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Relationships Between Genetic Variability and Life-History Features of Fishes Based on S7 Ribosomal Protein Gene

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Relationships Between Genetic Variability and Life-History Features of Fishes Based on S7 Ribosomal Protein Gene id7826125 pdfMachine by Broadgun Software - a great PDF writer! - a great PDF creator! - http://www.pdfmachine.com http://www.broadgun.com ISSN : 0974 - 7532 Volume 10 Issue 7 Research & Reviews in BBiiooSScciieenncceess Regular Paper RRBS, 10(7), 2015 [250-258] Relationships between genetic variability and life-history features of fishes based on S7 ribosomal protein gene Tangjie Zhang* College of Veterinary medicine, Yangzhou University, Jiangsu Yangzhou 225009, (CHINA) E-mail: [email protected] ABSTRACT KEYWORDS To research relationship between genetic variation and life-history vari- Genetic diversity; ables of Actinopterygii, as indicated by common length, maximum length, Actinopterygii; maximum weight and longevity, and environmental variation, as indicated Rps7; ’ living environments, we applied analysis of in- by three different fishes Life-history. dependent regression and phylogenetically-independent contrasts meth- ods to evaluate life-history variables correlations with rps7 neutral ge- netic diversity. Polymorphism datasets of rps7 gene, belonging to 48 genera, 25 families and 9 orders, of Actinopterygii, was obtained from Polymorphix and Popset of GenBank. Life-history variables were ob- tained from the AnAge database and fishbase. The results showed that neutral genetic diversity of fishes is significantly negatively associated with common length. No strong level of correlation was found between ’s neutral genetic diversity and maximum size, maximum weigh or fish maximum longevity. No correlation was found among neutral genetic di- ’ habits (marine, freshwater and marine-freshwater) ei- versity and fishes ther. 2015 Trade Science Inc. - INDIA INTRODUCTION mtDNA substitution rate variations, there are some hypotheses-related to life-history- have been pro- There are two principal types of genetic diver- posed: the generation time, the metabolic rate, and sity: adaptive and neutral. Interpreting the genetic the longevity have been advanced to explain varia- diversity in organisms with diverse life and popula- tion in DNA substitution rate[28]. In Actinopterygii, tion histories can be difficult since the mechanisms some studies showed that in marine fishes, the level and processes that regulate this diversity are com- of genetic diversity is higher and the level of popu- plex and still poorly. The causes of variation could lation divergence is lower than in freshwater spe- be sample error, variance in gene flow, natural se- cies, most likely due to the better dispersal capa- lection, genetic drift and so on. The relative impor- bilities and larger effective population sizes of ma- tance of these variation factors in shaping the ge- rine species[14, 37, 11]. netic structure of a population could depend on the Appropriate DNA markers must be selected for life history of the species. For example, to explain the phylogenetic and genetic diversity analyses of RRBS, 10(7) 2015 Tangjie Zhang 251 Regular Paper fishes. Mitochondrial DNA (mtDNA) is one of the MATERIALS AND METHODS most widely studied genetic markers in the fields of population genetics and phylogeography. However, Data collection a more serious criticism is that mtDNA, which is Polymorphism datasets of rps7 gene was ob- more prone to hitch-hiking because of the lack of tained from Polymorphix[3] and Popset of GenBank. recombination, may not conform to neutral expecta- Two sequences were taken not to be clustered if there tions[4, 13]. The RPS7 gene, which belongs to a fam- was a mismatch of >50nt with <80% similarity flank- ily of genes called RPS (ribosomal proteins), has ing the CLUSTALW program[35]. Such a mismatch is been the most popular marker[29, 26, 20] of nuclear neu- interpreted as evidence that the sequences represent tral molecular diversity in fishes for its high simi- duplicate genes in distinct genomic contexts. Se- larity in taxa[6]. In this study, the polymorphism of quences were inspected by eye and corrected when fish RPS7 gene was therefore used to be analyzed required. ’s molecular diversity. for fish Data: 146 species of fish belonging to 48 genera The DNA substitution rate is widely used for and 25 families and 9 orders. Each group was aligned the studies of genetic diversity, but accurate estima- by eye using CLUSTALW. Details of the species tion of mutation rate is obviously required for accu- sampled are listed in Appendix S. rate molecular dating. Another most fundamental in Polymorphism sequence data analyses population genetics is the mutation parameter or ge- ’s estima- è=4Neµ Genetic diversity measures -Watterson netic diversity under the assumption that è µ denotes the tor ( ) were calculated separately from the intron mutations are effectively neutral. Here w and synonymous sites of the analyzed fragments of expected number of mutations for an individual DNA same species, expressed in per-site level of diver- sequence per generation and Ne denotes the effec- è sity, and the no. of mutation and sites both synony- tive population size. The estimate of is based on ’s estimator è mous and nonsynonymous sites were counted simul- coalescent theory. Watterson ( ,) is com- w taneously. monly used for its simplicity. Under the standard neutral model, mutation rates will definitely posi- Life history data tively lead to polymorphism levels. Definitely, the Many researches have been done on life history ’ polymorphism, which are analysis of nuclear genes traits in fishes. Kawasaki (1980) suggested that the based on increasing molecular genetic data, are use- grouping of life history traits of fishes differed from ful to understand the mechanism of molecular diver- the traditional methods developed for terrestrial ani- sity because they offer broad and comprehensive mals[19]. In this study, common length, maximum coverage. length, maximum weight and longevity, data were Molecular genetic data have greatly improved obtained from the AnAge database[10] and fishbase ’ evo- our ability to test hypotheses about organisms (http://www.fishbase.org/home.htm). lution. A large amount of nuclear data has been col- Body length or size was usually used as a proxy ’s populations dramati- lected from diverse organism for abundance, given the expected negative relation- cally during past decade or so. In this study, we ana- ship between body size and abundance. Indeed, a lyzed genetic diversity by surveying polymorphism significant negative relationship between body size ’s rps7 gene. Our goal of this work was to of fish and genetic variation was found in mammals based ascertain if there is a relationship between single on allozymes[36]. We got two types of body length, nuclear gene (rps7) neutral diversity and life-his- common length and maximum length. Using common tory variables, such as common length, maximum length as a proxy for abundance allowed us to in- length, maximum weight and longevity, presented crease the number of species evaluated, as catch data ’s living en- above, and a relationship between fish are only available for a limited number of species. vironments and neutral genetic diversity. Statistical tests 252 Relationships between genetic va. riability and life-history features RRBS, 10(7) 2015 Regular Paper è [34] w were arc-sine transformed . Quantitative (logistic regressions) analyses and phylogenetically life-history variables were log transformed. We first regression of independent contrasts. Both the appli- è è calculated for synonymous sites and for intron cation of phylogenetically independent contrasts and s è èi è sites and weighted average of s or /and i from rps7 logistic regression analyses showed that w of for same species. Analysis of independent regres- weighted neutral sites was significantly negatively sion methods was applied to evaluate one or more associated with common length(n=67, p=0.031, life-history correlations with neutral genetic diver- n=67, p=0.011). No strong level of correlation was è è sity ( ) (synonymous and intron sites). found between w of weighted neutral sites and maxi- Phylogenetic reconstructions mum size, maximum weigh or maximum longevity (TABLE 1). ’s We created a phylogenetic hypothesis for the To investigate the relationship between fish species included in this study by grafting them onto living environments and neutral genetic diversity, we ’ diver- a higher-level phylogenetic supertree of correlated environments to all neutral sites [16] Actinopterygii using PhyloWidget . The topology sity of sampled S7 ribosomal protein gene on the was a composite of information drawn from basis of three entirely different environments: ma- TreeBASE (http://www.treebase.org/treebase- rine, freshwater and marine-freshwater (TABLE 1). web/home.html). Phylogenetically-independent The result showed that no correlation was found ’s habits contrasts (PIC) were conducted using Phylogenetic between neutral genetic diversity and fish Comparative Methods of COMPARE, version (n=143, p=0.120). 4.6b[23]. DISCUSSION RESULTS Early studies have revealed marked differences Neutral genetic diversity of fishes based on rps7 in the level of genetic differentiation and genetic di- A smaller amount of life-history data is avail- versity between populations of marine and fresh- able especially for max weight, which documented water species, with marine species generally exhib- only 17 species in 146 fish species. We thus focused iting lower levels of inter-population differentiation on the effects on maximum size and common length. and higher genetic diversity[14, 37, 11]. This general The common length, however, could
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