Agreements and misunderstandings among three scientific fields: Paleogenomics, archaeology, and human paleontology

The emergence of paleogenomics (the study and analysis of ancient genomes) has provided a new, powerful source of information that can be used to test previous hypotheses regarding human evolution. However, various misunderstandings concerning the interpretation of genetic data in an archaeological and paleontological context and the existence of different scientific goals tend to hinder the fluent and fruitful collaboration between these fields. Here we explore some of the subjects creating confusion, such as the problems associated with molecular clocks, the difference between sequence divergence and species divergence, and the limitations of the uniparental markers. Limited understanding of how the expression of a genome shapes the phenotype (including morphology and cognition) is the main obstacle to linking the genetic and the morphological evidence available. In the case of Neanderthals (and probably Denisovans, too), it is obvious that the conspicuous morphological differences cannot be explained by differences in a list of about 100 genes alone, thus suggesting that regulatory genomic elements must have been involved. A functional analysis of the genes involved as well as a study of the genomic architecture- a complexity level above the simple DNA message-could help us fill this gap. It is hoped that this future work will lead to the emergence of an interrelated and multidisciplinary view of the study of the past based on real collaborative efforts among disciplines. © 2013 by The Wenner-Gren Foundation for Anthropological Research. All rights reserved.My research is supported by a grant (BFU2012-34157) from the Ministerio de Economía y Competitividad of Spain.Peer Reviewe

Aplicaciones de las técnicas paleogenómicas a la reconstrucción del pasado

Ponencia presentada en el II Congreso de Prehistoria de Andalucía Movilidad, contacto y cambio, celebrado en Antequera del 15 al 17 de febrero de 2012.Durante años, la paleogenética (definida como la recuperación de ADN de restos del pasado), no ha cumplido algunas de las expectativas que los arqueólogos y antropólogos habían depositado en este campo científico . Esto es debido en parte a diferencias de intereses científicos pero también a dificultades técnicas aparentemente insalvables asociadas a la conservación del material genético y a la posibilidad de contaminación de las muestras con ADN humano moderno. Sin embargo, el desarrollo , en los últimos cinco años, de las llamadas plataformas de secuenciación masiva en paralelo (conocidas también com o técnicas de ultrasecuenciación) ha permitido generar, por vez primera, genomas completos de humanos del pasado y dotar así a la paleogenética de una potencialidad increíblemente mayor de la esperada, incluso por los propios expertos en el campo. En el futuro será posible progresar en el conocimiento genético de los humanos del pasado, algo que sin embargo requerirá una mayor integración y colaboración entre las diferentes áreas de estudio implicadas.Peer Reviewe

Els mamuts les preferien rosses...i també morenes

Els mamuts les preferien rosses...i també morene

Paleogenòmica

Des que es va recuperar per primer cop DNA d'una espècie extingida, l'any 1984, la paleogenòmica ha experimentat una autèntica revolució, gràcies a les tècniques d'ultraseqüenciació desenvolupades en els dos darrers anys. Això ha permès per primer cop assolir projectes genòmics d'espècies extingides com els mamuts i els neandertals. Aquest treball fa un repàs històric dels principals estudis paleogenòmics i es discuteixen les possibles aplicacions, així com les problemàtiques metodològiques.Since the first DNA retrievals from an extinct species, in 1984, palaeogenomics has experienced a real revolution, thanks to the new ultrasequencing techniques developed in the last two years. These techniques have allowed the launching of genomic projects from extinct species such as mammoths and Neandertals. This work is an historical review of the main paleogenomic studies. Possible applications as well as methodological problems are also discussed

The Neanderthal Genome project and beyond

No existeix actualment un consens per a una definició científica de la nostra pròpia espècie. Les anàlisi genòmiques de diferents poblacions humanes estan mostrant una variació interindividual més gran de l'esperada. Per tant, serà molt difícil, sinó impossible, posar un límit a aquesta variació només des dels estudis de les poblacions humanes contemporànies. Amb l'arribada de noves tecnologies d'ultraseqüenciació, ara som capaços de recuperar genomes complets d'espècies extingides, entre elles mamuts i neandertals. El genoma neandertal, recentment finalitzat, ens proporcionarà una referència evolutiva més propera a nosaltres en el temps, que ens ajudarà a descobrir quines variants genètiques estan compartides amb els neandertals i quines són exclusives dels humans moderns. Això ens permetrà generar una definició objectiva de la nostra espècie, si bé consistirà probablement en un complex llistat de variants genètiques en potser un centenar de gens.A consensus regarding a scientific definition of our own species does not exist. Genomic analyses from different human populations show an inter-individual variation that is higher than previously expected. Therefore, it will be difficult, if not impossible, to put a limit on this variation from the study of contemporary populations exclusively. With the advent of new ultrasequencing technologies, we are now able to retrieve complete genomes from extinct species, such as mammoths and Neanderthals. The recently completed Neanderthal genome will provide us with a close external evolutionary reference, helping us to identify those genetic variants shared with Neanderthals and those present in modern humans alone. This, in turn, will allow us to generate an objective definition of our own species, although it will probably be based on a complex list of genetic variants in some one hundred genes

A brief hiustory of palaeogenomics : how a young discipline revolutionised the syudy of the past

In only a few short years, the ancient DNA field has transformed from an anecdotal and artisanal discipline into one of the most dynamic current scientific fields, generating massive genomic data from hundreds of past individuals. These include extinct hominins such as Neanderthals and Denisovans and prehistoric humans, and have provided information about the recent settlement of the continents. The field of palaeogenomics gives direct space and time information about the adaptive and demographic aspects of human populations and reveals complex patterns of past migrations that can help us to understand our current diversity. The development of this discipline is a unique opportunity to establish partnerships with archaeologists and anthropologists and to build up a multidisciplinary approach to the study of the past

「ことば」で「学ぶ」ということ : ヨナとトゥエットの人生の物語から

In order to understand the genetic basis for the evolutionary success of modern humans, it is necessary to compare their genetic makeup to that of closely related species. Unfortunately, our closest living relatives, the chimpanzees, are evolutionarily quite distant. With the advent of ancient DNA study and more recently paleogenomics — the study of the genomes of ancient organisms — it has become possible to compare human genomes to those of much more closely related groups. Our closest known relatives are the Neanderthals, which evolved and lived in Europe and Western Asia, from about 600,000 years ago until their disappearance around 30,000 years ago following the expansion of anatomically modern humans into their range. The closely related Denisovans are only known by virtue of their DNA, which has been extracted from bone fragments dating around 30,000 to 50,000 years ago found in a single Siberian cave. Analyses of Neanderthal and Denisovan nuclear and mitochondrial genomes have revealed surprising insights into these archaic humans as well as our own species. The genomes provide a preliminary catalogue of derived amino acids that are specific to all extant modern humans, thus offering insights into the functional differences between the three lineages. In addition, the genomes provide evidence of gene flow between the three lineages after anatomically modern humans left Africa, drastically changing our view of human evolution

Genealogical Relationships between Early Medieval and Modern Inhabitants of Piedmont

Vai, Stefania et al.In the period between 400 to 800 AD, also known as the period of the Barbarian invasions, intense migration is documented in the historical record of Europe. However, little is known about the demographic impact of these historical movements, potentially ranging from negligible to substantial. As a pilot study in a broader project on Medieval Europe, we sampled 102 specimens from 5 burial sites in Northwestern Italy, archaeologically classified as belonging to Lombards or Longobards, a Germanic people ruling over a vast section of the Italian peninsula from 568 to 774. We successfully amplified and typed the mitochondrial hypervariable region I (HVR-I) of 28 individuals. Comparisons of genetic diversity with other ancient populations and haplotype networks did not suggest that these samples are heterogeneous, and hence allowed us to jointly compare them with three isolated contemporary populations, and with a modern sample of a large city, representing a control for the effects of recent immigration. We then generated by serial coalescent simulations 16 millions of genealogies, contrasting a model of genealogical continuity with one in which the contemporary samples are genealogically independent from the medieval sample. Analyses by Approximate Bayesian Computation showed that the latter model fits the data in most cases, with one exception, Trino Vercellese, in which the evidence was compatible with persistence up to the present time of genetic features observed among this early medieval population. We conclude that it is possible, in general, to detect evidence of genealogical ties between medieval and specific modern populations. However, only seldom did mitochondrial DNA data allow us to reject with confidence either model tested, which indicates that broader analyses, based on larger assemblages of samples and genetic markers, are needed to understand in detail the effects of medieval migration.This work was supported by the Italian Ministry for Universities and Research (MIUR), PRIN 2012 funds to DC, AA, AT and GB, FIRB funds “Futuro in Ricerca” 2008 (RBFR08U07M) and 2012 (RBFR126B8I) to AA, AO and ER; Compagnia di San Paolo, Turin to DC; the Anneliese Maier Research Award of the Alexander von Humboldt Foundation and the German Federal Ministry for Education and Research to PG; FEDER and Spanish Government grant BFU2012-34157 to CLF; European Research Council (ERC Advanced Grant No. 295733 “LanGeLin”) to GB.Peer reviewe