Four polymorphic microsatellite loci for the European wild rabbit, Oryctolagus cuniculus

Rico, Ciro; Rico, I.; Webb, Nicholas J.A.; Smith, Sophie; Bell, Diana; Hewitt, Godfrey M.

doi:10.1111/j.1365-2052.1994.tb00379.x

Cited by 60 publications

(29 citation statements)

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“…starcki , and 22 L . fagani for allelic variation at the following thirteen microsatellite loci: Sol08, Sol28, Sol30 Rico et al[88], Sol33 Surridge et al[89], Sat 2, Sat 8, and Sat 12 Mougel et al[90], Lsa 1, Lsa 2, Lsa 3, Lsa 6 and Lsa 8 Kryger[55], and INRACCDDV0001 (“Inra1”) Chantry-Darmon et al[91]; for PCR details see also Ben Slimen et al[37] and Suchentrunk et al [40,41]. PCR products were electrophoresed on a LI-COR 4200 automated sequencer along with fluorescently labelled size standard (30–350 bp sizing standard; LI-COR ® Biotechnology Division) and allele lengths were determined by the Gene ImageIR ver.…”

Section: Methodsmentioning

confidence: 99%

Mitochondrial and nuclear DNA reveals reticulate evolution in hares (Lepus spp., Lagomorpha, Mammalia) from Ethiopia

et al. 2017

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For hares (Lepus spp., Leporidae, Lagomorpha, Mammalia) from Ethiopia no conclusive molecular phylogenetic data are available. To provide a first molecular phylogenetic model for the Abyssinian Hare (Lepus habessinicus), the Ethiopian Hare (L. fagani), and the Ethiopian Highland Hare (L. starcki) and their evolutionary relationships to hares from Africa, Eurasia, and North America, we phylogenetically analysed mitochondrial ATPase subunit 6 (ATP6; n = 153 / 416bp) and nuclear transferrin (TF; n = 155 / 434bp) sequences of phenotypically determined individuals. For the hares from Ethiopia, genotype composition at twelve microsatellite loci (n = 107) was used to explore both interspecific gene pool separation and levels of current hybridization, as has been observed in some other Lepus species. For phylogenetic analyses ATP6 and TF sequences of Lepus species from South and North Africa (L. capensis, L. saxatilis), the Anatolian peninsula and Europe (L. europaeus, L. timidus) were also produced and additional TF sequences of 18 Lepus species retrieved from GenBank were included as well. Median joining networks, neighbour joining, maximum likelihood analyses, as well as Bayesian inference resulted in similar models of evolution of the three species from Ethiopia for the ATP6 and TF sequences, respectively. The Ethiopian species are, however, not monophyletic, with signatures of contemporary uni- and bidirectional mitochondrial introgression and/ or shared ancestral polymorphism. Lepus habessinicus carries mtDNA distinct from South African L. capensis and North African L. capensis sensu lato; that finding is not in line with earlier suggestions of its conspecificity with L. capensis. Lepus starcki has mtDNA distinct from L. capensis and L. europaeus, which is not in line with earlier suggestions to include it either in L. capensis or L. europaeus. Lepus fagani shares mitochondrial haplotypes with the other two species from Ethiopia, despite its distinct phenotypic and microsatellite differences; moreover, it is not represented by a species-specific mitochondrial haplogroup, suggesting considerable mitochondrial capture by the other species from Ethiopia or species from other parts of Africa. Both mitochondrial and nuclear sequences indicate close phylogenetic relationships among all three Lepus species from Ethiopia, with L. fagani being surprisingly tightly connected to L. habessinicus. TF sequences suggest close evolutionary relationships between the three Ethiopian species and Cape hares from South and North Africa; they further suggest that hares from Ethiopia hold a position ancestral to many Eurasian and North American species.

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Section: Methodsmentioning

confidence: 99%

Mitochondrial and nuclear DNA reveals reticulate evolution in hares (Lepus spp., Lagomorpha, Mammalia) from Ethiopia

et al. 2017

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“…These loci were developed for the European wild rabbit (Oryctolagus cuniculus-Sol03- Rico et al 1994;Sol44-Surridge et al 1997;Sat3, Sat7, Sat 12, Sat13-Mougel et al 1997 Korstanje et al 2003) and two South African hares (Lepus saxatilis and L. capensis-Lsa1, Lsa8- Kryger et al 2002). Samples were genotyped using fluorescent dye-labeled primers and an automated DNA sequencer (ABI 3130, Applied Biosystems, Foster City, CA).…”

Section: Sample Collection and Dna Extractionmentioning

confidence: 99%

Population genetic structure and history of fragmented remnant populations of the New England cottontail (Sylvilagus transitionalis)

et al. 2011

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The New England cottontail (Sylvilagus transitionalis) has suffered from extensive loss and fragmentation of its habitat and is now a species of conservation priority in the northeastern United States. Remnant New England cottontail populations currently occur in five geographically disjunct locations: southern Maine and southeastern New Hampshire (MENH); the Merrimack Valley in central New Hampshire (NH-MV); Cape Cod, Massachusetts (CC); parts of eastern Connecticut and Rhode Island (CTRI); and western Connecticut, southeastern New York and southwestern Massachusetts (CTNY). We used microsatellite genotyping to discern patterns of population structure, genetic variability, and demographic history across the species' range and to assess whether the observed patterns are a consequence of recent habitat loss and fragmentation. Our findings show that the geographic populations are highly differentiated (overall F ST = 0.145; P \ 0.001). Using Bayesian clustering analyses, we identified five genetic clusters, which corresponded closely to the geographic populations, but grouped MENH & NH-MV together (ME/NH) and identified an isolated population in eastern Connecticut (Bluff Point). The genetic clusters showed little evidence of recent gene flow and are highly influenced by genetic drift. The CC and Bluff Point populations show signs they experienced a genetic bottleneck, whereas the ME/NH population shows evidence of ongoing decline. Populations in Bluff Point, CC, and ME/NH also show significantly reduced genetic variation relative to the other clusters (CTNY and CTRI without Bluff Point). Without immediate human intervention, the short-term persistence of New England cottontail populations in Maine, New Hampshire and Cape Cod is at great risk. Conservation efforts at this time should focus on within-population sustainability and eventually restoring connectivity among these isolated populations.

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“…Eight microsatellite loci were amplified by PCR: SOL08, SOL28, SOL30 (Rico et al, 1994), SAT02, SAT05, SAT12 (Mougel et al, 1997), Lsa1 and Lsa2 (Kryger et al, 2002). PCR reaction was carried out in a total volume of 10 l, containing 1 l of extracted genomic DNA, 1 l of reaction buffer (10× buffer), 1 l dNTP (10 mM), 1 l of each primer (20 M) and 0.1 l of BioTherm TM DNA polymerase (5 U/l).…”

Section: Microsatellite Genotypingmentioning

confidence: 99%

MHC class II DQA gene variation across cohorts of brown hares (Lepus europaeus) from eastern Austria: Testing for different selection hypotheses

Campos¹,

Bellocq²,

Schaschl³

et al. 2011

Mammalian Biology

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a b s t r a c tWe have studied the temporal variation (1999)(2000)(2001)(2002)(2003)(2004)(2005)(2006)(2007) in the MHC class II DQA gene and 8 microsatellites across 8 cohorts in a population of brown hare (Lepus europaeus) from eastern Austria. Our results show no significant temporal changes in allele frequencies both in microsatellites and the DQA gene. Although positive selection on a larger evolutionary time scale has occurred in DQA, we have not observed evidence of contemporary balancing selection in this gene. Our results are not compatible with the negative frequency-dependent selection or the variable selection in time hypotheses within a timeframe of 8 consecutive generations. However, selection heterogeneity in space occurs. The studied cohorts have probably not been exposed to strong effects of parasites and pathogens during the period of this study, as indicated by our endoparasite counts and infection data. Furthermore, the most common DQA allele (Leeu-DQA*06) was found to be in a stable frequency equilibrium which is consistent with the occurrence of stabilizing selection. This could indicate that major selective agents have been rather constant in their frequency across our temporal samples.

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Four polymorphic microsatellite loci for the European wild rabbit, Oryctolagus cuniculus

Cited by 60 publications

References 1 publication

Mitochondrial and nuclear DNA reveals reticulate evolution in hares (Lepus spp., Lagomorpha, Mammalia) from Ethiopia

Mitochondrial and nuclear DNA reveals reticulate evolution in hares (Lepus spp., Lagomorpha, Mammalia) from Ethiopia

Population genetic structure and history of fragmented remnant populations of the New England cottontail (Sylvilagus transitionalis)

MHC class II DQA gene variation across cohorts of brown hares (Lepus europaeus) from eastern Austria: Testing for different selection hypotheses

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