Mapping the geographic origin of captive and confiscated Hermann’s tortoises: A genetic toolkit for conservation and forensic analyses

Biello, Roberto; Zampiglia, Mauro; Corti, Claudia; Deli, Gianluca; Biaggini, Marta; Crestanello, Barbara; Delaugerre, Michel; Tizio, Luciano Di; Leonetti, Francesco Luigi; Casari, Stefano; Olivieri, Oliviero; Pellegrino, Francesco; Romano, Antonio; Sperone, Emilio; Hauffe, Heidi C.; Trabalza‐Marinucci, Massimo; Bertorelle, Giorgio; Canestrelli, Daniele

doi:10.1016/j.fsigen.2020.102447

Cited by 16 publications

(54 citation statements)

References 46 publications

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“…Assigning individuals to their area of origin was highly accurate (100%) when we considered samples from wild populations. These results were also confirmed by using a panel of STR markers (Biello et al, 2021). This is in accordance with previous studies, which showed that reduced panels of highly informative SNPs (<100 SNPs) performed as well as or better than the traditional number (10-20) of STR loci used for individual identification (e.g., Glover et al, 2010).…”

Section: Test Of the Snp Panelsupporting

confidence: 91%

“…Within the T. h. hermanni group, six distinct clusters were identified: Italian Peninsula (ITP), North Calabria (NCA), Central Calabria (CCA), South Calabria (SCA), Sicily (SIC) and Sardinia (SAR). These results support a finer genetic structure than previously suggested using STRs (Biello et al, 2021;Perez et al, 2014). More specifically, SNPs allowed the identification of three clusters within the Calabria region (NCA, CCA, SCA) and a distinction between Sicily and Sardinia (SIC, SAR) (Figure 1b).…”

Section: Genetic Structure With Ddrad-seq and Comparison With Strssupporting

confidence: 88%

“…Furthermore, we performed assignment analysis using 7 STR loci on a subset of samples (68 samples) for which STR data were already available using the same methods and parameters used for the SNPs data. The STR database developed in Biello et al (2021) was used as a reference. Populations not included in the ddRAD-seq experiment were removed (e.g., France).…”

Section: Test and Validation Of The Snp Panelmentioning

confidence: 99%

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From STRs to SNPs via ddRAD-seq: geographic assignment of confiscated tortoises at reduced costs

Biello

Zampiglia

Fuselli

et al. 2021

Preprint

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Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost-effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD-seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3,182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro-area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re-assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than €15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in-situ of confiscated animals and their possible re-allocation in the wild. Our methodological pipeline can easily be extended to other species.

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Section: Test Of the Snp Panelsupporting

confidence: 91%

Section: Genetic Structure With Ddrad-seq and Comparison With Strssupporting

confidence: 88%

Section: Test and Validation Of The Snp Panelmentioning

confidence: 99%

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From STRs to SNPs via ddRAD-seq: geographic assignment of confiscated tortoises at reduced costs

Biello

Zampiglia

Fuselli

et al. 2021

Preprint

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“…This problem that has been resolved through the exchange of reference samples has been recently fixed by the set-up of an allelic ladder [60]. According to these authors, we constructed an allelic ladder for each locus to standardize a protocol between laboratories for conservation and forensic purposes.…”

Section: Discussionmentioning

confidence: 99%

Cross-Amplification in Strigiformes: A New STR Panel for Forensic Purposes

Giangregorio

Naldi

Mengoni

et al. 2021

Genes

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Strigiformes are affected by a substantial decline mainly caused by habitat loss and destruction, poaching, and trapping. Moreover, the increasing trend in bird trade and the growing interest in wild-caught rather than captive-bred birds are expected to encourage illegal trade. The biomolecular investigation represents a valuable tool to track illegal trade and to explore the genetic variability to preserving biodiversity. Microsatellite loci (STRs) are the most used markers to study genetic variability. Despite the availability of species-specific microsatellite loci in Strigiformes, a unique panel permitting the description of the genetic variability across species has not been identified yet. We tested 32 highly polymorphic microsatellite markers to evaluate the reliability of a unique microsatellite panel in different species of Strigiformes and its use for conservation and forensic purposes. We included in the study 84 individuals belonging to 28 parental groups and 11 species of Strigiformes. After screening polymorphic microsatellite loci, the description of genetic variability, and the kinship assessment, we characterized a final panel of 12 microsatellite loci able to identify individuals in 9 Strigiformes species. This STR panel might support the authorities in the forensic investigation for suspected smugglers and false parental claims; moreover, it can be useful to evaluate relatedness among individuals in captive-bred populations and to implement research projects finalized to the description of the genetic variability in wild populations.

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“…An example is Herman's tortoise (Testudo hermanni), that used to span much of the northern Mediterranean countries. To ensure that seized tortoise are correctly relocated to their correct geographical range, a panel of STR markers were applied for geographical provenance [22].…”

Section: Wildlife Str Typingmentioning

confidence: 99%

Animal Forensic Genetics

Linacre

2021

Genes

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Animal forensic genetics, where the focus is on non-human species, is broadly divided in two: domestic species and wildlife. When traces of a domestic species are relevant to a forensic investigation the question of species identification is less important, as the material comes from either a dog or a cat for instance, but more relevant may be the identification of the actual pet. Identification of a specific animal draws on similar methods to those used in human identification by using microsatellite markers. The use of cat short tandem repeats to link a cat hair to a particular cat paved the way for similar identification of dogs. Wildlife forensic science is becoming accepted as a recognised discipline. There is growing acceptance that the illegal trade in wildlife is having devasting effects on the numbers of iconic species. Loci on the mitochondrial genome are used to identify the most likely species present. Sequencing the whole locus may not be needed if specific bases can be targeted. There can be benefits of increased sensitivity using mitochondrial loci for species testing, but occasionally there is an issue if hybrids are present. The use of massively parallel DNA sequencing has a role in the identification of the ingredients of traditional medicines where studies found protected species to be present, and a potential role in future species assignments. Non-human animal forensic testing can play a key role in investigations provided that it is performed to the same standards as all other DNA profiling processes.

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Mapping the geographic origin of captive and confiscated Hermann’s tortoises: A genetic toolkit for conservation and forensic analyses

Cited by 16 publications

References 46 publications

From STRs to SNPs via ddRAD-seq: geographic assignment of confiscated tortoises at reduced costs

From STRs to SNPs via ddRAD-seq: geographic assignment of confiscated tortoises at reduced costs

Cross-Amplification in Strigiformes: A New STR Panel for Forensic Purposes

Animal Forensic Genetics

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