Population genetic structure in the endemic cyprinid fish Microphysogobio alticorpus in Taiwan: Evidence for a new phylogeographical area

The Formosa Bank is a significant zoogeographical barrier for the freshwater fish in Southern Taiwan. Here, we present population genetic structure analyses on Microphysogobio alticorpus populations in Taiwan, and biogeographic pattern to infer the relationship between historic dispersal geological dynamics. A total of 24 haplotypes were genotyped for mitochondrial CR + cyt b region in 134 specimens collected from 9 populations. Relatively high levels of haplotype diversity (h = 0.896) and low levels of nucleotide diversity (π = 0.005) were detected in M. alticorpus. Two major phylogenetic haplotype groups, Clade N1+N2 and S, were revealed and estimated to diverge about 0.121 myr (million years) ago. Haplotype network and population genetic analyses indicated significant genetic structure (F_ST = 0.876), largely concordant with the geographical location of the populations. According to SAMOVA analysis, M. alticorpus populations were divided into five units that can be explained by episodes of dispersal and population expansion followed by population fragmentation and restricted gene flow. The results of the topological pattern and network suggested that the Kaoping River was the first habitat colonized by the ancestor of M. alticorpus, before the northward dispersal.     

Genetic population structure of <Emphasis Type="Italic">Lefua echigonia</Emphasis> inferred from allozymic and mitochondrial cytochrome <Emphasis Type="Italic">b</Emphasis> variations

We examined the genetic population structure of Lefua echigonia (Japanese name, hotoke-dojo) using polymerase chain reaction restriction-fragment length polymorphisms (PCR-RFLPs) of the mitochondrial cytochrome b gene and two allozymic loci. The phylogenetic relationships of L. echigonia and those among L. echigonia, Lefua sp. (nagare hotoke-dojo), and L. nikkonis (ezo hotoke-dojo) were also investigated based on the nucleotide sequences of the cytochrome b gene. PCR-RFLP analysis revealed 18 mitotypes in L. echigonia, 2 in Lefua sp., and 1 in L. nikkonis. Phylogenetic trees based on the cytochrome b sequences indicated that the 18 mitotypes in L. echigonia were divided into five distinct groups (South-Kanto, North-Kanto, Tohoku, Echigo, and Tokai-Kinki clades) that differed by 8.5–15.3%, reflecting region-specific geographic distributions. The distributions of alleles in two allozymic loci roughly corresponded to those of the mitotype groups. The divergence times of the five groups were estimated to be about 3.4–7.7 million years ago by applying a general rate for mitochondrial DNA, suggesting that the divergence among them might have occurred in the late Tertiary. It can be inferred that the regional differentiation of each group was mainly due to geographic isolation and that this has been maintained, because the boundaries among the groups corresponded to geological features. The trees also supported the existence of three taxa, L. echigonia, Lefua sp., and L. nikkonis. We concluded that Lefua sp. was distinguished from other species in Lefua by morphological and ecological characters and also by genetic divergences of the cytochrome b gene. Our study also demonstrated the superior efficacy and simplicity of PCR-RFLP analysis as a method for detecting genetic variation in L. echigonia.     

Phylogeography of the capercaillie in Eurasia: what is the conservation status in the Pyrenees and Cantabrian Mounts?

The Western capercaillie (Tetrao urogallus) is a keystone species of Palearctic boreal and altitude coniferous forests. With the increase of mountain leisure activities and habitat loss, populations are declining in most mountain ranges in Western Europe. Recent work has shown that the populations from the Pyrenees and Cantabrian Mountains survived a severe bottleneck during the 19th century, and are still considered as threatened due to habitat fragmentation and isolation with other populations. We present an extensive phylogeographic study based on mitochondrial DNA sequence (control region) extracted non-invasively from faeces collected throughout the species range (from western European mountains to central and eastern Europe, Fenno-Scandia, Russia and Siberia). We also compared our results with DNA sequences of closely related black-billed capercaillie (T. parvirostris). We found that populations from Pyrenees and Cantabrians are closely related but are different from all other capercaillie populations that form a homogenous clade. Therefore, we consider that these South-Western populations should be considered as forming an Evolutionary Significant Unit that needs an appropriate management at a local scale. We also discuss the possible locations of glacial refugia and subsequent colonisation routes in Eurasia, with a Western “aquitanus” lineage from Iberia and Balkans, and an Eastern “urogallus” lineage from Southern Asia. This work might have important implication for capercaillie conservation strategies to define important areas for conservation, and to prevent possible exchange or introductions of individuals originated from other lineages. Electronic Supplementary Material The online version of this article (doi: ) contains supplementary material, which is available to authorized users.     

Mitochondrial phylogeography of the Dalmatian wall lizard, Podarcis melisellensis (Lacertidae)

A 903 bp section of the mitochondrial cytochrome b gene was sequenced from 73 specimens of Podarcis melisellensis collected at 52 localities distributed over the major part of the species’ range. In addition, parts of the 12S (about 470 bp) and 16S rRNA (about 500 bp) genes were analysed for 11 representative samples leading to a congruent phylogeny. Our study includes representatives of all 20 subspecies recognized today. The phylogenetic analysis of the sequence data revealed three main clades: mainland with nearby islands, Vis archipelago, and Lastovo archipelago. The degree of mitochondrial DNA divergence among these clades suggests a separation of the respective population groups during the earliest Pleistocene. The phylogenetic pattern observed within the species is in sharp contrast to the actual taxonomic division into subspecies. A correlation between genetic diversity of P. melisellensis populations and paleogeography of the regions they inhabit is discussed.     

Mitochondrial DNA reveals a mosaic pattern of phylogeographical structure in Atlantic and Mediterranean populations of anchovy (Engraulis encrasicolus)

This study extends the geographic coverage of a previous study of mitochondrial DNA restriction fragment length polymorphism in European anchovy. Both studies together include 24 samples representing 17 localities extending from the Black Sea, through the Mediterranean Sea to the eastern Atlantic as far south as Dakar, Senegal. Eighty-eight haplotypes define two clades (A and B) separated by 3.2% sequence divergence. Clade A has a star-like genealogy indicative of a recent population expansion. Clade B has a more complex genealogy, consisting of several haplotypes at intermediate frequencies. The distributions of these clades consist of a mosaic with abrupt changes between some areas and gradients between other areas. Clade A predominates the Black and Aegean seas, but is present throughout the Mediterranean. Unexpectedly, new data show that clade A is also at a high frequency in the Atlantic, from Portugal to at least Senegal. Overall, the level of genetic differentiation among populations is high (F(ST)=0.148, p<0.0001), with the greatest differences between basins. AMOVA reveals four main geographical groups: Atlantic, central Mediterranean, Aegean Sea, and Black Sea. Mismatch distribution clearly indicates historical bottleneck and population expansion for clade A, while for clade B such evidence is equivocal. This difference may reflect a range expansion for both clades, but with higher gene flow (Nm values) between demes for clade A. Both contemporary and historical processes are important in shaping the complex genetic population structure of European anchovy.     

Mitochondrial DNA diversity and origins of domestic goats in Southwest China (excluding Tibet)

Southwest China contains about one third Chinese indigenous goat breeds representing special economic and ecological characteristics. Mitochondrial DNA (mtDNA) D-loop sequences of 312 individuals (including 109 new individuals, 203 individuals retrieved from GenBank) from 18 Chinese domestic goat breeds were used to investigate breed genetic diversity, origin and phylogeography. All goat breeds in this study proved to be extremely diverse, average haplotype diversity and nucleotide diversity being 0.9829 ± 0.0027 and 0.03615 ± 0.03257, respectively. The 312 sequences gave 148 different haplotypes. Phylogenetic analyses revealed that there were two mtDNA haplogroups identified in domestic goats in Southwest China, in which haplogroup A was predominant. Mismatch analysis showed haplogroup A had experienced population expansion events, whereas haplogroup B did not. Amova analysis showed there was no significant geographical structuring. Almost 86.23% of genetic variation was included in the within-breed variance component and only 3.5% was observed among the four geographic provinces. The results of this study contribute to the knowledge of the genetic structure and origin of domestic goats in Southwest China.     

Phylogeography, genetic diversity and conservation of the large copper butterfly Lycaena dispar in Europe

We argue that insect species conservation at large scales should take account of the distribution of genetic diversity among populations. Maintenance of genetic diversity may be vital in retaining a species' adaptive capacity and evolutionary potential. We illustrate the concept using the example of the large copper butterfly Lycaena dispar in Europe. This species has become extinct in parts of its range and is declining rapidly in others, whilst conversely, increasing in many areas. The latter has recently reduced its conservation status. Mitochondrial DNA analysis is used to construct a phylogeography from a preliminary sample set obtained from across Europe. A cytochrome b fragment of 402 base pairs was sequenced and 10 haplotypes were found. Relatedness among populations suggest that those from northern and central Europe are closely related and probably form one evolutionary significant unit (ESU) reflecting post-glacial colonization from southeast Europe. In contrast, the sample from Italy is divergent and should be considered a separate ESU. Our results, combined with ecological data, suggest that conservation action for this species should be targeted on specific regions and populations.     

A new and unique species of the genus Aphanius Nardo, 1827 (Teleostei: Cyprinodontidae) from Southern Iran: A case of regressive evolution

A primarily vicariance-based speciation has been suggested for the killifish genus Aphanius Nardo, 1827, but ecological factors are likely to have promoted the speciation processes in addition. Here, we report on the discovery of a unique Aphanius species from Southern Iran and show that also regressive evolution has shaped the present-day diversity of Aphanius. The species is characterized by complete absence of scales and reduction in the biomineralization of hard structures, particularly of the caudal skeleton and jaw teeth. Based on mt-DNA sequences, morphometric and meristic data, osteology, jaw teeth and otoliths, it is described as Aphanius furcatus sp. n. The new species is sympatric with A. dispar (Rüppell, 1829) in salty rivers and hot sulphuric springs in the Hormuzgan Basin (Southern Iran), and is sister taxon to this species plus A. ginaonis Holly, 1929. Based on geological data we estimate that the divergence between the lineages of A. furcatus and A. dispar is about 12–14 million years old. We conclude that the reductive phenomena observed in A. furcatus have evolved as an evolutionary response to the extreme habitat conditions in order to save energy (because storage of Ca²⁺ is not necessary), and to transport oxygen efficiently. The results confirm that regressive evolution is an important factor in speciation and occurs independently in separate lineages.     

Phylogeographic genomics of mitochondrial DNA: Highly-resolved patterns of intraspecific evolution and a multi-species, microarray-based DNA sequencing strategy for biodiversity studies

Phylogeographic genomics, based on multiple complete mtDNA genome sequences from within individual vertebrate species, provides highly-resolved intraspecific trees for the detailed study of evolutionary biology. We describe new biogeographic and historical insights from our studies of the genomes of codfish, wolffish, and harp seal populations in the Northwest Atlantic, and from the descendants of the founding human population of Newfoundland. Population genomics by conventional sequencing methods remains laborious. A new biotechnology, iterative DNA “re-sequencing”, uses a DNA microarray to recover 30–300 kb of contiguous DNA sequence in a single experiment. Experiments with a single-species mtDNA microarray show that the method is accurate and efficient, and sufficiently species-specific to discriminate mtDNA genomes of moderately-divergent taxa. Experiments with a multi-species DNA microarray (the “ArkChip”) show that simultaneous sequencing of species in different orders and classes detects SNPs within each taxon with equal accuracy as single-species-specific experiments. Iterative DNA sequencing offers a practical method for high-throughput biodiversity genomics that will enable standardized, coordinated investigation of multiple species of interest to Species at Risk and conservation biologists.     

Phylogeography of Asian weaver ants, Oecophylla smaragdina

The phylogeography of Oecophylla smaragdina was studied using the mitochondrial cytochrome b gene (Cytb), cytochrome oxidase subunit I (COI), and nuclear long-wavelength opsin gene (LW Rh). Weaver ants were collected from 35 localities and from one to nine colonies per locality. Neighbor-joining trees inferred from 647 bp of Cytb and 1,026 bp of COI using Oecophylla longinoda as an outgroup indicated that the haplotypes of O. smaragdina were clearly separated into seven groups: group 1 of India excluding West Bengal; group 2 of Bengal, Indochinese Peninsula, Malay Peninsula and Greater Sunda Islands, including Lombok and Sumbawa; group 3 of the Philippines; group 4 of Flores; group 5 of Sulawesi; group 6 of Halmahera; and group 7 of New Guinea and Australia. This grouping was also supported by a strict consensus tree derived from maximum parsimony and maximum likelihood trees. In addition, two haplotypes of LW Rh were found in O. smaragdina: one in group 2 and another in all the other groups. Comparison to haplotypes in other hymenopteran species suggests that group 2 is younger than other groups of O. smaragdina. The clustering of the seven groups was coincident with geological evidence of the distribution of continents, islands, and seas during glacial periods.     

Distribution and Conservation of Genetic Diversity Among UK Calcareous Grassland Regions: A Case Study Using Insects

Conservation strategies for whole communities at the landscape scale have rarely been able to take into account genetic diversity because of the number of species involved. However, if species can be grouped together by geographic distribution of genetic diversity and patterns of relatedness, then landscape and genetic conservation might be more effectively combined to cope with problems of fragmentation. We report on a study that measures how genetic diversity is distributed at national and regional scales in four unrelated species of calcareous grassland insects. Samples were obtained from sites within six UK calcareous grassland regions. Genetic diversity was measured using mtDNA sequencing (four species) and allozyme analysis (two of the four species). A striking difference in mtDNA diversity was found between the chrysomelid beetle Aphthona herbigrada (23 haplotypes; mean per region 5.5) and the cicadellid bug Batracomorphus irroratus (27 haplotypes; mean per region 6.2), with high haplotype richness, and the brown argus butterfly Aricia agestis (4 haplotypes; mean per region 1.7) and the cistus forester moth Adscita geryon (5 haplotypes; mean per region 2.4) with low. At the UK scale, patterns of diversity were species specific with no general conservation strategy emerging for the community. However, there was little differentiation among regions and any splitting into more than one management unit was not clearly justified, questioning whether distribution of genetic diversity should be a concern at this spatial scale.     

Phylogeographic history of the New Zealand stick insect Niveaphasma annulata (Phasmatodea) estimated from mitochondrial and nuclear loci

We have assessed the utility of a single-copy nuclear locus and mitochondrial DNA (mtDNA) in a phylogeographic study of the New Zealand stick insect Niveaphasma annulata (Hutton). We amplified sequences from the mitochondrial cytochrome oxidase subunit I (COI) gene and the single-copy nuclear gene elongation factor-1α (EF1α) from 97 individuals. Allelic phase at the EF1α locus was determined using Denaturing Gradient Gel Electrophoresis. Phylogenetic analyses showed broad congruence between the geographic distribution of three major COI clades and EF1α alleles, which suggested that the phylogenetic patterns reflect population history rather than lineage sorting. However, the geographic boundaries of these clades were not always in exact agreement between the two loci. Our data indicate that Niveaphasma annulata was most likely separated into a number of refugia during Pleistocene glacial advances. Subsequent to glacial retreat these refugial populations have expanded and now form a number of zones of secondary contact. We contrast these patterns with those observed from other New Zealand taxa. Our study offers compelling evidence for the use of nuclear genes alongside mtDNA for future phylogeographic studies.     

Rearrangements of mitochondrial transfer RNA genes in marsupials

Summary The nucleotide sequences of the mitochondrial origin of light-strand replication and the five tRNA genes surrounding it were determined for three marsupials. The region was found to be rearranged, leaving only the tRNA^Tyr gene at the same position as in placental mammals andXenopus. Distribution of the same rearranged genotype among two marsupial families indicates that the events causing the rearrangements took place in an early marsupial ancestor. The putative mitochondrial light-strand origin of replication in marsupials contains a hairpin structure similar to other vertebrate origins and, in addition, extensive flanking sequences that are not found in other vertebrates. Sequence comparisons among the marsupials as well as placentals indicate that the tRNA^Tyr gene has been evolving under more constraints than the other tRNA genes.Deceased July 21, 1991     

黑嘴鸥种群的遗传分化与迁徙模式

用分子生物学方法研究了黑嘴鸥(Larus saundersi)种群的遗传结构和分化.对我国黑嘴鸥现存的3个地方种群50个样本的线粒体DNA控制区部分片段进行了序列测定,结合已公布的的两个韩国样本的序列,比对后所获得的550 bp的序列中,共发现49个变异位点,定义了37种线粒体单元型,其中仅1种为我国3个地方种群间共享单元型,多数为各地方种群内特有.我国3个地方种群内的单元型多样性和核苷酸多态性都很高;4个地方种群合并成一个大种群时, 其线粒体单元型多样性与核苷酸多样性仍很高,分别为0.974%±0.012%和0.510%±0.042%.进一步分析表明,4个地方种群间核苷酸歧异度在0.433%-0.585%之间,种群分化程度FST在-0.03176-0.48063之间,基因流Nm在1.03-33.79之间,平均遗传距离为0.0051±0.0011.UPGMA系统发生树及最大简约网络图表明, 黑嘴鸥的演化关系呈现星状辐射,单元型之间呈现一种混杂的分布格局,地方种群没有形成明显的系统地理结构.同时运用彩色旗标技术,初步掌握了4个地方种群迁徙规律.对比分子研究结果,验证了不同地方种群间的遗传分化与其迁徙模式基本一致,同时认为黑嘴鸥不同地方繁殖种群从越冬地返回繁殖地的过程中会发生交叉.最后,鉴于黑嘴鸥不同地方种群间的遗传分化不显著,其迁徙行为具有差异性,建议在保护和遗传管理中应分别对待.