Mammoth and Elephant Phylogenetic Relationships: Mammut Americanum, the Missing Outgroup

At the morphological level, the woolly mammoth has most often been considered as the sister-species of Asian elephants, but at the DNA level, different studies have found support for proximity with African elephants. Recent reports have increased the available sequence data and apparently solved the discrepancy, finding mammoths to be most closely related to Asian elephants. However, we demonstrate here that the three competing topologies have similar likelihood, bayesian and parsimony supports. The analysis further suggests the inadequacy of using Sirenia or Hyracoidea as outgroups. We therefore argue that orthologous sequences from the extinct American mastodon will be required to definitively solve this long-standing question

DNA from extinct giant lemurs links archaeolemurids to extant indriids

<p>Abstract</p> <p>Background</p> <p>Although today 15% of living primates are endemic to Madagascar, their diversity was even greater in the recent past since dozens of extinct species have been recovered from Holocene excavation sites. Among them were the so-called "giant lemurs" some of which weighed up to 160 kg. Although extensively studied, the phylogenetic relationships between extinct and extant lemurs are still difficult to decipher, mainly due to morphological specializations that reflect ecology more than phylogeny, resulting in rampant homoplasy.</p> <p>Results</p> <p>Ancient DNA recovered from subfossils recently supported a sister relationship between giant "sloth" lemurs and extant indriids and helped to revise the phylogenetic position of <it>Megaladapis edwardsi </it>among lemuriformes, but several taxa – such as the Archaeolemuridae – still await analysis. We therefore used ancient DNA technology to address the phylogenetic status of the two archaeolemurid genera (<it>Archaeolemur </it>and <it>Hadropithecus</it>). Despite poor DNA preservation conditions in subtropical environments, we managed to recover 94- to 539-bp sequences for two mitochondrial genes among 5 subfossil samples.</p> <p>Conclusion</p> <p>This new sequence information provides evidence for the proximity of <it>Archaeolemur </it>and <it>Hadropithecus </it>to extant indriids, in agreement with earlier assessments of their taxonomic status (Primates, Indrioidea) and in contrast to recent suggestions of a closer relationship to the Lemuridae made on the basis of analyses of dental developmental and postcranial characters. These data provide new insights into the evolution of the locomotor apparatus among lemurids and indriids.</p

Evidence of coat color variation sheds new light on ancient canids.

International audienceWe 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

Using Classical Population Genetics Tools with Heterochroneous Data: Time Matters!

BACKGROUND: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. METHODOLOGY/PRINCIPAL FINDINGS: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)). CONCLUSIONS/SIGNIFICANCE: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

The Microcephalin Ancestral Allele in a Neanderthal Individual

Background: The high frequency (around 0.70 worlwide) and the relatively young age (between 14,000 and 62,000 years) of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1) locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans.1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. Methodology/Principal Findings: Here we report the first PCR amplification and high- throughput sequencing of nuclear DNA at the microcephalin (MCPH1) locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy). We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH

Utilisation de l'ADN ancien en anthropologie

Abstract. — The discovery of DNA persistence in ancient remains enables a direct access to the genome of extinct species or populations. In this review we present the conditions of conservation of DNA throughout time as well as the favourable substrates and environments. We also discuss some technical problems specific to the retrieval of this DNA (amount of DNA, contaminations, PCR inhibitors). The various possible applications to archaeological deposits of the ancient DNA studies are presented: individual typing of ancient individuals, identification of familial relationship, sex determination, studies of the human migrations, origin of infectious or genetic diseases, domestication.Résumé. — La découverte de la persistance d'ADN dans les restes anciens a permis d'avoir directement accès au génome d'espèces ou de populations disparues. Dans cette revue, nous présentons tout d'abord les conditions de conservation de l'ADN au cours du temps ainsi que les substrats et les environnements favorables. Certains problèmes techniques spécifiques de la récupération d'ADN ancien (quantité d'ADN, contaminations, présence d'un inhibiteur de la PCR. . .) sont abordés. Les applications possible de l'étude de l'ADN ancien en anthropologie sont ensuite présentés : reconnaissance individuelle des individus, détermination de leurs liens de parenté, détermination du sexe, étude des migrations humaines, origine des maladies infectieuses ou domestication.Hänni Catherine. Utilisation de l'ADN ancien en anthropologie. In: Bulletins et Mémoires de la Société d'anthropologie de Paris, Nouvelle Série. Tome 6 fascicule 1-2, 1994. pp. 5-28

Révision taxonomique des Gadidae et puce à ADN pour l'identification d'espèces (de l'intérêt de la Systématique)

La systématique, discipline longtemps délaissée, connaît actuellement un essor considérable, essentiellement parce qu'elle a été renouvelée dans ses concepts et ses approches méthodologiques. Nous discutons l'ensemble de ces aspects à travers deux volets. Le premier est consacré à la révision taxonomique d'un groupe de poissons téléostéens, les Gadidae (morues, merlus), par des approches morphologiques (révision de l'ensemble des études portant sur ce groupe) et de phylogénie moléculaire (analyse des gènes Cyt b et COX I). Le second volet est consacré à l'utilisation de nos compétences en systématique pour la mise en place d'une puce à ADN pour la détection et l'identification d'espèces (animaux vertébrés) dans les produits transformés (agroalimentaire, fraudes, gestion de la biodiversité)LYON1-BU.Sciences (692662101) / SudocSudocFranceF

Systematics of the spiny mouse (Acomys : Muroidea) : molecular and biochemical evidences

International audienc

Origine évolutive et diversification des espèces animales (apports de l'ADN ancien)

Au milieu des années quatre-vingt, l'isolement de traces d'ADN à partir de fossiles a ouvert de nouvelles perspectives dans les Sciences de l'Évolution. Les paléontologues, qui ne disposaient alors que des caractères morphologiques pour décrypter l'origine évolutive des espèces éteintes, pouvaient désormais s'appuyer sur des séquences d'acides-nucléiques. A l'aide de la technologie de l'ADN ancien, nous avons résolu la position phylogénétique de plusieurs espèces disparues. Mais les séquences anciennes peuvent aussi servir à mieux comprendre les espèces actuelles en suivant comment elles se sont mises en place dans l'espace et dans le temps. Une séquence d'Homme de Néandertal nous a ainsi permis d'éclairer sous un jour nouveau l'origine de notre propre espèce. L'évolution de la diversité génétique des Ours des cavernes, suivie sur près de cent mille ans, nous a également révélé toute l'influence que les changements climatiques en cours pourraient exercer sur l'évolution des Mammifères.LYON1-BU.Sciences (692662101) / SudocPARIS-Museum-Bib. d'entomologie (751052305) / SudocSudocFranceF

Détection et identification de l'ADN dégradé (nouvelles approches moléculaires et biophysiques)

Species identification is a key issue in many topical fields such as food forensics, medicine, paleontology, etc.. In processed products (animal or plant), identification based on morphological characters is not possible because no diagnostic test is available, hence the need to use identification methods based on DNA amplification by PCR (DNA barcoding). However, in degraded substrates, this molecule is sometimes unavailable to PCR due to the presence of inhibitors and / or chemical modifications that block the activity of Taq polymerase. In the first part, this thesis develops a methodology for extracting and amplifying DNA from leather, taken as a model of a product which is highly resistant to molecular analysis due to the treatments used in its manufacture. Indeed, the DNA in worked skin is highly degraded, chemically modified and more specifically it is co-extracted with inhibitors of PCR (dyes and tannins). In addition to the important applications in fraud prevention and biodiversity protection, restoration of historical musical instruments was an important goal of our approach. As new enzymatic treatments (DNA repair) are currently limited to already amplifiable DNA substrates, it is necessary to develop a new approach for DNA inaccessible by PCR. Thus, the second part of this thesis develops a new non-enzymatic method. This physical detection of DNA is based on vibrational Raman spectroscopy (SERRS, Surface Enhanced Resonant Raman Spectroscopy). In the future, this approach could replace the PCR, and be applied for rapid and reliable molecular diagnosis, especially in medical tests.L'identification des espèces est une question essentielle dans de nombreux domaines actuels comme l'agro-alimentaire, la médecine, la paléontologie, etc. Dans les produits transformés (d origine animale ou végétale), l identification basée sur des caractères morphologiques n est pas possible car aucun critère diagnostique n est accessible, d où la nécessité d utilisation de méthodes d identification basées sur l amplification de l ADN par PCR (DNA barcoding). Cependant, dans des substrats dégradés, cette molécule est parfois inaccessible à la PCR en raison de la présence d inhibiteurs et/ou de modifications chimiques bloquant l activité de la Taq polymérase. Dans une première partie, cette thèse développe une méthodologie d extraction et d amplification de l ADN à partir des cuirs, pris comme modèle des produits les plus réfractaires à l analyse moléculaire, du fait des traitements utilisés lors de leurs fabrication. En effet, l'ADN présent dans la peau travaillée est fortement dégradé et chimiquement modifié et en particulier il est co-extrait avec des inhibiteurs de la PCR (colorants et tanins). Outre des applications importantes dans la répression des fraudes et la protection de la biodiversité, la restauration des instruments historiques de musique a été un objectif important de notre approche. Comme les nouveaux traitements enzymatiques (réparation de l ADN) sont pour l instant limités aux substrats d ADN déjà amplifiables, il est donc nécessaire de développer une nouvelle approche pour l ADN inaccessible par la PCR. Dans ce but, la deuxième partie de cette thèse développe une nouvelle méthode non enzymatique. Il s agit d une détection physique de l ADN, basée sur la spectroscopie vibrationnelle Raman (SERRS, Surface Enhanced Resonant Raman Spectroscopy). Dans l avenir, cette approche pourrait remplacer la PCR, et être appliquée pour les diagnostics moléculaires rapides et fiables, en particulier pour les analyses médicales.LYON-ENS Sciences (693872304) / SudocSudocFranceF