Median-joining Network Research Articles

Phylogenetic analysis of Myanmar indigenous chickens using mitochondrial D-loop sequence reveals their characteristics as a genetic resource.

Myanmar indigenous chickens play important roles in food, entertainment, and farm business for the people of Myanmar. In this study, complete mitochondrial D-loop sequences (1232 bp) were analyzed using 176 chickens, including three indigenous breeds, two fighting cock populations, and three indigenous populations to elucidate genetic diversity and accomplish a phylogenetic analysis of Myanmar indigenous chickens. The average haplotype and nucleotide diversities were 0.948 ± 0.009 and 0.00814 ± 0.00024, respectively, exhibiting high genetic diversity of Myanmar indigenous chickens. Sixty-four haplotypes were classified as seven haplogroups, with the majority being haplogroup F. The breeds and populations except Inbinwa had multiple maternal haplogroups, suggesting that they experienced no recent purifying selection and bottleneck events. All breeds and populations examined shared haplogroup F. When 232 sequences belonging to haplogroup F (79 from Myanmar and 153 deposited sequences from other Asian countries/region) were analyzed together, the highest genetic diversity was observed in Myanmar indigenous chickens. Furthermore, Myanmar indigenous chickens and red junglefowls were observed in the center of the star-like median-joining network of 37 F-haplotypes, suggesting that Myanmar is one of the origins of haplogroup F. These findings revealed the unique genetic characteristic of Myanmar indigenous chickens as important genetic resources.

Characterization of genetic diversity of an invasive Lessepsian Migrant, Nemipterus randalli Russell, 1986 from its native and non-native regions using mitochondrial DNA marker

This study assessed and compared the genetic diversity of Nemipterus randalli across its native and non-native regions analysing the mitochondrial DNA D-loop region. Including all the geographical population samples, 68 haplotypes were observed with an average haplotype diversity value of 0.92±0.04. Relatively, a smaller number of haplotypes was observed in the invasive range of the Mediterranean Sea. All other native geographical samples showed high haplotype and nucleotide diversity values. A significant high genetic differentiation value was observed between the native population samples of India and the invasive samples of the Mediterranean Sea. In the median-joining network tree, N. randalli from the Mediterranean Sea and the Red Sea formed a single haplogroup while other samples from India are clustered into two haplogroups.

PHYLOGENETIC ASSESSMENT OF TREE SPECIES OF ACONITUM L. FROM KAZAKHSTAN BY USING ITS AND MATK MARKERS

The Aconitum L. is a diverse genus consisting of more than 300 species all over the World, including 11 species grown in Kazakhstan. The phylogeny of the genus was mostly studied by using internal transcribed sequences (ITS) of the nuclear genome and maturase K (matK) of the chloroplast genome. Therefore, in this study it was decided to assess the phylogenetic position of three local species A. leucostomum, A. soongoricum and A. apetalum, by using ITS and matK. The application of Maximum-Likelihood (ML) method suggested that the A. soongoricum belong to subgenus Aconitum, and A. leucostomum and A. apetalum to the subgenus Lycoctonum, which was congruent to previous taxanomic studies for this genus. The Median-Joining network using ITS suggested that A. sachalinense belongs to the group of processors of the genus among species that were involved in the analysis. The study is the first attempt to understand phylogenetic relationship of three species of Aconitum grown in Kazakhstan.

Incursion and establishment of the Old World arbovirus vector Aedes (Fredwardsius) vittatus (Bigot, 1861) in the Americas

Routine biosurveillance efforts at the Naval Station Guantanamo Bay, Cuba, on 18 June 2019, detected two unusual mosquitos in a CO2-baited CDC light trap. Morphological and molecular analysis confirmed the presence of Aedes (Fredwardsius) vittatus (Bigot, 1861) – the first record of the Old World dengue, chikungunya, Zika and yellow fever virus vector into the Americas – and provides evidence for its establishment in Cuba. Newly submitted GenBank sequences from Dominican Republic further evidence its establishment in the Caribbean, and a median-joining network analysis using mitochondrial COI gene sequences clearly supports multiple introductions of Ae. vittatus into the Caribbean from the Indian subcontinent. It was determined that many Ae. vittatus COI barcode sequences in GenBank are currently misidentified as Aedes (Fredwardsius) cogilli Edwards, 1922.

The role of the south-western Alps as a unidirectional corridor for Mediterranean brown trout (Salmo truttacomplex) lineages

AbstractThe role of the south-western Alps as a corridor for Mediterranean trout (Salmo trutta complex Linnaeus, 1758) was evaluated in order to understand the influence of the last glacial events in shaping the spatial distribution of the genetic diversity of this salmonid. For this, the allochthonous hypothesis of a man-mediated French origin (19th century) of the Mediterranean trout inhabiting the Po tributaries in the Italian side of the south-western Alps was tested. A total of 412 individuals were analysed at the mitochondrial control region. The phylogenetic classification was carried out by using a Median-Joining Network analysis. Mismatch pair-wise analysis, molecular dating and Kernel density distribution analysis of the main mitochondrial lineages were evaluated to compare past demographic dynamics with the current spatial distribution of genetic diversity. The main outcomes resulted strongly in agreement with a biogeographic scenario where the south-western Alps acted as a unidirectional corridor that permitted the colonization of the upper Durance (Rhône River basin) by trout from the Po River basin. Therefore, the Mediterranean trout should be considered as native also along the Italian side of the south-western Alps and the allochthonous hypothesis should be rejected.

Phylogenomics and Phylodynamics of SARS-CoV-2 Genomes Retrieved From India

Background: This is the first phylodynamic study attempted on SARS-CoV-2 genomes from India to infer the current state of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution using phylogenetic network and growth trends. Materials & Methods: Out of 286 retrieved whole genomes from India, 138 haplotypes were used to build a phylogenetic network. The birth–death serial model (BDSIR) package of BEAST2 was used to calculate the reproduction number of SARS-CoV-2. Population dynamics were investigated using the stamp date method as implemented in BEAST2 and BEAST 1.10.4. Results: A median-joining network revealed two ancestral clusters. A high basic reproduction number of SARS-CoV-2 was found. An exponential rise in the effective population size of Indian isolates was detected. Conclusion: The phylogenetic network reveals dual ancestry and possibility of community transmission of SARS-CoV-2 in India.

Genetic diversity, population structure and ancestral origin of KwaZulu-Natal native chicken ecotypes using microsatellite and mitochondrial DNA markers

South African native chicken breeds are no exception to the declining of local domestic breeds that has long been recognised and found associated with the commercialisation of breeding in domestic animals. The aims of the study were: (i) to provide a comprehensive view of genetic variation in four KwaZulu-Natal indigenous chicken populations (Jozini, Newcastle, Pietermaritzburg, and Port Shepstone), and (ii) to estimate the extent of differentiation of the village populations from three conserved South African indigenous pure breeds (Potchefstroom koekoek, Ovambo, and Venda) by genotyping individuals at 19 autosomal microsatellite loci. Finally, (iii) new information to the history of KwaZulu-Natal indigenous chicken populations was made available by exploring their phylogenetic relationship and their possible maternal origin through the mitochondrial DNA. The results suggested noticeable genetic diversity within and between ecotypes with clear sub-structuring between them. The indigenous populations had high genetic diversity (observed heterozygosity ranging from 0.61 in Pietermaritzburg to 0.70 in Jozini) while conserved populations showed considerable within population inbreeding coefficient (from 0.01 in Potchefstroom koekoek to 0.18 in Ovambo). Median-joining network analyses indicated the dominance of haplogroup E suggesting a likely Southeast Asia and/or Indian subcontinent origin. The presence of haplogroup B and C not only emphasises multiple maternal origin but also highlights genetic introgression of local chickens with commercial genotypes. These results highlighted the importance of local breeds as a genetic reservoir; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers. Highlights The genetic variation and differentiation of KwaZulu-Natal indigenous chicken populations and pure South African chicken breeds is investigated. The village populations showed a noticeable genetic variability with clear sub-structuring between them. The results can be used to improve a sustainable breeding and conservation programs to control possible genetic dilution with commercial genotypes.

Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region.

Simple SummaryThis paper represents the first fundamental report of mtDNA diversity in Turkish indigenous donkey breeds and presents findings for the origin and genetic characterization of donkey populations dispersed in seven geographical regions in Turkey, and thus reveals insights into their genetic history. The median-joining network and phylogenetic tree exhibit two different maternal lineages of the 16 Turkish indigenous donkey populations.In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (πD), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions.

Phylogenetic differentiation between Awassi and Hamdani sheep using the mitochondrial 12S rRNA

This study was conducted to assess the role of the mitochondrial 12S rRNA variations in the phylogenetic discrimination between two Iraqi breeds of sheep that differ in geographical distribution. A total of 122 animals (68 Awassi and 54 Hamdani) were included in the study. Direct sequencing of amplicons followed by the construction of a median-joining network and several trees were performed to identify the possible phylogenetic differences between both involved breeds. Genetic diversity, relative frequencies, and analysis of molecular variance (AMOVA) were performed to assess the genetic correlation between both populations. The median-joining network and minimized tree values showed that all observed haplotypes were separated into two groups according to their breed. Comprehensive phylogenetic data revealed only one Asian ancestor for all observed haplotypes. As indicated by AMOVA, the observed diversity was mostly due to between-population variation (1.24836%), while within-population variation (0.91221%) accounted for much less. The currently investigated rRNA amplicons exhibited different mitochondrial manifestations between Awassi and Hamdani breeds. Due to the ability of these 12S rRNA amplicons to mimic the geographical diversity for the currently investigated breeds, it is highly recommended to be used as potent mitochondrial genetic markers among broader ovine sequences.

Mitochondrial DNA diversity and population structure of Laodelphax striatellus across a broad geographic area in China

The small brown planthopper (SBPH), Laodelphax striatellus Fallén (Hemiptera: Delphacidae), is a crucial devastating rice pest in East Asia. To effectively control this pest, we investigate the genetic diversity, genetic differentiation and genetic structure of 49 populations in China based on a 596 bp fragment of the mitochondrial DNA cytochrome c oxidase subunit I (mtDNA COI) gene. Overall, 83 haplotypes were detected in 1253 mtDNA COI sequences. High levels of genetic variability (Hd = 0.756 ± 0.009, π = 0.00416 ± 0.00011) and genetic differentiation (F ST = 0.262, p < .001) were observed. Bayesian inference phylogenetic and median-joining haplotype network analyses indicated no obvious geographical distribution pattern among haplotypes. Hierarchical AMOVA and SAMOVA revealed no genetically distinct groups and lack of obvious phylogeographic structure. Isolation by distance (IBD) analysis results demonstrated no correlation between genetic differentiation and geographic distance. Finally, the demographic history of SBPH examined by neutrality tests and mismatch distribution analyses illustrated a sudden population expansion at the large spatial scale in China.

Rare Bolivian wild chile Capsicum eshbaughii (Solanaceae) located again: open ending on its identity and conservation

A new finding of the rare chile Capsicum eshbaughii (Solanaceae), whose location in the field had repeatedly failed in the past, is here reported. The species is poorly known and therefore new data on flowers, fruits, seeds, and chromosome number are provided. The relationships of C. eshbaughii, particularly relative to C. eximium, are explored based on DNA sequence data. Phylogenetic relationships were reconstructed through Bayesian inference and maximum likelihood analyses using sequence data from four cpDNA intergenic spacers and nuclear waxy. Relationships among haplotypes, using sequences of five cpDNA intergenic spacers, were analysed through a median-joining network. The close affinity of C. eshbaughii with C. eximium is strongly supported although the results are not conclusive about the rank of C. eshbaughii, either as a separate species or as a variety of C. eximium. Issues regarding conservation of the species are also discussed.

Phylogenetic relationships investigation of Mycobacterium caprae strains from sympatric wild boar and goats based on whole genome sequencing.

Tuberculosis (TB) in wildlife challenges epidemiological surveillance and disease control. An outbreak of TB was detected in a free‐ranging wild boar population of a Natural Park in Catalonia (Spain) and the outbreak investigation was conducted in the area. During the study period (2015–2020), 278 wild boars were analysed by gross pathology, histopathology, mycobacterial culture and DVR‐spoligotyping. In addition, all cattle (49) and goat (47) herds of the area were tested with tuberculin skin test. TB compatible lesions were detected in 21 wild boars, and Mycobacterium caprae was isolated in 17 of them with two different spoligotypes: SB0415 (13) and SB1908 (4). Only two goat herds showed TB positive animals that were subsequently slaughtered. M. caprae with the spoligotypes SB0416 and SB0415 were isolated from these animals. To investigate the phylogenetic relationships and the transmission chain of the outbreak, nine strains isolated from six wild boars and three goats of the study area were analysed by whole genome sequencing (WGS) followed by single nucleotide polymorphism (SNP) analysis by maximum likelihood and median‐joining network inference methods. Results indicated that infected wild boars maintained M. caprae strains circulation in their own population and have likely transmitted the infection to goats, thus acting as TB reservoirs, compromising the success of livestock TB eradication campaigns and posing a risk for public health. The results also highlighted the usefulness of WGS followed by SNP analysis in providing relevant epidemiological information when detailed contact data are missing.

Evolutionary and Anthropogenic Factors Affecting the Mitochondrial D-loop Genetic Diversity of Apodemus and Myodes Rodents on the Northern Slope of Mt. Fuji

Nucleotide sequences of the mitochondrial D-loop region were examined in three wild rodents (Apodemus argenteus, Apodemus speciosus, and Myodes smithii) on the northern slope of Mt. Fuji, the highest mountain in Japan, to elucidate the past evolutionary and present anthropogenic processes shaping their genetic diversity. Nucleotide diversity, median-joining network, and mismatch distribution analyses suggested that A. argenteus has multiple divergent lineages, possibly due to multiple previous expansion events, whereas A. speciosus and M. smithii are younger lineages that could be derived from single expansion events. These findings indicate that Mt. Fuji plays an important role as a reservoir maintaining lineages through multiple past expansion events. Artificial infrastructure also affected the genetic diversity of the two Apodemus species, as populations of these species on the two sides of the Fuji Subaru Line roadway were genetically distinct. To construct a proper conservation strategy based on genetic diversity, we suggest that the past and present contributors to genetic diversity must be clarified. Such clarification is especially important for the Mt. Fuji environment, which harbors rich biodiversity but also incurs much human impact as a national park.

Distribution of maternal lineages in hunter-gatherer societies of the southern coast of Tierra del Fuego, Argentina.

The aim of this work is to explore the maternal genetic diversity of hunter-gatherers of the southern Tierra del Fuego, specifically the north coast of Beagle Channel, the Península Mitre, and Isla de los Estados through ancient mitochondrial DNA analysis. The hypervariable regions 1 and 2 of the mitochondrial genome of five individuals from the north coast of Beagle Channel, six individuals from Península Mitre, and one individual from Isla de los Estados were analyzed. Through diversity statistics, Analysis of Molecular Variance (AMOVA), and Median Joining networks analyses, maternal relationships in the region were evaluated and phylogenetic similarities between ancient and contemporary populations of Tierra del Fuego were determined. The mitochondrial DNA lineages from the ancient individuals analyzed reveals the presence of subclades C1b and D1g. Pattern of decreasing genetic diversity toward the South is observed. The AMOVAs performed found no statistically significant differences between individuals of the north coast of Beagle Channel and Península Mitre-Isla de los Estados, and modern Yámana populations. Median joining network of haplotypes of clades C1 and D1g, show the same results. Ethnohistoric and ethnographic records of Península Mitre show that this region was occupied during the 19th century by Haush or Manekenk populations, although their biological, cultural, and subsistence characterization is unclear. We explore their maternal lineages and encounter low levels of genetic diversity and the absence of population differentiation with modern Yámana groups. We suggest that Península Mitre-Isla de los Estado was part of the same hunting and gathering populations as those of the Beagle Channel.

Morphological, Molecular Identification and Distribution of Trypanosome-Transmitting Dipterans from Cattle Settlements in Southwest Nigeria.

Glossina spp. (Glossinidae), Tabanus spp. (Tabanidae), Ancala spp. (Tabanidae), Atylotus spp. (Tabanidae) and Stomoxys spp. (Muscidae) are important transmitting vectors of African animal trypanosomosis in sub-Saharan Africa. There is paucity of information on the distribution and identification of these flies in cattle settlements in southwest Nigeria. The distribution patterns, genetic variations and diversities of dipteran flies in southwest Nigeria were described and identified using morphological and molecular analysis of the 28S rDNA gene. Of the 13,895 flies examined morphologically between April 2016 and March 2017, tabanids were identified [Tabanus (0.34%), Ancala (0.03%), Atylotus (0.01%), Haematopota (0.014%) and Chrysops (0.11%)]. Two stomoxyine species were identified; Stomoxys niger niger Macquart (45.30%) and Stomoxys calcitrans Linnaeus (17.29%) and two Glossina spp. namely; Glossina p. gambiense Vanderplank, 1911 (0.46%) and Glossina tachinoides Westwood (0.51%) were identified. The identities were further confirmed in a BLAST search using their nucleotide sequences. The median-joining network of the 28S rDNA gene sequences indicated that fly species examined were genetically distinct. The apparent density of all the trapped flies was highest at a mean temperature of 26-28℃, humidity > 80% and rainfall of 150-220mm/month. The distribution of flies was observed to increase as vegetation increased in density and decreased in areas with relatively high human population density (> 100/km2). The population indices of the 28S rDNA gene of the flies suggest that analysis of nuclear DNA fragments may provide more information on the molecular ecology of these flies. Characterising fly species and assessing their impact are essential in distribution and monitoring AAT spread.

Preliminary information on the prevalence and molecular description of Taenia hydatigena isolates in Pakistan based on mitochondrial cox1 gene

Taenia hydatigena is a cestode of veterinary importance. Infection with the metacestode larval stage results in cysticercosis, which poses a serious challenge to the livestock industry worldwide. Globally, there are numerous reports on cysticercosis caused by T. hydatigena in sheep and goat but a lack of data on the prevalence and genetic diversity exists for Pakistan. We designed this study to provide an insight into the disease status as well as investigate the genetic variation among the recovered isolates based on the mitochondrial cox1 gene. In this study, we examined small ruminants (sheep and goats) slaughtered in Faisalabad in eastern Punjab province of Pakistan for T. hydatigena metacestodes and described the population structure and genetic variation using the cytochrome c oxidase subunit 1 (cox1) mitochondrial gene. Overall, a prevalence of 4.40% (goat =4.67% sheep = 4.07%) from a total of 2225 small ruminant carcasses (sheep = 983, goats = 1242) was observed. Based on the NCBI BLAST search and Bayesian phylogeny, the identity of all isolates was confirmed via their nucleotide sequences. The diversity indices indicated a high haplotype and a low nucleotide diversity with 43 haplotypes from 98 isolates. The results also show the existence of unique haplotypes of T. hydatigena in Pakistan as demonstrated by the significant negative values of Tajima's D and Fu's Fs neutrality test suggesting a recent population expansion. The median-joining network of the partial cox1 sequence dataset showed the existence of two main haplotypes detected in both sheep and goat populations. This study shows that the prevalence of cycticercosis due to T. hydatigena is below 5% in sheep and goats in Faisalabad, Punjab, Pakistan. The molecular analysis of the partial cox1 gene also indicates a high degree of genetic variation with the existence of rare haplotypes. These findings represent a preliminary report on the prevalence and genetic variation of T. hydatigena in Pakistan and serve as baseline information for future studies on the prevalence and population structure of T. hydatigena in the country.

Morphological and molecular variations within Helicotylenchus vulgaris

Helicotylenchus vulgaris is a plant-parasitic nematode reported from several countries in various biogeographical regions. During the survey on Helicotylenchus in Iran and the South African Plant-Parasitic Nematode Survey in South Africa, H. vulgaris was found in samples from northern and southern Iran and from two provinces in South Africa. Helicotylenchus vulgaris was identified based on morphological and molecular characteristics. The result based on the hierarchical clustering of the principal component analysis placed the South African and Iranian populations into different groups, while the British populations were put together with the Iranian populations. Besides, the phylogenetic analysis of four Iranian H. vulgaris based on 28S rDNA indicated that they group into two different clades. Median-joining network analysis using 28S rDNA grouped H. vulgaris into two different groups, with the South African (acc. nrs: HM014239 and HM014238) sequences having 65 and 67 step differences, whereas a population from Iran (MF996711) was placed in a different group. In conclusion, the results showed that variations exist among the diverse populations of H. vulgaris, as shown by both morphological and molecular characters. A detailed revision of the species is, however, should be studied using different genes.

A preliminary phylogenetic analysis of ribbed-pine-borer (Rhagium inquisitor) based on mitochondrial COI sequences

Abstract The increased volume of intercontinental-trade had facilitated the distribution of species, including invaders. Wooden packaging materials, goods and timber are being transported via international ports in East of the Marmara Basin, where has vast forests. That forests provide an appropriate-mediator for the introduction and invasion of wood-boring insects, which are the most common group being transported between continents. One of them is Rhagium inquisitor, which has a pivotal role in wood decay, nevertheless, it is detrimental for industrial wood. We analyzed the 654 bp length of cytochrome c oxidase I (COI) gene, to determine native and introduced haplotypes of the ribbed-pine-borer, to investigate their phylogenetic relationships and possibly cryptic speciation of the morphospecies. It was found out that sixteen haplotypes were divided into five haplogroups. The groups were assembled on two main lineages: Eurasian and American. The genetic distance between the American (Groups 1–3), Asian (Group-4) and European (Group-5) clusters ranged from 3 to 10%; between haplotypes ranged from 0.2 to 10.9%. The distances between the specimens of the Marmara Basin (H9-12, Group-4) were lower compared to H16, which nested in Group-5. That haplotype was sampled on imported timber and was found out that it is shared between France, Germany, Italy, and Austria. Maximum Likelihood, Neighbor-Joining and Bayesian Inference trees showed the same topologies, and Median-Joining network also supported them. Contrary to the usual, our findings point out that some species might have been introduced from Europe to Asia. Furthermore, the high genetic diversity of the bark-runner between continents could be a sign of cryptic-allopatric speciation.

Population Genetics of Phlebotomus papatasi from Endemic and Nonendemic Areas for Zoonotic Cutaneous Leishmaniasis in Morocco, as Revealed by Cytochrome Oxidase Gene Subunit I Sequencing.

Zoonotic cutaneous leishmaniasis (ZCL) caused by Leishmania major Yakimoff & Shokhor and transmitted by Phlebotomus papatasi (Scopoli) is a public health concern in Morocco. The disease is endemic mainly in pre-Saharan regions on the southern slope of the High Atlas Mountains. The northern slope of the High Atlas Mountains and the arid plains of central Morocco remain non-endemic and are currently considered high risk for ZCL. Here we investigate and compare the population genetic structure of P. papatasi populations sampled in various habitats in historical foci and non-endemic ZCL areas. A fragment of the mtDNA cytochrome oxidase I (COI) gene was amplified and sequenced in 59 individuals from 10 P. papatasi populations. Haplotype diversity was probed, a median-joining network was generated (FST) and molecular variance (AMOVA) were analyzed. Overall, we identified 28 haplotypes with 32 distinct segregating sites, of which seven are parsimony informative. The rate of private haplotypes was high; 20 haplotypes (71.4%) are private ones and exclusive to a single population. The phylogenetic tree and the network reconstructed highlight a genetic structuration of these populations in two well defined groups: Ouarzazate (or endemic areas) and Non-Ouarzazate (or nonendemic areas). These groups are separated by the High Atlas Mountains. Overall, our study highlights differences in terms of population genetics between ZCL endemic and non-endemic areas. To what extent such differences would impact the transmission of L. major by natural P. papatasi population remains to be investigated.

Comprehensive analysis of mitochondrial DNA based genetic diversity in Indian goats.

Thirty four distinct breeds and many non-descript populations represent the caprine diversity of India. Genetic characterization of breeds is an essential element in designing breeding strategies and preserving genetic diversity. Considering the popularity of mitochondrial DNA for phylogeographical studies, this study involved an extensive analysis of population structure and genetic diversity of 28 defined breeds and 5 lesser known populations representing all four major agro-climatic zones of India using mitochondrial DNA markers. Analysis of hypervariable region 1 of mtDNA control region in 443 goats together with 22 reference sequences, delineated 341 distinct haplotypes belonging to four maternal haplogroups; A, B, C and D, with haplogroup A representing 90% of the individuals. The haplotype and nucleotide diversity indices of Indian goats were 0.998±0.001 and 0.028±0.001, respectively indicating abundant genetic variability. Estimates of population demographic parameters from mismatch analysis suggested a relatively good fit to the model of either spatial or demographic expansion of Indian goats. AMOVA analysis and topology of MJ network suggested lack of phylogeographic structure in domestic goats, which can be attributed to unstructured animal breeding, dwindling pastures and nomadic pastoralism. Genetic differentiation between goats from different agro-ecological regions was in accordance with their geographical propinquity.