Francesca Gandini

• PhD in Genetics, Molecular and Cellular Biology
• Research Associate at University of Huddersfield

Background The Islamic influence on the Iberian Peninsula left an enduring legacy culturally and linguistically, however the demographic impact is less well understood. This study aims to explore the dynamics of gene flow and population structure in eastern Iberia from the early to late Medieval period through ancient DNA. Results Our comprehensiv...

The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (...

Significance The Orcadian Neolithic has been intensively studied and celebrated as a major center of cultural innovation, whereas the Bronze Age is less well known and often regarded as a time of stagnation and insularity. Here, we analyze ancient genomes from the Orcadian Bronze Age in the context of the variation in Neolithic Orkney and Bronze Ag...

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 Nor...

Human remains from the Iron Age in Atlantic Scotland are rare, which makes the assemblage of an adult female and numerous foetal bones at High Pasture Cave, on the Isle of Skye, particularly noteworthy. Archaeological evidence suggests that the female had been deposited as an articulated skeleton when the cave entrance was blocked off, marking the...

Two key moments shaped the extant South Asian gene pool within the last 10 thousand years (ka): the Neolithic period, with the advent of agriculture and the rise of the Harappan/Indus Valley Civilisation; and Late Bronze Age events that witnessed the abrupt fall of the Harappan Civilisation and the arrival of Indo-European speakers. This study focu...

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula.We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming.We reveal sporadic contacts be...

Background: India is a patchwork of tribal and non-tribal populations that speak many different languages from various language families. Indo-European, spoken across northern and central India, and also in Pakistan and Bangladesh, has been frequently connected to the so-called "Indo-Aryan invasions" from Central Asia ~3.5 ka and the establishment...

Recent and compelling archaeological evidence attests to human presence ∼14.5 thousand years ago (Kya) at multiple sites in South America and a very early exploitation of extreme high-altitude Andean environments. Considering that, according to genetic evidence, human entry into North America from Beringia most likely occurred ∼16 Kya, these archeo...

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 coales...

Supplement to Silva et al 2017

Sardinians are “outliers” in the European genetic landscape and, according to paleogenomic nuclear data, the closest to early European Neolithic farmers. To learn more about their genetic ancestry, we analyzed 3,491 modern and 21 ancient mitogenomes from Sardinia. We observed that 78.4% of modern mitogenomes cluster into 89 haplogroups that most li...

Rare mitochondrial lineages with relict distributions can sometimes be disproportionately informative about deep events in human prehistory. We have studied one such lineage, haplogroup R0a, which uniquely is most frequent in Arabia and the Horn of Africa, but is distributed much more widely, from Europe to India. We conclude that: (1) the lineage...

In the original article, one of the co-author’s (Ken Khong Eng) given name has been published incorrectly. The correct given name should be Ken Khong. The original article has been corrected.

There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally-driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question by using founder analysis of mitochondrial DNA (mtDNA...

Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock specie...

Background: Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information conc...

A novel heteroplasmic mitochondrial DNA (mtDNA) micro-deletion affecting the cytochrome b gene (MT-CYB) was identified in an Italian female patient with a multisystem disease characterized by sensorineural deafness, cataracts, retinal pigmentary dystrophy, dysphagia, postural and gait instability and myopathy with prominent exercise intolerance. Th...

Background An increasing number of mitochondrial DNA (mtDNA) mutations, mainly in complex I genes, have been associated with variably overlapping phenotypes of Leber’s hereditary optic neuropathy (LHON), mitochondrial encephalomyopathy with stroke-like episodes (MELAS) and Leigh syndrome (LS). We here describe the first case in which the m.4171C>A/...

In this study we evaluated migration models to the Americas by using the information contained in native mitochondrial genomes (mitogenomes) from North America. Molecular and phylogeographic analyses of B2a mitogenomes, which are absent in Eskimo-Aleut and northern Na-Dene speakers, revealed that this haplogroup arose in North America ∼11-13 ka fro...

The current human mitochondrial (mtDNA) phylogeny does not equally represent all human populations but is biased in favour of representatives originally from north and central Europe. This especially affects the phylogeny of some uncommon West Eurasian haplogroups, including I and W, whose southern European and Near Eastern components are very poor...

File containing Tables S1–S3. Table S1. Origin and subclade affiliation of haplogroup N1a1b1 and I mitogenomes considered in this study. Table S2. Origin and subclade affiliation of haplogroup W mitogenomes considered in this study. Table S3. Percentage frequency distribution of haplogroups I and W and the subclades I1a and W6. (DOCX)

Ethnic Belarusians make up more than 80% of the nine and half million people inhabiting the Republic of Belarus. Belarusians together with Ukrainians and Russians represent the East Slavic linguistic group, largest both in numbers and territory, inhabiting East Europe alongside Baltic-, Finno-Permic- and Turkic-speaking people. Till date, only a li...

MtDNA and NRY reference data used in PC analyses. (XLS)

Analysis of molecular variance in Belarusians. (DOCX)

Y-chromosome N1c(Tat) and N1b(P43) STR haplotypes in Belarusians. (XLSX)

Y-STR data used in Median-Joining Networks calculations. (XLSX)

Y-chromosome I2a(P37) STR haplotypes in Belarusians. (XLSX)

PC analysis based on mtDNA haplogroup frequencies in six Belarusian sub-populations. The distribution of the populations within 1–2 and 1–3 PCs is represented in the upper panels; the contribution of mtDNA haplogroups to each of the PCs is depicted in the lower panels. Sub-populations are designated as BeN – North, BeC – Centre, BeE – East, BeW – W...

PC analysis based on mtDNA haplogroup frequencies among eastern Europeans and Balkan populations. The contribution of each haplogroup to the first and the second PCs is shown in gray. The group “Other” includes “Other” from published data merged with uncommon haplogroups L1b, L2a and L3f. Frequencies of mtDNA haplogroups and references are listed i...

Spatial autocorrelation analysis for three major NRY haplogroups (N1c(Tat), I2a(P37) and R1a(SRY1532)) in Belarusians. Moran's I indices were calculated for three NRY haplogroups in six Belarusian sub-populations including also immediate neighbor populations (Ukraine, Poland, Lithuania, Latvia, Central Russia). Correlograms indicate that ‘gradient-...

Geographic origin of the Belarusian samples. (XLSX)

MtDNA control and coding region polymorphisms in Belarusians. (XLSX)

Pairwise population Fst calculated from NRY haplogroup frequencies in six Belarusian sub-populations. (DOCX)

The distribution of mtDNA haplogroup N3 in world populations retrieved from published data along with those generated in this study. Black squares refer to the screened population data; green circles mark regions where haplogroup N3 has been detected and a star sign denotes the geographic origin of N3 mtDNAs completely sequenced in this study. Numb...

MDS plot of pair-wise Rst values obtained from 13 Y-STRs in the six Belarusian sub-populations (stress = 0.0000048). Sub-populations are designated as follows: BeN – North, BeC – Centre, BeE – East, BeW – West, BeWP – West Polesie, BeEP – East Polesie. (DOCX)

Pairwise population Fst calculated from mtDNA haplogroup frequencies in six Belarusian sub-populations. (DOCX)

The distribution of N3 mtDNAs (T16086C, A16129G, T16172C, T16217C, G16230A, T16278C, C16311T) in world populations. (XLSX)

MtDNA haplogroups defining control (HVS-I: 16000–16400) and coding-region mutations relative to the RSRS and rCRS. (XLSX)

Complete haplotypes of N3 and N1a3 mtDNAs generated in this study. (XLSX)

WITH ANALYSES OF ENTIRE MITOGENOMES, STUDIES OF NATIVE AMERICAN MITOCHONDRIAL DNA (MTDNA) VARIATION HAVE ENTERED THE FINAL PHASE OF PHYLOGENETIC REFINEMENT: the dissection of the founding haplogroups into clades that arose in America during and after human arrival and spread. Ages and geographic distributions of these clades could provide novel clu...

Knowledge of high resolution Y-chromosome haplogroup diversification within Iran provides important geographic context regarding the spread and compartmentalization of male lineages in the Middle East and southwestern Asia. At present, the Iranian population is characterized by an extraordinary mix of different ethnic groups speaking a variety of I...

Phylogeny of Y-chromosome haplogroups observed the Iranian population. The markers M33 and M81 of haplogroup E, M287, L91, and L497 of haplogroups G, M323 of haplogroup Q and M18, M434 and M458 of haplogroup R were typed but not observed. A star (*) indicates a paragroup: a group of Y chromosomes not defined by any reported phylogenetic downstream...

J1-M267* reduced median network. The areas of circles and sectors are proportional to the haplotype frequency in the haplogroup and in the geographic area, respectively. (TIF)

Absolute frequencies of Y-chromosome haplogroups and subhaplogroups in the 44 populations included in the PCA. (XLSX)

Haplogroup J1-M267* frequencies and variances. (XLSX)

Human populations, along with those of many other species, are thought to have contracted into a number of refuge areas at the height of the last Ice Age. European populations are believed to be, to a large extent, the descendants of the inhabitants of these refugia, and some extant mtDNA lineages can be traced to refugia in Franco-Cantabria (haplo...

Recent analyses of mitochondrial genomes from Native Americans have brought the overall number of recognized maternal founding lineages from just four to a current count of 15. However, because of their relative low frequency, almost nothing is known for some of these lineages. This leaves a considerable void in understanding the events that led to...

Control-region haplotypes and haplogroup/sub-haplogroup classification of the 904 mtDNAs from the Marche region. (DOC)

CHAID diagrams assessing the association between T2DM complications and candidate haplogroups. Chi-squared Automatic Interaction Detector (CHAID) was used to develop decision-tree analyses for the evaluation of T2DM complications, using those haplogroups that were significant in logistic analyses (H3, H, U3 and V) as predictors. As shown on panels...

Frequencies of mtDNA haplogroups and sub-haplogroups in diabetic patients also affected by somatic neuropathy. (DOC)

Frequencies of mtDNA haplogroups and sub-haplogroups in diabetic patients also affected by retinopathy. (DOC)

Frequencies of mtDNA haplogroups and sub-haplogroups in diabetic patients also affected by Peripheral Artery Occlusive Disease (PAOD). (DOC)

Frequencies of mtDNA haplogroups and sub-haplogroups in diabetic patients also affected by renal failure. (DOC)

Frequencies of mtDNA haplogroups and sub-haplogroups in diabetic patients also affected by cardiac ischemia. (DOC)

Frequencies of mtDNA haplogroups and sub-haplogroups in diabetic patients also affected by nephropathy. (DOC)

Mitochondrial dysfunction has been implicated in rare and common forms of type 2 diabetes (T2DM). Additionally, rare mitochondrial DNA (mtDNA) mutations have been shown to be causal for T2DM pathogenesis. So far, many studies have investigated the possibility that mtDNA variation might affect the risk of T2DM, however, when found, haplogroup associ...