Phylogenetic relationships and intraspecific variations of loaches of the genus Lefua (Balitoridae,Cypriniformes)

Three nominal species are known in East Asian balitorid loaches of the genus Lefua, i.e. L. echigonia, L. nikkonis, and L. costata. Lefua echigonia, with large morphological variations was recently separated into two groups, L. echigonia including the holotype and L. sp., based on morphological and ecological traits. We performed protein and DNA analyses to elucidate phylogenetic relationships among loaches of the genus Lefua and to settle the taxonomic status of L. sp. We also investigated intraspecific variations in L. echigonia s. str. to shed light on the process of formation of freshwater fish fauna in Japan. Protein analyses using two-dimensional gel electrophoresis showed that genetic distances between L. sp. and L. echigonia s. str. and between L. sp. and L. nikkonis were as large as that between L. echigonia s. str. and L. nikkonis. DNA analyses of the mitochondrial D-loop region showed that L. sp. and L. echigonia s. str. were monophyletic, respectively, while neither L. nikkonis nor L. costata was monophyletic and these species formed together a clade. The results supported the specific status of L. sp. and proposed reevaluation of the taxonomic status of L. nikkonis and L. costata. DNA analyses also showed that L. sp. was more closely related to L. echigonia s. str. than to the L. nikkonis-L. costata complex, and four local populations were distinguished in L. echigonia s. str. Distribution patterns of the four local populations of L. echigonia s. str. in Japan were approximately congruent with those of the medaka, Oryzias latipes, suggesting that differentiation in the two distantly related fishes have a common historical background.     

Incongruence between mtDNA phylogeny and morphologial and ecological characters in loaches of the genus Lefua (Balitoridae, Cypriniformes)

To elucidate the phylogenetic position of Lefua loaches from Aichi and Shizuoka Prefectures of Honshu Island, Japan, we determined their nucleotide sequences for the mitochondrial D-loop region and compared these to sequences from four other Lefua species: L. costata, L. nikkonis, L. echigonia, and L. sp. Loaches identified as L. sp. on the basis of morphology comprised a clade (the L. sp. Tokai population) that grouped together with L. echigonia; hence, the processes involved in evolution within the genus Lefua were unclear. We performed randomly amplified polymorphic DNA (RAPD) analyses to obtain genetic information on nuclear DNA. The RAPD patterns of the L. sp. Tokai population differed from those of the local L. echigonia and L. sp. populations. The L. sp. Tokai population was similar to L. echigonia with regard to mitochondrial DNA but differed from L. echigonia and L. sp. with respect to nuclear DNA; this indicated that the evolutionary background of the L. sp. Tokai population was unique. We suggest that introgression of mitochondria occurred from L. echigonia to the L. sp. Tokai population, and speculate on the process of evolution of the latter population of Lefua. As with six L. echigonia populations and two L. sp. populations, we regard the L. sp. Tokai population as an evolutionary significant unit (ESU) that qualifies for protection as an endangered loach.     

Parallel evolution in eight-barbel loaches of the genus Lefua (Balitoridae, Cypriniformes) revealed by mitochondrial and nuclear DNA phylogenies

The evolutionary history of eight-barbel loaches of the genus Lefua contains important phylogenetic information that will aid in resolution of the faunal formations and evolutionary histories of Japanese and East Asian freshwater fishes. Our sequencing of the mitochondrial D-loop region in a large number of samples allowed construction of the most comprehensive phylogeny of these loaches to date; we demonstrated monophyly of five Lefua species and identified populations of Lufua. sp. and Lefua echigonia. Loaches inhabiting the Tokai region in Japan were morphologically and ecologically indistinguishable from Lefua sp. However, they were included in the L. echigonia lineage. We determined a novel phylogeny by sequencing the nuclear ribosomal S7 subunit and showed that nuclear DNA phylogeny essentially matched the mitochondrial DNA phylogeny. Loaches from the Tokai region were part of the L. echigonia lineage, indicating parallel evolution between Tokai loaches and Lefua sp. in western Japan. We presented the most robust phylogeny to date using concatenated mitochondrial and nuclear sequences. The wealth of molecular information allowed us to speculate on evolutionary processes in the genus Lefua.     

On the systematics and phylogeography of eight-barbel loaches the genus Lefua (Cobitoidea: Nemacheilidae): mtDNA typing of L. pleskei

Comparative analysis of personal sequence data for the mtDNA control region (926 to 928 bp) from eight-barbel loaches inhabiting eight localities in the Amur River basin (4) and the Sea of Japan (4) and the GeneBank/NCBI data for the Lefua individuals from the other regions of the world showed that eight-barbel loaches from Primorskii krai water basins were marked by a specific group of mtDNA haplotypes. This finding is considered as supporting the species status of L. pleskei. Genetic distances within L. pleskei are small (on average 0.355) and close to those within L. nikkonis (on average 0.48%). The distances between this species pair are the least (on average 2.15%) among all other pairs compared. In MP, ML, and Bayesian trees, L. pleskei and L. nikkonis haplotypes formed a common clade with high statistically significant support. In all tree variants, L. costata mtDNA haplotypes were located out of the group of interest. A clade consisting of highly diverged lineages of Lefua sp. and L. echigonia haplotypes occupied even more independent position. The mtDNA haplotypes of L. pleskei and L. costata from the Amur River basin were evolutionary young and derived from the haplotypes found in these species from the Sea of Japan (L. pleskei) or the Yellow Sea (L. costata) basins. It is thereby suggested that both species rather recently migrated into the Amur River system. According to the molecular clock data, basal diversification of the eight-barbel loach lineages took place at the end of middle Miocene (about 11 to 12 Myr ago), while divergence of L. pleskei and L. costata ancestral forms probably occurred approximately, 5 Myr ago. Since all main lineages of eight-barbel loaches were found in the Sea of Japan basin (continental coastline and the islands), the divergence order and dispersal patterns of the Lafua species might have been largely determined by the geological development pattern of this water body and the adjacent territories.     

中国北鳅谱系地理学分析

北鳅(Lefua costata)为冷水性鱼类,分布于淮河以北,分析遗传结构能够反映其适应环境变迁的响应.基于线粒体D-loop区211条序列分析了我国北鳅的谱系地理学和遗传多样性,样本采自9条水系共18个样点.单倍型分析显示共计55个单倍型,呈高单倍型多样性(h=0.9304)和高核苷酸多样性(π=0.0087).单...     

Phylogenetic analysis of Sarcocystis spp. of mammals and reptiles supports the coevolution of Sarcocystis spp. with their final hosts.

Sequences of the small subunit rRNA genes were obtained for two coccidians, Sarcocystis dispersa and an unnamed Sarcocystis sp. which parasitise the European barn owl and an African viperid snake as their final host, respectively, and share mouse as their intermediate host. Phylogenetic analysis of the sequence data showed that Sarcocystis sp. from the viperid snake is most closely related to another Sarcocystis sp. isolated from an American crotalid snake, while S. dispersa grouped with other bird-transmitted species. The available dataset failed to resolve the evolutionary relationships among four major branches into which all Sarcocystidae and Isospora spp. were split. However, within these branches, the phylogenetic relationships of the majority of analysed members of the genus Sarcocystis reflected coevolution with their final, rather than intermediate hosts.     

Evidence of complex phylogeographic structure for the threatened rodent <Emphasis Type="Italic">Leopoldamys neilli</Emphasis>, in Southeast Asia

Leopoldamys neilli is a threatened murine rodent species endemic to limestone karsts of Thailand. We have studied the phylogeography of L. neilli using two mitochondrial markers (cytb, COI) and one nuclear fragment (bfibr), in order to assess the influence of its endemicity to karst habitat. One hundred fifteen individuals of L. neilli were collected in 20 localities throughout the geographic range of this species in Thailand. Our study revealed strong geographic structure of the mtDNA genetic diversity: six highly differentiated, allopatric genetic lineages were observed in our dataset. They exhibit a very high degree of genetic divergence, low gene flow among lineages and low levels of haplotype and nucleotide diversities within lineages. Our results suggest that L. neilli’s populations are highly fragmented due to the scattered distribution of its karst habitat. The most divergent lineage includes the populations from western Thailand, which have been separated from the other genetic lineages since at least the Early Pleistocene. The other lineages are more closely related and have diverged since the Middle Pleistocene. This study revealed an unexpected high level of genetic differentiation within L. neilli and highlighted the high endemicity of this species to limestone karsts. Our results enhance the importance of protecting limestone habitats to preserve not only the species but also intraspecific diversity.     

The use and limits of ITS data in the analysis of intraspecific variation in Passiflora L. (Passifloraceae)

The discovery and characterization of informative intraspecific genetic markers is fundamental for evolutionary and conservation genetics studies. Here, we used nuclear ribosomal ITS sequences to access intraspecific genetic diversity in 23 species of the genus Passiflora L. Some degree of variation was detected in 21 of these. The Passiflora and Decaloba (DC.) Rchb. subgenera showed significant differences in the sizes of the two ITS regions and in GC content, which can be related to reproductive characteristics of species in these subgenera. Furthermore, clear geographical patterns in the spatial distribution of sequence types were identified in six species. The results indicate that ITS may be a useful tool for the evaluation of intraspecific genetic variation in Passiflora.     

Intraspecific phylogeography of Lacerta vivipara and the evolution of viviparity

The lacertid lizard Lacerta vivipara is one of the few squamate species with two reproductive modes. We present the intraspecific phylogeny obtained from neighbor-joining and maximum-parsimony analyses of the mtDNA cytochrome b sequences for 15 individuals from Slovenian oviparous populations, 34 individuals from western oviparous populations of southern France and northern Spain, 92 specimens from European and Russian viviparous populations, and 3 specimens of the viviparous subspecies L. v. pannonica. The phylogeny indicates that the evolutionary transition from oviparity to viviparity probably occurred once in L. vivipara. The western oviparous group from Spain and southern France is phylogenetically most closely related to the viviparous clade. However, the biarmed W chromosome characterizing the western viviparous populations is an apomorphic character, whereas the uniarmed W chromosome, existing both in the western oviparous populations and in the geographically distant eastern viviparous populations, is a plesiomorphic character. This suggests an eastern origin of viviparity. Various estimates suggest that the oviparous and viviparous clades of L. vivipara split during the Pleistocene. Our results are discussed in the framework of general evolutionary models: the concept of an oviparity-viviparity continuum in squamates, the cold climate model of selection for viviparity in squamates, and the contraction-expansion of ranges in the Pleistocene resulting in allopatric differentiation.     

Correlates of genetic differentiation and isolation by distance in 17 congeneric Silene species

The contemporary pattern of intraspecific genetic variation can indicate the relative role of gene flow and local differentiation in shaping the evolutionary history and future trajectory of a species. To assess the recent influence of contrasting life history and demographic characteristics on genetic structure within a group of closely related species, patterns of genetic differentiation (F(ST) and related statistics) and isolation by distance (IBD) were compared among 17 congeneric herbaceous plant species. Data came from 35 published studies of 16 species, and a previously unpublished analysis of chloroplast genetic variation in the rare endemic Silene rotundifolia. Among-population genetic variance was most strongly influenced by the type of genetic marker used; cytoplasmic markers showed larger values than allozyme and anonymous nuclear markers. Other independently significant factors were geographical range size and, for allozyme studies, reproductive system; in particular, endemism and hermaphroditism were associated with higher among-population genetic variance, whereas large native geographical range and dioecy were associated with lower among-population variance. Over equivalent spatial scales, dioecious populations also showed weaker IBD than hermaphrodites, perhaps because increased population transience and/or variance in the spatial pattern of gene flow are more closely associated with dioecy in this genus. Invasive populations had both highly variable among-population genetic variance, and no evidence for IBD, consistent with nonequilibrium conditions. Other analysed factors including predominant pollinator had no discernable influence on genetic structure or patterns of IBD. In general, this comparative approach appears to be valuable for synthesizing the complementary information provided by F-statistics and IBD, and for indicating the relative importance of particular biological factors in shaping genetic variation within different species of a closely related plant group.     

Phylogenetic Relationships among Asian species of Petaurista (Rodentia, Sciuridae), Inferred from Mitochondrial Cytochrome b Gene Sequences

To elucidate the phylogenetic relationships among four species belonging to the genus Petaurista (P. alborufus castaneus, P. alborufus lena, P. leucogenys leucogenys, P. leucogenys nikkonis, P. petaurista melanotus, and P. philippensis grandis), we investigated the partial sequences (1,068 bp) of the mitochondrial cytochrome b gene for these giant flying squirrels. Phylogenetic trees (NJ, MP, and ML trees) constructed from cytochrome b sequences indicated that P. leucogenys was grouped independently with other species, and that P. philippensis was most closely related to P. petaurista with 99-100% bootstrap values. In addition, two subspecies of P. alborufus did not form a single clade: P. alborufus castaneus from China was most distantly related to the other species, whereas P. alborufus lena from Taiwan was closely related to P. petaurista and P. philippensis with 82-90% bootstrap values. This result suggests that it is reasonable to regard P. alborufus lena as a distinct species from P. alborufus castaneus.     

Microevolutionary studies in nematodes: a beginning

Comparisons between related species often allow the detailed genetic analysis of evolutionary processes. Here we advocate the use of the nematode Caenorhabditis elegans (and several other rhabditid species) as model systems for microevolutionary studies. Compared to Drosophila species, which have been a mainstay of such studies, C. elegans has a self-fertilizing mode of reproduction, a shorter life cycle and a convenient cell-level analysis of phenotypic variation. Data concerning its population genetics and ecology are still scarce, however. We review molecular, behavioral and developmental intraspecific polymorphisms for populations of C. elegans, Oscheius sp. 1 and Pristionchus pacificus. Focusing on vulval development, which has been well characterized in several species, we discuss relationships between patterns of variations: (1) for a given genotype (developmental variants), (2) after mutagenesis (mutability), (3) in different populations of the same species (polymorphisms) and (4) between closely related species. These studies have revealed that evolutionary variations between sister species affect those characters that show phenotypic developmental variants, that are mutable and that are polymorphic within species.     

Genetic variation and recombination in Penicillium miczynskii and Eupenicillium species

Reproduction in the genus Penicillium is thought to be completely asexual. Sexual reproduction, as occurs in the related genus Eupenicillium, is thought to provide evolutionary benefits because it allows for new combinations of alleles and therefore increases the amount of variation within the species. This hypothesis was tested using inter-simple sequence repeats (ISSRs) to assess the amount of intraspecific and intra-population variation within Penicillium miczynskii and the closely related Eupenicillium shearii. The data for both genera were also used to test for clonal reproduction against the null hypothesis of panmixis, using measures of genotypic diversity, linkage disequilibrium and phylogenetic tree length. The ISSR fingerprints indicated that the 70 Eupenicillium strains actually included two distinct species, Eupenicillium shearii and Eupenicillium tropicum sp. nov., each represented by populations in both Costa Rica and India. While none of the species or populations were found to be randomly recombining, the relative strength of the clonal component differed among the species. Penicillium miczynskii had the smallest clonal component, with the highest genotypic diversity, lowest Index of Association, 40 % of alleles non-randomly associated, and phylogenetic tree length closer to that of recombined data sets than to the minimum possible. Eupenicillium tropicum showed nearly complete clonal reproduction with the lowest genotypic diversity and 100 % of alleles non-randomly associated in both populations. On the other hand, it also had the greatest amount of intraspecific variation, with as little as 38 % similarity among strains. The results indicate that Penicilliumspecies may, on rare occasion, genetically recombine; the regular occurrence of meiosis in the life cycle of Eupenicilliumspecies does not facilitate recombination; and the greatest amount of genetic variation was not associated with recombination, but with clonal propagation.     

Comparative population genetic structures and local adaptation of two mutualists

Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations.     

Interspecific delimitation and phylogenetic origin of Pugionium (Brassicaceae)

Pugionium (Brassicaceae) is a small genus that occurs in central Asian deserts. The interspecific delimitation and taxonomic treatments of this genus are disputed and its phylogenetic origin remains unknown.In the present study, we examined these issues based on morphological and molecular data obtained for the first time. We used statistical methods to examine inter- and intraspecific morphological variations. The results suggest that only two species, namely P. dolabratum and P cornutum, can be warranted for all examined populations and specimens, whereas three species (P. calcaratum, P. cristatum, and R pterocarpum) should be incorporated into P.dolabratum. This delimitation was further supported by the molecular data: all populations of P. dolabratum, P.calcaratum, P. cristatum, and P. pterocarpum shared the same internal transcribed spacer genotype, whereas those from P. cornutum had another type. Phylogenetic analyses of Pugionium and representative genera of Brassicaceae based on ndhF sequences suggest that this genus is sister to the genus Megacarpaea, which, together, comprise a well-supported lineage with Farsetia, Lobularia, Iberis, and Ionopsidium, whereas the two other genera that were previously suggested to be closely related to this genus (Isatis and Bunias) were placed in the other lineages. We further discuss the origin of Pugionium and suggest that it probably originated in central Asia when the climate became drier from the late Miocene.     

Population genetics and objectivity in species diagnosis

Species as evolutionary lineages are expected to show greater evolutionary independence from one another than are populations within species. Two measures of evolutionary independence that stem from the study of isolation-with-migration models, one reflecting the amount of gene exchange and one reflecting the time of separation, were drawn from the literature for a large number of pairs of closely related species and pairs of populations within species. Both measures, for gene flow and time, showed broadly overlapping distributions for pairs of species and for pairs of populations within species. Species on average show more time and less gene flow than populations, but the similarity of the distributions argues against there being a qualitative difference associated with species status, as compared to populations. The two measures of evolutionary independence were similarly correlated with F(ST) estimates, which in turn also showed similar distributions for species comparisons relative to population comparisons. The measures of gene flow and separation time were examined for the capacity to discriminate intraspecific differences from interspecific differences. If used together, the two measures could be used to develop an objective (in the sense of being repeatable) measure for species diagnosis.     

Morphological variation versus genetic divergence: a taxonomic implication for Mogannia species (Cicadidae: Cicadinae)

Species showing intraspecific morphological variation tend to be very difficult to identify using morphological characters. One such example is the cicada genus Mogannia where some species show considerable intraspecific variation mainly exhibited by wing pattern and body colouration. Thirty-one variants covering different putative species of Mogannia were recognized and illustrated in the present paper. Molecular data of mitochondrial COI and Cytb sequences were employed to test the level of variation and phylogeny of them. The existence of a ‘barcoding gap’ between intraspecific and interspecific genetic divergences and the reciprocally monophyletic clades indicate that all the closely related variants represent a single species, and that all these variants correspond to six species, respectively. However, the evolutionary relationships of intraspecific variants are not resolved possibly due to insufficient genetic variation among them. Our results indicated that some morphological characters, especially the wing pattern and body colouration, and even the number of apical processes of the aedeagus in a couple of related species, must be used with great caution in delimiting Mogannia species and their relatives. The factors responsible for intraspecific morphological variation and phylogeny of Mogannia spp. are preliminarily discussed.     

基于18S rDNA遗传距离与GC含量对游走类纤毛虫的分子系统学研究

为了揭示游走类纤毛虫的系统发生,对寄生于淡水鱼类的车轮虫科中的6种车轮虫进行了18S rDNA的测序并获得了9个序列。采用了最大似然法(ML)与贝叶斯法(BI)对GenBank中所有游走类纤毛虫的18S rDNA序列进行了系统树的构建,并首次将SPSS与18S rDNA遗传距离结合分析了游走类纤毛虫的系统发生。研究结果进一步证实了车轮虫属(Trichodina)的非单系发生与小车轮虫属 (Trichodinella) 的有效性。此外,研究结合18S rDNA 的GC含量与遗传距离分析提出了游走类纤毛虫科属及种间新的鉴定依据: 18S rDNA 的GC含量可用于游走类纤毛虫的科属区分,且与游走类纤毛虫的分化密切相关; 18S rDNA的遗传距离在游走类纤毛虫的不同阶元中具有一定的阈值范围,即通常种内遗传距离阈值范围为0.000-0.005,属种间阈值范围为0.005-0.150,当遗传距离大于0.150时,则达到了科间水平。     

New Species of Closely Related Endosymbiotic Dinoflagellates in the Greater Caribbean have Niches Corresponding to Host Coral Phylogeny

Symbiotic dinoflagellates in the genus Breviolum (formerly Symbiodinium Clade B) dominate coral communities in shallow waters across the Greater Caribbean. While some formally described species exist, mounting genetic, and ecological evidence indicate that numerous more comprise this genus, many of which are closely related. To test this, colonies of common reef‐building corals were sampled across a large geographical range. Phylogenetic and population genetic markers then used to examine evolutionary divergence and delineate boundaries of genetic recombination. Three new candidate species were distinguished by fixed differences in nucleotide sequences from nuclear and chloroplast DNA. Population connectivity was evident within each lineage over thousands of kilometers, however, substantial genetic structure persisted between lineages co‐occurring within sampling locations, signifying reproductive isolation. While geographically widespread with overlapping distributions, each species is ecologically distinct, exhibiting specific mutualisms with phylogenetically distinct coral hosts. Moreover, significant differences in mean cell sizes provide some morphological evidence substantiating formal species distinctions. In providing evidence that satisfies the biological, phylogenetic, ecological, and morphological species concepts, we classify and formally name Breviolum faviinorum n. sp., primarily associated with Caribbean corals belonging to the Caribbean subfamily Faviinae; B. meandrinium n. sp., associated with corals belonging to the family Meandrinidae; and B. dendrogyrum n. sp., a symbiont harbored exclusively by the threatened coral Dendrogyra cylindrus. These findings support the primary importance of niche diversification (i.e. host habitat) in the speciation of symbiotic dinoflagellates.     

荞麦属种间13S球蛋白基因序列比较研究

荞麦13S球蛋白是荞麦种子中的一类主要贮藏蛋白。本研究选用荞麦属植物甜荞栽培种及其野生类型、苦荞栽培种及其野生类型、毛野荞、左贡野荞、细柄野荞和硬枝万年荞6个种共44份材料,进行PCR特异性扩增、测序得到荞麦13S球蛋白基因的保守片段序列。对序列进行差异分析,结果发现44份供试材料13S球蛋白基因片段的285个排列位点中不变位点为24个,多态性位点S为261个(含简约信息位点数198个和单型可变位点63个),序列总突变位点Eta为503个。野生甜荞种内13S球蛋白基因序列差异明显高于栽培甜荞,但野生苦荞种内13S球蛋白基因序列差异仅稍高于栽培苦荞。推测其一方面可能与繁殖方式有关,另一方面可能与荞麦驯化过程中通常只有少数野生型群体被驯化有关。系统聚类分析发现栽培甜荞与野甜荞亲缘关系近,与左贡野荞亲缘关系次之;栽培苦荞与野苦荞亲缘关系近,与毛野荞亲缘关系次之;细柄野荞和硬枝万年荞的13S蛋白基因片段序列差异较小,说明其亲缘关系较近。上述结果为荞麦属种间遗传多样性与进化关系研究提供了理论依据。