Lounes CHIKHI | Université Paul Sabatier de Toulouse (original) (raw)
Papers by Lounes CHIKHI
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Molecular Ecology Resources, 2021
Genotyping‐by‐sequencing methods such as RADseq are popular for generating genomic and population... more Genotyping‐by‐sequencing methods such as RADseq are popular for generating genomic and population‐scale data sets from a diverse range of organisms. These often lack a usable reference genome, restricting users to RADseq specific software for processing. However, these come with limitations compared to generic next generation sequencing (NGS) toolkits. Here, we describe and test a simple pipeline for reference‐free RADseq data processing that blends de novo elements from STACKS with the full suite of state‐of‐the art NGS tools. Specifically, we use the de novo RADseq assembly employed by STACKS to create a catalogue of RAD loci that serves as a reference for read mapping, variant calling and site filters. Using RADseq data from 28 zebra sequenced to ~8x depth‐of‐coverage we evaluate our approach by comparing the site frequency spectra (SFS) to those from alternative pipelines. Most pipelines yielded similar SFS at 8x depth, but only a genotype likelihood based pipeline performed similarly at low sequencing depth (2–4x). We compared the RADseq SFS with medium‐depth (~13x) shotgun sequencing of eight overlapping samples, revealing that the RADseq SFS was persistently slightly skewed towards rare and invariant alleles. Using simulations and human data we confirm that this is expected when there is allelic dropout (AD) in the RADseq data. AD in the RADseq data caused a heterozygosity deficit of ~16%, which dropped to ~5% after filtering AD. Hence, AD was the most important source of bias in our RADseq data.
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Nature, 2019
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Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed through... more Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic explosion has prompted understandable concern that there has been substantial oversplitting in the mouse lemur clade. Here, we take an integrative approach to investigate species diversity in two pairs of sister lineages that occur in a region in northeastern Madagascar with high levels of microendemism and predicted habitat loss. We analyzed RADseq data with multispecies coalescent (MSC) species delimitation methods for three named species and an undescribed lineage previously identified to have divergent mtDNA. Marked differences in effective population sizes, levels of gene flow, patterns of isolation-by-distance, and species delimitation results were found among them. Whereas all tests support the recognition of the presently undescribed lineage as a separate species, the sp...
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Journal of Archaeological Science, 2019
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Trends in ecology & evolution, Jan 14, 2018
We challenge the view that our species, Homo sapiens, evolved within a single population and/or r... more We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the polycentric origin and persistence of regionally distinct Pleistocene material culture in a variety of paleoecological settings. Genetic studies also indicate that present-day population structure within Africa extends to deep times, paralleling a paleoenvironmental record of shifting and fractured habitable zones. We argue that these fields support an emerging view of a highly structured African prehistory that should be considered in human evolutionary inferences, prompting new interpretations, questions, and interdisciplinary research directions.
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Nature ecology & evolution, Jan 22, 2018
The plains zebra (Equus quagga) is an ecologically important species of the African savannah. It ... more The plains zebra (Equus quagga) is an ecologically important species of the African savannah. It is also one of the most numerous and widely distributed ungulates, and six subspecies have been described based on morphological variation. However, the within-species evolutionary processes have been difficult to resolve due to its high mobility and a lack of consensus regarding the population structure. We obtained genome-wide DNA polymorphism data from more than 167,000 loci for 59 plains zebras from across the species range, encompassing all recognized extant subspecies, as well as three mountain zebras (Equus zebra) and three Grevy's zebras (Equus grevyi). Surprisingly, the population genetic structure does not mirror the morphology-based subspecies delineation, underlining the dangers of basing management units exclusively on morphological variation. We use demographic modelling to provide insights into the past phylogeography of the species. The results identify a southern Afr...
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American journal of human genetics, Jan 16, 2017
Zoroastrianism is one of the oldest extant religions in the world, originating in Persia (present... more Zoroastrianism is one of the oldest extant religions in the world, originating in Persia (present-day Iran) during the second millennium BCE. Historical records indicate that migrants from Persia brought Zoroastrianism to India, but there is debate over the timing of these migrations. Here we present genome-wide autosomal, Y chromosome, and mitochondrial DNA data from Iranian and Indian Zoroastrians and neighboring modern-day Indian and Iranian populations and conduct a comprehensive genome-wide genetic analysis in these groups. Using powerful haplotype-based techniques, we find that Zoroastrians in Iran and India have increased genetic homogeneity relative to other sampled groups in their respective countries, consistent with their current practices of endogamy. Despite this, we infer that Indian Zoroastrians (Parsis) intermixed with local groups sometime after their arrival in India, dating this mixture to 690-1390 CE and providing strong evidence that Iranian Zoroastrian ancestry...
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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...
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Genome biology and evolution, Jan 11, 2015
A polymorphic inversion that lies on chromosome 17q21 comprises two major haplotype families (H1 ... more A polymorphic inversion that lies on chromosome 17q21 comprises two major haplotype families (H1 and H2) that not only differ in orientation but also in copy-number. While the processes driving the spread of the inversion-associated lineage (H2) in humans remain unclear, a selective advantage has been proposed for one of its subtypes. Here, we genotyped a large panel of individuals from previously overlooked populations using a custom array with a unique panel of H2-specific single nucleotide polymorphisms (SNPs) and found a patchy distribution of H2 haplotypes in Africa, with North Africans displaying a higher frequency of inverted subtypes, when compared to Sub-Saharan groups. Interestingly, North African H2s were found to be closer to "non-African" chromosomes further supporting that these populations may have diverged more recently from groups outside Africa. Our results uncovered higher diversity within the H2 family than previously described, weakening the hypothesis...
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Most species do not live in a constant environment over space or time. Their environment is often... more Most species do not live in a constant environment over space or time. Their environment is often heterogeneous with a huge variability in resource availability and exposure to pathogens or predators, which may affect the local densities of the species. Moreover, the habitat might be fragmented, preventing free and isotropic migrations between local sub-populations (demes) of a species, making some demes more isolated than others. For example, during the last ice age populations of many species migrated towards refuge areas from which re-colonization originated when conditions improved. However, populations that could not move fast enough or could not adapt to the new environmental conditions may face extinctions. Populations living in these types of dynamic environments are often referred to as metapopulations and modeled as an array of subdivisions (or demes) that exchange migrants with their neighbors. Several studies have focused on the description of their demography, probabili...
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Primate Conservation, 2014
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The Encyclopedia of Global Human Migration, 2013
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Encyclopedia of Life Sciences, 2006
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eLS, 2013
After having introduced the Hardy–Weinberg principle and its underlying assumptions, the authors ... more After having introduced the Hardy–Weinberg principle and its underlying assumptions, the authors describe the main causes of departures from equilibrium. They then stress the importance of species subdivision into different local subpopulations/demes. This geographical structure affects allele frequencies over space and consequently the proportions of different genotypes in the local populations. It leads to the Wahlund effect, which can be defined as the excess of homozygotes or the deficit in heterozygotes observed in a sample of individuals obtained from a structured population, even when the local populations are randomly mating. Finally, the authors briefly outline the extension of the Wahlund effect at two loci and its consequences in association studies. Key Concepts: The Hardy–Weinberg principle states that genotype frequencies can be predicted from gene/allele frequencies and remain constant over generations in random-mating populations under the simple assumptions of no mutation, selection or migration. Many deviations from random mating can be observed in natural populations, such as assortative mating or other mating systems that lead to inbreeding or outbreeding. Species subdivision (into subpopulations, social groups and families) is also a common pattern encountered in natural populations that can cause substantial spatial genetic structure and departure from random mating depending on the sampling unit. The Wahlund effect is both the apparent excess of homozygotes and the deficit of heterozygotes observed at single locus data in a large ‘sample’ of individuals due to the existence of population subdivision. The Wahlund effect can be extended at multiple loci where it leads to an apparent excess of double homozygotes and either an excess or a deficit of heterozygote combinations, depending on allele frequency variation at different loci across populations. An important consequence of the Wahlund effect due to unknown population stratification is the creation of allelic association or linkage disequilibrium between different loci in the total sample of individuals. Unknown population structure can, therefore, have a major impact on association studies by creating false-positive tests, and a large range of methods have been developed that allow to correct or control genetic structure. Population structure and sampling units (or sampling strategy) are increasingly recognised as important factors when making inference in population genetics under models that assume HW and ignore structure. Keywords: Hardy–Weinberg equilibrium; Wahlund effect; population subdivision; linkage disequilibrium; association studies
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Molecular Ecology Resources, 2021
Genotyping‐by‐sequencing methods such as RADseq are popular for generating genomic and population... more Genotyping‐by‐sequencing methods such as RADseq are popular for generating genomic and population‐scale data sets from a diverse range of organisms. These often lack a usable reference genome, restricting users to RADseq specific software for processing. However, these come with limitations compared to generic next generation sequencing (NGS) toolkits. Here, we describe and test a simple pipeline for reference‐free RADseq data processing that blends de novo elements from STACKS with the full suite of state‐of‐the art NGS tools. Specifically, we use the de novo RADseq assembly employed by STACKS to create a catalogue of RAD loci that serves as a reference for read mapping, variant calling and site filters. Using RADseq data from 28 zebra sequenced to ~8x depth‐of‐coverage we evaluate our approach by comparing the site frequency spectra (SFS) to those from alternative pipelines. Most pipelines yielded similar SFS at 8x depth, but only a genotype likelihood based pipeline performed similarly at low sequencing depth (2–4x). We compared the RADseq SFS with medium‐depth (~13x) shotgun sequencing of eight overlapping samples, revealing that the RADseq SFS was persistently slightly skewed towards rare and invariant alleles. Using simulations and human data we confirm that this is expected when there is allelic dropout (AD) in the RADseq data. AD in the RADseq data caused a heterozygosity deficit of ~16%, which dropped to ~5% after filtering AD. Hence, AD was the most important source of bias in our RADseq data.
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Nature, 2019
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Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed through... more Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic explosion has prompted understandable concern that there has been substantial oversplitting in the mouse lemur clade. Here, we take an integrative approach to investigate species diversity in two pairs of sister lineages that occur in a region in northeastern Madagascar with high levels of microendemism and predicted habitat loss. We analyzed RADseq data with multispecies coalescent (MSC) species delimitation methods for three named species and an undescribed lineage previously identified to have divergent mtDNA. Marked differences in effective population sizes, levels of gene flow, patterns of isolation-by-distance, and species delimitation results were found among them. Whereas all tests support the recognition of the presently undescribed lineage as a separate species, the sp...
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Journal of Archaeological Science, 2019
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Trends in ecology & evolution, Jan 14, 2018
We challenge the view that our species, Homo sapiens, evolved within a single population and/or r... more We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the polycentric origin and persistence of regionally distinct Pleistocene material culture in a variety of paleoecological settings. Genetic studies also indicate that present-day population structure within Africa extends to deep times, paralleling a paleoenvironmental record of shifting and fractured habitable zones. We argue that these fields support an emerging view of a highly structured African prehistory that should be considered in human evolutionary inferences, prompting new interpretations, questions, and interdisciplinary research directions.
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Nature ecology & evolution, Jan 22, 2018
The plains zebra (Equus quagga) is an ecologically important species of the African savannah. It ... more The plains zebra (Equus quagga) is an ecologically important species of the African savannah. It is also one of the most numerous and widely distributed ungulates, and six subspecies have been described based on morphological variation. However, the within-species evolutionary processes have been difficult to resolve due to its high mobility and a lack of consensus regarding the population structure. We obtained genome-wide DNA polymorphism data from more than 167,000 loci for 59 plains zebras from across the species range, encompassing all recognized extant subspecies, as well as three mountain zebras (Equus zebra) and three Grevy's zebras (Equus grevyi). Surprisingly, the population genetic structure does not mirror the morphology-based subspecies delineation, underlining the dangers of basing management units exclusively on morphological variation. We use demographic modelling to provide insights into the past phylogeography of the species. The results identify a southern Afr...
Bookmarks Related papers MentionsView impact
American journal of human genetics, Jan 16, 2017
Zoroastrianism is one of the oldest extant religions in the world, originating in Persia (present... more Zoroastrianism is one of the oldest extant religions in the world, originating in Persia (present-day Iran) during the second millennium BCE. Historical records indicate that migrants from Persia brought Zoroastrianism to India, but there is debate over the timing of these migrations. Here we present genome-wide autosomal, Y chromosome, and mitochondrial DNA data from Iranian and Indian Zoroastrians and neighboring modern-day Indian and Iranian populations and conduct a comprehensive genome-wide genetic analysis in these groups. Using powerful haplotype-based techniques, we find that Zoroastrians in Iran and India have increased genetic homogeneity relative to other sampled groups in their respective countries, consistent with their current practices of endogamy. Despite this, we infer that Indian Zoroastrians (Parsis) intermixed with local groups sometime after their arrival in India, dating this mixture to 690-1390 CE and providing strong evidence that Iranian Zoroastrian ancestry...
Bookmarks Related papers MentionsView impact
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...
Bookmarks Related papers MentionsView impact
Genome biology and evolution, Jan 11, 2015
A polymorphic inversion that lies on chromosome 17q21 comprises two major haplotype families (H1 ... more A polymorphic inversion that lies on chromosome 17q21 comprises two major haplotype families (H1 and H2) that not only differ in orientation but also in copy-number. While the processes driving the spread of the inversion-associated lineage (H2) in humans remain unclear, a selective advantage has been proposed for one of its subtypes. Here, we genotyped a large panel of individuals from previously overlooked populations using a custom array with a unique panel of H2-specific single nucleotide polymorphisms (SNPs) and found a patchy distribution of H2 haplotypes in Africa, with North Africans displaying a higher frequency of inverted subtypes, when compared to Sub-Saharan groups. Interestingly, North African H2s were found to be closer to "non-African" chromosomes further supporting that these populations may have diverged more recently from groups outside Africa. Our results uncovered higher diversity within the H2 family than previously described, weakening the hypothesis...
Bookmarks Related papers MentionsView impact
Most species do not live in a constant environment over space or time. Their environment is often... more Most species do not live in a constant environment over space or time. Their environment is often heterogeneous with a huge variability in resource availability and exposure to pathogens or predators, which may affect the local densities of the species. Moreover, the habitat might be fragmented, preventing free and isotropic migrations between local sub-populations (demes) of a species, making some demes more isolated than others. For example, during the last ice age populations of many species migrated towards refuge areas from which re-colonization originated when conditions improved. However, populations that could not move fast enough or could not adapt to the new environmental conditions may face extinctions. Populations living in these types of dynamic environments are often referred to as metapopulations and modeled as an array of subdivisions (or demes) that exchange migrants with their neighbors. Several studies have focused on the description of their demography, probabili...
Bookmarks Related papers MentionsView impact
Primate Conservation, 2014
Bookmarks Related papers MentionsView impact
The Encyclopedia of Global Human Migration, 2013
Bookmarks Related papers MentionsView impact
Encyclopedia of Life Sciences, 2006
Bookmarks Related papers MentionsView impact
eLS, 2013
After having introduced the Hardy–Weinberg principle and its underlying assumptions, the authors ... more After having introduced the Hardy–Weinberg principle and its underlying assumptions, the authors describe the main causes of departures from equilibrium. They then stress the importance of species subdivision into different local subpopulations/demes. This geographical structure affects allele frequencies over space and consequently the proportions of different genotypes in the local populations. It leads to the Wahlund effect, which can be defined as the excess of homozygotes or the deficit in heterozygotes observed in a sample of individuals obtained from a structured population, even when the local populations are randomly mating. Finally, the authors briefly outline the extension of the Wahlund effect at two loci and its consequences in association studies. Key Concepts: The Hardy–Weinberg principle states that genotype frequencies can be predicted from gene/allele frequencies and remain constant over generations in random-mating populations under the simple assumptions of no mutation, selection or migration. Many deviations from random mating can be observed in natural populations, such as assortative mating or other mating systems that lead to inbreeding or outbreeding. Species subdivision (into subpopulations, social groups and families) is also a common pattern encountered in natural populations that can cause substantial spatial genetic structure and departure from random mating depending on the sampling unit. The Wahlund effect is both the apparent excess of homozygotes and the deficit of heterozygotes observed at single locus data in a large ‘sample’ of individuals due to the existence of population subdivision. The Wahlund effect can be extended at multiple loci where it leads to an apparent excess of double homozygotes and either an excess or a deficit of heterozygote combinations, depending on allele frequency variation at different loci across populations. An important consequence of the Wahlund effect due to unknown population stratification is the creation of allelic association or linkage disequilibrium between different loci in the total sample of individuals. Unknown population structure can, therefore, have a major impact on association studies by creating false-positive tests, and a large range of methods have been developed that allow to correct or control genetic structure. Population structure and sampling units (or sampling strategy) are increasingly recognised as important factors when making inference in population genetics under models that assume HW and ignore structure. Keywords: Hardy–Weinberg equilibrium; Wahlund effect; population subdivision; linkage disequilibrium; association studies
Bookmarks Related papers MentionsView impact