6 research outputs found
Cães (Canis lupus familiaris) da Península Ibérica do período Calcolítico: uma abordagem genómica
Os cães existem na Península Ibérica pelo menos desde o Paleolítico Superior;
o resto arqueológico mais antigo data há cerca de 16,000 AP (Erralla, Espanha).
Existem diferentes teorias sobre a origem dos cães na Europa. Estudos
anteriores indicam que os cães podem ter chegado à Europa a partir de uma
população domesticada de lobos oriundos da Ásia Oriental, ou a partir de duas
populações de lobos geneticamente distintas da Eurásia Oriental e Ocidental,
domesticadas independentemente, e que mais tarde, a população de cães da
Eurásia Oriental se espalhou e substituiu parcialmente a população da Eurásia
Ocidental.
Um estudo recente focando na composição genética de 6 cães Ibéricos do
período Mesolítico, sugeriu que uma domesticação local na Península Ibérica
pode ter ocorrido na Europa pré-Neolítica. Considerando o debate mantido
sobre a origem dos cães, é crucial desvendar a composição genética de
populações passadas e periféricas da Europa – usando métodos específicos
para recuperar e analisar o DNA ancestral, de diferentes períodos, a fim de
investigar a origem e a trajetória evolutiva dos cães no seu global.
Nomeadamente, pode revelar-se importante por fornecer dados sobre uma
possível contribuição do lobo Ibérico para a origem dos primeiros cães Ibéricos
e informação genómica potencialmente útil para a detecção de eventos de
hibridação histórica entre o cão e o seu parente selvagem, o lobo Ibérico – uma
subespécie endêmica e atualmente considerada “Em perigo” de extinção. Esta
informação pode ser englobada aquando a definição de medidas de gestão e
conservação futuras para a espécie selvagem lobo Ibérico.
Neste trabalho, uma abordagem genómica (Next Generation Sequencing, NGS)
foi a escolhida para recuperar sequências do genoma mitocondrial (mt) e nuclear
de Canis de três sítios arqueológicos Ibéricos datados do Calcolítico [ca. 5,000-
4,000 anos atrás]: dois cães de Leceia em Oeiras, Portugal; dois cães de
Casetón de La Era em Valladolid, Espanha; e um lobo de Penedo de Lexim em
Mafra, Portugal. Utilizando as ferramentas de bioinformática actuais, esses
genomas foram identificados e compilados. Além disso, para entender a relação
de populações passadas/modernas, construiu-se uma rede filogenética
(baseada num fragmento parcial da região controlo do mtDNA) reunindo 254
sequências de Canis, bem como uma árvore filogenética de 23 mitogenomas de
Canis disponíveis em bases dados públicos.
Embora a recuperação e análise do genoma nuclear sejam um maior desafio se
proveniente de amostras ancestrais, este foi investigado para a identificação do
sexo molecular desses 5 espécimes.
Relativamente ao estudo dos cães pré-históricos da Ibéria, esta é a primeira
tentativa de aplicar com sucesso o método NGS para investigar a sua
composição genética. Neste estudo, foi possível: gerar sequências do genoma
mitocondrial (com 1x a 17x de cobertura) e recuperar entre 0.09% e 3.75% do
genoma nuclear endógeno das 5 amostras do Calcolítico; identificar haplótipos
de DNA mitocondrial e atribuí-los a dois (A e C) dos quatro principais
haplogrupos descritos para os cães (A, B, C e D); gerar dados genómicos de um
lobo Ibérico do Calcolítico que, tanto quanto investiguei, constituem os primeiros
dados genómicos de um espécime de lobo da Ibéria e desta cronologia. Os
resultados mostram que os cães Ibéricos do Calcolítico apresentavam a mesma
frequência de haplótipos do Haplogrupo A (Hg anteriormente presente neste
território, em contraste com as outras regiões da Europa), bem como do
Haplogrupo C (já presente em outras regiões da Europa desde o Paleolítico).Domestic dogs exist in the Iberian Peninsula at least since the Upper Late
Palaeolithic; the oldest remain dated to 16,000 BP years old (Erralla, Spain).
There are different theories about the origins of European dogs. Previous studies
indicated that dogs may arrived in Europe from an Eastern Asia domesticated
population of wolves, or that two genetically distinct wolf populations in Eastern
and Western Eurasia may have been independently domesticated, and that
afterwards the Eastern dog population spread and partially replaced an
indigenous Western Eurasian dog population.
A recent study focusing in the genetic composition of 6 Mesolithic Iberian dogs
reported that a local domestication in the Iberia Peninsula may have occurred in
pre-Neolithic Europe. Considering the debated origin of Iberian dogs, it is crucial
to unravel the genetic composition of past European peripheral populations -
using specific methods to recover and analyse ancient DNA, from different
periods in order to further investigate their origins and evolutionary trajectories.
Additionally, it may prove important to provide data on a possible contribution of
the Iberian wolf to the origin of the first Iberian dogs and genomic information
potentially useful for the detection of historical hybridization events between the
dog and its wild relative, the Iberian wolf – a subspecies and an endemism
currently considered “Endangered”. This information can be included in the
definition of future management and conservation measures for the wild Iberian
wolf species.
In this work, a genomic approach (Next Generation Sequencing, NGS) was
carried out to recover mitogenome and nuclear genomic data of Canis from three
Iberian archaeological sites dated to the Chalcolithic [ca. 5,000-4,000 years BP],
in particular: two dogs from Leceia in Oeiras, Portugal; two dogs from Casetón
de La Era in Valladolid, Spain; and one wolf from Penedo de Lexim in Mafra,
Portugal. Using the most up-to-date bioinformatic tools, their mitochondrial (mt)
and nuclear genomes were sequenced. In addition, to understand the
relationship of past/extant populations, a phylogenetic network (based on a
partial fragment of the mtDNA control region) comprising 254 Canis sequences,
as well as a phylogenetic tree of 23 Canis mitogenomes, publicly available, were
constructed. Furthermore, the nuclear genome, although more challenging to
recover and analyse from ancient samples, was investigated to molecularly
assess the sex of these 5 Canis specimens.
Regarding ancient Iberian dogs, this is the first attempt to successfully apply
NGS methods to investigate their genomic composition. In this study, it was
possible to: generate the draft of mitochondrial genomes (coverages ranged
between 1x and 17x) and recover between 0.09% and 3.75% of endogenous
nuclear genomic data of these 5 Canis specimens; identify mitochondrial DNA
haplotypes and assign those to 2 (A and C) of the four major dog haplogroups
described (A, B C and D); generate genetic data from a Chalcolithic wolf - to the
best of my knowledge this is the first genomic data available from an Iberian wolf
specimen from this chronology. The results shown that the Chalcolithic Iberian
dogs had about the same frequency of Haplogroup A (previously present in this
territory, but contrasting with other European regions), as well as of the
Haplogroup C (already present in other European regions since the Paleolithic).Mestrado em Ecologia Aplicad
Bioinformatic tools in the study of ancient dogs: preliminary results of an Iberian case study
In this study, we attempted to carry out a genomic amplification of ancient DNA from four pre-historic Iberian dogs using the Illumina sequencing method; to assign mtDNA sequences to the major dog haplogroups and to characterize some phenotypic traits of these dogs.This study is being developed within the Woof project - PTDC/HARARQ/29545/2017,
supported by national funds by FCT/MCTES and co-supported by Fundo Europeu de Desenvolvimento Regional (FEDER) throughout COMPETE - POCI – Programa Operacional Competividade e Internacionalização (POCI-01-0145 - FEDER- 029545 ), as well as by the post-doctoral grant SFRH/BPD/112653/2015 (AEPires), SFRH/BPD/108236/2015 (CDetry) and IF/00866/2014 (CGinja)info:eu-repo/semantics/publishedVersio
Iberian Chalcolithic Canis: a genomic approach to know them better
To our knowledge, for Iberian ancient dogs and wolves, this is the first attempt to successfully apply NGS methods.This study is being developed within the Woof project - PTDC/HISARQ/ 29545/2017 (CIBIO-InBIO), supported by portuguese funds by FCT/MCTES and co-supported by Fundo Europeu de Desenvolvimento Regional (FEDER) throughout COMPETE - POCI – Programa Operacional Competividade e Internacionalização (POCI-01-0145-FEDER-029545), as well as by the postdoctoral grant SFRH/BPD/112653/2015 (AEPires), SFRH/BPD/108236/2015 (CDetry) and IF/00866/2014 (CGinja).info:eu-repo/semantics/publishedVersio
Unraveling the genomes of ancient Iberian Canis
info:eu-repo/semantics/publishedVersio
Iberian dogs – a diachronic genomic analysis
Objectives: Dogs are an important genetic patrimony and in Portugal several functional breeds have been developed. The analysis of their genomes including those from ancient samples can provide a good opportunity to understand the origins and evolution of dogs from more peripheral regions, as well as to infer some of the morphological characteristics exhibited by past individuals.
Materials and Methods: We employed well-established molecular biology methods, such as high-throughput sequencing and a nuclear capture assay, in order to recover endogeneous ancient DNA (aDNA) and SNP data from 14 ancient specimens dated from Mesolithic (~8,000 yBP) through the Middle Ages. Whole genomes from present-day Iberian dogs (n=46) and Iberian wolves (n=2) were also retrieved for a comprehensive study of dog diversity. Regarding data analysis some specific scripts were improved by our team and adjusted to either modern or ancient samples.
Results: Although poorly preserved, aDNA was recovered. The endogenous content (%) is not correlated with the antiquity of each sample (r=-0,42, ns). Ancient dog mitogenomes (>90%, 3x coverage) are distributed within the variability of the A and C clades, while present-day dogs show a wider range of variability: clades A to D. WGS allowed the identification of 12 dogs (9 males, 3 females) and 3 ancient wolves (2, 1). Based on autosomal markers, ancient dogs show either a single or a mixed ancestry, while present-day dogs show a single ancestry/breed meaning they are genetically well-defined breeds. From 3 Roman dogs (Spain), 3-7 SNPs involved in determining the morphology were recovered whereas for one of the ancient wolves, only a single locus was recovered.
Conclusions: DNA (mitochondrial and nuclear) was recovered from Canis archaeological samples, and it helped in documenting the presence of dogs and describe their genomic composition in Iberia.
Keywords: Archaeogenomics; Dog; Evolution; Breeds.
Funding: Woof Project - POCI-01-0145-FEDER-029545 & PTDC/HAR-ARQ/29545/201
A multidisciplinary study of Iberian Chalcolithic dogs
Domesticated dogs have been present in the Iberian Peninsula long before other domesticated species, back to the late Palaeolithic period. Their origin is still uncertain, but dogs were already well established during the Chalcolithic period (ca. 5000–4000 BP). This study employed a multidisciplinary approach comprising osteometric, radiographic and palaeogenomic analyses to characterize Chalcolithic Iberian Canis remains. Two Chalcolithic archaeological sites – Leceia, Oeiras, in Portugal, and El Caset´on de la Era, Villalba de los Alcores, Valladolid, in Spain – were the main focus of this study. Osteometric and odontometric data from eleven other sites in Iberia were also included. Osteometric results show signs of phenotypic variability, likely the result of human-driven selective pressure. Dental radiographic and dental wear analyses allowed age at death estimation for four individuals (two juvenile and two adults). Three Chalcolithic Iberian dogs had their mitogenomes resequenced and the mitochondrial DNA analysis allowed to assign each individual to two of the major known haplogroups – A and C. Molecular sex infered by the chromosomeX/chromosome1 coverage ratio allowed to identify one female and two males. This study unveils some aspects of the Iberian Chalcolithic dogs: these dogs already exhibited various morphotypes whose profiles might be associated to the performance of certain tasks, as well as mitogenomes of two distinct lineages that help tracking the evolutionary paths of Iberian dogs.info:eu-repo/semantics/publishedVersio