Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and... more Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16-19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that - analysed alongside 100 published ones - enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the ...
The strong phylogenetic signal provided by mitochondrial deoxyribonucleic acid (mtDNA) sequences ... more The strong phylogenetic signal provided by mitochondrial deoxyribonucleic acid (mtDNA) sequences within species is being exploited to reconstruct the maternal genealogy and anchor it in space and time. This is the starting point for interpretations of the processes in population history that led to those patterns, as illustrated here for humans. Mitochondrial phylogeography began by revolutionising our view of modern human origins, with the demonstration that modern humans dispersed from Africa approximately 60 000 years ago. Now benefitting from the high genealogical and chronological resolution afforded by whole‐mtDNA sequences, and despite the advent of genome‐wide analyses, mtDNA continues to illuminate prehistoric settlement and dispersal history. It has often led to challenges to received wisdom, such as the stress on pre‐Neolithic dispersals at the end of the Ice Age in many parts of the world, and the database of contemporary variation is currently being augmented by rapidly increasing information from ancient DNA.
Phylogenetic and diversity analysis of the mtDNA control region sequence variation of 821 individ... more Phylogenetic and diversity analysis of the mtDNA control region sequence variation of 821 individuals from Europe and the Middle East distinguishes five major lineage groups with different internal diversities and divergence times. Consideration of the diversities and geographic distribution of these groups within Europe and the Middle East leads to the conclusion that ancestors of the great majority of modern, extant lineages entered Europe during the Upper Paleolithic. A further set of lineages arrived from the Middle East much later, and their age and geographic distribution within Europe correlates well with archaeological evidence for two culturally and geographically distinct Neolithic colonization events that are associated with the spread of agriculture. It follows from this interpretation that the major extant lineages throughout Europe predate the Neolithic expansion and that the spread of agriculture was a substantially indigenous development accompanied by only a relatively minor component of contemporary Middle Eastern agriculturalists. There is no evidence of any surviving Neanderthal lineages among modern Europeans.
Archaeogenetics was described by Renfrew as ‘the study of the human past using the techniques of ... more Archaeogenetics was described by Renfrew as ‘the study of the human past using the techniques of molecular genetics’ – involving the collaboration of geneticists with archaeologists, anthropologists, historical linguists, and climatologists. He traced its origins to the pioneering work of Cavalli-Sforza in the 1960s, using classical genetic markers (such as blood groups, etc.). Ammerman and Cavalli-Sforza developed a suite of new approaches, in particular the use of principal component maps, to evaluate the distribution of genetic variation in space. Their results on Europe, in particular, were taken to imply large-scale demic diffusion of farming communities from the Near East with the advent of the Neolithic. The discipline was then renewed in the 1980s by Wilson's work on mitochondrial DNA (mtDNA), as DNA sequencing started to become routine, making it possible for the first time to build genealogical trees of lineages within a species
Advances in intelligent systems and computing, Jun 22, 2019
Founder analysis is a sophisticated application of phylogeographic analysis. It comprises the est... more Founder analysis is a sophisticated application of phylogeographic analysis. It comprises the estimation of timing and impact of migrations in current populations by taking advantage of the non-recombining property of certain marker systems (in the first instance, mitochondrial DNA) and therefore the possibility of building realistic phylogenetic trees. Given two populations, a source and a sink, and an assumed direction of migration between them, we can identify founder haplotypes, date the founder clusters deriving from them, and also estimate the proportions of lineages in each migration event. Despite being a methodology dating back nearly two decades and having been featured in numerous research articles, its use has mostly been restricted to a handful of research groups due to the cumbersome and time-consuming calculations it entails, a hindrance which stems not only from the often prohibitively large volume of data being dealt with but also the intricacies involved in the detection of founders. We have developed a Python-based tool with a user-friendly interface in response to these issues, providing a fast, automatized approach to the founder analysis pipeline and additional useful features within this context, expediting this step efficiently and allowing more hypotheses to be tested in a reliable and easily reproducible manner.
Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and... more Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16-19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that - analysed alongside 100 published ones - enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the ...
The strong phylogenetic signal provided by mitochondrial deoxyribonucleic acid (mtDNA) sequences ... more The strong phylogenetic signal provided by mitochondrial deoxyribonucleic acid (mtDNA) sequences within species is being exploited to reconstruct the maternal genealogy and anchor it in space and time. This is the starting point for interpretations of the processes in population history that led to those patterns, as illustrated here for humans. Mitochondrial phylogeography began by revolutionising our view of modern human origins, with the demonstration that modern humans dispersed from Africa approximately 60 000 years ago. Now benefitting from the high genealogical and chronological resolution afforded by whole‐mtDNA sequences, and despite the advent of genome‐wide analyses, mtDNA continues to illuminate prehistoric settlement and dispersal history. It has often led to challenges to received wisdom, such as the stress on pre‐Neolithic dispersals at the end of the Ice Age in many parts of the world, and the database of contemporary variation is currently being augmented by rapidly increasing information from ancient DNA.
Phylogenetic and diversity analysis of the mtDNA control region sequence variation of 821 individ... more Phylogenetic and diversity analysis of the mtDNA control region sequence variation of 821 individuals from Europe and the Middle East distinguishes five major lineage groups with different internal diversities and divergence times. Consideration of the diversities and geographic distribution of these groups within Europe and the Middle East leads to the conclusion that ancestors of the great majority of modern, extant lineages entered Europe during the Upper Paleolithic. A further set of lineages arrived from the Middle East much later, and their age and geographic distribution within Europe correlates well with archaeological evidence for two culturally and geographically distinct Neolithic colonization events that are associated with the spread of agriculture. It follows from this interpretation that the major extant lineages throughout Europe predate the Neolithic expansion and that the spread of agriculture was a substantially indigenous development accompanied by only a relatively minor component of contemporary Middle Eastern agriculturalists. There is no evidence of any surviving Neanderthal lineages among modern Europeans.
Archaeogenetics was described by Renfrew as ‘the study of the human past using the techniques of ... more Archaeogenetics was described by Renfrew as ‘the study of the human past using the techniques of molecular genetics’ – involving the collaboration of geneticists with archaeologists, anthropologists, historical linguists, and climatologists. He traced its origins to the pioneering work of Cavalli-Sforza in the 1960s, using classical genetic markers (such as blood groups, etc.). Ammerman and Cavalli-Sforza developed a suite of new approaches, in particular the use of principal component maps, to evaluate the distribution of genetic variation in space. Their results on Europe, in particular, were taken to imply large-scale demic diffusion of farming communities from the Near East with the advent of the Neolithic. The discipline was then renewed in the 1980s by Wilson's work on mitochondrial DNA (mtDNA), as DNA sequencing started to become routine, making it possible for the first time to build genealogical trees of lineages within a species
Advances in intelligent systems and computing, Jun 22, 2019
Founder analysis is a sophisticated application of phylogeographic analysis. It comprises the est... more Founder analysis is a sophisticated application of phylogeographic analysis. It comprises the estimation of timing and impact of migrations in current populations by taking advantage of the non-recombining property of certain marker systems (in the first instance, mitochondrial DNA) and therefore the possibility of building realistic phylogenetic trees. Given two populations, a source and a sink, and an assumed direction of migration between them, we can identify founder haplotypes, date the founder clusters deriving from them, and also estimate the proportions of lineages in each migration event. Despite being a methodology dating back nearly two decades and having been featured in numerous research articles, its use has mostly been restricted to a handful of research groups due to the cumbersome and time-consuming calculations it entails, a hindrance which stems not only from the often prohibitively large volume of data being dealt with but also the intricacies involved in the detection of founders. We have developed a Python-based tool with a user-friendly interface in response to these issues, providing a fast, automatized approach to the founder analysis pipeline and additional useful features within this context, expediting this step efficiently and allowing more hypotheses to be tested in a reliable and easily reproducible manner.
Historical records document medieval immigration from North Africa to Iberia to create Islamic al... more Historical records document medieval immigration from North Africa to Iberia to create Islamic al-Andalus. Here, we present a low-coverage genome of an eleventh century CE man buried in an Islamic necropolis in Segorbe, near Valencia, Spain. Uniparental lineages indicate North African ancestry, but at the autosomal level he displays a mosaic of North African and European-like ancestries, distinct from any present-day population. Altogether, the genome-wide evidence, stable isotope results and the age of the burial indicate that his ancestry was ultimately a result of admixture between recently arrived Amazigh people (Berbers) and the population inhabiting the Peninsula prior to the Islamic conquest. We detect differences between our sample and a previously published group of contemporary individuals from Valencia, exemplifying how detailed, small-scale aDNA
A combined effect of functional constraints and random mutational events is responsible for the s... more A combined effect of functional constraints and random mutational events is responsible for the sequence evolution of the human mitochondrial DNA (mtDNA) control region. Most studies targeting this noncoding segment usually focus on its primary sequence information disregarding other informative levels such as secondary or tertiary DNA conformations. In this work, we combined the most recent developments in DNA folding calculations with a phylogenetic comparative approach in order to investigate the formation of intrastrand secondary structures in the human mtDNA control region. Our most striking results are those regarding a new cloverleaf-like secondary structure predicted for a 93-bp stretch of the control region 5'-peripheral domain. Randomized sequences indicated that this structure has a more negative folding energy than the average of random sequences with the same nucleotide composition. In addition, a sliding window scan across the complete mitochondrial genome revealed that it stands out as having one of the highest folding potential. Moreover, we detected several lines of evidence of both negative and positive selection on this structure with high levels of conservation at the structure-relevant stem regions and the occurrence of compensatory base changes in the primate lineage. In the light of previous data, we discuss the possible involvement of this structure in mtDNA replication and/or transcription. We conclude that maintenance of this structure is responsible for the observed heterogeneity in the rate of substitution among sites in part of the human hypervariable region I and that it is a hot spot for the 3' end of human mtDNA deletions.
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Papers by Martin B Richards