Microsatellite allele sequencing in population analyses of the South American cactophilic species Drosophila antonietae (Diptera: Drosophilidae)

Abstract

Drosophila antonietae belongs to the Drosophila buzzatii cluster, a cactophilic group of species naturally endemic to South America. Morphological and genetic analyses indicate that its populations are the most homogenous in the cluster and that the diversity observed is mainly a result of variation within populations. Seven polymorphic microsatellite loci were described for this species and used in the present study to investigate the genetic diversity of natural populations of D. antonietae by both length and sequence variation. The study aimed to understand how homoplasy and null alleles affect inferences about the population history of this species and to obtain an accurate interpretation of population inferences where these loci could be applied. The results provide useful information on the interpretation of genetic data derived from the microsatellite loci described for D. antonietae and on evolutionary aspects of cactophilic Drosophila. Importantly, the results indicate that size homoplasy and null alleles do not represent significant problems for the population genetics analyses because the large amount of variability at microsatellite loci compensate the low frequency of these problems in the populations.

Exploring the effect of microsatellite size homoplasy on reconstruction of phylogenetic relationships of picote splitfin Zoogoneticus quitzeoensis

“…These results are in agreement with the observations of Adams et al (2004), Barkley et al (2009), Machado et al (2010) and with the Estoup et al (2002) proposal that homoplasic microsatellites are not a significant problem in many types of population analyses, especially if mutation models that assume homoplasy are used to calculate genetic distances, as suggested by Barkley et al (2009).…”

“…Several studies have detected size homoplasy in microsatellites in different organisms (Primmer & Ellegren, 1998; Viard et al , 1998; Angers et al , 2000; Van Oppen et al , 2000; Culver et al , 2001; Adams et al , 2004; Yokoyama et al , 2004; Lia et al , 2007; Barkley et al , 2009; Machado et al , 2010). Only a few of these studies deal directly with the effect that these homoplasies have on the reconstruction of phylogenetic relationships or on the estimation of population parameters (Viard et al , 1998; Angers et al , 2000; Adams et al , 2004; Barkley et al , 2009; Machado et al , 2010) and have generally reached contradictory conclusions.…”

“…These authors also found that the use of homoplasious microsatellites may affect the reconstruction of phylogenetic relationships in the honey bee Apis mellifera . Two recent papers (Barkley et al , 2009; Machado et al , 2010) suggest, however, that homoplasic microsatellites have a moderate effect on the reconstruction of phylogenetic relationships or population genetic studies. Barkley et al (2009) suggest that the use of this type of microsatellite has a slight effect on the reconstruction of phylogenetic relationships within the genus Citrus and Machado et al (2010), analysing Drosophila antonietae populations, claim that neither size homoplasy nor null alleles represent significant problems for population genetic analyses, as they are compensated for by the high degree of microsatellite polymorphisms.…”

Spatial Variation of Genetic Diversity in Drosophila Species from Two Different South American Environments

“…According to Machado (2003), the presence of null alleles can explain the non amplification of Drosophila buzzatii microsatellite loci in D. antonietae. Machado et al (2010), analyzing the same seven microssatellite loci of D. antonietae, detected the presence of null allele in the AluRSAlanto-6 locus and size homoplasy in four out of seven loci. However, they concluded that null allele and size homoplasy do not appear to represent significant problems for the population genetics analyses because the large amount of variability at microsatellite loci can compensate the low frequency of these problems in the populations investigated.…”

Estrutura populacional e filogeografia de <i>Drosophila antonietae</i> Tidon & Sene

“…A partir de dados aloenzimáticos, Mateus & Sene (2007) sugerem que as populações de D. antonietae sofram efeito moderado do fluxo gênico sobreposto ao efeito de deriva genética, resultando em um gradiente genético. O fluxo gênico extensivo pela base dos rios Paraná-Paraguai, juntamente ao isolamento recente entre as populações Machado, Mateus, Sene & Manfrin, 2010;Mateus et al, 2013) ao gargalo genético recente causado pela contração da vegetação xerofítica depois do último período glacial (Ab'saber, 1977;Pennington et al, 2000), a manutenção do polimorfismo ancestral, e a seleção natural (Mateus & Sene, 2007;Machado et al, 2010) seriam as causas prováveis da baixa variabilidade genética e homogeneidade entre as populações, especialmente quando comparada às outras espécies do grupo.…”