Diversity and phylogenetic relationships of <Emphasis Type="Italic">Glossina</Emphasis> populations in Nigeria and the Cameroonian border region

Background

Tsetse flies are vectors of trypanosomes, parasites that cause devastating disease in humans and livestock. In the course of vector control programmes it is necessary to know about the Glossina species present in the study area, the population dynamics and the genetic exchange between tsetse fly populations.

Results

To achieve an overview of the tsetse fly diversity in Nigeria and at the Nigeria-Cameroon border, tsetse flies were trapped and collected between February and March 2014 and December 2016. Species diversity was determined morphologically and by analysis of Cytochrome C Oxidase SU1 (COI) gene sequences. Internal transcribed spacer-1 (ITS-1) sequences were compared to analyse variations within populations. The most dominant species were G. m. submorsitans, G. tachinoides and G. p. palpalis. In Yankari Game Reserve and Kainji Lake National Park, G. submorsitans and G. tachinoides were most frequent, whereas in Old Oyo National Park and Ijah Gwari G. p. palpalis was the dominant species. Interestingly, four unidentified species were recorded during the survey, for which no information on COI or ITS-1 sequences exists. G. p. palpalis populations showed a segregation in two clusters along the Cameroon-Nigerian border.

Conclusions

The improved understanding of the tsetse populations in Nigeria will support decisions on the scale in which vector control is likely to be more effective. In order to understand in more detail how isolated these populations are, it is recommended that further studies on gene flow be carried out using other markers, including microsatellites.

     

Diversity and phylogenetic relationships of Wolbachia in Drosophila and other native Hawaiian insects

Wolbachia is a genus of parasitic alphaproteobacteria found in arthropods and nematodes, and represents on of the most common, widespread endosymbionts known. Wolbachia affects a variety of reproductive functions in its host (e.g., male killing, cytoplasmic incompatibility, parthenogenesis), which have the potential to dramatically impact host evolution and species formation. Here, we present the first broad-scale study to screen natural populations of native Hawaiian insects for Wolbachia, focusing on the endemic Diptera. Results indicate that Wolbachia infects native Hawaiian taxa, with alleles spanning phylogenetic supergroups, A and B. The overall frequency of Wolbachia incidene in Hawaiian insects was 14%. The incidence of infection in native Hawaiian Diptera was 11% for individuals and 12% for all species screened. Wolbachia was not detected in two large, widespread Hawaiian dipteran families—Dolichopodidae (44 spp screened) and Limoniidae (12 spp screened). Incidence of infection within endemic Hawaiian lineages that carry Wolbachia was 18% in Drosophilidae species, 25% in Caliphoridae species, > 90% in Nesophrosyne species, 20% in Drosophila dasycnemia and 100% in Nesophrosyne craterigena. Twenty unique alleles were recovered in this study, of which 18 are newly recorded. Screening of endemic populations of D. dasycnemia across Hawaii Island revealed 4 unique alleles. Phylogenetic relationships and allele diversity provide evidence for horizontal transfer of Wolbachia among Hawaiian arthropod lineages.     

Diversity and phylogenetic relationships of Wolbachia in Drosophila and other native Hawaiian insects

Wolbachia is a genus of parasitic alphaproteobacteria found in arthropods and nematodes, and represents on of the most common, widespread endosymbionts known. Wolbachia affects a variety of reproductive functions in its host (e.g., male killing, cytoplasmic incompatibility, parthenogenesis), which have the potential to dramatically impact host evolution and species formation. Here, we present the first broad-scale study to screen natural populations of native Hawaiian insects for Wolbachia, focusing on the endemic Diptera. Results indicate that Wolbachia infects native Hawaiian taxa, with alleles spanning phylogenetic supergroups, A and B. The overall frequency of Wolbachia incidene in Hawaiian insects was 14%. The incidence of infection in native Hawaiian Diptera was 11% for individuals and 12% for all species screened. Wolbachia was not detected in two large, widespread Hawaiian dipteran families—Dolichopodidae (44 spp screened) and Limoniidae (12 spp screened). Incidence of infection within endemic Hawaiian lineages that carry Wolbachia was 18% in Drosophilidae species, 25% in Caliphoridae species, > 90% in Nesophrosyne species, 20% in Drosophila dasycnemia and 100% in Nesophrosyne craterigena. Twenty unique alleles were recovered in this study, of which 18 are newly recorded. Screening of endemic populations of D. dasycnemia across Hawaii Island revealed 4 unique alleles. Phylogenetic relationships and allele diversity provide evidence for horizontal transfer of Wolbachia among Hawaiian arthropod lineages.     

Genetic diversity and phylogenetic relationships of Malayan tapir (Tapirus indicus) populations in the Malay Peninsula based on mitochondrial DNA control region

Biodiversity and Conservation - The Malayan tapir (Tapirus indicus) is an endangered species in Southeast Asia (SEA). Over the years, there has only been a few reports on its population genetic...     

Diversity of mitochondrial DNA haplotypes in ethnic populations of the Volga-Ural region of Russia

The mtDNA polymorphism was analyzed in eight ethnic groups (N = 979) of the Volga-Ural region. Most mtDNA variants belonged to haplogroups H, U, T, J, W, I, R, and N1 characteristic of West Eurasian populations. The most frequent were haplogroups H (12-42%) and U (18-44%). East Eurasian mtDNA types (A, B, Y, F, M, N9) were also observed. Genetic diversity was higher in Turkic than in Finno-Ugric populations. The frequency of mtDNA types characteristic of Siberian and Central Asian populations substantially increased in the ethnic groups living closer to the Urals, a boundary between Europe and Asia. Geographic distances, rather than linguistic barriers, were assumed to play the major role in distribution of mtDNA types in the Volga-Ural region. Thus, as concerns the maternal lineage, the Finno-Ugric populations of the region proved to be more similar to their Turkic neighbors rather than to linguistically related Balto-Finnish ethnic groups.     

Reconstruction of phylogenetic relationships

In this paper, we provide an introductory overview to the field of phylogenetic analysis, which has wide applications in modern biology.     

喜马拉雅旱獭线粒体DNA控制区遗传多样性及系统发育

喜马拉雅旱獭是青藏高原的优势种,数量多、分布广,全面了解其遗传背景对该地区旱獭资源的保护与合理利用具有重要的意义。本研究以青藏高原云南、西藏和青海三省区共13个地理种群计258只旱獭为研究对象,PCR扩增获得线粒体DNA控制区基因部分序列(887 bp),并运用种群遗传学方法进行遗传多样性分析。结果显示:258份样品共发现了84个变异位点(9.40%),定义了68种单倍型,其单倍型多样性(h)平均值为0.968±0.003、核苷酸多样性(π)平均值为0.017 25±0.016 37,种群总体遗传多样性较高。AMOVA方差分析显示13个地理种群间存在着明显的遗传分化(Fst=0.620 67,P<0.001),种群间基因交流多数较低(Nm<1)。基于单倍型构建的系统发育树中13个地理种群的喜马拉雅旱獭聚为两支,其中来自青藏高原西南地区(西藏安多、青海格尔木、青海囊谦、云南迪庆)的18个单倍型聚成一个大的分支(A支),其余50个单倍型聚为一个大的分支(B支),在NETWORK网络图中也可见到相似网络拓扑结构。研究结果显示青藏高原喜马拉雅旱獭种群以唐古拉山脉为界分为两个大的种群,说明地理隔离是影响喜马拉雅旱獭种群动态变化的主要因素。     

Genetic variation in Glossina brevipalpis, G.longipennis and G.pallidipes, and the phenetic relationships of Glossina species

Glossina brevipalpis Newstead, G.longipennis Corti, and G.pallidipes Austen maintained at ILRAD, Nairobi, Kenya, were examined for genetic variation of fourteen enzyme loci, using polyacrylamide gel electrophoresis. G.brevipalpis had six polymorphic loci, an average of 1.46 effective alleles per locus and a mean heterozygosity per locus of 20.0 +/- 7.1%. The figures for the same parameters in G.longipennis were 3, 1.16 and 8.2 +/- 4.9%, and for G.pallidipes the figures were 7, 1.40 and 22.3 +/- 6.3%. Seven rare alleles were lost from the G.brevipalpis colony during a 1-year period, but no statistically significant changes were observed in the genetics of the colony during this period. Using allele frequency data for ten of the enzymes studied, and frequencies for these enzymes in other taxa, a phenogram was constructed that indicated that the subgenus Austenina (i.e. the fusca group) is the oldest of the three subgenera within the genus Glossina, and that the subgenus Glossina s.str. (i.e. the morsitans group) may be paraphyletic.     

Genetic differentiation of some Glossina morsitans morsitans populations

To study the population structure of Glossina morsitans morsitans Westwood (Diptera: Glossinidae), polymerase chain reaction (PCR) and singlestrand conformational polymorphism (SSCP) methods were used to estimate mitochondrial DNA diversity at four loci in six natural populations from Zambia, Zimbabwe and Mozambique, and in two laboratory cultures. The Zambian and Zimbabwean samples were from a single fly belt. Four alleles were recorded at 12S and 16S1, and five alleles at 16S2 and COI. Nucleotide sequencing confirmed their singularities. Chi-square contingency tests showed that allele frequencies differed significantly among populations. Mean allele diversities in populations averaged over loci varied from 0.14 to 0.61. Little loss in haplotype diversity was detected in the laboratory cultures thereby indicating little inbreeding. Wright's fixation index F(ST) in the natural populations was 0.088+/-0.016, the correlation of haplotypes within populations relative to correlations in the total. A function of its inverse allows an estimate of the mean equivalent number of females exchanged per population per generation, 5.2. No correlation was detected between pairwise genetic distance measures and geographical distances. Drift explains the high degree of differentiation.     

Diversity and phylogenetic relationships of entomopathogenic nematodes (Steinernematidae and Heterorhabditidae) from the Sky Islands of Southern Arizona

A survey for entomopathogenic nematodes was conducted in oak-juniper woodlands of four mountain ranges (Santa Rita, Santa Catalina, Pinale?o, and Chiricahuas), in southeastern Arizona. From a total of 120 soil samples, 23.3% were EPN-positive. Of them 78.5% were positive for Steinernema spp. and 21.5% were positive for Heterorhabditis spp. An integrated approach, combining both traditional (morphological) and molecular methods, was used for examining the diversity of species of these entomopathogenic nematodes. Two named-species S. oregonense and S. riobrave are reported for the first time in Arizona, expanding their currently known geographic range. In addition to this, three undescribed Steinernema and three Heterorhabditis spp. were recovered. Insular evolution, in part, could account for the geographic distribution of entomopathogenic nematodes in Arizona.     

Structure of mitochondrial DNA control region of Fenneropenaeus chinensis and phylogenetic relationship among different populations

This paper deals with the structure of mitochondrial DNA control region of Fenneropenaeus chinensis. The termination-associated sequence (TAS), cTAS, CSB-D-CSB-F, and CSB-1 are detected in the species. The results indicate that the structures of these parts are similar to those of most marine organisms. Two conserved regions and many stable conserved boxes are found in the extended TAS area, central sequences blocks, and conserved sequences blocks (CSBs). This is the special character of F. chinensis. All the mtDNA control region sequences do not have CSB2 and CSB3 blocks, which is quite different from most vertebrates. In addition, the complete mtDNA control region sequences are used to analyze the phylogenetic relationships of F. chinensis. The phylogenetic trees show a lack of genetic structure among populations, which is similar to many previous studies.     

Diversity and distribution of murid rodent populations between forest and derived savanna sites within south western Nigeria

Southward encroachment of the derived savanna zone with its attendant denudation of the rainforest in Nigeria adversely affects the diversity and distribution of mammals, particularly murid rodents. This study was carried out to establish the identities of murid rodent populations and to compare their diversity between forest and derived savanna sites within south western Nigeria. Identification of captured specimens was carried out by multivariate statistics of body and skull measurements, and also by analysis of certain discrete characters. Six species were identified: Praomys tullbergi, Hylomyscus stella, Mastomys natalensis, Arvicanthis rufinus, Lemniscomys striatus and Lophuromys sikapusi. Forest sites possessed a higher Shannon’s diversity index (1.685) than the derived savanna sites (0.978), containing a higher number of taxa and larger abundance of murid rodents. This underscores the negative impact that encroachment of the derived savanna has upon diversity of animals in areas that were once forest.     

On the phylogenetic relationships of Vincelestes neuquenianus

This short review paper compares the lower jaw and lower dentition of the small Mesozoic mammal Vincelestes neuquenianus with some other Laurasian and Gondwanan taxa. On this basis a set of 90 characters recognised by recent authors was assembled and used to construct a cladogram. The topology suggests that the early Cretaceous mammal from Patagonia, Vincelestes, is nested within a clade comprising ‘other Gondwanan mammals’, separated from Laurasian taxa. In general, because there is a lack of Mesozoic mammal skulls from Gondwana, meaning that the skull of Vincelestes can only be compared with cranial material from Laurasia, an incomplete understanding of relationships has resulted in earlier studies. The prototribosphenic condition of Vincelestes is supported by the cladistic analysis presented here and permits a number of interesting speculations because it is of later age than Jurassic tribosphenic mammals from Gondwana. It is proposed that the tribosphenic condition may have developed first amongst taxa on Pangea, before the separation of Laurasia and Gondwana.     

Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations

Nucleotide sequences of mitochondrial DNA (mtDNA) cytochrome B gene (1140 bp) and control region (707 bp) were used to determine the phylogenetic relationships among 51 pig samples representing ancient and current varieties of Iberian pigs (26), Spanish wild boars (seven) and other domestic pigs (18) of cosmopolitan (Duroc, Large White, Landrace, Pietrain and Meishan) and local (Spotted Black Jabugo, Basque and Mangalitza) breeds. A neighbour-joining tree constructed from pairwise distances provide evidence of the European origin of both Iberian pigs and Spanish wild boars. The introgression of Asian mtDNA haplotypes in the genetic pool of the Iberian breed seems unlikely. Four estimates of sequence divergence between European and Asian clades were calculated from the two main domains of the D-loop region and the synonymous and nonsynonymous nucleotide substitutions in the cytochrome B gene. The time since the divergence of pig ancestors was estimated at about 600,000 years before present.     

Exploring contradictory phylogenetic relationships in yeasts

Phylogenetic trees underlie our understanding of yeast evolution and are also proving instrumental in the development of a more robust yeast classification system based upon natural (i.e. evolutionary) relationships. In an effort to refine/improve taxonomic resolution, recent studies have focused on the use of multigene rather than single gene sequencing. Nevertheless, searches to determine 'the tree' remain problematic, as they can often overlook conflicts in the dataset. In such instances, phylogenetic networks such as neighbor-nets and consensus networks can provide a more useful and indeed more informative alternative means of analysis. In this study, we have used the latter two phylogenetic network techniques to reanalyze the multigene sequence dataset of Kurtzman & Robnett, which was used to redefine the taxonomy of the family Saccharomycetaceae. Results from our analyses show that, in general, established clades are robust. However, they also reveal conflict between mitochondrial- and nuclear-encoded genes and indicate the existence of complex patterns of hybridization and introgression not detected in the original study. These patterns are discussed in relation to how they may impact upon the current classification of this group of yeasts.     

Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus

Regions of rDNA are commonly used to infer phylogenetic relationships among fungal species and as DNA barcodes for identification. These regions occur in large tandem arrays, and concerted evolution is believed to reduce intragenomic variation among copies within these arrays, although some variation still might exist. Phylogenetic studies typically use consensus sequencing, which effectively conceals most intragenomic variation, but cloned sequences containing intragenomic variation are becoming prevalent in DNA databases. To understand effects of using cloned rDNA sequences in phylogenetic analyses we amplified and cloned the ITS region from pure cultures of six Laetiporus species and one Wolfiporia species (Basidiomycota, Polyporales). An average of 66 clones were selected randomly and sequenced from 21 cultures, producing a total of 1399 interpretable sequences. Significant variation (≥ 5% variation in sequence similarity) was observed among ITS copies within six cultures from three species clades (L. cincinnatus, L. sp. clade J, and Wolfiporia dilatohypha) and phylogenetic analyses with the cloned sequences produced different trees relative to analyses with consensus sequences. Cloned sequences from L. cincinnatus fell into more than one species clade and numerous cloned L. cincinnatus sequences fell into entirely new clades, which if analyzed on their own most likely would be recognized as "undescribed" or "novel" taxa. The use of a 95% cut off for defining operational taxonomic units (OTUs) produced seven Laetiporus OTUs with consensus ITS sequences and 20 OTUs with cloned ITS sequences. The use of cloned rDNA sequences might be problematic in fungal phylogenetic analyses, as well as in fungal bar-coding initiatives and efforts to detect fungal pathogens in environmental samples.     

Genotyping of Capreolus pygargus fossil DNA from Denisova cave reveals phylogenetic relationships between ancient and modern populations

Background

The extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia), where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved.

Methodology/Principal Findings

We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan), Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains) are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples.

Conclusion/Significance

Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian roe deer represent a complex and heterogeneous species with high migration rates and without evident subspecies structure. Low genetic diversity of the West Siberian Plain population indicates a recent bottleneck or founder effect.