Genetic diversity of aboriginal and invasive populations of four‐eyed fir bark beetle Polygraphus proximus Blandford (Coleoptera,Curculionidae, Scolytinae)

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Phylogeography of the giant wood spider (Nephila pilipes, Araneae) from Asian–Australian regions

Aim There are currently few population genetic studies on widely distributed SE Asian terrestrial organisms. We have studied the genetic diversification pattern of the giant wood spider, Nephila pilipes (Araneae: Tetragnathidae) to see whether fluctuations in rain forest extents generated by Quaternary climatic changes left signatures on populations of this agile terrestrial arthropod. Location The collecting localities were distributed in the following seven regions: (1) N Australia; (2) India (Calcutta, Karziranga and Sukna); (3) SE Asia (N Vietnam, Malaysia, Singapore and Bali); (4) SE China (Fujian, Guandong, Hong Kong and Hainan); (5) SW China (Guangxi and Yunnan); (6) E Asian islands (Ryukyu islands and Taiwan); and (7) the Philippine Islands. Methods A total of 374 specimens were collected from the East Asian continent and islands, SE Asia, India, and northern Australia. Mitochondrial cytochrome oxidase I gene partial sequences were used as the molecular marker to infer the phylogeographic diversification patterns. Results From the specimens collected, 67 haplotypes were identified, which could be grouped into five major clades. The dominant clade contained populations in regions ranging from Okinawa to Bali (spanning a distance of more than 4000 km), but their genetic variations were not structured and were not significantly associated with geographical distances. Three clades contained specimens collected from peripheral regions of the distribution range of N. pilipes, such as India, N Australia, and NE Asia. Members of the clade distributed in NE Asia were sympatric but those of the clades distributed in Australia and India were allopatric with those of the dominant clade. Main conclusions The results of this study indicate that, during Quaternary glacial periods, the rain forests in SE Asia might have been more or less continuous and thus generated an unstructured genetic diversification pattern of N. pilipes inhabiting this region. However, during such periods, populations in peripheral regions such as India, N Australia and NE Asia might have been isolated in refugia, thus accounting for the observed genetic divergence from populations in the SE Asian region.     

Understanding the genetic structure of <Emphasis Type="Italic">Symplocos laurina</Emphasis> Wall. Populations using nuclear gene markers

To characterize the genetic diversity of present populations of Symplocos laurina, which grow in the montane forests in India, we analyzed the DNA sequences of a nuclear gene. Using the 881 bp sequence of cytosolic Glyceraldehyde-3-phosphate dehydrogenase gene, we detected 24 haplotypes among 195 individuals sampled from 14 populations. Two dominant haplotypes were distributed over the entire range of this species in India and several private haplotypes were found. Low genetic diversity within population, high differentiation, number of population specific haplotypes and deviation from neutral evolution characterized the present populations of S. laurina. An analysis of molecular variance indicated the presence of geographic structure within the haplotype distribution. The occurrence of S. laurina preglaciation in India is the most parsimonious explanation for the current geographic structure observed. The populations are presumably ancient and might have spread across its extant distribution range in India through a recent range expansion event.     

入侵我国红火蚁的三种单倍型

红火蚁Solenopsis invicta Buren是重要的经济害虫,特别是在农业和生态系统危害方面。2004年底在广东和香港的部分地区发现红火蚁入侵。本文用线粒体细胞色素氧化酶Ⅰ（CO Ⅰ）基因对境内的13个种群进行了入侵蚁巢是否独立传入进行了分析。通过对共计28个蚁巢56个体的包含904个碱基的CO Ⅰ基因分析,发现入侵中国的红火蚁中存在3种单倍型。基于未修正的配对序列变异分析表明,单倍型Ⅱ与单倍型Ⅲ之间的变异最小。而香港种群同时具有这三种单倍型,是入侵中国的红火蚁种群中多样性最丰富的地区。这三种单倍型都分别在阿根廷红火蚁种群中有记录。同源性分析显示,中国的红火蚁可能起源于阿根廷或南美洲,而香港可能是所研究种群的第一入侵地点。     

Genetic differentiation and distribution of Pyropia acanthophora (Bangiales,Rhodophyta) in the Philippines

Pyropia acanthophora is a foliose Bangiales with widely known endemic populations in Indo-Pacific region. This alga has expanded its range recently as a consequence of introduction. In an attempt to explore the genetic diversity of Py. acanthophora within the Philippines and the impact of the introduction of the species from elsewhere, an examination of molecular differentiation and distribution was undertaken using the mitochondrial COI-5P and plastid rbcL gene sequences. The results revealed that the populations of Py. acanthophora in the Philippines exhibited high haplotypic and genetic diversities, and were found to be distinct from those previously reported as conspecific populations found in Taiwan, India, Japan, Hawaii, and from those introduced populations from Brazil. The network analyses as inferred from rbcL and from the combined COI-5P and rbcL genes showed evidence that the Philippine populations of Py. acanthophora exhibited a chaotic patchiness pattern characterized by a population with highly site-exclusive haplotypes, wide genetic variability and lack of local geographic patterns. The distribution of Py. acanthophora within the Philippines was also found to be greater than what was previously known, ranging from the extreme northwest to extreme northeast mainland Luzon coasts, including Camiguin Is., Cagayan. Understanding the genetic diversity and distribution of Py. acanthophora in the Philippines provides valuable information in relation to the conservation and effective resource management of native populations of Py. acanthophora in the tropical Asian region.     

Mitochondrial DNA variation in natural populations of endangered Indian Feather-Back Fish, Chitala chitala

Genetic variation at mitochondrial cytochrome b (cyt b) and D-loop region reveals the evidence of population sub-structuring in Indian populations of highly endangered primitive feather-back fish Chitala chitala. Samples collected through commercial catches from eight riverine populations from different geographical locations of India were analyzed for cyt b region (307 bp) and D-loop region (636–716 bp). The sequences of the both the mitochondrial regions revealed high haplotype diversity and low nucleotide diversity. The patterns of genetic diversity, haplotypes networks clearly indicated two distinct mitochondrial lineages and mismatch distribution strongly suggest a historical influence on the genetic structure of C. chitala populations. The baseline information on genetic variation and the evidence of population sub-structuring generated from this study would be useful for planning effective strategies for conservation and rehabilitation of this highly endangered species.     

Unique haplotypes in ant‐attended aphids and widespread haplotypes in non‐attended aphids

Aphid species within the genus Tuberculatus Mordvilko (Hemiptera: Aphididae) exhibit a variety of interactions with ants, ranging from close associations to non‐attendance. A previous study indicated that despite wing possession, ant‐attended Tuberculatus species exhibited low dispersal rates compared with non‐attended species. This study examined if presence or absence of mutualistic interactions and habitat continuity of host plants affected intraspecific genetic diversity and genetic differentiation in mitochondrial DNA cytochrome oxidase I (COI) sequences. Sympatric ant‐attended Tuberculatus quercicola (Matsumura) (Hemiptera: Aphididae) and non‐attended Tuberculatus paiki Hille Ris Lambers (Hemiptera: Aphididae) were collected from the daimyo oak Quercus dentata Thunberg (Fagales: Fagaceae) in Japan and examined for haplotype variability. Seventeen haplotypes were identified in 568 T. quercicola individuals representing 23 populations and seven haplotypes in 425 T. paiki representing 19 populations. Haplotype diversity, which indicates the mean number of differences between all pairs of haplotypes in the sample, and nucleotide diversity were higher in T. quercicola than T. paiki. Analysis of molecular variance (AMOVA) showed higher genetic differentiation among populations within groups of T. quercicola (39.8%) than T. paiki (22.6%). The effects of attendant ant species on genetic differentiation in T. quercicola were not distinguishable from geographic factors. Despite low dispersal rates, host plant habitat continuity might facilitate widespread dispersal of a T. quercicola haplotype in Hokkaido. These results suggested that following T. quercicola colonization, gene flow among populations was limited, resulting in genetic drift within populations. However, frequent T. paiki dispersal is clearly evident by low genetic differentiation among populations within groups, resulting in lower haplotype diversity.     

Two genetic divergence centers revealed by chloroplastic DNA variation in populations of <Emphasis Type="Italic">Cinnamomum kanehirae</Emphasis> Hay

Cinnamomum kanehirae Hayata (Lauraceae), the most valuable subtropical and temperate broadleaf timber tree in Taiwan, is rapidly disappearing from the wild. Taking advantage of a scion garden established by the Taiwan Forestry Research Institute, we examined patterns of chloroplast DNA (cpDNA) variations in 19 populations including 94 individuals. By sequencing two cpDNA fragments using universal primers (the trnL-trnF and petG-trnP intergenic spacers), we found eight polymorphic sites, six haplotypes, and extremely low nucleotide diversity (π = 0.00016) from 792 bp aligned sequences. The ancestral haplotype is widely distributed. Among the populations studied, three separated populations, at Yungfeng, Fuli, and Tahu have high nucleotide diversity. No phylogeographical structures of haplotypes were revealed because the tests of N _ST−G _ST for populations did not differ from zero in any situations; a ‘star-like’ genealogy is characteristic when all haplotypes rapidly coalesce and is a general outcome of population expansion. The neutrality test also suggested demographic expansion. The genetic divergence and diversity analyses suggested that two potential refugia existed during the last glaciation with a major one located in southeastern Taiwan and a minor one located in Tahu in north-central Taiwan in the Hsuehshan Range, west of the Central Mountain Range.     

Ventral coloration differentiation and mitochondrial sequences of the Chinese Cobra (<Emphasis Type="Italic">Naja atra</Emphasis>) in Taiwan

Differences in coloration between eastern and western populations of the Chinese cobra (Naja atra) in Taiwan have been noted by snake collectors, snake keepers, and users of Chinese traditional medicine, but have never been verified by scientific research. In this study, we quantified the amount of black pigment on ventral scales, and found prominent differences in ventral coloration of populations across Taiwan; populations in eastern Taiwan have black ventral scales while populations in the west are predominantly white. Previous studies have shown a similar east-west population differentiation in regards to venom components. We supplement these data with mitochondrial control region sequences, which show extremely low nucleotide diversity. Black-ventral and white-ventral snakes share major haplotypes and show no genetic differentiation. Nevertheless, moderate F_st and low N_m values between populations indicate low levels of gene flow. With a morphological fixation earlier than mitochondrial sequences on a relatively short evolutionary time scale, ventral coloration is potentially a result of local adaptation. Based upon the results of this study, along with traditional observations, we strongly recommend treating each of the four populations of the Chinese cobra in Taiwan as distinct ESUs. Reintroducing confiscated snakes from the illegal trade back into the wild needs to be halted to prevent artifical gene flow.     

Effects of habitat fragmentation on genetic diversity and gene flow among the Homidia socia (Collembola: Entomobryidae) populations in the Thousand Island Lake

In the present study, partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene of 22 island populations of the springtail Homidia socia in the Thousand Island Lake were sequenced. Across all sequences, 37 haplotypes were identified for the 510‐bp mitochondrial (mt) DNA COI gene. Haplotype 2 was the most common, and was distributed in the most of the 22 island populations. Haplotype diversity ranged from 0.065 to 0.733, and the total genetic diversity was 0.56216. The genetic characteristics of the 22 island populations were analyzed using the fixation index and gene flow, with values of 0.00043–0.94900 and 0.02703–703.72540, respectively. Comparison between (island area and isolations) with population genetic diversity revealed that there were no significant correlations between them, except for a significant correlation between the number of haplotypes and island area. Mantel tests showed that there was no significant correlation between geographic distance and genetic distance among various groups. All the results indicated that there were no obvious relationships between island characteristics and the genetic diversity of the springtails. We consider that the low dispersal capacity of springtails and the island patches surrounded by water in the Thousand Island Lake are the major factors affecting the genetic diversity of H. socia.     

Analysis of Amblyomma sculptum haplotypes in an area endemic for Brazilian spotted fever

Amblyomma sculptum (Ixodida: Ixodidae) Berlese, 1888, a member of the Amblyomma cajennense complex, is the major vector of Brazilian spotted fever (BSF) in southeastern Brazil. In this study, the genetic diversity of A. sculptum populations in the state of Rio de Janeiro (RJ), Brazil, was investigated because genetic variability in tick populations may be related to vector competence. Samples of A. sculptum from 19 municipalities in 7 regions of RJ were subjected to DNA extraction, amplification and sequencing of D‐loop, cytochrome oxidase II and 12S rDNA mitochondrial genes. These sequences were used to map the genetic diversity of this tick. Amblyomma sculptum populations are genetically diverse in RJ, especially in the South Centre and Highland regions. Few unique haplotypes were observed in all populations, and the majority of genetic variation found was among ticks within each population. Phylogenetic reconstruction reinforced the assumption that all the haplotypes identified in RJ belong to A. sculptum. However, some RJ haplotypes are closer to A. sculptum from Argentina than to A. sculptum from elsewhere in Brazil. In RJ, A. sculptum has high genetic diversity, although little genetic differentiation. Observations also indicated a high level of gene flow among the studied populations and no evidence of population structure according to region in RJ.     

Mitochondrial phylogeography of a Beringian relict: the endemic freshwater genus of blackfish Dallia (Esociformes)

Mitochondrial genetic variability among populations of the blackfish genus Dallia (Esociformes) across Beringia was examined. Levels of divergence and patterns of geographic distribution of mitochondrial DNA lineages were characterized using phylogenetic inference, median‐joining haplotype networks, Bayesian skyline plots, mismatch analysis and spatial analysis of molecular variance (SAMOVA) to infer genealogical relationships and to assess patterns of phylogeography among extant mitochondrial lineages in populations of species of Dallia. The observed variation includes extensive standing mitochondrial genetic diversity and patterns of distinct spatial segregation corresponding to historical and contemporary barriers with minimal or no mixing of mitochondrial haplotypes between geographic areas. Mitochondrial diversity is highest in the common delta formed by the Yukon and Kuskokwim Rivers where they meet the Bering Sea. Other regions sampled in this study host comparatively low levels of mitochondrial diversity. The observed levels of mitochondrial diversity and the spatial distribution of that diversity are consistent with persistence of mitochondrial lineages in multiple refugia through the last glacial maximum.     

Genetic variation among populations of the endangered fan mussel <Emphasis Type="Italic">Pinna nobilis</Emphasis> (Mollusca: Bivalvia) along the Tunisian coastline

The Mediterranean fan mussel Pinna nobilis is an endangered invertebrate due to overexploitation and habitat deterioration. In this species, two distinctive morphs, the “combed” and “straight and wide” forms, have been recorded and it is not known whether this morphometric variability is attributed to genetic or environmental factors. In this study, we used mitochondrial COI sequences to describe the genetic variability of five Pinna nobilis populations sampled along the northern, eastern, and southern Tunisian coastline, and to examine whether there is a genetic differentiation between the two forms of this species. DNA sequences of 675 bp from the mitochondrial COI gene have revealed 10 different haplotypes among 49 examined specimens. Haplotype diversity was high, ranging between 0.40441 and 0.80952, and showed a decreasing North-East gradient, which seems to be explained by the hydrogeography of the study area. The mitochondrial COI marker did not suggest a genetic distinctiveness between the two Pinna nobilis shell forms, “combed” and “straight and wide”. Although the morphometric plasticity of the fan mussel could be due to the influence of environmental factors, further genetic studies using nuclear markers are envisaged to investigate whether this differentiation is associated to gene flow restrictions.     

Genetic diversity in the bronze gudgeon, <Emphasis Type="Italic">Coreius heterodon</Emphasis>, from the Yangtze River system based on mtDNA sequences of the control region

The bronze gudgeon, Coreius heterodon (Bleeker), is an economically important species, which only inhabits the Yangtze River. The stock declined drastically in recent years due to dam construction, over-fishing, and pollution. Little is known about its population genetic structure. In this study, the sequences of the mitochondrial DNA (mtDNA) control regions of natural bronze gudgeon was determined for fish collected from four sites in the Yangtze River (n = 102). The molecular data were used to estimate the genetic diversity and differentiation of the bronze gudgeon. The results showed that 28 haplotypes and 22 variable sites were found, and the haplotype diversity (π) and nucleotide diversity (h) were 0.849 and 0.00257, respectively. A low level of genetic diversity exists in the bronze gudgeon. Analysis of molecular variance (AMOVA) suggests that 98.8% of the genetic variability occurred within the populations; the site of collection had little influence on diversity. Future research should focus on investigating the genetic divergence of populations in different tributaries and using additional polymorphic markers, such as microsatellite DNA, to verify the results and improve interpretation.     

Effect of the invasive bivalve Mytilopsis sallei on the macrofaunal fouling community and the environment of Yundang Lagoon,Xiamen, China

Mytilopsis sallei is a small marine bivalve and is considered as a serious pest. We assume that the invasive bivalve M. sallei changed the community structure of fouling macrofauna and reduced the species diversity index in Yundang Lagoon, Xiamen, China. In order to verify the above hypothesis, test panels were submerged seasonally at five stations during four seasons in Yundang Lagoon, and some chemical parameters were determined. The results showed there were significant differences in density and biomass of M. sallei and other fouling macrofauna with season and with station. The species diversity of the macrofaunal fouling community at stations B and F was low in summer, because high density of M. sallei was found at two stations. There were significantly positive correlations between density and biomass of M. sallei and water temperature and COD, and significantly negative correlations with pH. The results confirmed that this invasive species changed the density and biomass compositions of fouling macrofauna, reduced the species diversity index during the summer period, and somewhat worsened the aquatic environmental quality in Yundang Lagoon, because the pH and the DO were the lowest, and the BOD and the COD were the second lowest in summer among four seasons.     

Self‐fertilization,long‐distance flash invasion and biogeography shape the population structure of Pseudosuccinea columella at the worldwide scale

Population genetic studies are efficient for inferring the invasion history based on a comparison of native and invasive populations, especially when conducted at species scale. An expected outcome in invasive populations is variability loss, and this is especially true in self‐fertilizing species. We here focus on the self‐fertilizing Pseudosuccinea columella, an invasive hermaphroditic freshwater snail that has greatly expanded its geographic distribution and that acts as intermediate host of Fasciola hepatica, the causative agent of human and veterinary fasciolosis. We evaluated the distribution of genetic diversity at the largest geographic scale analysed to date in this species by surveying 80 populations collected during 16 years from 14 countries, using eight nuclear microsatellites and two mitochondrial genes. As expected, populations from North America, the putative origin area, were strongly structured by selfing and history and harboured much more genetic variability than invasive populations. We found high selfing rates (when it was possible to infer it), none‐to‐low genetic variability and strong population structure in most invasive populations. Strikingly, we found a unique genotype/haplotype in populations from eight invaded regions sampled all over the world. Moreover, snail populations resistant to infection by the parasite are genetically distinct from susceptible populations. Our results are compatible with repeated introductions in South America and flash worldwide invasion by this unique genotype/haplotype. Our study illustrates the population genetic consequences of biological invasion in a highly selfing species at very large geographic scale. We discuss how such a large‐scale flash invasion may affect the spread of fasciolosis.     

Genetic bottleneck in invasive species: the potato tuber moth adds to the list

The level of genetic diversity within populations of introduced species has received increasing attention as an important factor influencing their survival and adaptive potential. We examined this issue with the Guatemalan potato tuber moth Tecia solanivora, an agricultural pest which has successfully invaded South America and the Canary Islands within the last 20 years. To analyse changes in T. solanivora genetic diversity, the mitochondrial marker cytochrome b was sequenced from individuals collected across its known distribution area. High haplotypic diversity was observed in Guatemala, whereas only three haplotypes have been found in Venezuela and a single one in the remaining invaded South American countries and the Canary Islands. Invasive haplotypes were not observed in our samples from Guatemala but are closely related to Guatemalan haplotypes. These results are consistent with the hypotheses that (i) either a few individuals were introduced into Venezuela leading to a strong initial genetic bottleneck, or selection pressure may have lead to the disparition of all but a reduced number of introduced haplotypes, (ii) a second bottleneck occured between Venezuela and Colombia, and (iii) the invasion of the Canary Islands originated from South America. We further reviewed the recent literature to compare this change in genetic diversity with those reported for other invasive species. We quantified the changes in genetic diversity between native and introduced ranges for 57 biological invasions. We found that the genetic homogenization in T. solanivora was among the strongest reported and discuss factors that can explain the success of invasive populations with low genetic diversity.     

No genetic differentiation between geographically isolated populations of Clarias macrocephalus Günther in Malaysia revealed by sequences of mtDNA Cytochrome b and D‐loop gene regions

In the present study, we assessed the genetic variation of three Clarias macrocephalus Günther populations collected from Kedah, Perlis and Kelantan (Peninsular Malaysia) using sequences of partial mitochondrial cytochrome b (Cyt b) and D‐loop genes. A total of 57 individuals were sequenced and 1470 bp were obtained (1053 bp Cyt‐b; 417 bp D‐loop). The analysis revealed 21 haplotypes based on 81 polymorphic sites. Nucleotide diversity (π) was 0.003 in all populations while haplotype diversity ranged from 0.657 to 0.765. No significant genetic differentiation among the three populations was observed. Nevertheless, a number of private haplotypes was discovered, providing valuable information for selective breeding programs.     

Genetic and morphological assessment of a vulnerable large catfish,Silonia silondia (Hamilton, 1822), in natural populations from India

Silonia silondia is a commercially important fish distributed in Asian countries, which is under threat due to overexploitation. This study focuses on the morphological analysis and genetic variation of S. silondia individuals, through truss network and sequencing of two mitochondrial regions, respectively, from six wild populations of the Ganga and Mahanadi river systems in India. A total of 38 haplotypes was observed by analysing combined mitochondrial genes (cytochrome b + ATPase 6/8) in 247 individuals of S. silondia collected from six populations. Average haplotype and nucleotide diversities were 0.8508 and 0.00231, respectively. Genetic structure analysis showed the predominant cause of genetic variation to be within populations. The two clades were observed among the haplotypes and time of divergence from their most probable ancestor was estimated to be around 0.3949 mya. Analysis of combined mitochondrial genes in six populations of S. silondia resulted into three management units or genetic stocks. The truss network analysis was carried out by interconnecting 12 landmarks from digital images of specimens to identify phenotypic stocks. Sixty-five truss morphometric variables were analysed for geometric shape variation which revealed morphological divergence in River Son specimens. The present study presents molecular markers and genetic diversity data which can be critical input for conservation and management of differentiated populations and future monitoring of the genetic bottleneck. The morphological shape analysis clearly shows that variation in the insertion of adipose fin is an important parameter influencing the morphological discrimination.     

The origin of Indian Star tortoises (Geochelone elegans) based on nuclear and mitochondrial DNA analysis: A story of rescue and repatriation

The Indian Star tortoise (Geochelone elegans) belongs to the family Testunidae and is distributed in southwest India and Sri Lanka. In addition to facing loss of its natural habitat, the species is also illegally traded as food and as an exotic pet internationally. Here we report DNA-based analyses for identification and repatriation of these tortoises into their natural habitat. We have attempted to establish the geographical origin of these tortoises rescued from smugglers, by comparing the microsatellite and mitochondrial markers of rescued animals with animals of known provenance. Star tortoises exhibited strong genetic structure in India. The populations from western India were genetically distinct at microsatellite and mitochondrial loci from southern populations. The rescued individuals had similar multilocus genotypes and mitochondrial DNA haplotypes as the reference individuals from south India. However, the precise geographic origin of many of the rescued samples remains unresolved, because we could not assign them to southern populations and the Neighbor-Joining cluster analysis indicated that some of rescued tortoises formed distinct clusters. These data strongly suggest that the rescued group of tortoises is composed of a mix of individuals from differentiated source populations that are probably located in southern India and possibly Sri Lanka. Our study provides valuable information based on molecular markers for the assessment of genetic diversity in Indian Star tortoises.