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1.
Genome Biol ; 25(1): 201, 2024 Jul 30.
Artículo en Inglés | MEDLINE | ID: mdl-39080715

RESUMEN

BACKGROUND: North African human populations present a complex demographic scenario due to the presence of an autochthonous genetic component and population substructure, plus extensive gene flow from the Middle East, Europe, and sub-Saharan Africa. RESULTS: We conducted a comprehensive analysis of 364 genomes to construct detailed demographic models for the North African region, encompassing its two primary ethnic groups, the Arab and Amazigh populations. This was achieved through an Approximate Bayesian Computation with Deep Learning (ABC-DL) framework and a novel algorithm called Genetic Programming for Population Genetics (GP4PG). This innovative approach enabled us to effectively model intricate demographic scenarios, utilizing a subset of 16 whole genomes at > 30X coverage. The demographic model suggested by GP4PG exhibited a closer alignment with the observed data compared to the ABC-DL model. Both point to a back-to-Africa origin of North African individuals and a close relationship with Eurasian populations. Results support different origins for Amazigh and Arab populations, with Amazigh populations originating back in Epipaleolithic times, while GP4PG supports Arabization as the main source of Middle Eastern ancestry. The GP4PG model includes population substructure in surrounding populations (sub-Saharan Africa and Middle East) with continuous decaying gene flow after population split. Contrary to ABC-DL, the best GP4PG model does not require pulses of admixture from surrounding populations into North Africa pointing to soft splits as drivers of divergence in North Africa. CONCLUSIONS: We have built a demographic model on North Africa that points to a back-to-Africa expansion and a differential origin between Arab and Amazigh populations.


Asunto(s)
Genética de Población , Genoma Humano , Humanos , África del Norte , Población Negra/genética , Modelos Genéticos , Flujo Génico , Teorema de Bayes , Medio Oriente , Árabes/genética , Algoritmos , Pueblo Norteafricano
2.
Hum Genomics ; 18(1): 53, 2024 May 27.
Artículo en Inglés | MEDLINE | ID: mdl-38802968

RESUMEN

BACKGROUND: The human lineage has undergone a postcranial skeleton gracilization (i.e. lower bone mass and strength relative to body size) compared to other primates and archaic populations such as the Neanderthals. This gracilization has been traditionally explained by differences in the mechanical load that our ancestors exercised. However, there is growing evidence that gracilization could also be genetically influenced. RESULTS: We have analyzed the LRP5 gene, which is known to be associated with high bone mineral density conditions, from an evolutionary and functional point of view. Taking advantage of the published genomes of archaic Homo populations, our results suggest that this gene has a complex evolutionary history both between archaic and living humans and within living human populations. In particular, we identified the presence of different selective pressures in archaics and extant modern humans, as well as evidence of positive selection in the African and South East Asian populations from the 1000 Genomes Project. Furthermore, we observed a very limited evidence of archaic introgression in this gene (only at three haplotypes of East Asian ancestry out of the 1000 Genomes), compatible with a general erasing of the fingerprint of archaic introgression due to functional differences in archaics compared to extant modern humans. In agreement with this hypothesis, we observed private mutations in the archaic genomes that we experimentally validated as putatively increasing bone mineral density. In particular, four of five archaic missense mutations affecting the first ß-propeller of LRP5 displayed enhanced Wnt pathway activation, of which two also displayed reduced negative regulation. CONCLUSIONS: In summary, these data suggest a genetic component contributing to the understanding of skeletal differences between extant modern humans and archaic Homo populations.


Asunto(s)
Evolución Molecular , Proteína-5 Relacionada con Receptor de Lipoproteína de Baja Densidad , Hombre de Neandertal , Humanos , Proteína-5 Relacionada con Receptor de Lipoproteína de Baja Densidad/genética , Animales , Hombre de Neandertal/genética , Selección Genética/genética , Hominidae/genética , Haplotipos/genética , Densidad Ósea/genética , Genoma Humano/genética
3.
Nat Rev Genet ; 25(1): 61-78, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-37666948

RESUMEN

In population genetics, the emergence of large-scale genomic data for various species and populations has provided new opportunities to understand the evolutionary forces that drive genetic diversity using statistical inference. However, the era of population genomics presents new challenges in analysing the massive amounts of genomes and variants. Deep learning has demonstrated state-of-the-art performance for numerous applications involving large-scale data. Recently, deep learning approaches have gained popularity in population genetics; facilitated by the advent of massive genomic data sets, powerful computational hardware and complex deep learning architectures, they have been used to identify population structure, infer demographic history and investigate natural selection. Here, we introduce common deep learning architectures and provide comprehensive guidelines for implementing deep learning models for population genetic inference. We also discuss current challenges and future directions for applying deep learning in population genetics, focusing on efficiency, robustness and interpretability.


Asunto(s)
Aprendizaje Profundo , Genómica , Genética de Población , Genoma , Evolución Biológica
4.
Nat Ecol Evol ; 7(9): 1503-1514, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37500909

RESUMEN

Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.


Asunto(s)
Hominidae , Hombre de Neandertal , Animales , Humanos , Gorilla gorilla/genética , Pan paniscus/genética , Teorema de Bayes , Hominidae/genética , Pan troglodytes , Hombre de Neandertal/genética
5.
Eur J Hum Genet ; 30(12): 1439-1443, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36192439

RESUMEN

An important fraction of patients with rare disorders remains with no clear genetic diagnostic, even after whole-exome or whole-genome sequencing, posing a difficulty in giving adequate treatment and genetic counseling. The analysis of genomic data in rare disorders mostly considers the presence of single gene variants in coding regions that follow a concrete monogenic mode of inheritance. A digenic inheritance, with variants in two functionally-related genes in the same individual, is a plausible alternative that might explain the genetic basis of the disease in some cases. In this case, digenic disease combinations should be absent or underrepresented in healthy individuals. We develop a framework to evaluate the significance of digenic combinations and test its statistical power in different scenarios. We suggest that this approach will be relevant with the advent of new sequencing efforts including hundreds of thousands of samples.


Asunto(s)
Exoma , Herencia Multifactorial , Humanos , Análisis de Secuencia de ADN , Secuenciación del Exoma , Enfermedades Raras/genética
6.
Front Genet ; 13: 1100440, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36704333

RESUMEN

The genetic variation of the European population at a macro-geographic scale follows genetic gradients which reflect main migration events. However, less is known about factors affecting mating patterns at a micro-geographic scale. In this study we have analyzed 726,718 autosomal single nucleotide variants in 435 individuals from the catalan Pyrenees covering around 200 km of a vast and abrupt region in the north of the Iberian Peninsula, for which we have information about the geographic origin of all grand-parents and parents. At a macro-geographic scale, our analyses recapitulate the genetic gradient observed in Spain. However, we also identified the presence of micro-population substructure among the sampled individuals. Such micro-population substructure does not correlate with geographic barriers such as the expected by the orography of the considered region, but by the bishoprics present in the covered geographic area. These results support that, on top of main human migrations, long ongoing socio-cultural factors have also shaped the genetic diversity observed at rural populations.

7.
Nat Hum Behav ; 5(12): 1600-1601, 2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-34782731
8.
Eur J Hum Genet ; 29(10): 1557-1565, 2021 10.
Artículo en Inglés | MEDLINE | ID: mdl-33837278

RESUMEN

The area of the Spanish Pyrenees is particularly interesting for studying the demographic dynamics of European rural areas given its orography, the main traditional rural condition of its population and the reported higher patterns of consanguinity of the region. Previous genetic studies suggest a gradient of genetic continuity of the area in the West to East axis. However, it has been shown that micro-population substructure can be detected when considering high-quality NGS data and using spatial explicit methods. In this work, we have analyzed the genome of 30 individuals sequenced at 40× from five different valleys in the Spanish Eastern Pyrenees (SEP) separated by less than 140 km along a west to east axis. Using haplotype-based methods and spatial analyses, we have been able to detect micro-population substructure within SEP not seen in previous studies. Linkage disequilibrium and autozygosity analyses suggest that the SEP populations show diverse demographic histories. In agreement with these results, demographic modeling by means of ABC-DL identify heterogeneity in their effective population sizes despite of their close geographic proximity, and suggests that the population substructure within SEP could have appeared around 2500 years ago. Overall, these results suggest that each rural population of the Pyrenees could represent a unique entity.


Asunto(s)
Pool de Genes , Aislamiento Reproductivo , Población Rural , Haplotipos , Humanos , Desequilibrio de Ligamiento , Polimorfismo Genético , España , Secuenciación Completa del Genoma/estadística & datos numéricos
9.
Cell ; 184(10): 2565-2586.e21, 2021 05 13.
Artículo en Inglés | MEDLINE | ID: mdl-33930288

RESUMEN

The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.


Asunto(s)
Civilización/historia , Genoma Humano , Genoma Mitocondrial , Migración Humana/historia , ADN Antiguo , Antigua Grecia , Historia Antigua , Humanos
10.
Genome Med ; 13(1): 15, 2021 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-33517887

RESUMEN

BACKGROUND: Pancreatic cancer (PC) is a complex disease in which both non-genetic and genetic factors interplay. To date, 40 GWAS hits have been associated with PC risk in individuals of European descent, explaining 4.1% of the phenotypic variance. METHODS: We complemented a new conventional PC GWAS (1D) with genome spatial autocorrelation analysis (2D) permitting to prioritize low frequency variants not detected by GWAS. These were further expanded via Hi-C map (3D) interactions to gain additional insight into the inherited basis of PC. In silico functional analysis of public genomic information allowed prioritization of potentially relevant candidate variants. RESULTS: We identified several new variants located in genes for which there is experimental evidence of their implication in the biology and function of pancreatic acinar cells. Among them is a novel independent variant in NR5A2 (rs3790840) with a meta-analysis p value = 5.91E-06 in 1D approach and a Local Moran's Index (LMI) = 7.76 in 2D approach. We also identified a multi-hit region in CASC8-a lncRNA associated with pancreatic carcinogenesis-with a lowest p value = 6.91E-05. Importantly, two new PC loci were identified both by 2D and 3D approaches: SIAH3 (LMI = 18.24), CTRB2/BCAR1 (LMI = 6.03), in addition to a chromatin interacting region in XBP1-a major regulator of the ER stress and unfolded protein responses in acinar cells-identified by 3D; all of them with a strong in silico functional support. CONCLUSIONS: This multi-step strategy, combined with an in-depth in silico functional analysis, offers a comprehensive approach to advance the study of PC genetic susceptibility and could be applied to other diseases.


Asunto(s)
Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Neoplasias Pancreáticas/genética , Biomarcadores de Tumor/genética , Línea Celular Tumoral , Simulación por Computador , Redes Reguladoras de Genes , Genoma Humano , Humanos , Desequilibrio de Ligamiento/genética , Reproducibilidad de los Resultados , Transducción de Señal/genética
11.
Genes (Basel) ; 13(1)2021 12 24.
Artículo en Inglés | MEDLINE | ID: mdl-35052384

RESUMEN

The 1000 Genomes Project (1000G) is one of the most popular whole genome sequencing datasets used in different genomics fields and has boosting our knowledge in medical and population genomics, among other fields. Recent studies have reported the presence of ghost mutation signals in the 1000G. Furthermore, studies have shown that these mutations can influence the outcomes of follow-up studies based on the genetic variation of 1000G, such as single nucleotide variants (SNV) imputation. While the overall effect of these ghost mutations can be considered negligible for common genetic variants in many populations, the potential bias remains unclear when studying low frequency genetic variants in the population. In this study, we analyze the effect of the sequencing center in predicted loss of function (LoF) alleles, the number of singletons, and the patterns of archaic introgression in the 1000G. Our results support previous studies showing that the sequencing center is associated with LoF and singletons independent of the population that is considered. Furthermore, we observed that patterns of archaic introgression were distorted for some populations depending on the sequencing center. When analyzing the frequency of SNPs showing extreme patterns of genotype differentiation among centers for CEU, YRI, CHB, and JPT, we observed that the magnitude of the sequencing batch effect was stronger at MAF < 0.2 and showed different profiles between CHB and the other populations. All these results suggest that data from 1000G must be interpreted with caution when considering statistics using variants at low frequency.


Asunto(s)
Técnicas de Cultivo Celular por Lotes/métodos , Genética de Población , Genoma Humano , Genómica/normas , Polimorfismo de Nucleótido Simple , Programas Informáticos , Secuenciación Completa del Genoma/normas , Anciano , Femenino , Estudio de Asociación del Genoma Completo , Genotipo , Humanos , Masculino , Población Rural , España
12.
Genes (Basel) ; 13(1)2021 12 30.
Artículo en Inglés | MEDLINE | ID: mdl-35052433

RESUMEN

Attention-deficit hyperactivity disorder (ADHD) is a complex neurodevelopmental disorder characterized by hyperactivity, impulsivity, and/or inattention, which are symptoms also observed in many rare genetic disorders. We searched for genes involved in Mendelian disorders presenting with ADHD symptoms in the Online Mendelian Inheritance in Man (OMIM) database, to curate a list of new candidate risk genes for ADHD. We explored the enrichment of functions and pathways in this gene list, and tested whether rare or common variants in these genes are associated with ADHD or with its comorbidities. We identified 139 genes, causal for 137 rare disorders, mainly related to neurodevelopmental and brain function. Most of these Mendelian disorders also present with other psychiatric traits that are often comorbid with ADHD. Using whole exome sequencing (WES) data from 668 ADHD cases, we found rare variants associated with the dimension of the severity of inattention symptoms in three genes: KIF11, WAC, and CRBN. Then, we focused on common variants and identified six genes associated with ADHD (in 19,099 cases and 34,194 controls): MANBA, UQCC2, HIVEP2, FOPX1, KANSL1, and AUH. Furthermore, HIVEP2, FOXP1, and KANSL1 were nominally associated with autism spectrum disorder (ASD) (18,382 cases and 27,969 controls), as well as HIVEP2 with anxiety (7016 cases and 14,475 controls), and FOXP1 with aggression (18,988 individuals), which is in line with the symptomatology of the rare disorders they are responsible for. In conclusion, inspecting Mendelian disorders and the genes responsible for them constitutes a valuable approach for identifying new risk genes and the mechanisms of complex disorders.


Asunto(s)
Trastorno por Déficit de Atención con Hiperactividad/genética , Trastorno por Déficit de Atención con Hiperactividad/patología , Marcadores Genéticos , Neumonía por Aspiración/genética , Adolescente , Adulto , Anciano , Trastorno por Déficit de Atención con Hiperactividad/epidemiología , Estudios de Casos y Controles , Comorbilidad , Femenino , Humanos , Masculino , Persona de Mediana Edad , Fenotipo , Neumonía por Aspiración/patología , Secuenciación del Exoma , Adulto Joven
13.
Sci Rep ; 10(1): 8622, 2020 05 25.
Artículo en Inglés | MEDLINE | ID: mdl-32451437

RESUMEN

Attention-deficit/hyperactivity disorder (ADHD) is an impairing neurodevelopmental condition highly prevalent in current populations. Several hypotheses have been proposed to explain this paradox, mainly in the context of the Paleolithic versus Neolithic cultural shift but especially within the framework of the mismatch theory. This theory elaborates on how a particular trait once favoured in an ancient environment might become maladaptive upon environmental changes. However, given the lack of genomic data available for ADHD, these theories have not been empirically tested. We took advantage of the largest GWAS meta-analysis available for this disorder consisting of over 20,000 individuals diagnosed with ADHD and 35,000 controls, to assess the evolution of ADHD-associated alleles in European populations using archaic, ancient and modern human samples. We also included Approximate Bayesian computation coupled with deep learning analyses and singleton density scores to detect human adaptation. Our analyses indicate that ADHD-associated alleles are enriched in loss of function intolerant genes, supporting the role of selective pressures in this early-onset phenotype. Furthermore, we observed that the frequency of variants associated with ADHD has steadily decreased since Paleolithic times, particularly in Paleolithic European populations compared to samples from the Neolithic Fertile Crescent. We demonstrate this trend cannot be explained by African admixture nor Neanderthal introgression, since introgressed Neanderthal alleles are enriched in ADHD risk variants. All analyses performed support the presence of long-standing selective pressures acting against ADHD-associated alleles until recent times. Overall, our results are compatible with the mismatch theory for ADHD but suggest a much older time frame for the evolution of ADHD-associated alleles compared to previous hypotheses.


Asunto(s)
Trastorno por Déficit de Atención con Hiperactividad/genética , Genoma Humano , Genómica/métodos , Hombre de Neandertal/genética , Alelos , Animales , Trastorno por Déficit de Atención con Hiperactividad/historia , Trastorno por Déficit de Atención con Hiperactividad/patología , Teorema de Bayes , Bases de Datos Genéticas , Aprendizaje Profundo , Evolución Molecular , Historia Antigua , Humanos
14.
Eur J Hum Genet ; 28(3): 287-299, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-31488894

RESUMEN

Previous studies indicated existing, albeit limited, genetic-geographic population substructure in the Dutch population based on genome-wide data and a lack of this for mitochondrial SNP based data. Despite the aforementioned studies, Y-chromosomal SNP data from the Netherlands remain scarce and do not cover the territory of the Netherlands well enough to allow a reliable investigation of genetic-geographic population substructure. Here we provide the first substantial dataset of detailed spatial Y-chromosomal haplogroup information in 2085 males collected across the Netherlands and supplemented with previously published data from northern Belgium. We found Y-chromosomal evidence for genetic-geographic population substructure, and several Y-haplogroups demonstrating significant clinal frequency distributions in different directions. By means of prediction surface maps we could visualize (complex) distribution patterns of individual Y-haplogroups in detail. These results highlight the value of a micro-geographic approach and are of great use for forensic and epidemiological investigations and our understanding of the Dutch population history. Moreover, the previously noted absence of genetic-geographic population substructure in the Netherlands based on mitochondrial DNA in contrast to our Y-chromosome results, hints at different population histories for women and men in the Netherlands.


Asunto(s)
Cromosomas Humanos Y/genética , Polimorfismo de Nucleótido Simple , Población/genética , Haplotipos , Humanos , Masculino , Países Bajos
15.
Eur J Hum Genet ; 28(3): 399, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-31645767

RESUMEN

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

16.
Genome Biol ; 20(1): 77, 2019 04 26.
Artículo en Inglés | MEDLINE | ID: mdl-31023378

RESUMEN

BACKGROUND: Population demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level. RESULTS: Here, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, with the hunter-gatherer groups being more genetically differentiated and having larger effective population sizes throughout most modern-human history. Admixture signals are found between neighbor populations from both hunter-gatherer and agriculturalists groups, whereas North African individuals are closely related to Eurasian populations. Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage. CONCLUSION: The present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level.


Asunto(s)
Población Negra/genética , Flujo Génico , Migración Humana , África , Variación Genética , Humanos , Filogeografía , Densidad de Población , Secuenciación Completa del Genoma
17.
Forensic Sci Int Genet ; 41: 72-82, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-31003081

RESUMEN

Correct identification of different human epithelial materials such as from skin, saliva and vaginal origin is relevant in forensic casework as it provides crucial information for crime reconstruction. However, the overlap in human cell type composition between these three epithelial materials provides challenges for their differentiation and identification when using previously proposed human cell biomarkers, while their microbiota composition largely differs. By using validated 16S rRNA gene massively parallel sequencing data from the Human Microbiome Project of 1636 skin, oral and vaginal samples, 50 taxonomy-independent deep learning networks were trained to classify these three tissues. Validation testing was performed in de-novo generated high-throughput 16S rRNA gene sequencing data using the Ion Torrent™ Personal Genome Machine from 110 test samples: 56 hand skin, 31 saliva and 23 vaginal secretion specimens. Body-site classification accuracy of these test samples was very high as indicated by AUC values of 0.99 for skin, 0.99 for oral, and 1 for vaginal secretion. Misclassifications were limited to 3 (5%) skin samples. Additional forensic validation testing was performed in mock casework samples by de-novo high-throughput sequencing of 19 freshly-prepared samples and 22 samples aged for 1 up to 7.6 years. All of the 19 fresh and 20 (91%) of the 22 aged mock casework samples were correctly tissue-type classified. Moreover, comparing the microbiome results with outcomes from previous human mRNA-based tissue identification testing in the same 16 aged mock casework samples reveals that our microbiome approach performs better in 12 (75%), similarly in 2 (12.5%), and less good in 2 (12.5%) of the samples. Our results demonstrate that this new microbiome approach allows for accurate tissue-type classification of three human epithelial materials of skin, oral and vaginal origin, which is highly relevant for future forensic investigations.


Asunto(s)
Aprendizaje Profundo , Secuenciación de Nucleótidos de Alto Rendimiento , Microbiota , ARN Ribosómico 16S/genética , Análisis de Secuencia de ARN , Femenino , Genética Forense/métodos , Humanos , Masculino , Saliva/microbiología , Piel/microbiología , Vagina/microbiología
18.
Nat Commun ; 10(1): 246, 2019 01 16.
Artículo en Inglés | MEDLINE | ID: mdl-30651539

RESUMEN

Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes (Neanderthal and Denisova). Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics.

19.
Genes (Basel) ; 10(1)2018 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-30583455

RESUMEN

Evolutionary medicine applies the principles of evolutionary biology to understand why we get sick rather than how, and it has undergone an exponential growth since the early 1990s [...].

20.
Genes (Basel) ; 9(7)2018 Jul 18.
Artículo en Inglés | MEDLINE | ID: mdl-30022013

RESUMEN

The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH interbred with archaic hominins once they left the African continent. Current non-African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.

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