Determining the source of individuals: multilocus genotyping in nonequilibrium population genetics

Davies, Neil; Villablanca, Francis X.; Roderick, George

doi:10.1016/s0169-5347(98)01530-4

Cited by 197 publications

(171 citation statements)

References 28 publications

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“…Therefore, we think that the reduced levels of genetic variability found in populations of Ae. albopictus from Manaus may be attributed to a founder effect (i.e., populations founded by few individuals) (Davies et al, 1999;Martocq and Villablanca, 2001), which resulted in the loss of genetic variability through genetic drift, followed by the recent expansion of this species throughout neighborhoods of city (Fé et al, 2003). Furthermore, the recent expansion of this mosquito in Manaus may also explain the high Nm values and low levels of genetic variation found in these samples.…”

Section: Discussionmentioning

confidence: 99%

Reduced levels of genetic variation in Aedes albopictus (Diptera: Culicidae) from Manaus, Amazonas State, Brazil, based on analysis of the mitochondrial DNA ND5 gene

Maia¹,

Scarpassa²,

Maciel-Litaiff³

et al. 2009

Genet. Mol. Res.

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ABSTRACT. Aedes albopictus, a mosquito originally from Southeast Asia, is considered to be one of the main vectors of dengue fever, yellow fever and other arboviruses. We examined the genetic variability and population structure of 68 individuals of Ae. albopictus collected from five neighborhoods of the city of Manaus, based on the mitochondrial gene coding for NADH dehydrogenase subunit 5 (ND5). Two haplotypes were found, separated by a single mutational event (T ↔ C), with extremely low levels of genetic variability (h = 0.187 ± 0.059; π = 0.00044 ± 0.00014). Based on AMOVA, we concluded that most of the variation (99.08%) occurred within populations, though the levels of variation were not significant. Neutrality tests (Tajima's D and Fu's Fs) were non-significant, indicating that these populations are in genetic equilibrium. The most frequent haplotype (H1) is restricted to Brazilian populations of Ae. albopictus, while the rarer haplotype (H2) is shared with populations from the United States and Asia. We suggest that the reduced variability and low genetic structure identified in our study is a consequence of the recent introduction of this species in Manaus, possibly through a founder effect, followed by expansion throughout the city neighborhoods. Genetic similarity would therefore be due to insufficient time to have accumulated genetic differences between the populations of Ae. albopictus and not to extensive gene flow among them.

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Section: Discussionmentioning

confidence: 99%

Reduced levels of genetic variation in Aedes albopictus (Diptera: Culicidae) from Manaus, Amazonas State, Brazil, based on analysis of the mitochondrial DNA ND5 gene

Maia¹,

Scarpassa²,

Maciel-Litaiff³

et al. 2009

Genet. Mol. Res.

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“…Second, the gametic recapture, like assignment methods (e.g. Davies et al 1999), is not dependent on traditional population genetic assumptions about drift/mutation/ migration equilibrium (although the paternity calculations assume Hardy-Weinberg equilibrium, Marshall et al 1998). These advantages, however, can also be viewed as limitations.…”

Section: Reproductive Autonomy and Evolutionary Differentiationmentioning

confidence: 99%

Organismal and 'gametic' capture-recapture using microsatellite genotyping confirm low abundance and reproductive autonomy of humpback whales on the wintering grounds of New Caledonia

Garrigue¹,

Dodémont²,

Steel³

et al. 2004

Mar. Ecol. Prog. Ser.

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The abundance and reproductive autonomy of humpback whales from the New Caledonia (South Pacific) wintering grounds were investigated using capture-recapture models and paternity inference based on nuclear microsatellite genotyping, mitochondrial DNA sequencing, molecular sex identification and photographs of natural markings (photo-identification). The analyses included records of 213 individuals (excluding 16 calves used in paternity inference) identified by genotypes (9 loci), and 210 identified by fluke photographs, collected from 1995 to 2001. By comparing records of 175 individuals identified using both genotypes and photographs, a small number of errors were detected (and corrected) in the photo-identification catalogue and in the field and laboratory notes of the genotypes. Using the weighted mean of the Petersen capture-recapture model, the estimate of abundance based on genotyping (N = 533, CV = 0.15) was larger than the estimate based on photo-identification (N = 327, CV = 0.11). Sex-specific estimates of abundance based on genotypes were similar for males and females although the variance of the female estimate was greater than the male (N f = 248, CV = 0.30; N m = 288, CV = 0.18, respectively). The paternity of 5 calves from 16 sampled cow/calf pairs was inferred from the total sample of 133 non-calf males (one offspring each). The 16 sampled cow/calf pairs and the 5 inferred paternities were used for an alternate 'gametic recapture' estimate of male abundance. This gametic recapture estimate (N m = 379, CV = 0.30) was similar to the sex-specific estimate based on the organismal recapture using a 2-sample model (N m = 382, CV = 0.22). The close agreement of the organismal and gametic recapture estimates support the assumption that this humpback whale wintering ground represents an autonomous population unit that is relatively closed to demographic and reproductive interchange. The current low abundance of the New Caledonian breeding unit highlights the slow recovery of this and some other regional populations in the Southern Hemisphere following intensive 20th century commercial and illegal whaling.

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“…AMs use genetic information to ascertain population membership of individuals or groups of individuals. One approach, the 'assignment test' (AT; Box 1), has seen widespread use over the past decade [1][2][3][4][5][6][7]. More recent advances enable one to address questions such as, 'How many populations exist in my study area?'…”

mentioning

confidence: 99%

Assignment methods: matching biological questions with appropriate techniques

Manel

Gaggiotti

Waples

2005

Trends in Ecology & Evolution

649

684

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Times Cited: 83International audienceAssignment methods, which use genetic information to ascertain population membership of individuals or groups of individuals, have been used in recent years to study a wide range of evolutionary and ecological processes. In applied studies, the first step of articulating the biological question(s) to be addressed should be followed by selection of the method(s) best suited for the analysis. However, this first step often receives less attention than it should, and the recent proliferation of assignment methods has made the selection step challenging. Here, we review assignment methods and discuss how to match the appropriate methods with the underlying biological questions for several common problems in ecology and conservation (assessing population structure; measuring dispersal and hybridization; and forensics and mixture analysis). We also identify several topics for future research that should ensure that this field remains dynamic and productive

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Determining the source of individuals: multilocus genotyping in nonequilibrium population genetics

Cited by 197 publications

References 28 publications

Reduced levels of genetic variation in Aedes albopictus (Diptera: Culicidae) from Manaus, Amazonas State, Brazil, based on analysis of the mitochondrial DNA ND5 gene

Reduced levels of genetic variation in Aedes albopictus (Diptera: Culicidae) from Manaus, Amazonas State, Brazil, based on analysis of the mitochondrial DNA ND5 gene

Organismal and 'gametic' capture-recapture using microsatellite genotyping confirm low abundance and reproductive autonomy of humpback whales on the wintering grounds of New Caledonia

Assignment methods: matching biological questions with appropriate techniques

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