Recombination Drives Genetic Diversification of Streptococcus dysgalactiae Subspecies equisimilis in a Region of Streptococcal Endemicity

Infection of the skin or throat by Streptococcus dysgalactiae subspecies equisimilis (SDSE) may result in a number of human diseases. To understand mechanisms that give rise to new genetic variants in this species, we used multi-locus sequence typing (MLST) to characterise relationships in the SDSE population from India, a country where streptococcal disease is endemic. The study revealed Indian SDSE isolates have sequence types (STs) predominantly different to those reported from other regions of the world. Emm-ST combinations in India are also largely unique. Split decomposition analysis, the presence of emm-types in unrelated clonal complexes, and analysis of phylogenetic trees based on concatenated sequences all reveal an extensive history of recombination within the population. The ratio of recombination to mutation (r/m) events (11:1) and per site r/m ratio (41:1) in this population is twice as high as reported for SDSE from non-endemic regions. Recombination involving the emm-gene is also more frequent than recombination involving housekeeping genes, consistent with diversification of M proteins offering selective advantages to the pathogen. Our data demonstrate that genetic recombination in endemic regions is more frequent than non-endemic regions, and gives rise to novel local SDSE variants, some of which may have increased fitness or pathogenic potential.

Cryptic species and Miocene diversification of Palaearctic naked-toed geckos (Squamata: Gekkonidae) in the Indian dry zone

We sampled Palaearctic naked-toed geckos from across their range in India and used two mitochondrial and two nuclear genes to reconstruct relationships within a global phylogeny. Published sequences of Peninsular Indian Hemidactylus allow us to contrast these two groups in dating analyses - providing insights into the history of the Indian dry zone. Palaearctic naked-toed geckos first moved onto the Indian Plate in the Oligocene, with higher-level diversification probably linked to collision of the Indian and Eurasian plates, and subsequent dispersal into-India and diversification with increasing Miocene aridity. An independent gekkonid radiation with species in the dry zone, Hemidactylus diversified during the same period in Peninsular India. Our results demonstrate that dry zone taxa across India may date back to at least the Miocene, with a potential historical climatic barrier between the Indus and Peninsular Indian Divisions. `Cyrtopodion' aravallense is revealed to be a complex with seven genetically and environmentally divergent lineages that began diversifying in the late Miocene, congruent with increased aridity in north-western India. This discovery of cryptic diversity in the Indian dry zone represents the first terrestrial vertebrate radiation from north-western central India and highlights how little we understand of the regions' biodiversity, emphasizing the need for systematic geographic sampling and multiline evidence to reveal true patterns of diversity. The ancestor of `Cyrtopodion' aravallense came into the nascent Indian dry zone in the Miocene and has since diversified, potentially in the absence of any sympatric scansorial rupicolous geckos. Cyrtopodion scabrum represents a unique case of commensalism and shows phylogeographic structure in its presumed native range. The taxonomic implications of our study include a number of undescribed species, recognition of `Cyrtopodion' as a distinct lineage and the non-monophyly of Altiphylax.

A phylogeny of the only ground-dwelling radiation of Cyrtodactylus (Squamata, Gekkonidae): diversification of Geckoella across peninsular India and Sri Lanka

The subgenus Geckoella, the only ground-dwelling radiation within Cyrtodactylus, closely overlaps in distribution with brookii group Hemidactylus in peninsular India and Sri Lanka. Both groups have Oligocene origins, the latter with over thrice as many described species. The striking difference in species richness led us to believe that Geckoella diversity is underestimated, and we sampled for Geckoella across peninsular India. A multi-locus phylogeny reveals Geckoella diversity is hugely underestimated, with at least seven undescribed species, doubling previously known richness. Strikingly, the new species correspond to cryptic lineages within described Indian species (complexes); a number of these endemic lineages from the hills of peninsular India outside the Western Ghats, highlighting the undocumented diversity of the Indian dry zone. The Geckoella phylogeny demonstrates deep splits between the Indian species and Sri Lankan G. triedrus, and between Indian dry and wet zone clades, dating back to the late Oligocene. Geckoella and brookii group Hemidactylus show contrasting diversification patterns. Geckoella shows signals of niche conservatism and appears to have retained its ancestral forest habitat. The late Miocene burst in speciation in Geckoella may be linked to the expansion of rain forests during the mid-Miocene climatic optimum and subsequent fragmentation with increasing late Miocene aridification. (C) 2014 Elsevier Inc. All rights reserved.

Sun skink diversification across the Indian-Southeast Asian biogeographical interface

Aim Widespread, transcontinental vertebrate groups represent ideal systems for biogeographical studies, because they can shed light on a wide range of questions relating to species diversification across the geographical template. We combined extensive geographical and genetic sampling from across multiple biogeographical realms to examine the timing and location of diversification in Asian sun skinks, a clade characterized by problematic species boundaries and a particularly enigmatic evolutionary history. Location Indian subcontinent, the Philippines, Southeast Asia and Sundaland. Methods We sequenced one mitochondrial and nine nuclear genes for most species in the genus Eutropis, and estimated phylogenetic relationships and divergence times using coalescent methods. To investigate the location of diversification events, we also estimated ancestral geographical ranges using several methods. Finally, we explored patterns of genetic diversity within several poorly understood, but widely distributed species. Results Divergence-time estimates indicate that Eutropis began to diversify during the Eocene. Biogeographical reconstructions show that species diversification was associated with dispersal into three biogeographical realms: India, Sundaland and the Philippines. Main conclusions The results of this study clarify several questions related to the evolutionary history of Eutropis, and place them in the context of classic Southeast Asian biogeography. Our study represents one of the first to compile a heavily sampled multilocus dataset ranging across international boundaries in southern Asia that have historically prevented a unified understanding of biogeographical and evolutionary processes involving the Indian subcontinent, mainland southern Asia and the island archipelagos of Southeast Asia.

Diversification of aquaculture for empowerment to fisheries through institution village linkage programme (IVLP) in Kerala, India

Technology Assessment and Refinement through the Institution Village Linkage Programme (IVLP) is the latest participatory extension model successfully undertaken by the Indian Council of Agricultural Research in India. The Central Marine Fisheries Research Institute has been implementing IVLP since 2001 to assess and refine the technologies of the coastal agro ecosystems at Elamkunnapuzha village (Vypeen Island) in the Ernakulam District of Kerala. A series of need based location specific technology intervention plans have been introduced to overcome the social and biological constraints on farming practices in fisheries, livestock and agriculture, and implemented with the active participation of the stakeholders. The inferences drawn from IVLP ultimately form a package suitable for enhanced production in the costal agro ecosystem for replication to other areas with similar characteristics. This paper gives a brief account of the treatment packages applied in fisheries through various technological interventions and discusses the consequent yield and benefits obtained. The ‘integrated whole village development’ through the involvement of multi institutional teams and a participatory approach was accorded prime importance in the IVLP of Elamkunnapuzha, with a greater emphasis on marginal and small farmers and specifically focusing on women for poverty alleviation and equity under the coastal agro ec

Variety of antimicrobial peptides in the Bombina maxima toad and evidence of their rapid diversification

Antimicrobial peptides secreted by the skin of many amphibians play an important role in innate immunity. From two skin cDNA libraries of two individuals of the Chinese red belly toad (Bombina maxima), we identified 56 different antimicrobial peptide cDNA sequences, each of which encodes a precursor peptide that can give rise to two kinds of antimicrobial peptides, maximin and maximin H. Among these cDNA, we found that the mean number of nucleotide substitution per non-synonymous site in both the maximin and maximin H domains significantly exceed the mean number of nucleotide substitution per synonymous site, whereas the same pattern was not observed in other structural regions, such as the signal and propiece peptide regions, suggesting that these antimicrobial peptide genes have been experiencing rapid diversification driven by Darwinian selection. We cloned and sequenced seven genes amplified from skin or liver genomic DNA. These genes have three exons and share the same gene structure, in which both maximin and maximin H are encoded by the third exon. This suggests that alternative splicing and somatic recombination are less likely to play a role in creating the diversity of maximins and maximin Hs. The gene trees based on different domain regions revealed that domain shuffling or gene conversion among these genes might have happened frequently.