Tracking the origins of the cave bear (Ursus spelaeus) by mitochondrial DNA sequencing.

Hänni, Catherine; Laudet, Vincent; Stéhelin, D; Taberlet, Pierre

doi:10.1073/pnas.91.25.12336

Cited by 93 publications

(60 citation statements)

References 18 publications

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“…PCR conditions consisted of an 11-min activation step at 95°C followed by 55 cycles at 94°C for 30 s, corresponding annealing temperature for 30 s and 74°C for 30 s. All samples, with the exception of Aketegi II, Maza Cotina, La Paloma, and Villavieja, were amplified by using primers URSUSF1 136 -156/URSUSR1 273-290, OP54, and OP55. DNA of these four samples was amplified by using primers L16164/H16299 (31). This procedure was carried out as part of a previous study, and extracts were not available for secondary amplifications using the other primer sets used in this study.…”

Section: Dna Extraction From Ancient Brown Bears Samples (Ua1-ua4)mentioning

confidence: 99%

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Surprising migration and population size dynamics in ancient Iberian brown bears ( Ursus arctos )

Valdiosera

García-Garitagoitia

Garcı́a

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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The endangered brown bear populations (Ursus arctos) in Iberia have been suggested to be the last fragments of the brown bear population that served as recolonization stock for large parts of Europe during the Pleistocene. Conservation efforts are intense, and results are closely monitored. However, the efforts are based on the assumption that the Iberian bears are a unique unit that has evolved locally for an extended period. We have sequenced mitochondrial DNA (mtDNA) from ancient Iberian bear remains and analyzed them as a serial dataset, monitoring changes in diversity and occurrence of European haplogroups over time. Using these data, we show that the Iberian bear population has experienced a dynamic, recent evolutionary history. Not only has the population undergone mitochondrial gene flow from other European brown bears, but the effective population size also has fluctuated substantially. We conclude that the Iberian bear population has been a fluid evolutionary unit, developed by gene flow from other populations and population bottlenecks, far from being in genetic equilibrium or isolated from other brown bear populations. Thus, the current situation is highly unusual and the population may in fact be isolated for the first time in its history.bottleneck ͉ gene flow ͉ mitochondrial DNA ͉ ancient DNA ͉ serial coalescent simulations

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Section: Dna Extraction From Ancient Brown Bears Samples (Ua1-ua4)mentioning

confidence: 99%

“…Primers used were L16164 and H16299 from ref. 31. In this case, when conflict was observed among the data, a majority rule consensus was applied, considering two of three the correct sequence for analysis.…”

Section: Dna Extraction From Ancient Brown Bears Samples (Ua1-ua4)mentioning

confidence: 99%

Surprising migration and population size dynamics in ancient Iberian brown bears ( Ursus arctos )

Valdiosera

García-Garitagoitia

Garcı́a

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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“…Thus, the complete cycle was as follows: 94 C, 1 min; hybridization at 55-37 C, 1 min; 72 C, 1 min; 40 cycles. To avoid contamination, all of the RT-PCR reactions as well as RNA extraction were conducted in a special nucleic-acidfree room under positive air pressure and using specific reagents (Safi et al 1997, Hänni et al 1994. For each pair of primers used, we prepared a control reaction (without DNA) to check that our PCR reactions were not contaminated (in order to avoid spurious amplification of TRs from mammals routinely used in our laboratory).…”

Section: Ti(a/g)tg(c/t)ttic(g/t)g(a/t)a(a/g)tt(a/g)atmentioning

confidence: 99%

Molecular cloning and characterization of thyroid hormone receptors in teleost fish

Marchand¹,

Safi²,

Escrivà³

et al. 2001

Journal of Molecular Endocrinology

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108

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Thyroid hormones are pleiotropic factors important for many developmental and physiological functions in vertebrates. Their effects are mediated by two specific receptors (TR and TR ) which are members of the nuclear hormone receptor superfamily. To clarify the function of these receptors, our laboratory has started a comparative study of their role in teleost fish. This type of approach has been hampered by the isolation of specific clones for each fish species studied. In this report, we describe an efficient reverse transcription/PCR procedure that allows the isolation of large fragments corresponding to TR and TR of a wide range of teleost fish. Phylogenetic analysis of these receptors revealed a placement consistent with their origin, sequences from teleost fish being clearly monophyletic for both TR and TR . Interestingly, this approach allowed us to isolate (from tilapia and salmon) several new TR or TR isoforms resulting from alternative splicing. These isoforms correspond to expressed transcripts and thus may have an important physiological function. In addition, we isolated a cDNA encoding TR in the Atlantic salmon (Salmo salar) encoding a functional thyroid hormone receptor which binds specific thyroid hormone response elements and regulates transcription in response to thyroid hormones.

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“…The subterranean milieu ensures stable temperature (12-15°C) conditions, away from UV irradiation, but is still less favorable than permafrost for DNA preservation. Consequently, cave bear mitochondrial genome fragments have only been retrieved as short sequences that up to now could be assembled into a partial control region and a single protein coding gene (11,12), which together span Ͻ10% of the expected 17 kb mitochondrial genome. Phylogenetic analysis carried out using the available sequence information (12)(13)(14) supported one hypothesis drawn from morphometric studies of fossil records (10) arguing for an early split of the cave bear from the brown bear lineage.…”

mentioning

confidence: 99%

Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet

Bon

Caudy

Dieuleveult

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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Retrieving a large amount of genetic information from extinct species was demonstrated feasible, but complete mitochondrial genome sequences have only been deciphered for the moa, a bird that became extinct a few hundred years ago, and for Pleistocene species, such as the woolly mammoth and the mastodon, both of which could be studied from animals embedded in permafrost. To enlarge the diversity of mitochondrial genomes available for Pleistocene species, we turned to the cave bear (Ursus spelaeus), whose only remains consist of skeletal elements. We collected bone samples from the Paleolithic painted cave of Chauvet-Pont d'Arc (France), which displays the earliest known human drawings, and contains thousands of bear remains. We selected a cave bear sternebra, radiocarbon dated to 32,000 years before present, from which we generated overlapping DNA fragments assembling into a 16,810-base pair mitochondrial genome. Together with the first mitochondrial genome for the brown bear western lineage, this study provides a statistically secured molecular phylogeny assessing the cave bear as a sister taxon to the brown bear and polar bear clade, with a divergence inferred to 1.6 million years ago. With the first mitochondrial genome for a Pleistocene carnivore to be delivered, our study establishes the Chauvet-Pont d'Arc Cave as a new reservoir for Paleogenetic studies. These molecular data enable establishing the chronology of bear speciation, and provide a helpful resource to rescue for genetic analysis archeological samples initially diagnosed as devoid of amplifiable DNA.ancient DNA ͉ pleistocene ͉ Ursus spelaeus

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Tracking the origins of the cave bear (Ursus spelaeus) by mitochondrial DNA sequencing.

Cited by 93 publications

References 18 publications

Surprising migration and population size dynamics in ancient Iberian brown bears ( Ursus arctos )

Surprising migration and population size dynamics in ancient Iberian brown bears ( Ursus arctos )

Molecular cloning and characterization of thyroid hormone receptors in teleost fish

Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet

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