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Title |
The limitations of kinship determinations using STR data in ill-defined populations |
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2020 |
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International Journal of Legal Medicine |
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134 |
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6 |
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1981-1990 |
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Abstract |
The likelihood ratio (LR) method is commonly used to determine kinship in civil, criminal, or forensic cases. For the past 15 years, our research group has also applied LR to ancient STR data and obtained kinship results for collections of graves or necropolises. Although we were able to reconstruct large genealogies, some pairs of individuals showed ambiguous results. Second-degree relationships, half-sibling pairs for example, were often inconsistent with detected first-degree relationships, such as parent/child or brother/sister pairs. We therefore set about providing empirical estimations of the error rates for the LR method in living populations with STR allelic diversities comparable to that of the ancient populations we had previously studied. We collected biological samples in the field in North-Eastern Siberia and West Africa and studied more than 800 pairs of STR profiles from individuals with known relationships. Because commercial STR panels were constructed for specific regions (namely Europe and North America), their allelic makeup showed a significant deficit in diversity when compared to European populations, replicating a situation often faced in ancient DNA studies. We assessed the capacity of the LR method to confirm known relationships (effectiveness) and its capacity to detect those relationships (reliability). Concerns over the effectiveness of LR determinations are mostly an issue in forensic studies, while the reliability of the detection of kinship is an issue for the study of necropolises or other large gatherings of unidentified individuals, such as disaster victims or mass graves. We show that the application of LR to both test populations highlights specific issues (both false positives and false negatives) that prevent the confirmation of second-degree kinship or even full siblingship in small populations. Up to 29% of detected full sibling relationships were either overestimated half-sibling relationships or underestimated parent-offspring relationships. The error rate for detected half-sibling relationships was even higher, reaching 41%. Only parent-offspring pairs were reliably detected or confirmed. This implies that, in populations that are small, ill-defined, or for which the STR loci analyzed are inappropriate, an examiner might not be able to distinguish a pair of full siblings from a pair of half-siblings. Furthermore, half-sibling pairs might be overlooked altogether, an issue that is exacerbated by the common confusion, in many languages and cultures, between half-siblings and full siblings. Consequently, in the study of ancient populations, human remains of unknown origins, or poorly surveyed modern populations, we recommend a conservative approach to kinship determined by LR. Next-generation sequencing data should be used when possible, but the costs and technology involved might be prohibitive. Therefore, in potentially contentious situations or cases lacking sufficient external information, uniparental markers should be analyzed: ideally, complete mitochondrial genomes and Y-chromosome haplotypes (STR, SNP, and/or sequencing). |
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1437-1596 |
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8059 |
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Author |
Clark Melody S, Thorne Michael A S, Toullec Jean-Yves, Meng Yan, Guan Le Luo, Peck Lloyd S, Moore Stephen, |
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Title |
Antarctic krill 454 pyrosequencing reveals chaperone and stress transcriptome.
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2011 |
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PloS one |
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6 |
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1 |
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e15919 -e15919 |
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The Antarctic krill Euphausia superba is a keystone species in the Antarctic food chain. Not only is it a significant grazer of phytoplankton, but it is also a major food item for charismatic megafauna such as whales and seals and an important Southern Ocean fisheries crop. Ecological data suggest that this species is being affected by climate change and this will have considerable consequences for the balance of the Southern Ocean ecosystem. Hence, understanding how this organism functions is a priority area and will provide fundamental data for life history studies, energy budget calculations and food web models.
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444 |
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2010 |
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yes |
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2616 |
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Author |
Lorenzo Ricci |
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2011 |
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Isolation, temperature and thermal steadiness provided by Antarctic Ocean make it a particularly favourable environment for studying of genetic adaptations to cold and stenothermy. The impact, on a very long-range, of Antarctic climate, has led, for several species, to the loss of the universal Heat Shock Response (HSR). Such an evolution results, on the molecular level, from changes in function and/or nature of Hsps, especially in the subfamily of Hsps70. The characterization of three Hsps70 genes and, at least, one Hsp90 in krill Euphausia superba, a key-species of this regional trophic web, authorized a functional study, involving RT-qPCR technics, of Hsps regulation in response to a heat stress. This approach showed the preservation of the HSR in E. superba, despite the fact that this species inhabits Antarctic Ocean for several million years. Even though conditions for transcriptional inducibility or constitutivity remain hard to determine, especially for Hsps70, results from E. superba experiments, juxtaposed to current knowledge about krill ecology and physiology, led to hypothesis about HSR preservation in a thermally cold and steady environment. These findings can also be of great interest for larger studies about global warming impact on Antarctic fauna. A parallel study at structural and phylogenetic level led to confirm functional results. |
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1039 |
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yes |
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3730 |
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Author |
Toullec JY, Clark M, Kawaguchi S,Tanguy A. & Jollivet D. |
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Title |
Krill responses to environmental temperature variations |
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Conference - International - Poster |
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2011 |
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Communication at the Krill in Changing Ocean WOrkshop: Texel May 2011 |
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1039 |
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3731 |
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Lorenzo RICCI, Melody CLARK, So KAWAGUCHI, Arnaud TANGUY and Jean-Yves TOULLEC |
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Responses of Antarctic krill (Euphausia superba) to variations of environmental temperature. CAREX Conference on Life in Extreme Environments, Dublin, Ireland: 18-20 October 2011 |
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2011 |
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1039 |
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3789 |
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Flores H, Atkinson A, Kawaguchi S, Krafft B A, Milinevsky G, Nicol S, Reiss C, Tarling G A, Werner R, Rebolledo E Bravo, Cirelli V, CuzinRoudy J, Fielding S, Groeneveld J J, Haraldsson M, Lombana A, Marschoff E, Meyer B, Pakhomov E A, Rombol E, Schmidt K, Siegel V, Teschke M, Tonkes H, Toullec J Y, Trathan P N, Tremblay N, Putte A P Van de, Franeker J A van, Werner T, |
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Impact of climate change on Antarctic krill
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2012 |
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MARINE ECOLOGY-PROGRESS SERIES |
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0171-8630 |
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458 |
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1-19 |
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1039 |
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4294 |
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Toullec JY, Hourdez S., Lallier F.H. et Jollivet D. |
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2012 |
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BIOFUTUR |
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336 |
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40-43 |
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1039 |
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0294-3506 |
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4295 |
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Claire Papot |
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2012 |
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4296 |
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Jean-Yves TOULLEC |
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Conference - International - Communication |
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2012 |
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4297 |
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