. Among 13 haplotypes, 45 nucleotide positions were polymorphic and most of the polymorphic nucleotide positions localized at peptide-binding region (PBR). Rates of nonsynonymous substitutions were significantly higher than synonymous substitutions at PBR. Phylogenetic analysis of the haplotypes showed that 10 haplotypes of the gazelles were clustered together while three were clustered with ovine and bovine haplotypes. The results indicated that at least 13 haplotypes at exon 2 of MHC class-II DRB gene were showing high degree of nucleotide and amino acid diversity, and certain haplotypes of G. subgutturosa were more similar to haplotypes from sheep or cattle than to each other. Rates of synonymous and nonsynonymous substitutions suggested that positive selection was a driving force for diversity at this locus in G. subgutturosa.     

Mitochondrial COI and 16sRNA Evidence for a Single Species Hypothesis of E. vitis,J. formosana and E. onukii in East Asia

Tea green leafhopper is one of the most damaging tea pests in main tea production regions of East Asia. For lack of recognized morphological characters, the dominant species of tea green leafhoppers in Mainland China, Taiwan and Japan have always been named as Empoasca vitis Göthe, Jacobiasca formosana Paoli and Empoasca onukii MATSUDA, respectively. Furthermore, nothing is known about the genetic relationships among them. In this study, we collected six populations from Mainland China, four populations from Japan and one population from Taiwan, and examined the genetic distances in the COI and 16sRNA regions of mtDNA among them. The results showed that the genetic distances based on single gene or the combined sequences among eleven leafhopper populations were 0.3–1.2%, which were all less than the species boundary of 2%. Moreover, there were at least two haplotypes shared by two distinct populations from different regions. The phylogenetic analysis based on single gene or combined sets also supported that tea green leafhoppers from Mainland China, Taiwan and Japan were closely related to each other, and there were at least two specimens from different regions clustered ahead of those from the same region. Therefore, we propose that the view of recognizing the dominant species of tea green leafhoppers in three adjacent tea production regions of East Asia as different species is unreliable or questionable and suggest that they are a single species.     

基于线粒体DNA控制区的斑翅草螽不同地理种群遗传分化研究

采用PCR扩增结合DNA克隆测序技术,分析了斑翅草螽Conocephalus maculates 9个地理种群mtDNA控制区序列的变异及遗传多样性。切除侧翼RNA基因序列后,最终获得的斑翅草螽mtDNA控制区比对后全长为676 bp,平均碱基组成T(37.8%),C(11.7%),A(41.3%)和G(9.1%)。共检测到98个可变位点,占总位点数的14.5%,其中,9处碱基插入/缺失,74处转换(40个T/C,34个A/G),50处颠换(18个A/T,11个T/G,15个A/C,6个C/G)。共定义46个单倍型,其中,4个为种群间共享单倍型(H02、H05、H08和H10),其余42个为各种群独有单倍型,包括6个种群内共享单倍型(H09、H11、H15、H18、H26和H38)。单倍型总数占实验个体总数的69.7%,除四川峨眉山外,其余种群单倍型百分比均﹥50%。通过两两地理种群间的FST值差异显著性检验,将这些群体分为4组,分别为SC+CQ,GX+FLB+HN+YN,XZ和HB。以长瓣草螽C.gladiatus、峨眉草螽C.emeiensis、悦鸣草螽C.melaenus、竹草螽C.bambusanus为外群,构建的斑翅草螽mtDNA控制区单倍型NJ法系统树形成3个自举支持度较高的分支,其中,分支A由28种单倍体组成,包括本研究中除四川峨眉山(SC)和重庆万州(CQ)以外的7个种群;分支B由12种单倍体组成,包含除菲律宾拉乌尼翁(FLB)和江西南昌(JX)以外的7个种群;分支C由6种单倍型组成,全部来自西藏林芝(XZ)的单倍型。聚类结果表明,斑翅草螽不同地理种群间的遗传分化并不明显,即使是两两群体间FST值差异显著的群体,也未能形成完全独立的分支。     

Phylogenetic Relationships Among Fragmented Asian Black Bear (Ursus Thibetanus) Populations in Western Japan

The number of Asian black bears (Ursus thibetanus) in Japan has been reduced and their habitats fragmented and isolated because of human activities. Our previous study examining microsatellite DNA loci revealed significant genetic differentiation among four local populations in the western part of Honshu. Here, an approximate 700-bp nucleotide sequence of mitochondrial DNA (mtDNA) control region was analysed in 119 bears to infer the evolutionary history of these populations. Thirteen variable sites and variation in the number of Ts at a T-repeat site were observed among the analysed sequences, which defined 20 mtDNA haplotypes with the average sequence divergence of 0.0051 (SD = 0.00001). The observed haplotype frequencies differed significantly among the four populations. Phylogeographic analysis of the haplotypes suggested that black bears in this region have gone through two different colonisation histories, since the observed haplotypes belonged to two major monophyletic lineages and the lineages were distributed with an apparent border. The spatial genetic structure revealed by using mtDNA was different from that observed using microsatellite DNA markers, probably due to female philopatry and male-biased dispersal. Since nuclear genetic diversity will be lost in the three western populations because of the small population size and genetic isolation, their habitats need to be preserved, and these four populations should be linked to each other by corridors to promote gene flow from the easternmost population with higher nuclear genetic diversity.     

油松遗传结构与地理阻隔因素的相关性

油松(Pinus tabulaeformis)是我国特有广布树种。秦岭是我国亚热带和暖温带气候的重要分界线,贺兰山是我国西北干旱区与半干旱区的分界线。旨在以分布于秦岭、贺兰山和晋陕两省的10个天然油松种群为研究对象,通过对其线粒体DNA(nad1和matR内含子)的序列,探讨地理阻隔对油松遗传结构的影响。结果表明,10个天然油松种群的100个个体中共检测到27个单倍型,多态位点172个,简约信息位点35个,单一多态性位点137个。其中1个单倍型为全部种群共有,4个单倍型为2-5个种群共有,其余22个单倍型为各个种群所独有。在这10个种群中,有8个种群分别具有1-4个独有单倍型。尽管秦岭南侧种群和北侧种群分别具有两个和一个独有单倍型; 贺兰山东侧种群和西侧种群均具有3个独有单倍型;但是与晋陕种群(即油松分布区中心种群)相比,其种群独有单倍型平均数目则明显较少。与此同时,不仅秦岭南北两侧或贺兰山东西两侧种群的独有单倍型的进化关系往往较近,而且秦岭北侧或贺兰山东侧种群的独有单倍型与油松分布区中心种群的某些独有单倍型的关系亦较近。从而导致秦岭南北两侧或贺兰山东西两侧种群与油松分布区中心种群之间表现出比较复杂的聚类关系。由此可见,油松的遗传结构与山脉屏障的存在没有明显关系。     

Finding copepod footprints: a protocol for molecular identification of diapausing eggs in lake sediments

Even though calanoid copepods produce diapausing eggs that stay alive in lake sediments, these eggs have rarely been used paleolimnologically, as they lack diagnostic morphological features. In this study, we developed a method to identify copepod diapausing eggs in Japan as a clue toward reconstructing past plankton populations. We first determined a 28S ribosomal DNA (rDNA) (i.e., nc28S) regional sequence library (240 bp) of various calanoid copepod species using ethanol-fixed plankton samples collected from across the Japanese archipelago. Then we applied the UltraSHOT method to extract DNA from an individual diapausing egg. Finally, the nc28S region of diapausing eggs collected from various lakes was sequenced and compared with the regional library for species identification. In total, 21 haplotypes of the nc28S region were recovered from planktonic samples of 11 Japanese freshwater calanoid copepod species. Despite the short length of this region, no identical haplotypes were shared among the species analyzed, including the Acanthodiaptomus pacificus complex treated as a species. Even different lineages of A. pacificus could be separated. These results indicate that the nc28S region can be used as a barcode in Japan. A total of 112 diapausing eggs collected from various lakes and ponds was processed, and the nc28S region of each was successfully sequenced. All of these egg sequences matched one or the other of the nc28S haplotypes in the regional library mentioned above. The set of protocols we applied (i.e., preparing a comprehensive regional sequence library and sequencing egg DNA) is thus useful for involving copepod diapausing eggs in paleolimnological studies in lakes. The nc28S region treated in this study has a strong potential to uncover the paleodiversity of copepods, at least in Japan.     

Phylogeography of lateral plate dimorphism in the freshwater type of ninespine sticklebacks, genus Pungitius

The freshwater type of ninespine sticklebacks, genus Pungitius, is widely distributed in northern Japan and reproductively isolated from other genetically divergent types endemic to small regions in Japan. This type expresses dimorphism in its lateral plate morphology: complete and partial row morphs. The two morphs show a parapatric distribution in Japan. To clarify the process involving the distribution of these two morphs, we examined their phylogeography based on restriction fragment length polymorphism of an entire mitochondrial DNA (mtDNA). The survey was carried out with seven restriction enzymes on the populations of the freshwater type collected from 41 localities across the distribution range in Japan, and 6 further Pungitius populations from the Okhotsk Sea coast of Russia were appended. An unweighted pair-group method with arithmetic averages (UPGMA) tree among 54 mtDNA haplotypes resolved eight clustering groups that differed in sequence divergence by approximately 1.3%–2.1%. Two of the eight groups were found only in Russia. mtDNA phylogenies constructed by neighbor-joining and Wagner parsimony methods suggested that the haplotypes of each plate morph were polyphyletic. The geographic distribution pattern of these groups suggests that they should be classified into two broad categories, one with extensive distribution and the other with localized distribution of the constituent haplotypes within a group. The former groups were found mainly in the populations with the completely plated morph and the latter groups with the partially plated morph. It is supposed that twice dispersals of dimorphic or complete plated ancestors and genetic differentiation during the interglacial played an important role in the formation of the present distribution of the two morphs in Japan. Received: March 28, 2000 / Revised: November 3, 2000 / Accepted: January 16, 2001     

Occurrence of a novel strain of Scirtothrips dorsalis (Thysanoptera: Thripidae) in Japan and development of its molecular diagnostics

Scirtothrips dorsalis Hood is a cosmopolitan and polyphagous thrips species. Recently, a novel strain of S. dorsalis attacking capsicum crops was found in Japan. A molecular phylogenetic analysis using mitochondrial cytochrome c oxidase subunit I sequences revealed that the capsicum-associated populations were genetically different from Japanese native strains and were closely related to Southeast Asian populations. We named the capsicum-associated populations “strain C” and the Japanese native ones “strain YT”. A total of 10 haplotypes were found in strain C and 26 in strain YT. To differentiate the two strains, we developed a multiplex-PCR method using the ribosomal ITS2 region.     

基于细胞色素b基因的中国岩羊不同地理种群遗传差异分析

为了揭示中国岩羊不同地理种群的遗传差异,探讨岩羊亚种分化的分子机制,采用中国岩羊不同地理种群的细胞色素b(Cyt b)基因的全序列,分析了碱基变异情况、遗传距离以及核苷酸序列差异。用最大似然法和贝叶斯法构建分子系统树并对获得的拓扑结构进行分析。结果发现,西藏亚种与四川亚种Cyt b基因平均序列差异为4.2%(±0.007),处于偶蹄目亚种的序列差异范围内,支持了目前对岩羊西藏亚种的分类地位。四川亚种内部各地理种群之间的遗传距离(0.033±0.0 111)与它们分别到西藏种群的遗传距离(0.042±0.007)差异不显著(t=1.824,P=0.084),说明四川亚种内部各地理种群间已经发生较显著的遗传分化。其中,四川、甘肃和青海种群亲缘关系较近,并与四川亚种内部的其它种群已产生了显著的遗传分化。因此认为四川亚种内部各地理种群的种下分化需要深入研究。     

Identity and genetic structure of eggplant fruit and shoot borer,Leucinodes orbonalis Guenée (Lepidoptera:Crambidae) populations in the Philippines inferred from morphological traits and COI sequence data

Morphological and molecular analysis of 15 Philippine populations of eggplant fruit and shoot borer (EFSB), Leucinodes orbonalis Guenée were conducted to determine if these populations are constituted singly by L. orbonalis or by different species and to assess the level of variability among them. Morphometric analysis of five genital traits of 850 male adult EFSB from field populations and analysis of the COI gene sequence of 879 F₁ EFSB larvae from 15 main eggplant-producing provinces identified all individuals as belonging to L. orbonalis. Principal Component Analysis of five morphometric genital characters revealed high similarity among the EFSB populations regardless of geographic location. Thirteen (13) sequence variants (haplotypes) were identified, with one haplotype predominant and widespread throughout the country. The remaining haplotypes occurred rarely and differed from the widespread haplotype by one mutation. Overall, the EFSB populations from Philippines exhibited low nucleotide and haplotype diversity, indicating low genetic diversity. Topologies from a maximum likelihood tree indicate all thirteen haplotypes cluster in a single clade with EFSB populations from India and other South-East Asian countries. Further analysis with the Generalized Mixed Yule Coalescent (GMYC) method classified the different haplotypes into a single GMYC entity. Combined with morphometric analysis, differences between haplotypes are not suggestive of any subspecies. Negative values of Tajima's D and Fu's F_s tests combined with the phylogenetic analysis and overall low genetic diversity of Philippine populations support the hypothesis that EFSB is not endemic but introduced to the Philippines.