Maria Pala

University of Huddersfield · School of Applied Sciences

The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture¹. The extent to which migration from continental Europe mediated these transitions is a matt...

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 (...

The remarkable archaeological record of Neolithic Orkney has ensured that these islands play a prominent role in narratives of European late prehistory, yet knowledge of the subsequent Bronze Age is comparatively poor. The Bronze Age settlement and cemetery at the Links of Noltland, on the island of Westray, offers new evidence, including aDNA, tha...

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...

The novel coronavirus SARS-CoV-2 emerged from a zoonotic transmission in China towards the end of 2019, rapidly leading to a global pandemic on a scale not seen for a century. InN order to cast fresh light on the spread of the virus and on the effectiveness of the containment measures adopted globally, we used 26,869 SARS-CoV-2 genomes to build a p...

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...

Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersa...

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...

Analysis of human mitochondrial DNA (mtDNA) variation plays an important role in forensic genetic investigations, especially in degraded biological samples and hair shafts. There are many issues of the mtDNA phylogeny that are of special interest to the forensic community, such as haplogroup classification or the post hoc investigation of potential...

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...

There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The “out-of-Taiwan” model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely...

The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match...

The development of agriculture has often been described as the most important change in all of human history. Volume 2 of The Cambridge World History explores the origins and impact of agriculture and agricultural communities, and also discusses issues associated with pastoralism and hunter-fisher-gatherer economies. To capture the patterns of this...

The development of agriculture has often been described as the most important change in all of human history. Volume 2 of The Cambridge World History explores the origins and impact of agriculture and agricultural communities, and also discusses issues associated with pastoralism and hunter-fisher-gatherer economies. To capture the patterns of this...

Giara and Sarcidano are 2 of the 15 extant native Italian horse breeds with limited dispersal capability that originated from a larger number of individuals. The 2 breeds live in two distinct isolated locations on the island of Sardinia. To determine the genetic structure and evolutionary history of these 2 Sardinian breeds, the first hypervariable...

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...

The archaeogenetics of Europe remains deeply controversial. Advances in ancient deoxyribonucleic acid (DNA) analysis have suggested gene flow between Neanderthals and modern humans, who arrived in Europe <50 000 years ago, but have so far failed to support evolution of Neanderthals from a population of Homo heidelbergensis represented by remains in...

Obituary in memory of our colleague and friend Laura Morelli (1967-2013)

The origins of Ashkenazi Jews remain highly controversial. Like Judaism, mitochondrial DNA is passed along the maternal line. Its variation in the Ashkenazim is highly distinctive, with four major and numerous minor founders. However, due to their rarity in the general population, these founders have been difficult to trace to a source. Here we sho...

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)

Complex I (CI) deficiency is a frequent cause of mitochondrial disorders and, in most cases, is due to mutations in CI subunit genes encoded by mitochondrial DNA (mtDNA). In this study, we establish the pathogenic role of the heteroplasmic mtDNA m.3890G>A/MT-ND1 (p.R195Q) mutation, which affects an extremely conserved amino acid position in ND1 sub...

Leber's hereditary optic neuropathy (LHON) is a maternally inherited blinding disorder, which in over 90% of cases is due to one of three primary mitochondrial DNA (mtDNA) point mutations (m.11778G>A, m.3460G>A and m.14484T>C, respectively in MT-ND4, MT-ND1 and MT-ND6 genes). However, the spectrum of mtDNA mutations causing the remaining 10% of cas...

Degree of conservation of amino acid positions contiguous to non-conserved polymorphic variants. (PDF)

Pedigrees of LHON families. Family ID numbers, mtDNA mutations and haplogroup affiliations are reported. Symbol definitions are also indicated. Probands are identified by black arrows. (PDF)

Epidemiologic data of LHON diagnosis in the involved centers. (PDF)

PCR oligonucleotides and restriction enzymes employed to evaluate heteroplasmy of LHON rare mutations. (PDF)

Case reports: clinical details of patients. (PDF)

Conservation analysis and pathogenicity prediction of mtDNA polymorphic nucleotide changes. (PDF)

List of mitochondrial haplotypes found in the Bulgarian sample

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...

For millennia, the southern part of the Mesopotamia has been a wetland region generated by the Tigris and Euphrates rivers before flowing into the Gulf. This area has been occupied by human communities since ancient times and the present-day inhabitants, the Marsh Arabs, are considered the population with the strongest link to ancient Sumerians. Po...

MtDNA control-region data of the samples reported in Table 1. The file provides information about the mtDNA control-region haplotypes observed in the subjects of the present study.

Y-chromosome markers examined in this study. The file provides information on the Y-chromosome markers examined in the present study.

Y-STR haplotypes associated with J1-M267* and J1-Page08. The file provides the Y-chromosome STR haplotypes used for the construction of the networks illustrated in Figure 4.

Absolute frequencies of Y-chromosome haplogroups and sub-haplogroups in the 48 populations included in the PCA. The file provides the list of the populations and Y-chromosome haplogroups, along with their frequencies, used in the PCA analysis.

Frequencies of Y-chromosome haplogroup J1-M267 and J1-Page08 from published sources and present study used for Figure 6. The file provides the data used for constructing the maps illustrated in Figure 6.

Y-chromosome haplogroup J1-Page-08 microsatellite variance from published sources and present study used for Figure 6. The file provides the data used for constructing the map illustrated in Figure 6.

Y-chromosome J1 sub-haplogroups variance, divergence and expansion times based on six STR loci. The file provides the variance, divergence and expansion times of the two J1 sub-haplogroups.

Absolute frequencies of mtDNA haplogroups and sub-haplogroups in the 35 populations included in the PCA. The file provides the list of the populations and mtDNA haplogroups, along with their frequencies, used in the PCA analysis.

Y-chromosome haplogroup J1-M267* microsatellite variance from published sources and present study used for Figure 6. The file provides the data used for constructing the map illustrated in Figure 6.

To define the matrilineal relationships between Bulgarians and other European populations, we have evaluated the mitochondrial DNA (mtDNA) variation in a sample of 855 Bulgarian subjects from the mtDNA perspective. The molecular survey was performed by sequencing ∼750 bp of the control region, which resulted in 557 different haplotypes, and by a su...

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)