Ancient mtDNA Research Articles

Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases.

Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases—and profiling, in certain conditions—especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven’s grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.

No evidence for recent introgressive hybridization between the European and Siberian roe deer in Poland

Wildlife translocations increase the rate of introgressive hybridization between closely related species. In this study, we investigated the population genetic structure of the European roe deer (Capreolus capreolus) in Poland, affected by widespread ancient mtDNA introgression from Siberian roe deer (C. pygargus), for signs of recent human-mediated admixture. We analysed two nuclear gene sequences (FPGT and LRRIQ3) and 10 microsatellite loci in 258 European roe deer and 78 introgressed individuals (C. capreolus with mtDNA of C. pygargus) collected from 16 populations from Poland. Eighteen Siberian roe deer from Russia were also genotyped. Population genetic structure, assessed using Bayesian analysis and Principal Coordinate Analysis, indicated the existence of one genetic cluster in the European roe deer in Poland and gave no evidence for recent introgression in nuclear markers. Measures of genetic diversity for pure C. capreolus and introgressed individuals did not differ, while species lineages exhibited significant high genetic differentiation from one another (FST = 0.271; P < 0.001). The discordance between previous mtDNA results and the present study based on nuclear markers confirms the impact of ancient natural hybridization process on the genetic structure of European roe deer populations in Poland.

Maternal lineage of Okinawa indigenous Agu pig inferred from mitochondrial DNA control region.

ObjectiveThe Agu is the only native pig breed in Japan, which is reared in Okinawa prefecture, the southernmost region in Japan. Its origins are considered to be of Asian lineage; however, the genetic background of the Agu is still unclear. The objective of this study was to elucidate the maternal lineage of the Okinawa indigenous Agu pig with the use of the mitochondrial DNA (mtDNA) control region.MethodsThe mtDNA control regions of Agu pigs were sequenced and the phylogenetic relationship among Agu, East Asian and European pigs was investigated with the use of 78 Agu individuals.ResultsTwenty-seven polymorphic sites and five different haplotypes (type 1 to type 5) were identified within the Agu population. Phylogenetic analysis indicated that types 1 and 2 were included in East Asian lineages; however, the remaining types 3, 4, and 5 were of European lineages, which showed a gene flow from European pigs in the 20th century. Sixty-seven out of 78 Agu individuals (85.9%) possessed mtDNA haplotypes 1 and 2 of the East Asian lineage, which were identical to two haplotypes of ancient mtDNA (7,200 to 1,700 years before the present) excavated at archaeological sites in Okinawa.ConclusionThis study confirmed that the East Asian lineage is dominant in the maternal genetic background of the Agu population, supporting the hypothesis that the ancestors of the Agu pig were introduced from the Asian continent.

Cranio-morphometric and aDNA corroboration of the Austronesian dispersal model in ancient Island Southeast Asia: Support from Gua Harimau, Indonesia.

The Austronesian language is spread from Madagascar in the west, Island Southeast Asia (ISEA) in the east (e.g. the Philippines and Indonesian archipelagoes) and throughout the Pacific, as far east as Easter Island. While it seems clear that the remote ancestors of Austronesian speakers originated in Southern China, and migrated to Taiwan with the development of rice farming by c. 5500 BP and onto the northern Philippines by c. 4000 BP (the Austronesian Dispersal Hypothesis or ADH), we know very little about the origins and emergence of Austronesian speakers in the Indonesian Archipelago. Using a combination of cranial morphometric and ancient mtDNA analyses on a new dataset from Gua Hairmau, that spans the pre-Neolithic through to Metal Period (5712—5591cal BP to 1864—1719 cal BP), we rigorously test the validity of the ADH in ISEA. A morphometric analysis of 23 adult male crania, using 16 of Martin’s standard measurements, was carried out with results compared to an East and Southeast Asian dataset of 30 sample populations spanning the Late Pleistocene through to Metal Period, in addition to 39 modern samples from East and Southeast Asia, near Oceania and Australia. Further, 20 samples were analyzed for ancient mtDNA and assigned to identified haplogroups. We demonstrate that the archaeological human remains from Gua Harimau cave, Sumatra, Indonesia provide clear evidence for at least two (cranio-morphometrically defined) and perhaps even three (in the context of the ancient mtDNA results) distinct populations from two separate time periods. The results of these analyses provide substantive support for the ADH model in explaining the origins and population history of ISEA peoples.

Ancient Roman mitochondrial genomes and isotopes reveal relationships and geographic origins at the local and pan-Mediterranean scales

Rome initiated several campaigns to expand, conquer, and enslave local Italic populations following the establishment of the republic in 504 BCE. However, the cultural and biological changes resulting from Roman subjugation across Italy remain a topic of intense historical debate. Although important, historic and archaeological lines of evidence fail to track the impact of forced enslavement and enculturation at individual and broader genetic scales and, more generally, offer fewer clues regarding the potential affinities of Roman period Italians to European, Near Eastern, western Asian and North African populations at this time.In this paper, we present the whole mitochondrial (mtDNA) genomes of 30 Roman period (1st–4th centuries CE) individuals buried in the Vagnari necropolis in southern Italy. We integrate the mtDNA data with previously published bioarchaeological and isotope (δ18O and 87Sr/86Sr) data for the Vagnari assemblage and compare Roman haplogroup composition to 15 newly sequenced mitochondrial genomes obtained from a pre-Roman Iron Age skeletal assemblage, located in close proximity to Vagnari. Additionally, we contrast our South Italian dataset with a further 332 complete ancient mtDNA genomes from the pan-Mediterranean region, Europe, western Asia and North African regions.Population pairwise ΦST values suggest that Roman Italians share closer genetic similarity to Neolithic, Bronze Age, and Armenian Iron Age populations from western and central Eurasia than with Iron Age Italians, Ptolemaic, and Roman period Egyptians. Vagnari individuals with δ18O, 87Sr/86Sr, and mtDNA data suggest a predominantly local demographic was employed at the site. However, two individuals belong to eastern Eurasian haplogroup D4b1c, indicating that the maternal ancestors of these two individuals migrated to South Italy prior to the 1st century CE. Additionally, we provide the first genetic evidence for possible maternal relatedness in a Roman period skeletal assemblage. Our research highlights the significance of integrating multiple lines of bioarchaeological data to inform interpretations about Roman colonial expansion and its impact on population structure.

Association Between Mitochondrial DNA Haplogroup Variation and Autism Spectrum Disorders

Autism spectrum disorders (ASD) are characterized by impairments in social interaction, communication, and repetitive or restrictive behavior. Although multiple physiologic and biochemical studies have reported defects in mitochondrial oxidative phosphorylation in patients with ASD, the role of mitochondrial DNA (mtDNA) variation has remained relatively unexplored. To assess what impact mitochondrial lineages encompassing ancient mtDNA functional polymorphisms, termed haplogroups, have on ASD risk. In this cohort study, individuals with autism and their families were studied using the Autism Genetic Resource Exchange cohort genome-wide association studies data previously generated at the Children's Hospital of Philadelphia. From October 2010 to January 2017, we analyzed the data and used the mtDNA single-nucleotide polymorphisms interrogated by the Illumina HumanHap 550 chip to determine the mtDNA haplogroups of the individuals. Taking into account the familial structure of the Autism Genetic Resource Exchange data, we then determined whether the mtDNA haplogroups correlate with ASD risk. Odds ratios of mitochondrial haplogroup as predictors of ASD risk. Of 1624 patients with autism included in this study, 1299 were boys (80%) and 325 were girls (20%). Families in the Autism Genetic Resource Exchange collection (933 families, encompassing 4041 individuals: 1624 patients with ASD and 2417 healthy parents and siblings) had been previously recruited in the United States with no restrictions on age, sex, race/ethnicity, or socioeconomic status. Relative to the most common European haplogroup HHV, European haplogroups I, J, K, O-X, T, and U were associated with increased risk of ASD, as were Asian and Native American haplogroups A and M, with odds ratios ranging from 1.55 (95% CI, 1.16-2.06) to 2.18 (95% CI, 1.59-3) (adjusted P < .04). Hence, mtDNA haplogroup variation is an important risk factor for ASD. Because haplogroups I, J, K, O-X, T, and U encompass 55% of the European population, mtDNA lineages must make a significant contribution to overall ASD risk.

Cheek tooth morphology and ancient mitochondrial DNA of late Pleistocene horses from the western interior of North America: Implications for the taxonomy of North American Late Pleistocene Equus.

Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to the end-Pleistocene extinction. Based on the morphological and molecular data analyzed, a caballine (Equus ferus) and a non-caballine (E. conversidens) species were identified from different localities across most of the Western Interior. A second non-caballine species (E. cedralensis) was recognized from southern localities based exclusively on the morphological analyses of the cheek teeth. Notably the separation into caballine and non-caballine species was observed in the Bayesian phylogenetic analysis of ancient mtDNA as well as in the geometric morphometric analyses of the upper and lower premolars. Teeth morphologically identified as E. conversidens that yielded ancient mtDNA fall within the New World stilt-legged clade recognized in previous studies and this is the name we apply to this group. Geographic variation in morphology in the caballine species is indicated by statistically different occlusal enamel patterns in the specimens from Bluefish Caves, Yukon Territory, relative to the specimens from the other geographic regions. Whether this represents ecomorphological variation and/or a certain degree of geographic and genetic isolation of these Arctic populations requires further study.

Ancient mtDNA diversity reveals specific population development of wild horses in Switzerland after the Last Glacial Maximum.

On large geographical scales, changes in animal population distribution and abundance are driven by environmental change due to climatic and anthropogenic processes. However, so far, little is known about population dynamics on a regional scale. We have investigated 92 archaeological horse remains from nine sites mainly adjacent to the Swiss Jura Mountains dating from c. 41,000–5,000 years BP. The time frame includes major environmental turning points such as the Last Glacial Maximum (LGM), followed by steppe vegetation, afforestation and initial re-opening of the landscape by human agricultural activities. To investigate matrilinear population dynamics, we assembled 240 base pairs of the mitochondrial d-loop. FST values indicate large genetic differentiation of the horse populations that were present during and directly after the LGM. After the retreat of the ice, a highly diverse population expanded as demonstrated by significantly negative results for Tajima’s D, Fu’s FS and mismatch analyses. At the same time, a different development took place in Asia where populations declined after the LGM. This first comprehensive investigation of wild horse remains on a regional scale reveals a discontinuous colonisation of succeeding populations, a pattern that diverges from the larger Eurasian trend.

MtDNA meta-analysis reveals both phenotype specificity and allele heterogeneity: a model for differential association

Human mtDNA genetic variants have traditionally been considered markers for ancient population migrations. However, during the past three decades, these variants have been associated with altered susceptibility to various phenotypes, thus supporting their importance for human health. Nevertheless, mtDNA disease association has frequently been supported only in certain populations, due either to population stratification or differential epistatic compensations among populations. To partially overcome these obstacles, we performed meta-analysis of the multiple mtDNA association studies conducted until 2016, encompassing 53,975 patients and 63,323 controls. Our findings support the association of mtDNA haplogroups and recurrent variants with specific phenotypes such as Parkinson’s disease, type 2 diabetes, longevity, and breast cancer. Strikingly, our assessment of mtDNA variants’ involvement with multiple phenotypes revealed significant impact for Caucasian haplogroups H, J, and K. Therefore, ancient mtDNA variants could be divided into those that affect specific phenotypes, versus others with a general impact on phenotype combinations. We suggest that the mtDNA could serve as a model for phenotype specificity versus allele heterogeneity.

First analysis of ancient mtDNA genetic diversity in Northern coast of Argentinean Patagonia

In the past decades, archaeological research advances in different Patagonian sectors have contributed to the knowledge of lifestyle and evolution of pre-Columbian populations in these regions. The San Matías Gulf archaeological record (Río Negro province, Northern Patagonia, Argentina) shows that humans occupied the area from Middle Holocene to contact period, where palaeodietary and technological changes are evident from around 1700 14C BP. Nevertheless, few studies have been done on biological origin and evolution of these populations. For this reason and in order to investigate mitochondrial genetic variability in comparison with other ancient and contemporary Patagonian populations, we analyzed ancient DNA on human skeletal remains belonging to different chronologies of this area. We found a prevalence of founding lineages C1, D1 (D1g and D1j subclades) and D4h3a, low frequency of A2 and absence of B2. This supports the hypothesis of genetic drift acting on populations of the Southern Cone of South America. Individuals analyzed present similar haplotypes, indicating a possible temporal and regional continuity or a common population origin. Those lineages are also present in Tehuelche and Mapuche contemporary populations. However, B2 is highly represented in these extant groups possibly as a consequence of recent migrations related with Araucanization process.

Ancient Out-of-Africa Mitochondrial DNA Variants Associate with Distinct Mitochondrial Gene Expression Patterns.

Mitochondrial DNA (mtDNA) variants have been traditionally used as markers to trace ancient population migrations. Although experiments relying on model organisms and cytoplasmic hybrids, as well as disease association studies, have served to underline the functionality of certain mtDNA SNPs, only little is known of the regulatory impact of ancient mtDNA variants, especially in terms of gene expression. By analyzing RNA-seq data of 454 lymphoblast cell lines from the 1000 Genomes Project, we found that mtDNA variants defining the most common African genetic background, the L haplogroup, exhibit a distinct overall mtDNA gene expression pattern, which was independent of mtDNA copy numbers. Secondly, intra-population analysis revealed subtle, yet significant, expression differences in four tRNA genes. Strikingly, the more prominent African mtDNA gene expression pattern best correlated with the expression of nuclear DNA-encoded RNA-binding proteins, and with SNPs within the mitochondrial RNA-binding proteins PTCD1 and MRPS7. Our results thus support the concept of an ancient regulatory transition of mtDNA-encoded genes as humans left Africa to populate the rest of the world.

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

In Western Europe, the Middle to Upper Paleolithic transition is associated with the disappearance of Neandertals and the spread of anatomically modern humans (AMHs). Current chronological, behavioral, and biological models of this transitional period hinge on the Châtelperronian technocomplex. At the site of the Grotte du Renne, Arcy-sur-Cure, morphological Neandertal specimens are not directly dated but are contextually associated with the Châtelperronian, which contains bone points and beads. The association between Neandertals and this "transitional" assemblage has been controversial because of the lack either of a direct hominin radiocarbon date or of molecular confirmation of the Neandertal affiliation. Here we provide further evidence for a Neandertal-Châtelperronian association at the Grotte du Renne through biomolecular and chronological analysis. We identified 28 additional hominin specimens through zooarchaeology by mass spectrometry (ZooMS) screening of morphologically uninformative bone specimens from Châtelperronian layers at the Grotte du Renne. Next, we obtain an ancient hominin bone proteome through liquid chromatography-MS/MS analysis and error-tolerant amino acid sequence analysis. Analysis of this palaeoproteome allows us to provide phylogenetic and physiological information on these ancient hominin specimens. We distinguish Late Pleistocene clades within the genus Homo based on ancient protein evidence through the identification of an archaic-derived amino acid sequence for the collagen type X, alpha-1 (COL10α1) protein. We support this by obtaining ancient mtDNA sequences, which indicate a Neandertal ancestry for these specimens. Direct accelerator mass spectometry radiocarbon dating and Bayesian modeling confirm that the hominin specimens date to the Châtelperronian at the Grotte du Renne.

Ancient mtDNA sequences from the First Australians revisited

The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537-542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the "Out of Africa" model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains.

Temporal fluctuation in North East Baltic Sea region cattle population revealed by mitochondrial and Y-chromosomal DNA analyses.

BackgroundAncient DNA analysis offers a way to detect changes in populations over time. To date, most studies of ancient cattle have focused on their domestication in prehistory, while only a limited number of studies have analysed later periods. Conversely, the genetic structure of modern cattle populations is well known given the undertaking of several molecular and population genetic studies.ResultsBones and teeth from ancient cattle populations from the North-East Baltic Sea region dated to the Prehistoric (Late Bronze and Iron Age, 5 samples), Medieval (14), and Post-Medieval (26) periods were investigated by sequencing 667 base pairs (bp) from the mitochondrial DNA (mtDNA) and 155 bp of intron 19 in the Y-chromosomal UTY gene. Comparison of maternal (mtDNA haplotypes) genetic diversity in ancient cattle (45 samples) with modern cattle populations in Europe and Asia (2094 samples) revealed 30 ancient mtDNA haplotypes, 24 of which were shared with modern breeds, while 6 were unique to the ancient samples. Of seven Y-chromosomal sequences determined from ancient samples, six were Y2 and one Y1 haplotype. Combined data including Swedish samples from the same periods (64 samples) was compared with the occurrence of Y-chromosomal haplotypes in modern cattle (1614 samples).ConclusionsThe diversity of haplogroups was highest in the Prehistoric samples, where many haplotypes were unique. The Medieval and Post-Medieval samples also show a high diversity with new haplotypes. Some of these haplotypes have become frequent in modern breeds in the Nordic Countries and North-Western Russia while other haplotypes have remained in only a few local breeds or seem to have been lost. A temporal shift in Y-chromosomal haplotypes from Y2 to Y1 was detected that corresponds with the appearance of new mtDNA haplotypes in the Medieval and Post-Medieval period. This suggests a replacement of the Prehistoric mtDNA and Y chromosomal haplotypes by new types of cattle.

Distribution of East Eurasian Y-Chromosome and Mitochondrial DNA Haplogroups across Eurasia: Insights into the Genetic Ancestry of Bulgarians

The modern Bulgarian mitochondrial DNA (mtDNA) and Y-chromosome gene pools predominantly consist of Western Eurasian haplogroups. In contrast, the Eastern Eurasian lineages are found at very low frequencies in Bulgarians, being represented only by mtDNA haplogroups C (0.2%), D (0.4%) and Z (0.1%) (Karachanak et al., 2012) and Y-chromosome haplogroups C, N and Q (each 0.5%) (Karachanak et al., 2013). A similar pattern is observed in ancient mtDNA samples of proto-Bulgarian human remains, which belong exclusively to Western Eurasian mtDNA haplogroups (Nesheva et al., 2015). In order to investigate Bulgarian ancestry from the perspective of Eastern Eurasian haplogroups, we have analyzed the distribution of Y-chromosome haplogroups C, N and Q and mtDNA haplogroups C, D and Z across Eurasia. The survey was performed using literature data for more than 15,000 individuals from different Eurasian (sub-) populations for each of these haplogroups. The collected data were used to construct Eurasian frequency maps of the considered haplogroups and to test the significance of their incidence between Bulgarians and Europeans, European neighboring populations of Bulgaria and populations, which according to some historical conceptions could have common ancestry with proto-Bulgarians, namely: Altaian, Caucasus, Siberian and Central Asian populations. The spatial distribution of mtDNA haplogroups C, D and Z and Y-chromosome haplogroups C, N and Q contrasts their high frequency among Altaic populations and their occasional appearance in Bulgarians. Furthermore, the comparison of the occurrence of these haplogroups shows no link between Bulgarians and Altaic and Caucasus populations. Based on the substantial genetic input of proto-Bulgarians to the modern Bulgarian gene pool, the present study confirms the nonexistence of a close Y-chromosomal or mtDNA link between proto-Bulgarians on the one hand and Altaic and Caucasus populations on the other.

Ancient DNA from the Schild site in Illinois: Implications for the Mississippian transition in the Lower Illinois River Valley.

Archaeologists have long debated whether rapid cultural change in the archaeological record is due to in situ developments, migration of a new group into the region, or the spread of new cultural practices into an area through existing social networks, with the local peoples adopting and adapting practices from elsewhere as they see fit (acculturation). Researchers have suggested each of these explanations for the major cultural transition that occurred at the beginning of the Mississippian period (AD 1050) across eastern North America. In this study, we used ancient DNA to test competing hypotheses of migration and acculturation for the culture change that occurred between the Late Woodland (AD 400-1050) and Mississippian (AD 1050-1500) periods in the Lower Illinois River Valley. We obtained sequences of the first hypervariable segment of the mitochondrial genome (mtDNA) from 39 individuals (17 Late Woodland, 22 Mississippian) interred in the Schild cemetery in western Illinois, and compared these lineages to ancient mtDNA lineages present at other sites in the region. Computer simulations were used to test a null hypothesis of population continuity from Late Woodland to Mississippian times at the Schild site and to investigate the possibility of gene flow from elsewhere in the region. Our results suggest that the Late Woodland to Mississippian cultural transition at Schild was not due to an influx of people from elsewhere. Instead, it is more likely that the transition to Mississippian cultural practices at this site was due to a process of acculturation.

Tamil merchant in ancient Mesopotamia.

Recent analyses of ancient Mesopotamian mitochondrial genomes have suggested a genetic link between the Indian subcontinent and Mesopotamian civilization. There is no consensus on the origin of the ancient Mesopotamians. They may be descendants of migrants, who founded regional Mesopotamian groups like that of Terqa or they may be merchants who were involved in trans Mesopotamia trade. To identify the Indian source population showing linkage to the ancient Mesopotamians, we screened a total of 15,751 mitochondrial DNAs (11,432 from the literature and 4,319 from this study) representing all major populations of India. Our results although suggest that south India (Tamil Nadu) and northeast India served as the source of the ancient Mesopotamian mtDNA gene pool, mtDNA of these ancient Mesopotamians probably contributed by Tamil merchants who were involved in the Indo-Roman trade.

First ancient mitochondrial human genome from a prepastoralist southern African.

The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semidesert regions of Namibia and Botswana, whereas archeological, historical, and genetic evidence promotes a once broader southerly dispersal of click-speaking peoples including southward migrating pastoralists and indigenous marine-foragers. No genetic data have been recovered from the indigenous peoples that once sustained life along the southern coastal waters of Africa prepastoral arrival. In this study we generate a complete mitochondrial genome from a 2,330-year-old male skeleton, confirmed through osteological and archeological analysis as practicing a marine-based forager existence. The ancient mtDNA represents a new L0d2c lineage (L0d2c1c) that is today, unlike its Khoe-language based sister-clades (L0d2c1a and L0d2c1b) most closely related to contemporary indigenous San-speakers (specifically Ju). Providing the first genomic evidence that prepastoral Southern African marine foragers carried the earliest diverged maternal modern human lineages, this study emphasizes the significance of Southern African archeological remains in defining early modern human origins.

Phylogeography of Hepialus humuli (L.) (Lepidoptera: Hepialidae) in Europe: short distance vs. large scale postglacial expansions from multiple Alpine refugia and taxonomic implications

We explore the phylogeography of the common ghost moth, Hepialus humuli (Linnaeus) in Europe based on 1451 bp Cytochromeoxydase Subunit 1 (COI) mtDNA and 617 bp Ribosomal protein Subunit 5 (RpS5) ntDNA with special focus on populations in the Alps and surrounding regions, as well as northern Europe. While RpS5 fails to recover any phylogeographic signal, COI reveals a remarkable pattern with central European populations separated in four well-defined groups. The most divergent group is restricted to northern Italy and southern Austria and geographically isolated from the others; one group is found only in the central-northern region south of Lake Constance (Liechtenstein, western Austria) and co-occurs with the two other groups, from north-eastern Alps and north-western Alps respectively. We conclude that the southern and central groups are relicts from a previous Pleistocene glacial maximum, whereas the two latter groups were isolated during the last glacial maximum in a western and an eastern refugium respectively, the exact extends of these refugia are uncertain. The central group has subsequently interbred with the two other northern groups and probably only exists today as ancient mtDNA haplotypes. The north-western and north-eastern groups have spread considerably and overlap over a large part of their range in the Alps and surrounding areas. Following the last glacial maximum, the north-western group spread into western Europe as far as Normandy, but the English Channel has apparently acted as a dispersal barrier. The north-eastern group spread into eastern and northern Europe, including Scandinavia, and possibly into the Balkans as well. The British Isles as well as the North Atlantic islands groups, the Faroese and Shetlands were colonised from southern Scandinavia or northern Germany, likely via Doggerland. Despite the deep divergence in mtDNA between the populations in Italy and southern Austria, and the remaining populations, there are no consistent morphological differences, and we conclude that there is no evidence that the southern populations should be considered a separate species. Although the populations in the Shetland and Faroese islands are phenotypically distinct from most other populations, we find no genetic or genitalia morphological differences between these populations and the rest. We therefore conclude that they display what can be termed cryptic genetic homogeneity. As the phenotypic variation is not unique to these populations either, we synonymise the North Atlantic subspecies H. humuli thulensis Newman syn.n. with H. humuli humuli.

Aspects of ancient mitochondrial DNA analysis in different populations for understanding human evolution.

The evolution of modern humans is a long and difficult process which started from their first appearance and continues to the present day. The study of the genetic origin of populations can help to determine population kinship and to better understand the gradual changes of the gene pool in space and time. Mitochondrial DNA (mtDNA) is a proper tool for the determination of the origin of populations due to its high evolutionary importance. Ancient mitochondrial DNA retrieved from museum specimens, archaeological finds and fossil remains can provide direct evidence for population origins and migration processes. Despite the problems with contaminations and authenticity of ancient mitochondrial DNA, there is a developed set of criteria and platforms for obtaining authentic ancient DNA. During the last two decades, the application of different methods and techniques for analysis of ancient mitochondrial DNA gave promising results. Still, the literature is relatively poor with information for the origin of human populations. Using comprehensive phylogeographic and population analyses we can observe the development and formation of the contemporary populations. The aim of this study was to shed light on human migratory processes and the formation of populations based on available ancient mtDNA data.