1. Molecular identification of animal or plant species in fresh and degraded products (e.g. food, faeces, hair and other organic remains) has become a very important issue in both conservation ...biology and food science. 2. In this proof-of-concept study, we developed a microarray-based method using cytochrome b-derived probes to identify the main commercial and/or endangered vertebrate species in both food and forensic samples. 3. This method allowed the unambiguous identification of 71 out of 77 species tested. In the remaining six cases, identification was hampered due to false sequences deposited in GenBank and high intraspecific variability. Our evaluation of this DNA chip for routine control demonstrated its effectiveness for the simultaneous identification of at least five species, and that its sensitivity varied according to the type of sample analysed. 4. Synthesis and applications. Taken together, our results suggest that cytb-based microarray is a reliable and powerful identification tool for vertebrates, and more generally highlights the significant role of both molecular and traditional taxonomy in the development of molecular identification methods.
Morphological traits typical of Neanderthals began to appear in European hominids at least 400,000 years ago and about 150,000 years ago in western Asia. After their initial appearance, such traits ...increased in frequency and the extent to which they are expressed until they disappeared shortly after 30,000 years ago. However, because most fossil hominid remains are fragmentary, it can be difficult or impossible to determine unambiguously whether a fossil is of Neanderthal origin. This limits the ability to determine when and where Neanderthals lived. To determine how far to the east Neanderthals ranged, we determined mitochondrial DNA (mtDNA) sequences from hominid remains found in Uzbekistan and in the Altai region of southern Siberia. Here we show that the DNA sequences from these fossils fall within the European Neanderthal mtDNA variation. Thus, the geographic range of Neanderthals is likely to have extended at least 2,000 km further to the east than commonly assumed.
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DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid ...phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of EQUUS: In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.
In this study, we integrate osteometric and palaeogenetic data to investigate dog variability in the Roman Empire in Iberia and North Africa. Osteometry was used to distinguish the status—domestic or ...wild, of approximately 2000 years old Canis remains and to understand to what extent teeth and long bones varied in dogs in the Roman provinces of Mauretania Tingitana, Lusitania and Tarraconensis. High-throughput 454-DNA sequencing technology was used to obtain mitochondrial DNA (mtDNA) sequences from 15 bone and teeth samples. We identified five dog haplotypes from partial sequences of the hypervariable D-loop region. MtDNA haplotypes were grouped into two of the four major clades found in present-day dogs. We detected three clade A haplotypes in 12 samples from Portugal, Spain and Morocco, and a single clade D haplotype in 3 samples from Spain. So far, this is the oldest evidence for the presence of dog clade D in Iberia. It is dated to the late Roman occupation in the 4th-5th cent. AD (ca. 1,600 years ago).
Our results confirm the existence of distinct dog morphotypes in Roman times that also harboured distinct genetic lineages. According to our data, dogs from distinct mtDNA lineages (clades A and D) have been continuously bred in the Iberian Peninsula since at least 1600 years ago. Moreover, the sharing of matrilines between dogs from Spain and North Africa may indicate gene flow. Dogs could have been easily transported between these regions by humans along maritime and terrestrial trade routes. These results provide new insights into pre-Roman and Roman domestication practices, confirming selection practices were extensively applied to dogs during the first centuries of our era in the Iberian Peninsula. We show that the greater size variability of teeth length (and consequently cranium) and long bone breadths (and consequently phenotype) of Roman dogs in the Iberian Peninsula, is concomitant with the detection of diverse and rare maternal lineages. This would reflect an intensification of dog breeding and the use of non-local dogs for breeding.
The genetic diversity of present‐day brown bears (Ursus arctos) has been extensively studied over the years and appears to be geographically structured into five main clades. The question of the past ...diversity of the species has been recently addressed by ancient DNA studies that concluded to a relative genetic stability over the last 35 000 years. However, the post‐last glacial maximum genetic diversity of the species still remains poorly documented, notably in the Old World. Here, we analyse Atlas brown bears, which became extinct during the Holocene period. A divergent brown bear mitochondrial DNA lineage not present in any of the previously studied modern or ancient bear samples was uncovered, suggesting that the diversity of U. arctos was larger in the past than it is now. Specifically, a significant portion (with respect to sequence divergence) of the intraspecific diversity of the brown bear was lost with the extinction of the Atlas brown bear after the Pleistocene/Holocene transition.
New polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA). However, ...classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. Here, we characterize the extent of such possible biases using serial coalescent simulations.
We first use a coalescent framework to generate datasets assuming no or different levels of heterochrony and contrast most classical population genetic statistics. We show that even weak levels of heterochrony ( approximately 10% of the average depth of a standard population tree) affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism theta, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck). Substantial departures of the tests are detected in the opposite direction for more heterochroneous and equilibrated datasets, with balanced trees mimicking in particular population contraction, balancing selection, and population differentiation. We therefore introduce simple corrections to classical estimators of polymorphism and of the genetic distance between populations, in order to remove heterochrony-driven bias. Finally, we show that these effects do occur on real aDNA datasets, taking advantage of the currently available sequence data for Cave Bears (Ursus spelaeus), for which large mtDNA haplotypes have been reported over a substantial time period (22-130 thousand years ago (KYA)).
Considering serial sampling changed the conclusion of several tests, indicating that neglecting heterochrony could provide significant support for false past history of populations and inappropriate conservation decisions. We therefore argue for systematically considering heterochroneous models when analyzing heterochroneous samples covering a large time scale.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Middle East brown bears (Ursus arctos syriacus Hemprich and Ehrenberg, 1828) are presently on the edge of extinction. However, little is known of their genetic diversity. This study investigates that ...question as well as that of Middle East brown bear relationships to surrounding populations of the species. Middle East region of south-western Asia. We performed DNA analyses on 27 brown bear individuals. Twenty ancient bone samples (Late Pleistocene to 20th century) from natural populations and seven present-day samples obtained from captive individuals were analysed. Phylogenetic analyses of the mitochondrial sequences obtained from seven ancient specimens identify three distinct maternal clades, all unrelated to one recently described from North Africa. Brown bears from Iran exhibit striking diversity (three individuals, three haplotypes) and form a unique clade that cannot be linked to any extant one. Individuals from Syria belong to the Holarctic clade now observed in Eastern Europe, Turkey, Japan and North America. Specimens from Lebanon surprisingly appear as tightly linked to the clade of brown bears now in Western Europe. Moreover, we show that U. a. syriacus in captivity still harbour haplotypes closely linked to those found in ancient individuals. This study brings important new information on the genetic diversity of brown bear populations at the crossroads of Europe, Asia and Africa. It reveals a high level of diversity in Middle East brown bears and extends the historical distribution of the Western European clade to the East. Our analyses also suggest the value of a specific breeding programme for captive populations.
The analysis of ancient or processed DNA samples is often a great challenge, because traditional Polymerase Chain Reaction - based amplification is impeded by DNA damage. Blocking lesions such as ...abasic sites are known to block the bypass of DNA polymerases, thus stopping primer elongation. In the present work, we applied the SERRS-hybridization assay, a fully non-enzymatic method, to the detection of DNA refractory to PCR amplification. This method combines specific hybridization with detection by Surface Enhanced Resonant Raman Scattering (SERRS). It allows the detection of a series of double-stranded DNA molecules containing a varying number of abasic sites on both strands, when PCR failed to detect the most degraded sequences. Our SERRS approach can quickly detect DNA molecules without any need for DNA repair. This assay could be applied as a pre-requisite analysis prior to enzymatic reparation or amplification. A whole new set of samples, both forensic and archaeological, could then deliver information that was not yet available due to a high degree of DNA damage.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We have used a paleogenetics approach to investigate the genetic landscape of coat color variation in ancient Eurasian dog and wolf populations. We amplified DNA fragments of two genes controlling ...coat color, Mc1r (Melanocortin 1 Receptor) and CBD103 (canine-β-defensin), in respectively 15 and 19 ancient canids (dogs and wolf morphotypes) from 14 different archeological sites, throughout Asia and Europe spanning from ca. 12 000 B.P. (end of Upper Palaeolithic) to ca. 4000 B.P. (Bronze Age). We provide evidence of a new variant (R301C) of the Melanocortin 1 receptor (Mc1r) and highlight the presence of the beta-defensin melanistic mutation (CDB103-K locus) on ancient DNA from dog-and wolf-morphotype specimens. We show that the dominant K(B) allele (CBD103), which causes melanism, and R301C (Mc1r), the variant that may cause light hair color, are present as early as the beginning of the Holocene, over 10,000 years ago. These results underline the genetic diversity of prehistoric dogs. This diversity may have partly stemmed not only from the wolf gene pool captured by domestication but also from mutations very likely linked to the relaxation of natural selection pressure occurring in-line with this process.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Equus hydruntinus inhabited Europe and the Middle East for more than 300 000 years. For a long time, palaeontological data failed to place E. hydruntinus into the equid phylogenetic tree, confronted ...with the fact that it shares primitive Equus characters with both zebras and asses, and derived characters with asses and hemiones. However, the study of a recently discovered skull points to a relationship with hemiones. Extraction of DNA from ancient samples from Crimea (E. hydruntinus) and Iran (E. cf. hydruntinus) yielded 134–288 bp of the mtDNA control region and 143 bp of the cytochrome b gene. This DNA analysis supports the proximity of E. hydruntinus and Equus hemionus suggested by skull and limb bone analyses, and rejects proximity to either Equus burchelli or the asses suggested by tooth morphology. Dental morphology may thus be of poor taxonomical value if used alone for establishing equid phylogenetic relationships. Furthermore, the small genetic distance between E. cf. hydruntinus of Iran and the classical E. hydruntinus of Crimea suggests that both samples belong to the same species. Accordingly, the geographic range of E. hydruntinus— until now believed to be restricted to Europe, Israel, and Turkey — can be extended towards East as far as Iran.
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