Distribution of Selected Single Nucleotide Polymorphisms in the Brahmin, Rajput and Bania Populations of Jammu District of Jammu and Kashmir, North India

ABSTRACTA total of 461 randomly selected unrelated subjects belonging to three selected castes populations of Jammu district of Jammu and Kashmir (J&K) viz., the Brahmin, Rajput, and Bania were typed using standard PCRRFLP technique for a battery of five SNPs (Single Nucleotide Polymorphisms) namely NAT2, ADH2, PSCR, T2, and ALAD. The objective of the present study was to characterize these populations genetically and assess the degree of genetic differentiation and genetic affinities among them. The results revealed that the present caste populations were moderately differentiated (GST = 0.0105).The genetic distance analysis demonstrated that the Rajput and Bania were in close genetic affinities while the Brahmin population was somewhat distant. In conclusion, the present investigation documented the underlying genomic uniformity in the people of the Jammu district.

Distribution of Human-specific Alu InDel Polymorphisms in the Brahmin and Rajput Populations of Kangra District of Himachal Pradesh, North India

ABSTRACT The genetic constitution of two endogamous caste populations viz., the Brahmin (n=250) and Rajput (n=250) of Kangra district of the North Indian state of Himachal Pradesh was studied using six autosomal Alu InDel (insertion/deletion) markers viz., ACE, APO, PV92, CD4, PLAT, and TPA25 All markers were found to be polymorphic. Except for Alu APO and PV92 in the Rajput, genotype frequencies of other markers were in the Hardy-Weinberg equilibrium in both the populations. The average heterozygosity (H) was observed higher in the Brahmin (0.4134) compared to the Rajput (0.3809) and the degree of genic differentiation was low between them (GST =0.00898). The genetic distance analysis revealed close genetic affinities of the present Rajput population with the Gaddi Rajput and Gaddi Brahmin populations reported earlier from the district but the present Brahmin population was found distant from them.

Monitoring genetic diversity across Pinus tabuliformis seed orchard generations using SSR markers

The maintenance of genetic diversity across seed orchard generations is an important management objective. Here, we used Pinus tabuliformis as a model to explore the extent of genetic diversity across the species’ breeding activities through their corresponding seed orchards generations. We utilized a large number of SSR markers selected from <i></i>Pinus tabuliformis<i></i> transcriptomic data, and then assessed the effect of marker number on genetic diversity and individuals’ genetic relationships across orchards’s generations. In total, we designed 125 simple sequence repeat (SSR) markers, from which 39 SSRs were polymorphic and used in the present study. The genetic diversity and genetic distance parameters tended to increase with thean increase ofin markerloci numbers and a stable trend was reached at 24 SSRs. The selected optimal 24 SSR markers were further used to assess the genetic diversity across seed orchards’s generations, and a decreasing trend was detected with the advancement of orchards’s generations. Genetic distance analysis indicated that individuals in the 2nd generation orchard was more closely related as compared to those of the 1st- and 1.5-generations. This study provided valuable information on the effect of selection and breeding on genetic diversity and highlighted its role for effective seed orchards management.

New color patterns and new synonym of Odontolabis sinensis (Westwood, 1848) (Coleoptera: Lucanidae): insights from a multilocus phylogeny and species delimitation

Taxonomy of Odontolabis sinensis (Westwood, 1848) and Odontolabis fallaciosa Boileau, 1901 has long been a controversial issue due to their highly morphological similarity except for elytral color patterns. In the present work, we assessed their taxonomic status by combining molecular phylogeny and species delimitation based on multilocus datasets (COI, 16S rDNA, Cytb, CAD, Wingless). Phylogenetic analyses under both Maximum Likelihood inference and Bayesian inference recovered identical topologies. All the examined individuals in the clade of O. sinensis and O. fallaciosa formed into five subclades belonging to four color patterns, respectively. The Kimura-2-Parameter (K2P) genetic distance analysis yielded a low mean value (0.0108−0.0295). The multiple species delimitations (ABGD, PTP and GMYC) reinforced them to be one MOTU. Our results suggest that these clades belong to the same species, and thus we propose O. fallaciosa to be a junior subjective synonym of O. sinensis. We also found two new color patterns corresponding to two clades from Southwestern China (north of 20°N and east of 105°E), respectively displaying the reddish-orange, slenderly rimmed patch and brownish-orange broad patches along the elytral edge, which was probably attributable to both historical and ecological factors in this particular region.

Morphological and Molecular Description of a New Species of Myxobolus (Myxosporea: Myxobolidae) Infecting Planiliza Macrolepis (Smith, 1846) From India

The present paper describes a novel species of Myxobolus parasitizing the gill filaments of the largescale mullet, Planiliza macrolepis from Cochin backwaters, Kerala, India. The parasite develops in the gill filaments; plasmodia elongated, milky white, measured 1.37 – 2.18 (1.78 ± 0.35) mm x 0.07-0.12 (0.10 ± 0.02) mm in size. Mature myxospores ovoid in valvular view, biconvex in sutural view with smooth shell valves and measured 6.24 - 7.02 (6.63 ± 0.23) × 5.01 - 6.18 (5.68 ± 0.25) μm in size. Polar capsules equal, oval with pointed anterior ends, 3.07 – 3.58 (3.33 ± 0.12) × 1.68 – 2.42 (2.09 ± 0.18) μm in size. Polar filaments with 4 coils, measured 29.61 ± 4.75 μm in length when extruded. Sporoplasm binucleate with a rudimentary nucleus and a vacuole. A comparison with related Myxobolus species revealed significant morphological & morphometric differences. In BLASTN and genetic distance analysis, the present parasite showed high divergence with other myxosporean sequences, indicating its molecular uniqueness. In Maximum Likelihood and Bayesian Interference analysis, the present species stands out with M. ramadus as sister branch within the Myxobolus clade. In infected gill filaments, the plasmodia caused swelling/deformation, compression of lamellae and reduction in respiratory surface area. Three of 222 P. macrolepis screened were infected, indicating a prevalence of 1.3%. Considering the morphological, morphometric, molecular and phylogenetic differences with the previously described species of myxosporeans, along with the dissimilarities in host and geographical locations, the present parasite is treated as a new species and the name Myxobolus cochinensis n. sp. is proposed.

Genetic structure analysis of cultivated and wild chestnut populations reveals gene flow from cultivars to natural stands

Japanese chestnut (Castanea crenata Sieb. et Zucc.), the only fruit tree species domesticated in Japan, has been cultivated alongside natural stands since prehistorical times. Understanding the genetic diversity of this species and the relationships between cultivated and wild chestnut is important for clarifying its breeding history and determining conservation strategies. We assessed 3 chestnut cultivar populations and 29 wild chestnut populations (618 accessions). Genetic distance analysis revealed that wild populations in the Kyushu region are genetically distant from other populations, whereas other wild and cultivar populations are comparatively similar. Assignment tests suggested that cultivars were relatively similar to populations from central to western Honshu. Bayesian structure analyses showed that wild individuals were roughly classified according to geographical distribution along the Japanese archipelago, except that some wild individuals carried the genetic cluster prevalent in cultivars. Parentage analyses between cultivars and wild individuals identified 26 wild individuals presumed to have a parent–offspring relationship with a cultivar. These results suggested that the genetic structure of some wild individuals in natural stands was influenced by gene flow from cultivars. To conserve wild individuals carrying true “wild” genetic clusters, these individuals should be collected and preserved by ex situ conservation programs.

Apophysomyces jiangsuensis sp. nov., a Salt Tolerant and Phosphate-Solubilizing Fungus from the Tidelands of Jiangsu Province of China

A newly isolated phosphate-solubilizing fungus from the topsoil of Spartina alterniflora habitats in Yancheng coastal salt marsh was cultivated. Scanning electron microscopy observation revealed that the sporangia are nearly spherical, peach-shaped, and the spores formed on the top of sporangia. The spores are ellipsoidal with raised white nubbins on the surface. Based on a polyphasic study and the genetic distance analysis referring to the sequence analysis of ITS (ITS1 + 5.8S + ITS2) and 28S rDNA (D1/D2 domains) genes, the novel species belongs to the genus Apophysomyces and is named as A. jiangsuensis. The optimum growth temperature and salinity of the new species were 28 °C and 1.15% NaCl, respectively. A study of its phosphate-solubilizing ability revealed that the fungus had an obvious decomposition effect on lecithin, Ca3(PO4)2, and AlPO3, respectively. The pH of the fermented liquid progressively decreased from 6.85 to 2.27 after 7 days of incubation, indicating that the low molecular weight organic acids excreted into the culture liquor were oxalic, succinic, and malic acids and a trace amount of citric acid. Among these, oxalic acid was the major organic acid, and its amount reached 652.5 mg/L. These results indicated that the main mechanism underlying the dissolved phosphorus was related to the secretion of large amounts of organic acids.

A review of the damselfly genus Megalestes Selys, 1862 (Insecta: Odonata: Zygoptera: Synlestidae) using integrative taxonomic methods

We used morphological and molecular characters to review the classification of damselflies in the genus Megalestes Selys, 1862 (Zygoptera: Odonata). Several methods were used for this review, including morphology, cladistics, genetic distance analysis, and molecular taxonomy. Six species were newly defined as junior synonyms (Megalestes palaceus to Megalestes haui, Megalestes chengi to Megalestes micans, Megalestes discus to Megalestes micans, Megalestes raychoudhurii to M. micans, Megalestes maai to Megalestes riccii, and Megalestes tuska to M. riccii). The total species number in Megalestes was reduced from 18 to 12. The importance of an objective species diversity measure is discussed.

Morphometrics and genetics variations of mullets (Pisces: Mugillidae) from Aceh waters. Indonesia

Yulianto D, Batubara IIAS, Nur FM, Rizal S, Siti-Azizah MN, Muchlisin ZA. 2020. Morphometrics and genetics variations of mullets (Pisces: Mugilidae) from Aceh waters, Indonesia. Biodiversitas 21: 3422-3430. Mullets are one of the commercial groups of coastal fish living in Aceh waters, in Indonesia. Presently, there is limited information on the bioecology, especially on the genetics and morphometrics of these fishes. Therefore, the objective of this study is to examine the morphology and genetic variations of Liza macrolepis, Liza tade, and Moolgarda engeli mullets. This study was conducted from January 2018 to July 2019 in four locations along the northern and eastern coasts of Aceh. Data were obtained by measuring the morphometrics of a total of 180 samples of the species in equal ratios. The data were analyzed using the ANOVA and Discriminate function analysis (DFA). The ANOVA test showed that at least 75% of characters are not significantly different among the mullets. Meanwhile, the discriminant function analysis produces the two functions with Eigenvalue of 0.627 and 0.107 with 85.5% and 17.2% total variants, respectively. Function 1 discriminates the mullet samples into two groups; the first was L. tade, and the second belonged to L. macrolepis and M. engeli. In addition, a total of 18 samples of mullets consisting of 8 samples of the L. macrolepis, 2 samples of the L tade, and 8 samples of the M. engeli were successfully amplified from the 5' region of the mitochondrial cytochrome oxidase subunit I (COX1) gene using a pair of primers (Fish F1 and Fish R1). Furthermore, a total of 7 haplotype sequences were produced from the ingroup where L. tade has one haplotype, L. macrolepis and M. engeli had three haplotypes, respectively. The genetic distance analysis showed that the interspecific distance was 0.38% and intraspecific was 8.2%. Therefore, the COI gene successfully discriminated against the mullet into three valid species.

Whole Genome Characterization and Genetic Evolution Analysis of a New Ostrich Parvovirus

Ostrich diseases characterized by paralysis have been breaking out in broad areas of China since 2015, causing major damage to the ostrich breeding industry in China. This report describes a parvovirus detected in ostriches from four different regions. The entire genomes of four parvovirus strains were sequenced following amplification by PCR, and we conducted comprehensive analysis of the ostrich parvovirus genome. Results showed that the length genomes of the parvovirus contained two open reading frames. Ostrich parvovirus (OsPV) is a branch of goose parvovirus (GPV). Genetic distance analysis revealed a close relationship between the parvovirus and goose parvovirus strains from China, with the closest being the 2016 goose parvovirus RC16 strain from Chongqing. This is the first report of a parvovirus in ostriches. However, whether OsPV is the pathogen of ostrich paralysis remains uncertain. This study contributes new information about the evolution and epidemiology of parvovirus in China, which provides a new way for the study of paralysis in ostriches.