Rita Rasteiro | University of Bristol (original) (raw)
Papers by Rita Rasteiro
Molecular Ecology Resources, Nov 14, 2023
Throughout Earth’s natural history, habitats have undergone drastic changes in quality and extent... more Throughout Earth’s natural history, habitats have undergone drastic changes in quality and extent, influencing the distribution of species and their diversity. In the last few hundred years, human activities have destroyed natural habitats at an unprecedent rate, converting continuous habitat into fragmented and isolated patches. Recent global metanalyses suggest that habitat loss and fragmentation (HL&F) has negatively impacted the genetic diversity of many taxa across the world. These conclusions have been drawn by comparing present-day genetic patterns from populations occurring in continuous and fragmented landscapes. In this work, we attempted to go beyond ‘pattern’ and investigate through simulations some of the ‘processes’ that influence genetic variation in the context of HL&F. Since most species have a geographically restricted dispersal (known as “isolation-by-distance”, IBD), we studied the impact of HL&F on isolation-by-distance. We characterised the behaviour of IBD in ...
Natural climate change and recent anthropogenic activities have largely contributed to habitat lo... more Natural climate change and recent anthropogenic activities have largely contributed to habitat loss and fragmentation across the world, leading to 70% of worldwide remaining forests to be within 1 km of forest’s edges (Haddad et al., 2015). Ecological studies have shown that edge-effect influences ecological communities, species richness and abundance across many taxa, contributing to worldwide decline in biodiversity. Since edge-effect reduces species abundance and connectivity, it is also expected to negatively influence species genetic variation. In fact, previous theoretical studies had showed that populations closer to the edges of a finite stepping-stone model tends to have shorter coalescence times, and therefore, lower genetic diversity, than central populations. However, predicting the impact of edge effect on local genetic diversity remains challenging in realistic and more complex habitat fragments, where the additive effect of multiple edges is expected to take place. In...
Background: Rab proteins are regulators of vesicular trafficking, requiring a lipid modification ... more Background: Rab proteins are regulators of vesicular trafficking, requiring a lipid modification for proper function, prenylation of C-terminal cysteines. This is catalysed by a complex of a catalytic heterodimer (Rab Geranylgeranyl Transferase-RabGGTase) and an accessory protein (Rab Escort Protein. REP). Components of this complex display domain insertions relative to paralogous proteins. The function of these inserted domains is unclear. Results: We profiled the domain architecture of the components of the Rab prenylation complex in evolution. We identified the orthologues of the components of the Rab prenylation machinery in 43 organisms, representing the crown eukaryotic groups. We characterize in detail the domain structure of all these components and the phylogenetic relationships between the individual domains. Conclusion: We found different domain insertions in different taxa, in α-subunits of RGGTase and REP. Our results suggest that there were multiple insertions, expansions and contractions in the evolution of this prenylation complex.
Journal of Archaeological Science: Reports, 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 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.
Journal of Archaeological Science, 2019
Royal Society Open Science, 2016
More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, ... more More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine...
Scientific reports, Jan 17, 2018
The origin of the elephant on the island of Borneo remains elusive. Research has suggested two al... more The origin of the elephant on the island of Borneo remains elusive. Research has suggested two alternative hypotheses: the Bornean elephant stems either from a recent introduction in the 17th century or from an ancient colonization several hundreds of thousands years ago. Lack of elephant fossils has been interpreted as evidence for a very recent introduction, whereas mtDNA divergence from other Asian elephants has been argued to favor an ancient colonization. We investigated the demographic history of Bornean elephants using full-likelihood and approximate Bayesian computation analyses. Our results are at odds with both the recent and ancient colonization hypotheses, and favour a third intermediate scenario. We find that genetic data favour a scenario in which Bornean elephants experienced a bottleneck during the last glacial period, possibly as a consequence of the colonization of Borneo, and from which it has slowly recovered since. Altogether the data support a natural colonizat...
CHC22 clathrin plays a key role in intracellular membrane trafficking of the insulin-responsive g... more CHC22 clathrin plays a key role in intracellular membrane trafficking of the insulin-responsive glucose transporter GLUT4, and so in post-prandial clearance of glucose from human blood. We performed population genetic and phylogenetic analyses of the CLTCL1 gene, encoding CHC22, to gain insight into its functional evolution. Analysis of 58 vertebrate genomes showed independent loss of CLTCL1 in at least two lineages after it arose from a gene duplication during the emergence of jawed vertebrates. All vertebrates studied retain the parent CLTC gene encoding CHC17 clathrin, which mediates endocytosis and other housekeeping pathways of membrane traffic, as performed by the single type of clathrin in non-vertebrate eukaryotes. For those species retaining CLTCL1, preservation of CHC22 functionality was supported by strong evidence for purifying selection over phylogenetic timescales, as seen for CLTC. Nonetheless, CLTCL1 showed considerably greater allelic diversity than CLTC in humans a...
Nature Communications
Advances in phenology (the annual timing of species’ life-cycles) in response to climate change a... more Advances in phenology (the annual timing of species’ life-cycles) in response to climate change are generally viewed as bioindicators of climate change, but have not been considered as predictors of range expansions. Here, we show that phenology advances combine with the number of reproductive cycles per year (voltinism) to shape abundance and distribution trends in 130 species of British Lepidoptera, in response to ~0.5 °C spring-temperature warming between 1995 and 2014. Early adult emergence in warm years resulted in increased within- and between-year population growth for species with multiple reproductive cycles per year (n = 39 multivoltine species). By contrast, early emergence had neutral or negative consequences for species with a single annual reproductive cycle (n = 91 univoltine species), depending on habitat specialisation. We conclude that phenology advances facilitate polewards range expansions in species exhibiting plasticity for both phenology and voltinism, but may...
Ethnic and Racial Studies, 2015
The differences between copies of the human genome are very small, but tend to cluster in differe... more The differences between copies of the human genome are very small, but tend to cluster in different populations. So, despite the fact that low inter-population differentiation does not support a biological definition of races statistical methods are nonetheless claimed to be able to predict successfully the population of origin of a DNA sample. Such methods are employed in commercial genetic ancestry tests, and particular genetic signatures, often in the male-specific Y-chromosome or maternally-inherited mitochondrial DNA, have become widely identified with particular ancestral or existing groups, such as Vikings, Jews, or Zulus. Here, we provide a primer on genetics, and describe how genetic markers have become associated with particular groups. We describe the conflict between population genetics and individual-based genetics and the pitfalls of over-simplistic genetic interpretations, arguing that although the tests themselves are reliable, the interpretations are unreliable and strongly influenced by cultural and other social forces.
The arrival of agriculture into Europe during the Neolithic transition brought a significant shif... more The arrival of agriculture into Europe during the Neolithic transition brought a significant shift in human lifestyle and
subsistence. However, the conditions under which the spread of the new culture and technologies occurred are still
debated. Similarly, the roles played by women and men during the Neolithic transition are not well understood, probably
due to the fact that mitochondrial DNA (mtDNA) and Y chromosome (NRY) data are usually studied independently rather
than within the same statistical framework. Here, we applied an integrative approach, using different model-based
inferential techniques, to analyse published datasets from contemporary and ancient European populations. By integrating
mtDNA and NRY data into the same admixture approach, we show that both males and females underwent the same
admixture history and both support the demic diffusion model of Ammerman and Cavalli-Sforza. Similarly, the patterns of
genetic diversity found in extant and ancient populations demonstrate that both modern and ancient mtDNA support the
demic diffusion model. They also show that population structure and differential growth between farmers and hunter-
gatherers are necessary to explain both types of data. However, we also found some differences between male and female
markers, suggesting that the female effective population size was larger than that of the males, probably due to different
demographic histories. We argue that these differences are most probably related to the various shifts in cultural practices
and lifestyles that followed the Neolithic Transition, such as sedentism, the shift from polygyny to monogamy or the
increase of patrilocality.
Cultural practices can deeply influence genetic diversity patterns. The Neolithic transitions tha... more Cultural practices can deeply influence genetic diversity patterns. The Neolithic transitions that took place at
different times and locations around the world led to major cultural and demographic changes that influenced
and therefore left their marks on human genetic diversity patterns. Several studies on the European Neolithic
transition suggest that mitochondrial DNA (mtDNA) and Y-chromosome data can exhibit different patterns,
which could be owing to different demographic histories for females and males. Archaeological and anthro-
pological data suggest that the transition from hunter–gatherers (HGs) to farmers’ societies is probably
associated with changes in social organization, particularly in post-marital residence (PMR) rules (i.e. patri-
locality, matrilocality or bilocality). The movements of humans and genes associated with these rules can be
seen as sex-biased short-range migrations. We developed a new individual-based simulation approach to
explore the genetic consequences of 45 different scenarios, where we varied the patterns of PMR and admix-
ture between HGs and farmers. We recorded mtDNA and Y-chromosome data and analysed their diversity
patterns within and between populations, through time and space. We also collected published mtDNA and
Y-chromosome data from European and Near-Eastern populations in order to identify the scenarios that
would best explain them. We show that: (i) different PMR systems can lead to different patterns of genetic
diversity and differentiation, (ii) asymmetries between mtDNA and Y-chromosome can be owing to different
behaviours between males and females, but also to different mutations rates, and (iii) patrilocality in farmers
explains the present patterns of genetic diversity better than matrilocality or bilocality. Moreover, we found
that (iv) the genetic diversity of farmers change depending on the HGs PMR rules even though they are
assumed to disappear more than 5000 years ago in our simulations.
Molecular Ecology Resources, Nov 14, 2023
Throughout Earth’s natural history, habitats have undergone drastic changes in quality and extent... more Throughout Earth’s natural history, habitats have undergone drastic changes in quality and extent, influencing the distribution of species and their diversity. In the last few hundred years, human activities have destroyed natural habitats at an unprecedent rate, converting continuous habitat into fragmented and isolated patches. Recent global metanalyses suggest that habitat loss and fragmentation (HL&F) has negatively impacted the genetic diversity of many taxa across the world. These conclusions have been drawn by comparing present-day genetic patterns from populations occurring in continuous and fragmented landscapes. In this work, we attempted to go beyond ‘pattern’ and investigate through simulations some of the ‘processes’ that influence genetic variation in the context of HL&F. Since most species have a geographically restricted dispersal (known as “isolation-by-distance”, IBD), we studied the impact of HL&F on isolation-by-distance. We characterised the behaviour of IBD in ...
Natural climate change and recent anthropogenic activities have largely contributed to habitat lo... more Natural climate change and recent anthropogenic activities have largely contributed to habitat loss and fragmentation across the world, leading to 70% of worldwide remaining forests to be within 1 km of forest’s edges (Haddad et al., 2015). Ecological studies have shown that edge-effect influences ecological communities, species richness and abundance across many taxa, contributing to worldwide decline in biodiversity. Since edge-effect reduces species abundance and connectivity, it is also expected to negatively influence species genetic variation. In fact, previous theoretical studies had showed that populations closer to the edges of a finite stepping-stone model tends to have shorter coalescence times, and therefore, lower genetic diversity, than central populations. However, predicting the impact of edge effect on local genetic diversity remains challenging in realistic and more complex habitat fragments, where the additive effect of multiple edges is expected to take place. In...
Background: Rab proteins are regulators of vesicular trafficking, requiring a lipid modification ... more Background: Rab proteins are regulators of vesicular trafficking, requiring a lipid modification for proper function, prenylation of C-terminal cysteines. This is catalysed by a complex of a catalytic heterodimer (Rab Geranylgeranyl Transferase-RabGGTase) and an accessory protein (Rab Escort Protein. REP). Components of this complex display domain insertions relative to paralogous proteins. The function of these inserted domains is unclear. Results: We profiled the domain architecture of the components of the Rab prenylation complex in evolution. We identified the orthologues of the components of the Rab prenylation machinery in 43 organisms, representing the crown eukaryotic groups. We characterize in detail the domain structure of all these components and the phylogenetic relationships between the individual domains. Conclusion: We found different domain insertions in different taxa, in α-subunits of RGGTase and REP. Our results suggest that there were multiple insertions, expansions and contractions in the evolution of this prenylation complex.
Journal of Archaeological Science: Reports, 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 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.
Journal of Archaeological Science, 2019
Royal Society Open Science, 2016
More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, ... more More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine...
Scientific reports, Jan 17, 2018
The origin of the elephant on the island of Borneo remains elusive. Research has suggested two al... more The origin of the elephant on the island of Borneo remains elusive. Research has suggested two alternative hypotheses: the Bornean elephant stems either from a recent introduction in the 17th century or from an ancient colonization several hundreds of thousands years ago. Lack of elephant fossils has been interpreted as evidence for a very recent introduction, whereas mtDNA divergence from other Asian elephants has been argued to favor an ancient colonization. We investigated the demographic history of Bornean elephants using full-likelihood and approximate Bayesian computation analyses. Our results are at odds with both the recent and ancient colonization hypotheses, and favour a third intermediate scenario. We find that genetic data favour a scenario in which Bornean elephants experienced a bottleneck during the last glacial period, possibly as a consequence of the colonization of Borneo, and from which it has slowly recovered since. Altogether the data support a natural colonizat...
CHC22 clathrin plays a key role in intracellular membrane trafficking of the insulin-responsive g... more CHC22 clathrin plays a key role in intracellular membrane trafficking of the insulin-responsive glucose transporter GLUT4, and so in post-prandial clearance of glucose from human blood. We performed population genetic and phylogenetic analyses of the CLTCL1 gene, encoding CHC22, to gain insight into its functional evolution. Analysis of 58 vertebrate genomes showed independent loss of CLTCL1 in at least two lineages after it arose from a gene duplication during the emergence of jawed vertebrates. All vertebrates studied retain the parent CLTC gene encoding CHC17 clathrin, which mediates endocytosis and other housekeeping pathways of membrane traffic, as performed by the single type of clathrin in non-vertebrate eukaryotes. For those species retaining CLTCL1, preservation of CHC22 functionality was supported by strong evidence for purifying selection over phylogenetic timescales, as seen for CLTC. Nonetheless, CLTCL1 showed considerably greater allelic diversity than CLTC in humans a...
Nature Communications
Advances in phenology (the annual timing of species’ life-cycles) in response to climate change a... more Advances in phenology (the annual timing of species’ life-cycles) in response to climate change are generally viewed as bioindicators of climate change, but have not been considered as predictors of range expansions. Here, we show that phenology advances combine with the number of reproductive cycles per year (voltinism) to shape abundance and distribution trends in 130 species of British Lepidoptera, in response to ~0.5 °C spring-temperature warming between 1995 and 2014. Early adult emergence in warm years resulted in increased within- and between-year population growth for species with multiple reproductive cycles per year (n = 39 multivoltine species). By contrast, early emergence had neutral or negative consequences for species with a single annual reproductive cycle (n = 91 univoltine species), depending on habitat specialisation. We conclude that phenology advances facilitate polewards range expansions in species exhibiting plasticity for both phenology and voltinism, but may...
Ethnic and Racial Studies, 2015
The differences between copies of the human genome are very small, but tend to cluster in differe... more The differences between copies of the human genome are very small, but tend to cluster in different populations. So, despite the fact that low inter-population differentiation does not support a biological definition of races statistical methods are nonetheless claimed to be able to predict successfully the population of origin of a DNA sample. Such methods are employed in commercial genetic ancestry tests, and particular genetic signatures, often in the male-specific Y-chromosome or maternally-inherited mitochondrial DNA, have become widely identified with particular ancestral or existing groups, such as Vikings, Jews, or Zulus. Here, we provide a primer on genetics, and describe how genetic markers have become associated with particular groups. We describe the conflict between population genetics and individual-based genetics and the pitfalls of over-simplistic genetic interpretations, arguing that although the tests themselves are reliable, the interpretations are unreliable and strongly influenced by cultural and other social forces.
The arrival of agriculture into Europe during the Neolithic transition brought a significant shif... more The arrival of agriculture into Europe during the Neolithic transition brought a significant shift in human lifestyle and
subsistence. However, the conditions under which the spread of the new culture and technologies occurred are still
debated. Similarly, the roles played by women and men during the Neolithic transition are not well understood, probably
due to the fact that mitochondrial DNA (mtDNA) and Y chromosome (NRY) data are usually studied independently rather
than within the same statistical framework. Here, we applied an integrative approach, using different model-based
inferential techniques, to analyse published datasets from contemporary and ancient European populations. By integrating
mtDNA and NRY data into the same admixture approach, we show that both males and females underwent the same
admixture history and both support the demic diffusion model of Ammerman and Cavalli-Sforza. Similarly, the patterns of
genetic diversity found in extant and ancient populations demonstrate that both modern and ancient mtDNA support the
demic diffusion model. They also show that population structure and differential growth between farmers and hunter-
gatherers are necessary to explain both types of data. However, we also found some differences between male and female
markers, suggesting that the female effective population size was larger than that of the males, probably due to different
demographic histories. We argue that these differences are most probably related to the various shifts in cultural practices
and lifestyles that followed the Neolithic Transition, such as sedentism, the shift from polygyny to monogamy or the
increase of patrilocality.
Cultural practices can deeply influence genetic diversity patterns. The Neolithic transitions tha... more Cultural practices can deeply influence genetic diversity patterns. The Neolithic transitions that took place at
different times and locations around the world led to major cultural and demographic changes that influenced
and therefore left their marks on human genetic diversity patterns. Several studies on the European Neolithic
transition suggest that mitochondrial DNA (mtDNA) and Y-chromosome data can exhibit different patterns,
which could be owing to different demographic histories for females and males. Archaeological and anthro-
pological data suggest that the transition from hunter–gatherers (HGs) to farmers’ societies is probably
associated with changes in social organization, particularly in post-marital residence (PMR) rules (i.e. patri-
locality, matrilocality or bilocality). The movements of humans and genes associated with these rules can be
seen as sex-biased short-range migrations. We developed a new individual-based simulation approach to
explore the genetic consequences of 45 different scenarios, where we varied the patterns of PMR and admix-
ture between HGs and farmers. We recorded mtDNA and Y-chromosome data and analysed their diversity
patterns within and between populations, through time and space. We also collected published mtDNA and
Y-chromosome data from European and Near-Eastern populations in order to identify the scenarios that
would best explain them. We show that: (i) different PMR systems can lead to different patterns of genetic
diversity and differentiation, (ii) asymmetries between mtDNA and Y-chromosome can be owing to different
behaviours between males and females, but also to different mutations rates, and (iii) patrilocality in farmers
explains the present patterns of genetic diversity better than matrilocality or bilocality. Moreover, we found
that (iv) the genetic diversity of farmers change depending on the HGs PMR rules even though they are
assumed to disappear more than 5000 years ago in our simulations.