Catarina Ginja graduated in Zootechnical Engineering from the University of Tras-os-Montes e Alto Douro-UTAD (Portugal) in 2000. She obtained an MSc degree in Animal Science (UTAD 2002), completed a PhD degree in Animal Breeding and Genetics from the Technical Univ. of Lisbon-UTL and the Univ. of California in Davis in 2009, and was invited to work as a Research Assistant at UCDavis (2008-2010). In 2015 she was awarded a 5-year research assistant contract grant within the competitive IF Programme funded by the Portuguese Foundation for Science and Technology. She is the PI of the Archaeogenetics research group at CIBIO-InBIO, at the University of Porto. She leads the ARCHAIC project since June 2016 to carry out an Archaeogenetics study of Iberian and North African cattle. C Ginja was invited as chairperson and cattle representative of the FAO/ISAG Committee on Animal Genetic Diversity (2014). Phone: +351252660411 Address: CIBIO/InBIO-Universidade do Porto Campus Agrário de Vairão, Rua Padre Armando Quintas, 7 4485-661 Vairão, Portugal
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....
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.
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.
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
BACKGROUND: American Creole cattle presumably descend from animals imported from the Iberian Peni... more BACKGROUND: American Creole cattle presumably descend from animals imported from the Iberian Peninsula during the period of colonization and settlement, through different migration routes, and may have also suffered the influence of cattle directly imported from Africa. The introduction of European cattle, which began in the 18th century, and later of Zebu from India, has threatened the survival of Creole populations, some of which have nearly disappeared or were admixed with exotic breeds. Assessment of the genetic status of Creole cattle is essential for the establishment of conservation programs of these historical resources. METHODOLOGY/PRINCIPAL FINDINGS: We sampled 27 Creole populations, 39 Iberian, 9 European and 6 Zebu breeds. We used microsatellite markers to assess the origins of Creole cattle, and to investigate the influence of different breeds on their genetic make-up. The major ancestral contributions are from breeds of southern Spain and Portugal, in agreement with the historical ports of departure of ships sailing towards the Western Hemisphere. This Iberian contribution to Creoles may also include some African influence, given the influential role that African cattle have had in the development of Iberian breeds, but the possibility of a direct influence on Creoles of African cattle imported to America can not be discarded. In addition to the Iberian influence, the admixture with other European breeds was minor. The Creoles from tropical areas, especially those from the Caribbean, show clear signs of admixture with Zebu. CONCLUSIONS/SIGNIFICANCE: Nearly five centuries since cattle were first brought to the Americas, Creoles still show a strong and predominant signature of their Iberian ancestors. Creole breeds differ widely from each other, both in genetic structure and influences from other breeds. Efforts are needed to avoid their extinction or further genetic erosion, which would compromise centuries of selective adaptation to a wide range of environmental conditions
To our knowledge, for Iberian ancient dogs and wolves, this is the first attempt to successfully ... more To our knowledge, for Iberian ancient dogs and wolves, this is the first attempt to successfully apply NGS methods.
Measurements taken on 47 complete and 44 distal fragments of cattle metacarpals from 17th century... more Measurements taken on 47 complete and 44 distal fragments of cattle metacarpals from 17th 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.
El presente estudio sobre la variacion osteometrica de los restos de oveja y vacuno recuperados d... more El presente estudio sobre la variacion osteometrica de los restos de oveja y vacuno recuperados de yacimientos arqueologicos del sur de Portugal — region que fue controlada por los musulmanes — revela que durante el periodo andalusi se produjo un incremento en la talla de la oveja, seguido tras la reconquista por un subsiguiente aumento del tamano del vacuno. El analisis de ADN antiguo de un conjunto de metacarpos de vacuno del siglo XV procedentes de Beja ha confirmado una interpretacion osteometrica previa: el aumento de la talla del vacuno no fue consecuencia de un cambio en la proporcion de los sexos. Tanto los metacarpos mas pequenos (vaca) como los mas grandes (toro/buey) aumentaron de tamano en epoca post-andalusi. Se ha asumido que estos incrementos en el tamano de las cabanas ovina y vacuna reflejan su mejora. El aumento de tamano de la oveja es facil de entender dada la preferencia de los musulmanes por la carne de ovino. Sin embargo, el posterior aumento de talla del gana...
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragmen... more Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The...
Note S1. Brief description of the Iberian native cattle breeds sampled in our study. Table S1. Ib... more Note S1. Brief description of the Iberian native cattle breeds sampled in our study. Table S1. Iberian breeds databases. Table S2. Individual sample information. The Y-chromosome haplogroups in bold were determined in this study (n.a.: not applicable). Table S3. FST values between taurine breeds. The highest value is shown in bold and the lowest in italic. Figure S1. Average error rate per sample. Figure S2. Population structure plots determined by NGSadmix; each individual is represented by a stacked column for 3, 4, 6 and 8 proportions. Other K values are shown in Fig. 1b. Figure S3. Principal component analysis done with PCAngsd (components 1 and 2 are shown in Fig. 1c). Variance explained by each component is shown in parenthesis. Figure S4. Differences in Tajima's D between autosomes and sex chromosome X (calculated using only the female individuals). Figure S5. D-statistics determined as in [4] using genome-wide data. Positive values indicate an excess of derived alleles s...
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....
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.
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.
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
BACKGROUND: American Creole cattle presumably descend from animals imported from the Iberian Peni... more BACKGROUND: American Creole cattle presumably descend from animals imported from the Iberian Peninsula during the period of colonization and settlement, through different migration routes, and may have also suffered the influence of cattle directly imported from Africa. The introduction of European cattle, which began in the 18th century, and later of Zebu from India, has threatened the survival of Creole populations, some of which have nearly disappeared or were admixed with exotic breeds. Assessment of the genetic status of Creole cattle is essential for the establishment of conservation programs of these historical resources. METHODOLOGY/PRINCIPAL FINDINGS: We sampled 27 Creole populations, 39 Iberian, 9 European and 6 Zebu breeds. We used microsatellite markers to assess the origins of Creole cattle, and to investigate the influence of different breeds on their genetic make-up. The major ancestral contributions are from breeds of southern Spain and Portugal, in agreement with the historical ports of departure of ships sailing towards the Western Hemisphere. This Iberian contribution to Creoles may also include some African influence, given the influential role that African cattle have had in the development of Iberian breeds, but the possibility of a direct influence on Creoles of African cattle imported to America can not be discarded. In addition to the Iberian influence, the admixture with other European breeds was minor. The Creoles from tropical areas, especially those from the Caribbean, show clear signs of admixture with Zebu. CONCLUSIONS/SIGNIFICANCE: Nearly five centuries since cattle were first brought to the Americas, Creoles still show a strong and predominant signature of their Iberian ancestors. Creole breeds differ widely from each other, both in genetic structure and influences from other breeds. Efforts are needed to avoid their extinction or further genetic erosion, which would compromise centuries of selective adaptation to a wide range of environmental conditions
To our knowledge, for Iberian ancient dogs and wolves, this is the first attempt to successfully ... more To our knowledge, for Iberian ancient dogs and wolves, this is the first attempt to successfully apply NGS methods.
Measurements taken on 47 complete and 44 distal fragments of cattle metacarpals from 17th century... more Measurements taken on 47 complete and 44 distal fragments of cattle metacarpals from 17th 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.
El presente estudio sobre la variacion osteometrica de los restos de oveja y vacuno recuperados d... more El presente estudio sobre la variacion osteometrica de los restos de oveja y vacuno recuperados de yacimientos arqueologicos del sur de Portugal — region que fue controlada por los musulmanes — revela que durante el periodo andalusi se produjo un incremento en la talla de la oveja, seguido tras la reconquista por un subsiguiente aumento del tamano del vacuno. El analisis de ADN antiguo de un conjunto de metacarpos de vacuno del siglo XV procedentes de Beja ha confirmado una interpretacion osteometrica previa: el aumento de la talla del vacuno no fue consecuencia de un cambio en la proporcion de los sexos. Tanto los metacarpos mas pequenos (vaca) como los mas grandes (toro/buey) aumentaron de tamano en epoca post-andalusi. Se ha asumido que estos incrementos en el tamano de las cabanas ovina y vacuna reflejan su mejora. El aumento de tamano de la oveja es facil de entender dada la preferencia de los musulmanes por la carne de ovino. Sin embargo, el posterior aumento de talla del gana...
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragmen... more Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The...
Note S1. Brief description of the Iberian native cattle breeds sampled in our study. Table S1. Ib... more Note S1. Brief description of the Iberian native cattle breeds sampled in our study. Table S1. Iberian breeds databases. Table S2. Individual sample information. The Y-chromosome haplogroups in bold were determined in this study (n.a.: not applicable). Table S3. FST values between taurine breeds. The highest value is shown in bold and the lowest in italic. Figure S1. Average error rate per sample. Figure S2. Population structure plots determined by NGSadmix; each individual is represented by a stacked column for 3, 4, 6 and 8 proportions. Other K values are shown in Fig. 1b. Figure S3. Principal component analysis done with PCAngsd (components 1 and 2 are shown in Fig. 1c). Variance explained by each component is shown in parenthesis. Figure S4. Differences in Tajima's D between autosomes and sex chromosome X (calculated using only the female individuals). Figure S5. D-statistics determined as in [4] using genome-wide data. Positive values indicate an excess of derived alleles s...
Bioinformatics Open Days, 21 e 22 de Fevereiro 2019, Universidade do Minho (Braga, Portugal), 2019
For Iberian ancient dogs, this is the first attempt to successfully apply NGS methods.
Ancient DN... more For Iberian ancient dogs, this is the first attempt to successfully apply NGS methods. Ancient DNA analyses and bioinformatic tools are very powerful to unravel genetic variants from past populations. Some optimization of the analyses is still necessary to guarantee that the generated consensus sequences are reliable. Regarding nuclear genes, this is an ongoing study but the preliminary results for the Chalcolithic dog samples show that DNA is poorly preserved for some genes of interest related to coat color, coat texture and body size. In this way, these preliminary results have shown that NGS Illumina applied on ancient DNA has potential to provide data to further investigations in domestication and evolutionary trajectories of dogs.
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Papers by Catarina Ginja
Ancient DNA analyses and bioinformatic tools are very powerful to unravel genetic variants from past populations.
Some optimization of the analyses is still necessary to guarantee that the generated consensus sequences are reliable.
Regarding nuclear genes, this is an ongoing study but the preliminary results for the Chalcolithic dog samples show that DNA is poorly preserved for some genes of interest related to coat color, coat texture and body size.
In this way, these preliminary results have shown that NGS Illumina applied on ancient DNA has potential to provide data to further investigations in domestication and evolutionary trajectories of dogs.