Cleia Detry | Universidade de Lisboa (original) (raw)

Papers by Cleia Detry

Ÿ Ancestral samples has a crucial role uncovering details of dog domestication and its evolution,... more Ÿ Ancestral samples has a crucial role uncovering details of dog domestication and its evolution, which can no longer be recovered by studies based only on modern samples (Larson et al. 2012). Ÿ DNA extracted from tissues such as bones and/or teeth present in low quantity and highly degraded (Lindahl 1993). Ÿ Bioinformatic tools has revealed new insights into genomics of ancient specimen (Shendure & Ji 2008). Ÿ Domestic dogs exist in the Iberian Peninsula at least since the Upper Late Paleolithic (Vigne 2005). Ÿ Genetic studies of Iberian extant dogs revealed the existence of four haplogroups A, B, C, D-haplogroup A is the most frequent whereas D is the least represented (Pires et al. 2006,2017). Ÿ Archaeological remains from Iberian dogs dated to the Chalcolithic period already exhibited a large phenotypic variability-indicating that human driven selection acted towards the appearance of different dog types for the performance of various tasks (e.g. hunting, livestock guarding, defense) (Pires et al. 2001; Arana & Rodríguez 2013). Ÿ We carried out Next-Generation Sequencing-Illumina (Fig. 3), and used the most up-to-date bioinformatic tools (Fig. 4) to recover and analyze mitochondrial and nuclear ancient DNA for 4 Chalcolithic Iberian dogs. Ÿ Consensus sequence from NGS analysis for each Chalcolithic dog sample was used to infer evolutionary relationships by the construction of an haplotype network including reference data (

Measurements taken on 47 complete and 44 distal fragments of cattle metacarpals from 17 th centur... more Measurements taken on 47 complete and 44 distal fragments of cattle metacarpals from 17 th century AD Carnide, Lisbon, separate into two groups. Comparison with 21 ancient DNA sexed specimens and modern specimens of known sex (seven Barrosã cows and a Barrosã bull), indicates that the Carnide metacarpals probably belonged to both cows and bulls/oxen. We use the 47 complete metacarpals as a "sexed reference sample" in order to find which measurements generally taken by zooarchaeologists on the distal metacarpal help separate males from females. Widths appear to be most useful. The modern Barrosã cattle in our collection, selected for their meat, have wider metacarpals than the ones from Carnide; the latter were perhaps more generalist animals.

Studies undertaken several years ago indicated little change in cattle size in Portugal before th... more Studies undertaken several years ago indicated little change in cattle size in Portugal before the fifteenth century AD, indeed even Roman cattle were not very different from preceding Iron Age ones. The Roman province of Lusitania com- prised the southwestern part of the Iberian Peninsula (present-day central and southern Portugal and Spanish Extremad- ura). Here we present some evidence of cattle size increase in the newly founded Lusitanian Roman cities, that is, those with no previous occupation. These cities include, for example, Emerita Augusta (Mérida, Spain) and ancient Ammaia (near Marvão, Portugal). We compare their measurements with those from smaller Roman towns and sites from other periods. Our hypothesis is that the size increase reflects better nourishment or the presence of different cattle morpho- types (by selection or introduction of new animals). Osteometric analyses suggest that cattle from the main Roman cities were generally bigger in Roman newly founded cities, contrary to sites with pre-Roman occupation. Innovations could have been implemented via the import of new stock and/or new breeding strategies.

Naturwissenschaften, Oct 11, 2018

New finds ofbones ofthe Egyptian Mongoose (Herpestes ichneumon), one from Portugal and one from S... more New finds ofbones ofthe Egyptian Mongoose (Herpestes ichneumon), one from Portugal and one from Spain, were directly 14C dated to the first century AD. While the Portuguese specimen was found without connection to the Chalcolith ic occupation ofthe Pedra Furada cave where it was recovered, the Spanish fmd, collected in the city of Mérida, comes from a ritual pit that also contained three human and 40 dog burials. The finds rep0l1ed here show that the Egyptian mongoose, contrary to the traditional and predominant view, did not first atTive in the lbetian Peninsula during the Muslim occupation of lberia. lnstead, our findings are consistent with the hypothesis that the species was first introduced by the Romans, or at least sometime during the Roman occupation of H ispania. Therefore, rad iocarbon dating of new archaeological finds of bones of the Egyptian Mongoose (Herpestes ichneumon) in the lberian Peninsula pusb back the confimled presence ofthe species in tlle region by approximately eight centuries, as the previously oldest dated record is from the ninth century. With these new dates, there are now a total offour 14C dated specimens of Egyptian mongooses from the lberian Peninsula, and ali ofthese dates fali within the last 2000 years. Tms offers support for the hypothesis that the presence ofthe species in lberia is due to hi storical introductions and is at odds with a scenario of natural sweepstake dispersai across the Straits of Gibraltar in the Late Pleistocene (126,000-11 ,700 years ago), recently proposed based on genetic data.

Quaternary International, Mar 1, 2018

In this study, we integrate osteometric and palaeogenetic data to investigate dog variability in ... more 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 statusddomestic 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. Highthroughput 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.

Journal of Archaeological Science, May 1, 2012

Journal of Archaeological Science: Reports, Oct 1, 2022

Inheritable traits of cattle were modified in various ways at different times by diverse cultures... more Inheritable traits of cattle were modified in various ways at different times by diverse cultures. A large collection of seventeenth century cattle remains excavated from 71 silos in the Largo do Coreto in Carnide, Lisbon, included 47 com- plete and 44 distal ends of metacarpals. These provide an opportunity to make a detailed osteometric and archaeogenetics study. While morphological changes such as size increase, as detected in bone measurements, indicate improvement for larger animals, ancient DNA is useful for studying evolutionary trajectories and modes of improvement of domestic animals. High-throughput sequencing can show evolutionary processes at unprecedented resolution. We generated whole-genome shotgun resequencing data for 6 Carnide specimens on the Illumina HiSeq X Ten platform. Mean en- dogenous DNA content for these samples varied between 1% (CAR008) and 4% (CAR014), and their mitogenomes were sequenced to between 3.56x and 33.44x mean depth of coverage, respectively. The Carnide cattle belong to the Europe- an-T3 (CAR002 and CAR021) and African-T1 haplogroups (CAR008, CAR009, CAR014, and CAR016). These haplogroups are also present in extant native breeds from the Iberian Peninsula, corroborating the hypothesis of a genetic continuity of maternal lineages over time. The admixture of African taurine cattle observed in these specimens from the Modern period supports the idea that current genetic diversity of Iberian cattle derives from the dispersal of a heterogeneous population since early times along the Mediterranean basin. In addition, the biological sex of the Carnide specimens was consistently determined by our genomic analysis and osteometric measurements. Further analyses of whole-genome nuclear data are needed to infer specific biological properties, for example, the coat color of these animals, as well as the variability of genes linked to body size, meat, and milk production traits.

Journal of Archaeological Science: Reports, Apr 1, 2022

Domesticated dogs have been present in the Iberian Peninsula long before other domesticated speci... more 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 Casetón de la Era, Villalba de los Alcores, Valladolid, in Spainwere 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.

Zooarchaeological studies undertaken several years ago indicated little change in cattle body siz... more Zooarchaeological studies undertaken several years ago indicated little change in cattle body size in southern Portugal before the 15th century AD. Subsequent analysis of several animal bone assemblages from cities of the Roman province Lusitânia (south-western part of the Iberian Peninsula) showed increase in cattle size during Roman times. These cities include present-day Mérida (Emerita Augusta), ancient Ammaia (both founded in the 1st century BC) and Lisbon (Olissipo). This last was a very important urban centre in Roman times, but its occupation began much earlier, in the Palaeolithic. Here we consider measurements of cattle bones recovered from excavations in these Roman cities and compare them with results from smaller towns and from other previous and subsequent periods. The measurements of cattle bones reveal some signs of size increase (and subsequently improvement) during the Roman occupation, which are more apparent in the newly founded Roman cities. Preliminary results of ancient DNA studies indicate a continuity through time of maternal lineages, supporting the hypothesis of local improvement. Forthcoming genomic analyses should provide more detailed information on the introduction of new breeding stock and modes of improvement.Peer reviewe

Ÿ Unfortunately, due to the endogenous DNA poor preservation, variants within specific nuclear ge... more Ÿ Unfortunately, due to the endogenous DNA poor preservation, variants within specific nuclear genes related to coat color, coat texture or body size could not be recovered (no coverage). A comparison between the nuclear genome-recovered from NGS analysis-and the reference dog genome revealed SNPsof possibly high impact, which are being assigned to genes. Ÿ Regarding sex determination, comparing the proportion reads/Mbp (Fig. 5) for each chromosome we observed that: 1) for LYEP9, LYEP11, LYEP53 and LYEP27 only half of the reads/Mbp aligned with the X chromosome, in contrast to the proportion observed for the autosomal chromosomes. Fewer reads aligned against Y chromosome because the reference used here is only a part of the dog Y chromosome (its real size is not know, but is expected to be ~20Mbp long); 2) LYEP51 has the same proportion of reads/Mbp aligning along all the chromosomes, including the X chromosome.

Cattle played a major role in the Roman economy. The zooarchaeological record indicates a general... more Cattle played a major role in the Roman economy. The zooarchaeological record indicates a general size increase across Europe, and many urban sites display higher cattle frequency remains compared to previous and later periods. The reasons for this size increase remains unknown: was it the result of the import of new lineages, related to wider mobility and trade networks? Or a consequence of selection and improvement of local stock using new breeding strategies? Or both? While morphological changes such as size increase, as detected in bone measurements, indicate improvement for larger animals, ancient DNA enables tracking changes in genomic diversity associated with mobility and animal selection traits. We aim to understand whether the Roman state enhanced cattle genetic diversity in the Western periphery using genomics. We generated whole-genome shotgun resequencing data (Illumina HiSeqX) to analyze around 100 cattle remains dating from the Roman period collected at archaeological sites in Portugal, Spain and Italy. Here we present and discuss the preliminary results of our analysis. For example, cattle mitochondrial DNA is geographically structured and it is, therefore, possible to associate maternal lineages to specific regions. Mitochondrial genome coverages for these specimens were between 1x and 100x, which allowed to determine the distribution of major haplogroups. Endogenous DNA content ranged between 0.5% and 50%. We will briefly discuss nuclear whole-genome data and their use to model genomic variation over time and investigate genetic relationships between past and extant cattle from these regions.Peer reviewe

Due to the endogenous DNA poor preservation (Table 1), variants within specific nuclear genes rel... more Due to the endogenous DNA poor preservation (Table 1), variants within specific nuclear genes related to coat color, coat texture or body size could not be recovered (very low coverage). A comparison between the nuclear genome-recovered from NGS analysis-and the reference dog genome revealed SNPs of possible high impact, which are being analysed. Ÿ Regarding sex determination, comparing the proportion of reads/Mbp (Fig. 5) for each chr, we observed that: 1) for LYEP9, LYEP11, LYEP53and LYEP27 only half of the reads/Mbp aligned with the X chr, in contrast to the proportion observed for the autosomes. Fewer reads aligned against Y chr because the reference used here is only a part of the dog Y chr (its real size is not know, but is expected to be ~20Mbp long); 2) LYEP51 has the same proportion of reads/Mbp aligning along all the autosomal and X chr. Ÿ We successfully applied NGS methods to recover ancient DNA-mitogenomes from Iberian dogs and wolves remains. Ÿ Chalcolithic Iberian dogs harboured haplotypes segregating within haplogroups A and C Their European counterparts exibited more diversity (Hg A, B, C and D were presented). Ÿ The distinct genetic composition of Iberian dogs is under investigation. Ÿ The coverage of nuclear genome needs to be improved in order to study some genes related with phenotype. Ÿ NGS Illumina applied on ancient DNA has potential to provide data for further investigations concerning domestication and evolutionary trajectories of dogs in Iberian.

Arqueologia em Portugal 2020 - Estado da Questão - Textos

We present the results obtained from the analysis of unpublished faunal remains from the Bronze A... more We present the results obtained from the analysis of unpublished faunal remains from the Bronze Age settlement of Outeiro do Circo (Beja). The materials provenance is diverse, corresponding mainly to one pit/ silo from trench 3 and the areas near the defensive systems designated trench 7 and 8. Hunting strategies are complementary in the assemblage, with a predominance of sheep and goat remains, followed by cattle and swine. Kill-off patterns with the presence of young and adult individuals are suggestive of a mixed economy with the exploitation of primary and secondary resources. Although highly fragmented and affected by postdepositional processes it was possible to record several anthropization indicators related to the butchering process and thermo-alteration of remains by fire

A escavação do Largo do Coreto em Carnide (2012) identificou diversos silos no interior dos quais... more A escavação do Largo do Coreto em Carnide (2012) identificou diversos silos no interior dos quais foram recuperados diversos elementos da cultura material, datados entre os finais do século XVI e meados do século XVII. A cerâmica comum, destinada à preparação e consumo de alimentos, é certamente o tipo mais abundante com diversos tipos recipientes. Panelas, tachos, frigideiras, cuscuzeiras, assadores, entre outros, demonstram que a preparação de alimentos passava por diferentes processos de confecção. O cruzamento das informações obtidas através das formas cerâmicas, combinadas com os vestígios faunísticos e os diversos livros de cozinha da época permitem inferir sobre que tipo de alimentos estariam à mesa dos habitantes de Carnide na Idade Moderna. The excavation of the Largo do Coreto in Carnide (2012) permitted the identification of several storage pits. Inside these silos several material culture elements were recovered, dated from late 16th to mid 17th century. Redwares, the mo...

Journal of Archaeological Science: Reports

Cattle and People

Applied Sciences

This paper presents the facial reconstruction of a Mesolithic dog whose skeleton was recovered fr... more This paper presents the facial reconstruction of a Mesolithic dog whose skeleton was recovered from the Muge shell middens (Portugal) in the 19th century. We used the anatomical deformation approach based on a collection of computer tomography images as an attempt to reconstruct the Muge dog’s head appearance. We faced a few challenges due to the level of bone displacement and the absence of some cranium anatomical parts, as well as accurate information on soft tissue thickness for modern dogs. This multidisciplinary study combined anatomical, veterinary, zooarchaeological, artistic and graphic aspects to allow for the facial reconstruction of the Muge dog. Albeit an approximation, it confers a recognition to this prehistoric finding.

University College Dublin, 2021

Quaternaire, 2021

A fossil remain of porcupine, a large-sized rodent hitherto unknown in Portugal, was identified d... more A fossil remain of porcupine, a large-sized rodent hitherto unknown in Portugal, was identified during the 2010-13 excavation of the Last Interglacial deposit of Figueira Brava cave. The specimen is a left hemimandible retaining the PM/4 to M/2 series but lacking the incisor and the M/3. Based on the analysis of its morphological and odontometric features, we assign the fossil to Hystrix cristata (Linnaeus, 1758). Nowadays, H. cristata is found in Africa as well as, recently introduced, in Italy. Most Late Pleistocene occurrences of the genus are assigned to the species Hystrix (Acanthion) vinogradovi but, as demonstrated by the fossil discovered in Figueira Brava, H. cristata once existed in Europe.