Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus , and brown bear, Ursus arctos , lineages

Abstract

The cave bear, Ursus spelaeus, represents one of the most frequently found paleontological remains from the Pleistocene in Europe. The species has always been confined to Europe and was contemporary with the brown bear, Ursus arctos. Relationships between the cave bear and the two lineages of brown bears defined in Europe, as well as the origins of the two species, remain controversial, mainly due to the wide morphological diversity of the fossil remains, which makes interpretation difficult [1, 2]. Sequence analysis of ancient DNA is a useful tool for resolving such problems because it provides an independent source of data [3]. We previously amplified a short DNA fragment of the mitochondrial DNA control region (mt control region) of a 40,000-year-old Ursus spelaeus sample [4]. In this paper, we describe the DNA analysis of two mtDNA regions, the control region and the cytochrome b gene. Control region sequences were obtained from ten samples of cave bears ranging from 130,000 to 20,000 years BP, and one particularly well-conserved sample gave a complete cyt b sequence. Our data demonstrate that cave bears split largely before the lineages of brown bears around 1.2 million years ago. Given its abundance, its wide distribution in space and time, and its large morphological diversity, the cave bear is a promising model for direct observation of the evolution of sequences throughout time, extinction periods, and the differentiation of populations shaped by climatic fluctuations during the Pleistocene.

Divergent mtDNA lineages of goats in an Early Neolithic site, far from the initial domestication areas

“…4 and 5 and Table 3, which are published as supporting information on the PNAS web site). The high rate of success (83%) indicates good preservation of ancient DNA in the samples, which is exceptional although not surprising because of their origin from a cave-like deposit (27)(28)(29)(30).…”

Typing single polymorphic nucleotides in mitochondrial DNA as a way to access Middle Pleistocene DNA

“…However, when higher stringency was applied to these types of study, it became evident that several of the oldest DNA sequences were based on contaminating DNA (Zischler et al 1995;Austin et al 1997). Most ancient DNA sequences that have been thoroughly authenticated are less than 100 000 years, with only a few exceptions (Loreille et al 2001;Willerslev et al 2003). The number of copies should increase with decreased fragment size, as DNA in ancient tissue is degraded (Smith et al 2003;Noonan et al 2005).…”

“…These two lineages diverged in Eurasia about 1.2 million years ago (Loreille et al 2001), and their common ancestor has been suggested to be the so-called Etruscan bear, Ursus etruscus (Soergel 1912). Ursus dolinensis has been recently suggested to represent the earliest member of the speleoid lineage (García & Arsuaga 2001).…”

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

“…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. However, considering the accumulating evidence demonstrating that long sequences are often necessary to obtain correct phylogenies (5), it is highly desirable to better characterize the cave bear mitochondrial genome.…”