RAPD analysis of Nectomys squamipes (Rodentia, Sigmodontinae) populations

Abstract

Random amplified of polymorphic DNA (RAPD) analysis was used to assess genetic distance and the genetic structure of populations of Nectomys squamipes, a semiaquatic rodent species distributed along watercourses. DNA samples of five populations were analyzed using three primers, producing 45 scorable bands, 31 of which were polymorphic. There was a significant differentiation among populations [F ST = 0.17; phiST = 0.14 (P < 0.004)] but gene flow (Nm = 1.25) was sufficient to overcome genetic drift effects. No fixed specific markers were found for any population. The Mantel's test and UPGMA cluster analysis showed a lack of relationship between genetic and geographic distances. The apparent homogeneity indicated by RAPD markers coincided with morphometric data, despite the wide geographic range of N. squamipes. Alternative hypotheses for explaining our results include recurrent processes of local extinction and recolonization or a recent and sudden increase in the geographic distribution of this species.<br>Uma análise baseada em amplificação aleatória de ADN polimórfico (random amplified polymorphic DNA, RAPD) foi feita a fim de se estimar distâncias genéticas e a estruturação da variabilidade genética em populações de Nectomys squamipes, uma espécie de roedor de hábito semi-aquático, que está sempre associada a cursos d'água. Amostras de ADN de cinco populações foram analisadas utilizando-se três primers, que produziram um total de 45 bandas úteis, sendo 69% delas polimórficas. Os resultados mostraram uma diferenciação significativa entre as populações [F ST = 0,17; fiST = 0,14 (P < 0,004)], mas com uma taxa de fluxo gênico suficiente (Nm = 1,25) para minimizar os efeitos da deriva genética. Não foram encontrados marcadores exclusivos para nenhuma das populações. O teste de Mantel e a análise de agrupamento por UPGMA não evidenciaram relação entre as distâncias genéticas e as geográficas, indicando que não há um padrão de isolamento por distância. A aparente homogeneidade indicada pelos marcadores de RAPD vai ao encontro de dados morfométricos prévios, que não indicaram uma diferenciação substancial na extensa área de distribuição de N. squamipes. Algumas hipóteses alternativas podem ser levantadas para explicar estes resultados, como processos recorrentes de extinção e recolonização locais, ou um aumento súbito e recente da distribuição geográfica desta espécie

Population structure and genetic variability of mainland and insular populations of the Neotropical water rat, Nectomys squamipes (Rodentia, Sigmodontinae)

“…The microsatellite loci used in this study showed differentiation indexes (q = 0.100 and r = 0.086) smaller than the index (F ST = 0.17) obtained in the previous RAPD analysis that included most of the mainland populations studied here (Almeida et al, 2000a). Differentiation estimates related to the F-statistics are negatively correlated with the product of the effective population size (Ne), and the mutation rate (m) plus the migration rate (m) (Wright, 1943).…”

“…Based on these results and theoretical models, wider areas would be expected to exhibit a higher degree of differentiation among sites. Contrary to these expectations, however, the morphology of N. squamipes was found to be fairly homogeneous across its wide geographic range (Bonvicino, 1994) and this low degree of differentiation between populations was confirmed by random amplified polymorphic DNA (RAPD) studies (Almeida et al, 2000a). Since morphology may be subject to balancing selection and RAPD markers have well known limitations and are less efficient in detecting differentiation than microsatellite markers (Lynch and Milligan, 1994;Ross et al, 1999;Lougheed et al, 2000), we decided to use microsatellite markers to re-analyze the population samples previously studied using RAPD.…”

“…Voucher specimens were deposited in the Museu Nacional, Rio de Janeiro, Brazil. Samples from GL, FU, SU, PD and FC had previously been analysed using RAPD (Almeida et al, 2000a). Geographic distances between mainland localities ranged from 23.7 to 741.5 km.…”

Random Amplified Polymorphic Dna (Rapd) Based Molecular Characterization of Evolutionary Advancement Amongst Hierarchal Five Vertebrate Species

“…However, lower frequencies of non-parental RAPD bands were found in beetles (Nicrophorus tomentosus) and strawberries (Fragaria vesca) [23]. In a study conducted in Nectomys squamipes, a semiaquatic rodent species distributed along watercourses using RAPD analysis in order to assess genetic distance and the genetic structure of populations [24]. In another study, the molecular characterization of Dicentrarchus labrax embryonic cells (DLEC) was done using Random amplified polymorphic deoxyribonucleic acid analysis by PCR (RAPD-PCR) to detect DNA alterations in environmental genotoxic studies [25].Similarly, in another study on Zebra fish was done, where in RADP primers were identified in laboratory strains of zebra fish which have shown extensive genetic polymorphism in developmental stages [26].…”

Identification of microsatellite loci in the water‐rat Nectomys squamipes (Rodentia, Sigmodontinae)

“…These characteristics make the presence of water‐rat populations a complicated factor for schistosomiasis control. Several populations of N. squamipes studied with random amplified polymorphic DNA (RAPD) showed limited differentiation indicating effects of migration or recent range expansion (Almeida et al , in press). Microsatellites were developed as a tool for studying migration patterns of N. squamipes and for evaluating its potential in spreading infection.…”