Overcoming the dichotomy between open and isolated populations using genomic data from a large European dataset

Anagnostou, Paolo; Dominici, Valentina; Battaggia, Cinzia; Pagani, Luca; Vilar, Miguel G.; Wells, R. Spencer; Pettener, Davide; Sarno, Stefania; Boattini, Alessio; Francalacci, Paolo; Colonna, Vincenza; Vona, Giuseppe; Calò, Carla Maria; Destro-Bisol, Giovanni; Tofanelli, Sergio

doi:10.1038/srep41614

Cited by 16 publications

(19 citation statements)

References 57 publications

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“…Other studies carried out on a regional scale in other geographical contexts have shown that linguistic diversity alone may not be an effective factor of population differentiation (e.g. Anagnostou et al, 2017;Capocasa et al, 2013Capocasa et al, , 2014.…”

Section: Discussionmentioning

confidence: 98%

Berbers and Arabs: Tracing the genetic diversity and history of Southern Tunisia through genome wide analysis

Anagnostou

Dominici

Battaggia

et al. 2020

American J Phys Anthropol

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Objectives: Tunisia has been a crossroads for people from Africa, Europe, and the Middle East since prehistoric times. At present, it is inhabited by two main ethnic groups, Arabs and Berbers, and several minorities. This study aims to advance knowledge regarding their genetic structure using new population samplings and a genome-wide approach. Materials and Methods: We investigated genomic variation, estimated ancestry components and dated admixture events in three Berber and two Arab populations from Southern Tunisia, mining a dataset including Middle Eastern, sub-Saharan, and European populations. Results: Differences in the proportion of North African, Arabian, and European ancestries and the varying impact of admixture and isolation determined significant heterogeneity in the genetic structure of Southern Tunisian populations. Admixture time estimates show a multilayer pattern of admixture events, involving both ethnolinguistic groups, which started around the mid XI century and lasted for nearly five centuries. Discussion: Our study provides evidence that the relationships between genetic and cultural diversity of old and new inhabitants of North Africa in southern Tunisia follow different patterns. The Berbers seem to have preserved a significant part of their common genomic heritage despite Islamization, Arab cultural influence, and linguistic diversity. Compared to Morocco and Algeria, southern Tunisian Arabs have retained a higher level of Arabian ancestry. This is more evident in the semi-nomad R'Baya, who have kept their original Bedouin lifestyle, than in the population from Douz, who have undergone multiple events of stratification and admixture.

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Section: Discussionmentioning

confidence: 98%

Berbers and Arabs: Tracing the genetic diversity and history of Southern Tunisia through genome wide analysis

Anagnostou

Dominici

Battaggia

et al. 2020

American J Phys Anthropol

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“…2007) under default parameter settings. SNPs were considered to be part of a homozygous segment, when the proportion of overlapping homozygous windows was above 5% (Anagnostou et al. 2017).…”

Section: Methodsmentioning

confidence: 99%

Dissecting the Pre-Columbian Genomic Ancestry of Native Americans along the Andes–Amazonia Divide

Gnecchi‐Ruscone

Sarno

Fanti

et al. 2019

Molecular Biology and Evolution

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Extensive European and African admixture coupled with loss of Amerindian lineages makes the reconstruction of pre-Columbian history of Native Americans based on present-day genomes extremely challenging. Still open questions remain about the dispersals that occurred throughout the continent after the initial peopling from the Beringia, especially concerning the number and dynamics of diffusions into South America. Indeed, if environmental and historical factors contributed to shape distinct gene pools in the Andes and Amazonia, the origins of this East-West genetic structure and the extension of further interactions between populations residing along this divide are still not well understood. To this end, we generated new high-resolution genome-wide data for 229 individuals representative of one Central and ten South Amerindian ethnic groups from Mexico, Peru, Bolivia, and Argentina. Low levels of European and African admixture in the sampled individuals allowed the application of fine-scale haplotype-based methods and demographic modeling approaches. These analyses revealed highly specific Native American genetic ancestries and great intragroup homogeneity, along with limited traces of gene flow mainly from the Andes into Peruvian Amazonians. Substantial amount of genetic drift differentially experienced by the considered populations underlined distinct patterns of recent inbreeding or prolonged isolation. Overall, our results support the hypothesis that all non-Andean South Americans are compatible with descending from a common lineage, while we found low support for common Mesoamerican ancestors of both Andeans and other South American groups. These findings suggest extensive back-migrations into Central America from non-Andean sources or conceal distinct peopling events into the Southern Continent.

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“…The p.Thr367Ile mutation appears to recur in VARS2 -related encephalopathy in Sardinia. North Sardinians are an inbred and isolated population [1]. Selective centuries-old environmental pressures have also contributed to the high genetic peculiarity that renders Sardinians susceptible to several multifactorial conditions including multiple sclerosis and type 1 diabetes [11, 12].…”

Section: Discussionmentioning

confidence: 99%

VARS2-linked mitochondrial encephalopathy: two case reports enlarging the clinical phenotype

et al. 2019

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Background Mitochondrial respiratory chain consists of five complexes encoded by nuclear and mitochondrial genomes. Mitochondrial aminoacyl-tRNA synthetases are key enzymes in the synthesis of such complexes. Bi-allelic variants of VARS2 , a nuclear gene encoding for valyl-tRNA (Val-tRNA) synthetase, are associated to several forms of mitochondrial encephalopathies or cardiomyoencephalopathies. Among these, the rare homozygous c.1100C > T (p.Thr367Ile) mutation variably presents with progressive developmental delay, axial hypotonia, limbs spasticity, drug-resistant epilepsy leading, in some cases, to premature death. Yet only six cases, of which three are siblings, harbouring this homozygous mutation have been described worldwide. Case presentation Hereby, we report two additional cases of two non-related young girls from Sardinia, born from non-consanguineous and healthy parents, carrying the aforesaid homozygous VARS2 variant. At onset both the patients presented with worsening psychomotor delay, muscle hypotonia and brisk tendon reflexes. Standard genetic tests were normal, as well as metabolic investigations. Brain MRI showed unspecific progressive abnormalities, such as corpus callosum hypoplasia (patient A) and cerebellar atrophy (patient A and B). Diagnosis was reached by adopting massive parallel next generation sequencing. Notably clinical phenotype of the first patient appears to be milder compared to previous known cases. The second patient eventually developed refractory epilepsy and currently presents with severe global impairment. Because no specific treatment is available as yet, both patients are treated with supporting antioxidant compounds along with symptomatic therapies. Conclusions Given the paucity of clinical data about this very rare mitochondrial encephalopathy, our report might contribute to broaden the phenotypic spectrum of the disorder. Moreover, noteworthy, three out of five pedigrees so far described belong to the Northern Sardinia ethnicity.

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Overcoming the dichotomy between open and isolated populations using genomic data from a large European dataset

Cited by 16 publications

References 57 publications

Berbers and Arabs: Tracing the genetic diversity and history of Southern Tunisia through genome wide analysis

Berbers and Arabs: Tracing the genetic diversity and history of Southern Tunisia through genome wide analysis

Dissecting the Pre-Columbian Genomic Ancestry of Native Americans along the Andes–Amazonia Divide

VARS2-linked mitochondrial encephalopathy: two case reports enlarging the clinical phenotype

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