Mean Genetic Divergence Research Articles

The use of mtCOI gene sequences in identifying Butis species in the Southwest of Vietnam

Butis genus is characterised by their small body size and morphological variability, allowing them to adapt to different habitats. This paper analyses the mitochondrial cytochrome C oxidase subunit I gene sequences and morphology of Butis for identification purposes and to understand genetic relationships. The morphological characteristics of Butis koilomatodon differed obviously from Butis humeralis and Butis butis. After classification based on morphology, the total deoxyribonucleic acid of fish samples was isolated, and the mitochondrial cytochrome C oxidase subunit I genes were successfully amplified using the polymerase chain reaction method. At approximately 617bp, the obtained mitochondrial cytochrome C oxidase subunit I gene sequences were highly similar to the reference sequences on Genbank (85.90–100%). The phylogenetic graphic was divided into five distinct groups, where B. koilomatodon was grouped in one group; and B. humeralis and B. butis were grouped together. The results suggest that B. humeralis was an entirely different species from B. butis, with a mean genetic divergence of up to 14%. However, further studies using a combination of other types of deoxyribonucleic acid barcoding together with morphological features should be undertaken to confirm these findings.

A new species of Versteria (Cestoda: Taeniidae) parasitizing Galictis cuja (Carnivora: Mustelidae) from Patagonia, Argentina: Morphological and molecular characterization.

Via morphological and molecular analysis, we describe a new species of taeniid from Patagonia (Argentina): Versteria cuja n. sp., parasitizing the Lesser grison Galictis cuja (Molina) (Carnivora: Mustelidae). This is the first report of a species of Versteria in Argentina and for a native mustelid. The new species (the third in the genus Versteria) is proposed using an integrative taxonomic approach, based on traditional morphology (distinctive morphological and morphometric diagnostic characters), genetic distances and phylogeny based on molecular data, the distinct geographical distribution, and the different definitive host species. Versteria cuja n. sp. mainly differs from Versteria mustelae (Gmelin, 1790) (from Europe) in the number of testes (54–85 vs. 83–127 in V. mustelae), the rostellum size (39–75 vs. 85–180 μm in V. mustelae), the genital atrium size (170–420 vs. 68-91 μm in V. mustelae) and in the hooks’ shape. It also differs from the African species Versteria brachyacantha (Baer and Fain, 1951) by having smaller measurements regarding the main diagnostic characters, i.e. size of scolex, rostellum and suckers, number, size and shape of rostellar hooks, number of testes, and by having smooth cirrus (vs. cirrus covered with hair-like bristles in V. brachyacantha). Phylogenetical analysis using cox1 showed our specimens clustering with North American isolates of Versteria sp. in a well-supported American clade (mean genetic divergence 0.024), separated from another clade composed of different isolates of V. mustelae (0.093). The close relationship between the new species and the North American species, known as “zoonotic” Versteria sp., and responsible for fatal infections by metacestodes in free-ranging wildlife (rodents), captive primates and immunosuppressed people, lead us to think that the zoonotic potential of Versteria cuja n. sp. should not be discarded.

Genomic phylogenetic analyses of four major hand, foot and mouth disease-related enteroviruses.

Enteroviruses had diverged into many types, some of which cause hand, foot and mouth disease (HFMD) in children. The predominant enterovirus types associated with HFMD are EVA71, CVA16, CVA6 and CVA10. Four enterovirus types were classified into subtypes based on VP1 sequences. However, the phylogenetics of these enteroviruses is rarely concerned at the genomic level. In this study, we performed the phylogenetic analyses of the EVA71, CVA16, CVA6 and CVA10 using available full-length genomic sequences. We found that the topologies of phylogenetic trees of full-length genomic sequences and VP1 sequences were almost consistent, except few subtypes of EVA71 and CVA10. The mean genetic divergence was 15.8-27% between subtypes and less than 12% within subtypes/sub-subtypes at genomic level. Comparison of phylogenetic topologies between genomic and VP1 sequences helped us to identify two new EVA71 inter-subtype recombinants RF01_CC4 and RF02_CC4. Furthermore, EVA71 subtypes C1 and C2 and CVA10 subtype D were found to originate through inter-subtype recombination. The genomic reference sequences of these enteroviruses are provided here for subtyping. The results provide important insights into the understanding of the evolution and epidemiology of the four enteroviruses. Keywords: enterovirus; hand; foot and mouth disease; classification; genetic distance; recombination.

DNA barcoding and phylogenetic relationship of shrimps (Crustacea: Decapoda) of Bangladesh

We adopted DNA barcoding technique using a 658-bp fragment of the mitochondrial cytochrome c oxidase I (COI) gene to identify shrimp species collected from the different areas of Bangladesh. A total of 24 sequences were generated belonging to 14 species including four new records- Macrobrachium nipponense, Macrobrachium kistnense, Exopalaemon carinicauda and Alpheus malleator. Genetic distance measured with Kimura 2 parameter showed that genetic divergence increased with higher taxonomic rank. The mean genetic divergence was evaluated and found to be 0.935%, 22.67% and 30.92% within species, genus and family, respectively. In addition to the barcode-based species identification system, phylogenetic relationships were established where individuals belonging to the same species were grouped under the same clade. Maximum likelihood (ML) was preferred as the statistical method and as expected, the phylogenetic tree complemented and ensured the conventional taxonomy. The present study evidently showed that DNA barcoding can be served as an effective tool to discriminate the shrimp species and this will enhance the understanding on evolution and conservation biology.
 Bioresearch Commu. 7(1): 941-946, 2021 (January)

Capoeta baliki Turan, Kottelat, Ekmekçi & Imamoglu, 2006 a junior synonym of Capoeta tinca (Heckel, 1843) (Teleostei: Cyprinidae)

Capoeta baliki was described from Sakarya basin, Turkey. It was distinguished from its nearest congener i.e. C. tinca based on a combination of characters, including fewer serrae along posterior margin of last simple dorsal-fin ray, modally fewer scale rows between lateral line and dorsal-fin origin, fewer vertebrae, deeper and shorter head and slenderer caudal peduncle. We examined the synonymy hypothesis of C.­ baliki and C. tinca by comparing their morphometric, meristic and molecular characters. Based on the results, their morphometric and meristic characters largely overlapped and no character was found to distinguish them. In addition, a low K2P mean genetic divergence of 0.37% C. baliki and C. tinca based on cyt b gene and clustering in same clad showed that they are identical in molecular characters. As no character could be found to clearly distinguish these species, we treat C. baliki as a junior synonym of C. tinca .

Species–genetic diversity correlation in phyllostomid bats of the Bodoquena plateau, Brazil

Recent theories suggest that processes shaping species diversity are the same shaping genetic diversity, leading to a correlation between the two levels of diversity. Using Neotropical bat assemblages, and considering the genetic diversity of two co-distributed Chiroptera species with distinct life-history traits, Artibeus planirostris and Carollia perspicillata, we evaluated the correlation between metrics of taxonomic (species richness, evenness, and community divergence) and genetic diversity (number of haplotypes, haplotype diversity, allelic richness, expected heterozygosity and genetic divergence) in these two species. Landscape variables potentially affecting those correlations (distance to the nearest conservation unit, forest area, forest border length and number of forest fragments) were also analysed. For A. planirostris, we found a negative correlation between evenness and expected heterozygosity and also between mean presence-absence assemblage divergence and mean genetic divergence based on microsatellites. Our results indicate that the genetic diversity in A. planirostris is not explained by the landscape variables considered. For C. perspicillata, we found a positive correlation between species richness and haplotype richness and between evenness and expected heterozygosity. Genetic differentiation based on microsatellites in C. perspicillata was positively related to geographic distance and landscape differentiation. Allelic richness and expected heterozygosity in C. perspicillata were negatively related to distance from the conservation unit and forest area, but significance changed according to the spatial scale. We conclude that species-genetic diversity correlations may vary according to the species under study. Thus, A. planirostris appears to be ecologically different to other species in assemblages, while C. perspicillata seems to be ecologically similar.

A new species of Scapholeberis Schoedler, 1858 (Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon basin highlighted by DNA barcodes and morphology.

BackgroundThe Amazon basin is recognized as one of the most complex and species-rich freshwater environments globally. The diversity of zooplankton here remains unknown, with many species undescribed.MethodsHere, we describe a new species of Scapholeberis Schoedler, 1858 (Cladocera: Anomopoda: Daphniidae: Scapholeberinae) from the Colombian Amazon Basin, collected with recently designed light traps. The description is based on detailed morphology (based on SEM and light microscopy) of parthenogenetic females, ephippial females, males, and molecular data based on the COI gene.ResultsScapholeberis yahuarcaquensis n. sp. has a combination of characters present in Scapholeberis kingi Sars, 1888 and Scapholeberis armata freyi Dumont & Pensaert, 1983. These are a trilobate rostrum, with the middle lobe well developed with sides straight to relatively rounded, the presence of an elongated slit frontal head pore, a dorsal pore in the juncture of the cephalic shield and the valves, and a single denticulate membrane at the posterior rim of the valves, with stronger setae in the last third. The unique characters of the parthenogenetic females are ventral sucker with delicate triangles. Each has a filament-like projection in the lamellae’s inner side and an external section forming convex folds with denticle-like projections in the middle zone of the sucker-plate. There is a peculiar pitted sculpture in the ephippial females and a strong projection in the front of it. The male hook on the limb I with a blunt tip, a quirky lamella-like outgrow in the proximal side, and a paddle with well-developed spines scattered on its surface. The ventral sucker-lamellae in the male is much more developed than the female. The COI gene sequences showed an interspecific mean genetic divergence of 16.4% between S. yahuarcaquensis n. sp. and the closest species S. freyi from Mexico, supporting our results. A coalescence analysis and Barcode Index Number also support the new species based on the DNA sequences. New methods of collecting and integrative biology will give important support to recognize the fauna from the Amazon Basin, one of the most important sources of fresh water in the world that remains unknown in many respects.

<strong>Hidden but not enough: DNA barcodes reveal two new species in <em>Hygrobates fluviatilis </em>complex from Iran (Acariformes, Hydrachnidia, Hygrobatidae)</strong>

Water mites of the Hygrobates fluviatilis complex are common in Palaearctic inhabiting mainly running and slowly flowing waters. In this study, we examined the specimens collected in a stream in Golestan Province of Iran which is currently the easternmost distribution limit of the latter species complex. We used a fragment of the mtDNA COI gene and the D2 region of 28S rDNA to test the genetic structure. Molecular analyses revealed presence of two new well-supported species with a mean genetic divergence of 12.80% and 14.66% COI, respectively, from their closest relatives. Phylogenetic analysis based on COI and nuclear DNA data placed H. grabowskii sp. nov. as the sister species of H. persicus, and H. ulii sp. nov. as the sister species of H. turcicus. Discriminant statistical analysis revealed that the two newly discovered species could be separated on the basis of morphometric characters, but robust morphological differences were not found. Yet we were able to show that diversity in water mites is underestimated and that species delimitation requires an integrative approach.

Phylogeny of the genus Hypophthalmus Cuvier, 1829 (Pimelodidae – Siluriformes), based on a multilocus analysis, indicates diversification and introgression in the Amazon basin

The genus Hypophthalmus encompasses four valid South American freshwater catfish species: H. marginatus, H. edentatus, H. fimbriatus, and H. oremaculatus. More recently two new species were proposed Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2. While Hypophthalmus species are a fundamentally important resource for the commercial fisheries that operate in the continental waters of the Amazon basin, their phylogenetic relationships and the true diversity of the genus have yet to be defined conclusively. Given this, the present study analyzed sequences of the mitochondrial COI gene and four nuclear markers (RAG2, Myh6, Plagl2 and Glyt) to evaluate the phylogenetic relationships and the diversity of the species of this genus. All the analyses showed that Hypophthalmus is monophyletic, and the species delimitation tests recovered all the Hypophthalmus taxa as distinct species. The putative new species Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2 presented mean genetic divergence similar to or greater than that observed between valid Hypophthalmus taxa. All the analyses showed that H. oremaculatus is the sister group of H. n. sp. 1, which together group with H. fimbriatus. This clade is the sister group of the clade containing H. edentatus and H. n. sp. 2. One specimen, morphologically identified as H. oremaculatus, presented the nuclear genome of this species and the mitochondrial genome of H. n. sp. 1; while another specimen, morphologically identified as H. n. sp. 2, presented the nuclear Myh6 of H. n. sp. 2 and the mitochondrial and RAG2 genome of H. edentatus. These results indicate that hybridization and introgression has occurred between species in Hypophthalmus. The findings of this study indicate that the diversity of the Hypophthalmus is underestimated, emphasize the need for a taxonomic review of the genus, and a more systematic evaluation of the hybridization patterns found, to understanding the role of hybridization and introgression in the evolution of the genus.

DNA barcoding identified selected ornamental fishes in Murti river of East India

Nomenclature for the nameless is one of the successful events after the invention of the DNA barcoding technique in biodiversity research. The ornamental fish species are frequently hunted from the east and northeast India and trafficked with various elusive names and high demanding values. Such illegitimate trading stimulated the severe threats on the native freshwater ecosystems and their indigenous biodiversity. Both traditional taxonomy and DNA barcoding technique successfully identified 11 ornamental fish species from a small riverine system, Murti river; linked up with three protected areas in the northern part of West Bengal. To test the efficacy of DNA barcode data for species identification, the generated sequences were subjected to similarity search results, and Neighbour-Joining tree clustering and genetic divergences. The mean genetic divergence was 21.3% and the interspecific genetic distance was ranging from 17.8% to 28.7% in the studied dataset. The detected high intraspecific genetic divergence in Opsarius barna (14.1%) and Channa gachua (6.4%) in the present dataset suggested further genetic investigation from their known distributions.

A continental-wide molecular approach unraveling mtDNA diversity and geographic distribution of the Neotropical genus Hoplias.

With an estimate of around 9,000 species, the Neotropical region hosts the greatest diversity of freshwater fishes of the world. Genetic surveys have the potential to unravel isolated and unique lineages and may result in the identification of undescribed species, accelerating the cataloguing of extant biodiversity. In this paper, molecular diversity within the valuable and widespread Neotropical genus Hoplias was assessed by means of DNA Barcoding. The geographic coverage spanned 40 degrees of latitude from French Guiana to Argentina. Our analyses revealed 22 mitochondrial lineages fully supported by means of Barcode Index Number, Automatic Barcode Gap Discovery and phylogenetic analyses. This mtDNA survey revealed the existence of 15 fully supported mitochondrial lineages within the once considered to be the continentally distributed H. malabaricus. Only four of them are currently described as valid species however, leaving 11 mitochondrial lineages currently “masked” within this species complex. Mean genetic divergence was 13.1%. Barcoding gap analysis discriminated 20 out of the 22 lineages tested. Phylogenetic analyses showed that all taxonomically recognized species form monophyletic groups. Hoplias malabaricus sensu stricto clustered within a large clade, excluding the representatives of the La Plata River Basin. In the H. lacerdae group, all species but H. curupira showed a cohesive match between taxonomic and molecular identification. Two different genetic lineages were recovered for H. aimara. Given the unexpected hidden mitochondrial diversity within H. malabaricus, the COI sequence composition of specimens from Suriname (the type locality), identified as H. malabaricus sensu stricto, is of major importance.

Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size

Diazotrophic Actinobacteria of the genus Frankia represent a challenge to classical bacterial taxonomy as they include many unculturable strains. As a consequence, we still have a poor understanding of their diversity, evolution and biogeography. In this study, a Multi-Locus Sequence Analysis (MLSA) using atpD, dnaA, ftsZ, pgk, and rpoB loci was done on a large set of cultured and uncultured strains, compared to 16S rRNA and correlated to Average Nucleotide Identity (ANI) from available Frankia genomes. MLSA provided a robust resolution of Frankia genus phylogeny and clarified the status of unresolved species and complex of species.The robustness of single-gene topologies and their congruence with the MLSA tree were tested. Lateral Gene Transfers (LGT) were few and scattered, suggesting they had no impact on the concatenate topology. The pgk marker – providing the longest sequence, highest mean genetic divergence and least occurrence of LGT – was used to survey an unequalled number of Alnus-infective Frankia — mainly uncultured strains from a broad range of host-species and geographic origins. This marker allowed reliable Single-Locus Strain Typing (SLST) below the species level, revealed an undiscovered taxonomical diversity, and highlighted the effect of cultivation, sporulation phenotype and host plant species on symbiont richness, diversity and phylogeny.

Molecular and Morphological Characterization of a Brazilian Lineage of Plasmodium ( Novyella) Unalis in Turdus Spp. (Passeriformes) of the Atlantic Forest, with Remarks on New Hosts and High Genetic Variation.

Plasmodium spp. are haemosporidian protozoans that alternate their live cycles between bloodsucking Culicidae dipterans and vertebrate hosts (mammals, reptiles, and birds). In birds, these parasites are the causative agents of the so-called avian malaria, a disease associated with considerable declines and extinctions in the avifauna in different geographical regions. In this work, we applied a multidisciplinary approach, light microscopy and cytochrome oxidase b (cyt b) gene sequence analysis, for characterization of Plasmodium spp. found in association with wild birds of the genus Turdus, collected in Atlantic forest fragments of southeastern Brazil. From the total 90 analyzed birds, 58 (47 Turdus rufiventris, 9 Turdus leucomelas, 1 Turdus albicollis, and 1 Turdus flavipes) were positively infected with Plasmodium unalis, a haemosporidian that was previously detected in Turdus fuscater in Colombia and in penguins in Brazil, but has never been found in association with these Turdus species of this present work. Moreover, all 7 new sequences of P. unalis cyt b gene clustered into a monophyletic clade with previously characterized P. unalis sequences with a mean genetic divergence of 1.6% and with a maximum divergence of 3.1%, indicating for a high degree of intraspecific polymorphism within this parasitic species. Together, our data highlight the existence a high degree of intraspecific variation within P. unalis and highlight the importance of integrative taxonomy to an accurate identification and characterization of avian haemosporidian parasites.

Multidisciplinary re-description of Plasmodium (Novyella) paranucleophilum in Brazilian wild birds of the Atlantic Forest kept in captivity.

Haemosporidian blood parasites of the Plasmodium genus are the causative agents of avian malaria in many parts of the world. Despite the great diversity of Brazilian avifauna, few studies have been conducted to examine the haemosporidians of wild birds found in the Brazilian Atlantic Forest, especially those kept in captivity. This study aimed to re-examine and further characterize the South American avian parasite Plasmodium paranucleophilum using a multidisciplinary approach. Blood samples were collected from 68 captive birds representing 15 species found in the Atlantic Forest of southeastern Brazil. Morphometric and morphological characterization was performed, in addition to PCR and sequencing of the mitochondrial cytochrome b gene and subsequent phylogenetic analysis. The overall prevalence of P. paranucleophilum infection in the study was 13.23% (n=9), with a mean parasitemia of 0.58%. We observed the highest parasitemia of 3.88% in Rupornis magnirostris. In our phylogenetic analysis, P. paranucleophilum and P lasmodium nucleophilum formed distinct, highly supported clades, with a mean genetic divergence of 2.48%. This study provides new morphological and molecular data, expanding our knowledge of the haemosporidians of wild birds in Brazil and highlighting the need for further investigation. The true depth of diversity in Brazilian avian haemosporidians remains largely unknown, and given the enormous variety of vectors and avian species, there may be many more species of these blood parasites yet to be described.

Distinct parasite populations infect individuals identified through passive and active case detection in a region of declining malaria transmission in southern Zambia

BackgroundSubstantial reductions in the burden of malaria have been documented in parts of sub-Saharan Africa, with elimination strategies and goals being formulated in some regions. Within this context, understanding the epidemiology of low-level malaria transmission is crucial to achieving and sustaining elimination. A 24 single-nucleotide-polymorphism Plasmodium falciparum molecular barcode was used to characterize parasite populations from infected individuals identified through passive and active case detection in an area approaching malaria elimination in southern Zambia.MethodsThe study was conducted in the catchment area of Macha Hospital in Choma District, Southern Province, Zambia, where the parasite prevalence declined over the past decade, from 9.2% in 2008 to less than 1% in 2013. Parasite haplotypes from actively detected, P. falciparum-infected participants enrolled in a serial cross-sectional, community-based cohort study from 2008 to 2013 and from passively detected, P. falciparum-infected individuals enrolled at five rural health centres from 2012 to 2015 were compared. Changes in P. falciparum genetic relatedness, diversity and complexity were analysed as malaria transmission declined.ResultsActively detected cases identified in the community were most commonly rapid diagnostic test negative, asymptomatic and had submicroscopic parasitaemia. Phylogenetic reconstruction using concatenated 24 SNP barcode revealed a separation of parasite haplotypes from passively and actively detected infections, consistent with two genetically distinct parasite populations. For passively detected infections identified at health centres, the proportion of detectable polyclonal infections was consistently low in all seasons, in contrast with actively detected infections in which the proportion of polyclonal infections was high. The mean genetic divergence for passively detected infections was 34.5% for the 2012–2013 transmission season, 37.8% for the 2013–2014 season, and 30.8% for the 2014–2015 season. The mean genetic divergence for actively detected infections was 22.3% in the 2008 season and 29.0% in the 2008–2009 season and 9.9% across the 2012–2014 seasons.ConclusionsDistinct parasite populations were identified among infected individuals identified through active and passive surveillance, suggesting that infected individuals detected through active surveillance may not have contributed substantially to ongoing transmission. As parasite prevalence and diversity within these individuals declined, resource-intensive efforts to identify the chronically infected reservoir may not be necessary to eliminate malaria in this setting.

Phylogenetic analysis of the genus Laparocerus, with comments on colonisation and diversification in Macaronesia (Coleoptera, Curculionidae, Entiminae).

The flightless Entiminae weevil genus Laparocerus is the species-richest genus, with 237 species and subspecies, inhabiting Macaronesia (Madeira archipelago, Selvagens, Canary Islands) and the continental ‘Macaronesian enclave’ in Morocco (one single polytypic species). This is the second contribution to gain insight of the genus and assist in its systematic revision with a mitochondrial phylogenetic analysis. It centres on the Canarian clade, adding the 12S rRNA gene to the combined set of COII and 16S rRNA used in our first contribution on the Madeiran clade (here re-analysed). The nuclear 28S rRNA was also used to produce an additional 4-gene tree to check coherency with the 3-gene tree.A total of 225 taxa (95%) has been sequenced, mostly one individual per taxa. Plausible explanations for incoherent data (mitochondrial introgressions, admixture, incomplete lineage sorting, etc.) are discussed for each of the monophyletic subclades that are coincident with established subgenera, or are restructured or newly described. The overall mean genetic divergence (p-distance) among species is 8.2%; the mean divergence within groups (subgenera) ranks from 2.9 to 7.0% (average 4.6%), and between groups, from 5.4% to 12.0% (average 9.2%). A trustful radiation event within a young island (1.72 Ma) was used to calibrate and produce a chronogram using the software RelTime.These results confirm the monophyly of both the Madeiran (36 species and subspecies) and the Canarian (196 species and subspecies) clades, which originated ca. 11.2 Ma ago, and started to radiate in their respective archipelagos ca. 8.5 and 7.7 Ma ago. The Madeiran clade seems to have begun in Porto Santo, and from there it jumped to the Desertas and to Madeira, with additional radiations. The Canarian clade shows a sequential star-shape radiation process generating subclades with a clear shift from East to West in coherence with the decreasing age of the islands. Laparocerus garretai from the Selvagens belongs to a Canarian subclade, and Laparocerus susicus from Morocco does not represent the ancestral continental lineage, but a back-colonisation from the Canaries to Africa. Dispersal processes, colonisation patterns, and ecological remarks are amply discussed. Diversification has been adaptive as well as non-adaptive, and the role of ’geological turbulence’ is highlighted as one of the principal drivers of intra-island allopatric speciation.Based on the phylogenetic results, morphological features and distribution, five new monophyletic subgenera are described: Aridotrox subg. n., Belicarius subg. n., Bencomius subg. n., Canariotrox subg. n., and Purpuranius subg. n., totalling twenty subgenera in Laparocerus.

Molecular based phylogenetic species recognition in the genus Pampus (Perciformes: Stromateidae) reveals hidden diversity in the Indian Ocean

Pomfrets (Genus Pampus) are commercially important fishes in the Indo Pacific region. The systematics of this genus is complicated due to morphological similarities between species. The silver pomfret from Indian waters has long been considered to be Pampus argenteus. The objective of the study was to utilize the mitochondrial COI gene to establish the molecular identity of the silver pomfret distributed in Indian waters and to resolve the phylogenetic relationships among Pampus species in the world based on sequence data in the NCBI database. Seven valid Pampus species are identified in this study. The mean genetic divergence value calculated between clades representing these species was 7.9%. The mean genetic distance between the so-called Pampus argenteus from Indian waters and sequences attributed to P. argenteus from the South China Sea, where the neotype of this species was collected, was found to be greater than 12%, strongly supporting the likelihood of the Indian species being distinct. The Indian Pampus species show very close affinity to P. cinereus, with inter species differences less than 2%. The taxonomic identity of the silver pomfret in India is also discussed here, in light of molecular and morphological evidence.

Candidate adaptive genes associated with lineage divergence: identifying SNPs via next-generation targeted resequencing in mule deer (Odocoileus hemionus).

Mule deer (Odocoileus hemionus) are an excellent nonmodel species for empirically testing hypotheses in landscape and population genomics due to their large population sizes (low genetic drift), relatively continuous distribution, diversity of occupied habitats and phenotypic variation. Because few genomic resources are currently available for this species, we used exon data from a cattle (Bos taurus) reference genome to direct targeted resequencing of 5935 genes in mule deer. We sequenced approximately 3.75Mbp at minimum 20X coverage in each of the seven mule deer, identifying 23204 single nucleotide polymorphisms (SNPs) within, or adjacent to, 6886 exons in 3559 genes. We found 91 SNP loci (from 69 genes) with putatively fixed allele frequency differences between the two major lineages of mule deer (mule deer and black-tailed deer), and our estimate of mean genetic divergence (genome-wide FST =0.123) between these lineages was consistent with previous findings using microsatellite loci. We detected an over-representation of gamete generation and amino acid transport genes among the genes with SNPs exhibiting potentially fixed allele frequency differences between lineages. This targeted resequencing approach using exon capture techniques has identified a suite of loci that can be used in future research to investigate the genomic basis of adaptation and differentiation between black-tailed deer and mule deer. This study also highlights techniques (and an exon capture array) that will facilitate population genomic research in other cervids and nonmodel organisms.

Phylogenetic Position of Psittacula Parakeet Bird from Enggano Island, Based on Analyses of Mitochondrial Cytochrome B Gene

Enggano Island of Indonesia has Psittacula parakeet bird; namely Psittacula longicauda modesta. Phylogenetically, the position of the bird has not been studied yet. The present study used DNA sequences of mitochondrial cytochrome b (cyt b) gene to analyze phylogenetic relationships within Psittacula parakeet birds; especially to reveal the phylogenetic position of Psittacula longicauda modesta. Blood samples were collected from two Psittacula species; Psittacula alexandri from Jawa island, and Psittacula longicauda (Psittacula longicauda modesta from Enggano island and P. l. defontainei from Natuna island). Blood samples were taken from each bird and DNA was extracted from each blood sample. PCR was performed to amplify a single fragment of cyt b gene, by using a pair of nucleotide primer. The DNA targets were then be sequenced. Totally 868-bp of cyt b was used to calculate genetic divergence within and between Psittacula parakeet, and to construct phylogenetic trees. DNA sequence data from others Psittacula species were taken from GenBank. Columba livia, Accipiter, and Cacatua were used as outgroup species. The mean genetic divergence within Psittacula longicauda was 2.16% for P. l. modesta vs P. l. defontainei, 2.37% for P. l. modesta vs P. l. longicauda, and 1.51% for P. l. defontainei vs P. l. longicauda. The mean genetic divergences within Psittacula were 0.0512 ± 0.0051. Both Phylogenetic (NJ and ML) trees showed that P. l. defontainea (Natuna is.) and P. l. longicauda grouped together and to be sister group, while the position of Psittacula parakeet from Enggano island (P. l. modesta) was distant from and as a sister group of (P. l. defontainei and P. l. longicauda). P. longicauda and P. alexandri group together and appeared to be sister group.

DNA barcoding reveals high levels of genetic diversity in the fishes of the Itapecuru Basin in Maranhão, Brazil

DNA barcoding is a useful complementary tool for use in traditional taxonomic studies due to its ability to detect cryptic species, and may be particularly efficient in the identification of fish species. The fish fauna of the Itapecuru River represents an important fishery resource in the Brazilian State of Maranhão, although it is currently suffering increasing degradation as a result of anthropogenic impacts. Therefore, DNA barcoding was used in the present study to identify fish species and establish a database of the rich freshwater fish fauna of Maranhão. A total of 440 specimens were analyzed, corresponding to 64 species belonging to 59 genera, 31 families, and 10 orders. Overall, 92.19% of these species could be identified by DNA barcoding, and were characterized by low levels (average 0.80%) of intra-specific divergence. However, five species (Anableps anableps, Gymnotus carapo, Sciades couma, Pseudauchenipterus nodosus, and Leporinus piau) presented values of mean genetic divergence above 3%, indicating the existence of cryptic diversity in these fishes. The DNA barcoding approach permitted the analysis of a large number of specimens and facilitated the discrimination and identification of closely related fish species in the Itapecuru Basin.