Defining the orientation of the tandem fusions that occurred during the evolution of Indian muntjac chromosomes by BAC mapping

The Indian muntjac (Muntiacus muntjak vaginalis) has a karyotype of 2n=6 in the female and 7 in the male, the karyotypic evolution of which through extensive tandem fusions and several centric fusions has been well-documented by recent molecular cytogenetic studies. In an attempt to define the fusion orientations of conserved chromosomal segments and the molecular mechanisms underlying the tandem fusions, we have constructed a highly redundant (more than six times of whole genome coverage) bacterial artificial chromosome (BAC) library of Indian muntjac. The BAC library contains 124,800 clones with no chromosome bias and has an average insert DNA size of 120 kb. A total of 223 clones have been mapped by fluorescent in situ hybridization onto the chromosomes of both Indian muntjac and Chinese muntjac and a high-resolution comparative map has been established. Our mapping results demonstrate that all tandem fusions that occurred during the evolution of Indian muntjac karyotype from the acrocentric 2n=70 hypothetical ancestral karyotype are centromere-telomere (head-tail) fusions.

Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups

Background: It is widely accepted that the ancestors of Native Americans arrived in the New World via Beringia approximately 10 to 30 thousand years ago (kya). However, the arrival time(s), number of expansion events, and migration routes into the Western

Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian Muntjac (Muntiacus muntjak vaginalis)

The karyotype of Indian muntjacs (Muntiacus muntjak vaginalis) has been greatly shaped by chromosomal fusion, which leads to its lowest diploid number among the extant known mammals. We present, here, comparative results based on draft sequences of 37 bac

Generic allocation of Indian and Sri Lankan Philautus (Anura: Rhacophoridae) inferred from 12S and 16S rRNA genes

The generic allocation of Indian and Sri Lankan Philautus needs further examination. In this study, a comprehensive understanding of the phylogeny of Indian and Sri Lankan Philautus is obtained based on 125 and 16S rRNA genes. All phylogenetic analyses indicate that Indian-Sri Lankan Philautus, Philautus menglaensis, Philautus longchuanensis, and Philautus gryllus form a well supported clade, separate from Philautus of Sunda Islands that form another well supported clade representing true Philautus. This result supports the designation of the genus Pseudophilautus to accommodate the Indian and Sri Lankan species. Pseudophilautus consists of two major lineages, one comprises the majority of Indian species, Chinese species, and Southeast Asian species, and one comprises all Sri Lankan species and a few Indian species. Pseudophilautus may have originated in South Asia and dispersed into Southeast Asia and China. Based on the results, we further suggest that Philautus cf. gryllus (MNHN1997.5460) belongs to the genus Kurixalus. (C) 2010 Published by Elsevier Ltd.

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A > T, C > G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA. (c) 2008 Published by Elsevier Inc.

Influence of selected Indian immunostimulant herbs against white spot syndrome virus (WSSV) infection in black tiger shrimp, Penaeus monodon with reference to haematological, biochemical and immunological changes

Immunostimulants are the substances, which enhance the non-specific defence mechanism and provide resistance against the invading pathogenic micro-organism. In order to increase the immunity of shrimps against the WSSV, the methanolic extracts of five different herbal medicinal plants like Cyanodon dactylon, Aegle marmelos, Tinospora cordifolia, Picrorhiza kurooa and Eclipta alba were selected and mixed thoroughly in equal proportion. The mixed extract was supplemented with various concentrations viz. 100 (A), 200 (B), 400 (C), and 800 (D) mg kg(-1) through artificial diets individually. The prepared diets (A-D) were fed individually to WSSV free healthy shrimp Penaeus monodon with an average weight of 8.0 +/- 0.5 g for 25 days. Control diet (E), devoid of herbal extract was also fed to shrimps simultaneously. After 25 days of feeding experiment, the shrimps were challenged with WSSV, which were isolated and propagated from the infected crustaceans. The shrimps succumbed to death within 7 days when fed on no herbal immunostimulant diet (E). Among the different concentrations of herbal immunostimulant supplemented diets, the shrimps fed on diet D (800 mg kg(-1)) significantly (P < 0.0001) had more survival (74%) and reduction in the viral load. Also the better performance of haematological, biochemical and immunological parameters was found in the immunostimulant incorporated diets fed shrimps. The present work revealed that the application of herbal immunostimulants will be effective against shrimp viral pathogenesis and they can be recommended for shrimp culture. (c) 2006 Published by Elsevier Ltd.

角蟾科（Megophryidae; Anura）蝌蚪的形态多样性和生态适应

角蟾科（Megophryidae）是以角蟾属（Megophrys Kuhl and Van Hasselt, 1822）为模式属而建立的，隶于无尾目（Anura），变凹型亚目（Anomocoela）。角蟾科包括2 亚科11 属142 种，分布于东洋界，从巴基斯坦、中国西部向东直到菲律宾和苏达群岛；中国有9 属75 种分布于华中和华南地区。角蟾科被认为是原始的两栖动物之一，其分类学、系统学、生态学、动物地理学的研究均深受中外科学家的瞩目。近年来，通过形态学、古生物学、细胞学、生态学、支序系统学的研究，角蟾科的分类与系统学研究取得了较大进展。与成体形态和分子系统学研究结果相比较，蝌蚪的研究存在更多的问题和挑战，尚需深入研究：（1）角蟾科蝌蚪的形态多样性分析；（2）角蟾科的系统发育关系与蝌蚪的演化，以及口漏斗的起源；（3）角蟾科蝌蚪表型分化与栖息环境和觅食行为的适应演化。针对上述问题，本文对角蟾科9 属30 种蝌蚪的形态特征，包括外部宏观形态和口器外部结构特征、口器内部显微结构、唇齿和角质颌的亚显微结构作了深入细致、多层次的比较研究；通过12s rRNA 和cytochrome b 基因构建最大简约树，采用贝叶斯系统发育进行分析，蝌蚪型的演化采用祖先性状的重建方法分析；得到如下结论：1）初步将角蟾科蝌蚪分为4 种类型；并且建立了2 种新的角蟾科蝌蚪类型。A 型：拟髭蟾型蝌蚪，该型蝌蚪包括拟髭蟾属、髭蟾属、齿蟾属和齿突蟾属的物种；B 型：新类型，掌突蟾型蝌蚪，该型蝌蚪在本文中包括掌突蟾属、小臂蟾属的物种；C 型：新类型，短腿蟾型蝌蚪，一种特化类型，该型蝌蚪在本文中仅包括短腿蟾属的物种；D 型：角蟾型蝌蚪，该型蝌蚪在本文中包括无耳蟾属、小口拟角蟾属和异角蟾属的物种。2）对角蟾科的分类进行了修订：（1）支持角蟾科两个亚科的分类系统；（2）角蟾亚科包括拟角蟾属、异角蟾属、无耳蟾属和短腿蟾属；该亚科形态差异小，系统学关系比较复杂，暂不作族级分类的再划分；（3）拟髭蟾亚科分为2 个族：拟髭蟾族，该族物种具有类型A 的蝌蚪，包括4 个属：拟髭蟾属、髭蟾属、齿蟾属、齿突蟾属；掌突蟾族，该族物种具有类型B 的蝌蚪，包括2 个属：掌突蟾属和小臂蟾属。3）结合分子系统进化关系探讨了4 种蝌蚪类型的演化。（1）角蟾科蝌蚪的最近共同祖先来自于一类具有拟髭蟾型蝌蚪性状的蝌蚪；（2）掌突蟾型蝌蚪和角蟾亚科的蝌蚪是由具有拟髭蟾型蝌蚪性状的祖先蝌蚪分别演化而来；（3）短腿蟾型蝌蚪是角蟾型蝌蚪的一种特化类型；（4）外群蝌蚪具有与拟髭蟾型蝌蚪相似的性状，进一步印证了类拟髭蟾型蝌蚪是角蟾科蝌蚪的最近共同祖先的假说；（5）具有口漏斗的蝌蚪类型是由不具口漏斗的蝌蚪类型演化而来，在角蟾科中口漏斗是一种衍生性状。4）分析了角蟾科四种蝌蚪类型与栖息环境的适应演化。（1）角蟾科蝌蚪的口部和体形的变化反映了该科蝌蚪由缓流向类似静水生境的回水凼的渐变式适应，角蟾科蝌蚪的形态显示了多方面的适应变化；（2）随着蝌蚪类型由A 向D的演化，当水速较大时，拟髭蟾型的蝌蚪营流水攀吸型生活方式；当水速递减时，掌突蟾型蝌蚪营流水附着型生活方式；当水速进一步递减时，具有较小口漏斗的短腿蟾型蝌蚪和具有大漏斗的角蟾型蝌蚪营流水浮泳型生活。角蟾科蝌蚪对于水流递减的适应演化说明蝌蚪的生态学适应是具有进化意义的；（3）蝌蚪口器内部结构的分化揭示了蝌蚪和食性的适应关系，蝌蚪以口部的唇齿与角质颌刮取或吞吸水中的物质，然后，通过口乳突有选择地过滤进入口腔中食物。拟髭蟾亚科蝌蚪的唇齿多而窄，唇齿间距宽，颌鞘粗而稀，反映了其植食性为主的特点；它们的舌前乳突一般为指状，在口腔入口处所占面积小，其机械过滤的作用很多被唇齿和角质颌分担了；而角蟾亚科的蝌蚪，其角质颌弱，其舌前乳突一般为匙状，几乎填满了口腔入口处，因此舌前乳突起了主要的机械过滤作用。The family Megophryidae is the largest and most diverse families inArchaeobatrachia, and most of its species occur in India, Pakistan, and eastward intoChina, Southeast Asia, Borneo and the Philippines to the Sunda Islands. Currently thefamily includes 142 species have been grouped into two subfamilies, Megophryinaeand Leptobrachiinae. The mountains of central and southern China are rich in speciesof Megophryidae, 75 species belong to 9 genera and two subfamilies.The family was supposed to be ideal materials of studies in many fields of biology,such as taxonomy, evolution, systematics, ecology, and biogeography. Recently, therehave a great development in taxonomy and systematics of megophryids throughstudied by morphology, paleontology, cytology, ecology, and cladistics. However,larvae of megophryids were generally unknown, although the tadpoles might be veryimportant for above studies.In this paper, we examined the evolutionary scenario of the tadpoles’ morphologyin the context of a phylogenetic framework. Our objectives are (1) to evaluate thedivergence of larval body shape and oral discs in the family Megophryidae, (2) toexplore the evolutionary trends of the larvae in megophryidae, and test if thefunnel-shaped oral disc is apomorphic, and (3) to explore the relationship of the larvalstructure, diet and microhabitat.We examined larval morphology of 30 megophryid species, the larval body shape,oral discs, the buccopharyngeal cavity, and jaw sheaths and denticles of the Chinesemegophryid frogs were re-examined. We constructed a phylogeny of the species on thebasis of published mitochondrial cytochrome b and 16S rRNA gene segments usingpartitioned Bayesian analyses. Furthermore, hypothetical changes of larval morphologywere inferred using parsimony principle on the phylogeny. The results showed that:1) Four tadpole types in Megophryidae. The larval morphological charactersseries in Chinese megophryids fall into four general categories according to the bodyshape and oral discs: (A) Leptobrachiini type, species from genera Leptobrachium,Oreolalax, Scutiger and, Vibrissaphora share this type of tadpoles. (B) Leptolalax type,species of genus Leptolalax have this type of tadpoles. (C) Brachytarsophrys type,species of the genus Brachytarsophrys have this type of tadpoles. (D) Megophryinitype, species of the genera Atympanophrys, Ophryophryne, and Xenophrys share this type of tadpoles. Of which B and C are two novel types.2）Taxonomic implications. The present study leads us to reconsider the generalclassification of tribes attributed to members of Megophryidae. More specifically,concerning the phylogenetic relationships and the two novel tadpole types describedherein, we propose a provisional taxonomy for the family but suggest that further taxasampling of other megophryids be performed to confirm this taxonomic change. TheMegophryidae is composed of two subfamilies (Leptobrachiinae and Megophryinae).The Leptobrachiinae was recogonized the two tribes: (1) tribe Leptobrachiini sensuDubois, corresponding to the tadpole of type A, including four genera, i.e.,Leptobrachium, Oreolalax, Scutiger and, Vibrissaphora; (2) tribe Leptolalaxini,corresponding to the tadpole of novel type B, including two genera, i.e., Leptolalaxand Leptobrachella. However, the relationships among the genera of Megophryinaewere largely unresolved, they recognized no monophyletic groups above the generalevel. A more thorough sampling will likely foster a better taxonomic solution.3) The larval evolutionary scenario in Megophryidae.Type A is characteristicof normal-mouthed with multiple tooth rows, representing the tadpole type of theMRCA of Chinese megophryids. Type B is characteristic of normal-mouthed withreduced tooth rows, prolonging labium, and integumetary glands. Type C ischaracteristic of no labial teeth and smaller umbeliform oral disc. Type D ischaracteristic of no labial teeth, enlarged umbeliform oral disc, representing the tadpoleof the MRCA of subfamily Megophryinae. A previous hypothesis, referring tofunnel-shaped oral discs as an apomorphy, is supported.4) The larval adaptation to habitats in Megophryidae. Tadpoles generallyadhere to substrates using their mouths, and the microhabitat that the tadpoles occupyreflects the degree of adhesion and oral complexity. The morphological changes inmegophryid tadpoles virtually allow a progressive adaptation to a changing habitatfrom faster water to slower water. Within the tadpoles of Type A to type D, the TOTbecomes smaller and smaller, and the oral disc orientates from anteroventral toumbelliform upturned, and eye position orientates from dorsal to lateral, and the trunkis more and more depressed and tail becomes relatively longer and slender. Within therunning water, the normal-mouthed with multiple tooth rows of Leptobrachiini tadpoles are correlated with lotic-suctorial, benthic feeders with anteroventral oraldisc and the largest body. With the water’s velocity decreasing, the lotic-adherentfeeders of Leptolalax tadpoles have tube-shaped labium with reduced tooth rows andintegumetary glands. And then, the smaller umbeliform in Brachytarsophrys tadpolesand the enlarged umbeliform oral disc in the Megophryini tadpoles are inhabitmicrohabitats of non-flowing backwaters of rivers, indicative of adaptive traits oflotic-neustonic surface feeders. The scheme of megophryid tadpoles andmicrohabitats provided the first clear evidence which congruent with the hypothesis ofAltig and Johnston (1989). The ecological divergence plays a general role in thedivergence and evolution of megophrid larvae. There is a definite correlation amongthe buccopharyngeal cavity, diet and feeding mechanisms, the tadpole graze orswallow the food particles, then through papillae which like a sieve and sort out foodparticles to the oesophagus. The tadpole of Leptobrachiinae possess multiple toothrows, wide intertooth distance as well as thick and sparse jaw sheath, these tadpolesinhabit bottom of the streams and graze on epiphyton or major detritus of organicmatter on the substrates, their prelingual papillae like single finger, the mechanicalpurpose of papillae served share in by tooth and jaw. The tadpoles of Megophryinaeoccur near the water surface of small streams and are the filter feeder, their dietincludes plankton and organic debris floating on the water surface, those tadpolepossess weak jaw, their prelingual papillae like spoon, the mechanical purpose ofpapillae served mostly for sieve.