Isolation and characterization of six polymorphic microsatellite loci for the Malagasy spider tortoise, Pyxis arachnoides and cross-amplification in Pyxis planicauda

Orozco‐terWengel, Pablo; Chiari, Ylenia; Vieites, David R.; Pedrono, Miguel; Louis, Edward E.

doi:10.1163/15685381-00002866

Cited by 7 publications

(7 citation statements)

References 9 publications

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“…Extracted genomic DNA was used as template DNA in the PCR. Twenty two microsatellite DNA loci, which were successful in previous testudines population genetics studies [115][116][117][118][119][120][121] were tested. They were tested on the target animal using PCR, with all forward primers labelled fluorescently with different dye probes (primer details and optimal annealing temperatures are given in Additional file 7: Table S14).…”

Section: Microsatellite Dna Genotypingmentioning

confidence: 99%

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

et al. 2020

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Background Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa. Results We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group. Conclusion Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-A.

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Section: Microsatellite Dna Genotypingmentioning

confidence: 99%

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

et al. 2020

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“…Extracted genomic DNA was used as template DNA in the PCR. Twenty two microsatellite DNA loci, which were successful in previous testudines population genetics studies [114,115,116,117,118,119,120) were tested. They were tested on the target animal using PCR, with all forward primers labelled uorescently with different dye probes (primer details and optimal annealing temperatures are given in Supplementary Table S14).…”

Section: Microsatellite Dna Genotypingmentioning

confidence: 99%

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of tent tortoise (Psammobates tentorius) species complex in Southern Africa

Zhao

Heideman

Bester

et al. 2020

Preprint

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Background Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots of in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa.Results We investigated genetic structure, population dynamics, and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group. Conclusion Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis, population dynamics, and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the population dynamics of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly C1–C3, C5 and C6.

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“…The cross-amplification of nonspecific markers (i.e., markers designed for a different species but can be amplified in a taxon of interest) may reduce genotyping costs, allowing the development of population genetic studies in otherwise uncharacterized taxa. A high rate of cross-amplification has already been reported for many animal species, such as tortoises (Orozco-terWengel et al, 2013), apes (Deka et al, 1994), canids (Fontoura-Rodrigues et al, 2008), and ungulates (Leite et al, 2007;Shafer et al, 2012). The rate of cross-amplification in Artiodactyla is surprisingly high, even between different families (e.g., Cervidae and Bovidae), indicating high genome similarity (Leite et al, 2007).…”

Section: Introductionmentioning

confidence: 91%

Cross-amplification of nonspecific microsatellites markers: a useful tool to study endangered/vulnerable species of southern Andes deer

Marín¹,

Orozco‐terWengel²,

Romero³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Thirty-nine microsatellite loci that are highly conserved in red deer, sika deer, reindeer, Soay sheep, and other artiodactyls were tested in two vulnerable and endangered Neotropical deer (pudu: Pudu puda and huemul: Hippocamelus bisulcus) with the aim of producing a standardized set of markers that can be used successfully in noninvasive samples from these species. We also compared these nonspecific loci against eight polymorphic loci that were recently developed for huemul to determine whether the nonspecific markers could reflect the huemul's genetic variation that was observed with the specific loci. We identified 10 suitable loci, six of which constitute a standardized set for the two species and can be used to identify them in the absence of phenotypic data. The expected heterozygosity per locus for the panel of six loci ranged from 0.461 to 0.889 (average 0.665), and the maximum probability of identity value was 6.9 x 10 -6 and 3.2 x 10 -4 in pudu and huemul, respectively. This set of loci has potential applications in evolutionary, ecological, forensic, and conservation studies in pudu and huemul.

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Isolation and characterization of six polymorphic microsatellite loci for the Malagasy spider tortoise, Pyxis arachnoides and cross-amplification in Pyxis planicauda

Cited by 7 publications

References 9 publications

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of tent tortoise (Psammobates tentorius) species complex in Southern Africa

Cross-amplification of nonspecific microsatellites markers: a useful tool to study endangered/vulnerable species of southern Andes deer

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