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- Bouakaze, Caroline, et al.
(författare)
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Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex) : Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters
- 2020
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Ingår i: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 48
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Tidskriftsartikel (refereegranskat)abstract
- We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.
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| 2. |
- Poulet, Nicolas, et al.
(författare)
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Genetic structure and dynamics of a small introduced population : the pikeperch, Sander lucioperca, in the Rhone delta
- 2009
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Ingår i: Genetica. - : Springer Science and Business Media LLC. - 0016-6707 .- 1573-6857. ; 135:1, s. 77-86
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Tidskriftsartikel (refereegranskat)abstract
- Genetic data on introduced populations may help us to understand how these species succeed in colonising new territories. The pikeperch is a predatory fish widely introduced in Europe and has at times been considered as an invasive species. However, little is known about the genetics of both native and introduced populations. In the present study, we surveyed an introduced pikeperch population from the Rhone River delta, a habitat that has been highly modified for agricultural purposes. Using six microsatellites, we genotyped 93 individuals distributed among four hydraulically connected water bodies: the Rhone River, an irrigation canal, a drainage canal and a brackish lagoon. Population isolation were revealed by significant genetic distances and bottleneck highlighted by population monitoring. However, values of allelic richness and unbiased expected heterozygosity observed in these populations were similar, or even higher, compare to 18 native populations from the Baltic Sea drainage. It may be explained by multiple introductions in the Rhonee drainage but also by demographic strategy that would have facilitated population persistence in this fragmented habitat. Similarly, heterozygote deficits (revealed by F-IS values) have been detected, but were also found in native populations suggesting that mating among relatives could also result from a mating behavior of the species, maybe reinforce here by the reduced carrying capacity of the artificial canals and their respective isolation. Despite harsh environmental conditions and suspected inbreeding, the pikeperch has successfully maintained viable populations in the Rhone delta. Our study suggests that one of the factors in this invasive success, apart from its ecology, could be the maintenance of a good level of genetic diversity in introduced pikeperch populations. This genetic diversity probably stem from both its popularity as game fish and food resource which led to numerous stocking and an increasing propagule pressure and the reproductive strategy of the species.
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