Søren Nørby

Tracing European Founder Lineages in the Near Eastern mtDNA Pool

Founder analysis is a method for analysis of nonrecombining DNA sequence data, with the aim of identification and dating of migrations into new territory. The method picks out founder sequence types in potential source populations and dates lineage clusters deriving from them in the settlement zone of interest. Here, using mtDNA, we apply the approach to the colonization of Europe, to estimate the proportion of modern lineages whose ancestors arrived during each major phase of settlement. To estimate the Palaeolithic and Neolithic contributions to European mtDNA diversity more accurately than was previously achievable, we have now extended the Near Eastern, European, and northern-Caucasus databases to 1,234, 2, 804, and 208 samples, respectively. Both back-migration into the source population and recurrent mutation in the source and derived populations represent major obstacles to this approach. We have developed phylogenetic criteria to take account of both these factors, and we suggest a way to account for multiple dispersals of common sequence types. We conclude that (i) there has been substantial back-migration into the Near East, (ii) the majority of extant mtDNA lineages entered Europe in several waves during the Upper Palaeolithic, (iii) there was a founder effect or bottleneck associated with the Last Glacial Maximum, 20,000 years ago, from which derives the largest fraction of surviving lineages, and (iv) the immigrant Neolithic component is likely to comprise less than one-quarter of the mtDNA pool of modern Europeans.

Y-Chromosomal Diversity in Europe Is Clinal and Influenced Primarily by Geography, Rather than by Language

Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift.

mtDNA Variation among Greenland Eskimos: The Edge of the Beringian Expansion

The Eskimo-Aleut language phylum is distributed from coastal Siberia across Alaska and Canada to Greenland and is well distinguished from the neighboring Na Dene languages. Genetically, however, the distinction between Na Dene and Eskimo-Aleut speakers is less clear. In order to improve the genetic characterization of Eskimos in general and Greenlanders in particular, we have sequenced hypervariable segment I (HVS-I) of the mitochondrial DNA (mtDNA) control region and typed relevant RFLP sites in the mtDNA of 82 Eskimos from Greenland. A comparison of our data with published sequences demonstrates major mtDNA types shared between Na Dene and Eskimo, indicating a common Beringian history within the Holocene. We further confirm the presence of an Eskimo-specific mtDNA subgroup characterized by nucleotide position 16265G within mtDNA group A2. This subgroup is found in all Eskimo groups analyzed so far and is estimated to have originated <3,000 years ago. A founder analysis of all Eskimo and Chukchi A2 types indicates that the Siberian and Greenland ancestral mtDNA pools separated around the time when the Neo-Eskimo culture emerged. The Greenland mtDNA types are a subset of the Alaskan mtDNA variation: they lack the groups D2 and D3 found in Siberia and Alaska and are exclusively A2 but at the same time lack the A2 root type. The data are in agreement with the view that the present Greenland Eskimos essentially descend from Alaskan Neo-Eskimos. European mtDNA types are absent in our Eskimo sample.

mtDNA Haplogroups and Frequency Patterns in Europe

To the Editor: Recently, an article by Simoni et al. (2000), who used (i) SAAP analysis to analyze the population frequencies of mtDNA haplogroups and (ii) AIDA analysis to examine both the frequency and the sequence similarity of truncated mtDNA sequences, appeared in this Journal. The main outcome of their study was that “the overall patterns of mtDNA diversity appear to be poorly significant in Europe.” The raw data comprised 2,619 hypervariable segment I (HVS-I) sequences (denoted as “HVR-I” [hypervariable region I] sequences by Simoni et al. [2000]) that were obtained from 36 regions or populations of Europe, the Near East, and the Caucasus and that were collected from both the literature and unpublished sources. Simoni et al. ostensibly grouped the HVS-I sequences according to haplogroup motifs proposed elsewhere (Richards et al. 1998), and they reported the resulting frequencies for each region/population in table 3 in their study. We have checked the input data displayed in table 3 and have found serious technical errors affecting numerous entries. More critically, the mtDNA categories that they report correspond neither to their own criteria nor to the haplogroup definitions established in the literature (to which they refer). Furthermore, their decision to truncate HVS-I information (and to disregard RFLP information) renders these data inadequate to differentiate even African and East Asian sequences from European sequences in many cases. Inspection of table 3 in the study by Simoni et al. (2000) reveals that (i) the data in the “Galicia” and “Spain: Central” rows have been, in part, crossed-over, (ii) the data in the “Belgium,” “Alps,” and “Turkey” rows have been computed with the use of sample sizes smaller than those reported in table 1 in the same study, (iii) the haplogroup “J” column has been totally randomized, and (iv) the “Other” column is complementary to the last four “superhaplogroup” columns but not to the first 11 haplogroup columns. As for item (iii), almost all positive entries in the haplogroup “J” column have been either displaced or calculated with the use of sample sizes corresponding to nearby rows. Hence, most entries in this column diverge widely from the real haplogroup J frequencies (see the last column of table 1 in the present study). Table 1 Haplogroup J Frequencies According to Simoni et al. (2000), a Crude Default Criterion, and Inference in the Present Study As an example of their haplogroup assignment, Simoni et al. (2000) specifically referred to the motif 16069T–16126C for haplogroup J, but they overlooked the fact that this criterion cannot formally be applied to the sequences in the study by Richards et al. (1996), since these were reported only between 16090 and 16365. This might explain some of the many “0” entries in the haplogroup “J” column of table 3 in the Simoni et al. study (see table 1 in the present study). Simoni et al. should have either adopted the haplogroup J frequencies reported by Richards et al. (1996), excluded these population samples from their study, or trimmed all data to the shortest common segment. In the latter case, by employing the motif 16126C–16294C, one could take the default cluster JT-T (comprising all JT sequences that are not T) as a crude default criterion for haplogroup J (see table 1 in the present study). The discrepancies in haplogroup frequencies are by no means restricted to haplogroup J. Table 2 in the present study shows the marked contrast between published haplogroup frequencies and those assumed by Simoni et al. (2000) for the well-characterized Tuscan, Druze, and Adygei samples (which were typed for RFLPs as well as for HVS-I sequences by Torroni et al. [1996] and Macaulay et al. [1999]). The large differences in frequency for haplogroup H, the most-common European haplogroup, are due to the premise of Simoni et al. (2000) that haplogroup “H contains all sequences . . . that show none of the 22 substitutions considered in this study.” This extreme simplification results, on the one hand, in the dumping of large numbers of haplogroup H mtDNAs mainly into the default category “Other” and, on the other hand, in the inclusion of several non-H sequences within their haplogroup H category. For instance, by their criterion, 10/20 haplogroup H mtDNAs from the Tuscan sample (Torroni et al. 1996) would no longer be scored as “H,” whereas the U sequence 16051G–16309G–16318C would be scored as “H.” In consequence, the haplogroup H category described by Simoni et al. (2000) is bound to be highly polyphyletic in the mtDNA genealogy and does not reflect the spatial patterns of haplogroup H. Table 2 Haplogroup Frequencies, According to Simoni et al. (2000) vs. the Original Studies, in Tuscan, Druze, and Adygei Populations At this point, it is important to clarify what haplogroup classification entails. An mtDNA haplogroup, when properly defined, is a monophyletic clade of the mtDNA genealogy. Originally, high-resolution RFLP analysis (employing 14 enzymes) had been used for identification of clades by signature sites (Torroni et al. 1992, 1993, 1994a, 1994b, 1996; Chen et al. 1995), and current haplogroup nomenclature originated in that context. In retrospect, this approach is indeed quite reliable, although recurrent changes at a few sites, such as 10394 DdeI, may occasionally cause problems. Potential ambiguities can largely be resolved by incorporation of information from other segments of mtDNA sequences or specific positions of the coding regions (Torroni et al. 1997; Brown et al. 1998; Starikovskaya et al. 1998; Macaulay et al. 1999; Quintana-Murci et al. 1999; Schurr et al. 1999). For instance, haplogroup K is now understood to be a clade (as are U1–U6) within haplogroup U. HVS-I data in combination with partial RFLPs can sometimes serve as a satisfactory substitute for a full RFLP analysis (Rando et al 1998, 2000; Kivisild et al. 1999a, 1999b). Unfortunately, HVS-I data alone, which have been produced en masse, often do not contain sufficient information for confident assignment of haplogroup affiliation. The truncation of the HVS-I data to only 13–22 variant positions, as performed by Simoni et al. (2000), yields even poorer results. For example, the motif 16223T–16278T, which was used by Simoni et al. to identify haplogroup X, would transfer most African L1/L2 sequences (Watson et al. 1997; Rando et al. 1998) into the then artefactual category “X.” For Europe, this is relevant insofar as a few L1/L2 sequences are present in Iberia (Rocha et al. 1999), and there even resides an African L1c sequence with the motif 16223T–16278T in the British data (Piercy et al. 1993). In addition, as was previously pointed out (Torroni et al. 1996; Macaulay et al. 1999), one has to be prepared for recurrent mutations in the HVS-I motifs (compare also figs. 4, 5, 8, and 9 of the study by Richards et al. [1998]). For instance, the frequency discrepancy (17.8% vs. 26.7%) for haplogroup X in the Druze sample (see table 2 in the present study) is due to the fact that Simoni et al. did not include four haplogroup X mtDNAs that have mutated to 16223C. Another of the many possible examples of misclassification caused by the use of truncated motifs is illustrated by 16129A–16223T, the motif used by Simoni et al. for classification of haplogroup I mtDNAs. Use of this truncated motif has led them to classify both the Asian haplogroup C mtDNAs (16129A–16223T–16298C–16327T) of the Adygei (6.0%) and the East African haplogroup M1 mtDNA (16129A–16189C–16223T–16249C–16311C–16359C) of the Druze (2.2%) as members of haplogroup I (see table 2 in the present study). The issue of haplogroups only affects the SAAP analysis. However, there are also serious difficulties with the AIDA analysis. Ideally, AIDA should be applied to full DNA-sequence data, but Simoni et al. (2000) included only 22/241 variant positions. One cannot expect that such a truncated data set would show much evidence of geographic patterns within Europe. Most of the haplogroup diagnostic variants in western Eurasian mtDNA are very ancient, and they probably evolved in the Near East and subsequently spread to Europe (Torroni et al. 1998; Macaulay et al. 1999); at any event, they occur throughout western Eurasia. The more recent “rare substitutions,” which have evolved since the earlier dispersals and which Simoni et al. (2000) discarded as “statistical noise,” are precisely those that are most likely to show regional distributions. The exclusion of such mutations severely restricts the capacity to identify phylogeographic units and, thus, is bound to have seriously reduced the power of the approach to detect autocorrelation. Even when haplogroup assignment is done with care, failure to detect significant clines in haplogroup frequencies does not prove the absence of any spatial structure in the mtDNA pool. Such structure would rather be manifest at a phylogenetically finer scale (defined on the basis of more-recent mutations). In any case, one would not expect that meaningful patterns of mtDNA diversity could emerge from analyses based on categories with no demonstrable phylogenetic support.

Mitochondrial DNA haplogroup distribution within Leber hereditary optic neuropathy pedigrees

. eber hereditary optic neuropathy (LHON; OMIM #535000) is a mitochondrial genetic disease that causes blindness in young adults, with an estimated minimum prevalence of 3.2 per 100 000 in the north east of England. 1 It classically presents as bilateral subacute loss of central vision due to the focal neurodegeneration of the retinal ganglion cell layer. Over 95% of cases are principally due to one of three ‘‘primary’’ mtDNA point mutations: 3460GRA, 11778GRA, and 14484TRC, all of which involve genes that encode complex I subunits of the mitochondrial respiratory chain. However, less than ,50% of male and ,10% of female LHON carriers will develop the optic neuropathy. 23

Juvenile Kearns-Sayre syndrome initially misdiagnosed as a psychosomatic disorder.

We have investigated a 15 year old girl with progressive external ophthalmoplegia, including bilateral ptosis and retinal rod and cone cell dysfunction with atypical retinal pigmentation, complicated by cerebellar ataxia, partial cardiac conduction block, and diabetes mellitus. In infancy she had a severe crisis of bone marrow depression, and as a child she suffered from hypersensitivity to light, increasing fatigue, and vertigo, signs that were initially though to be psychosomatic. Histological examination showed mitochondrial myopathy, and subsequent mitochondrial DNA (mtDNA) analysis showed a deletion of approximately 5500 base pairs in 35 to 40% of her muscle mtDNA. We therefore conclude that this patient has developed the Kearns-Sayre syndrome after a Pearson syndrome-like crisis in her first year of life.

Autosomal dominant polycystic kidney disease in the 1980's

Since it is one of the commonest hereditary diseases, causing serious illness in adulthood, autosomal dominant polycystic kidney disease (ADPKD) is a problem for both the affected families and for the health economy of the society. The current management of ADPKD is reviewed with emphasis on the development of predictive DNA analyses, the recently discovered genetic heterogeneity, and ethical perspectives. Insurance aspects are discussed, and the need for access to selective reproductive prevention as well as for improvement of conventional therapeutic measures is stressed.

Y-chromosomal STR haplotypes in Inuit and Danish population samples

Nineteen Y-chromosomal short tandem repeats (STRs), DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS388, DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, DYS460, DYS461 and DYS462 were typed in Inuit (n=70) and Danish (n=62) population samples.

Prevalence and Genetics of Leber Hereditary Optic Neuropathy in the Danish Population.

PURPOSE In Denmark, the occurrence of Leber hereditary optic neuropathy (LHON) has continuously been monitored since 1944. We provide here a summary of 70 years of data collection including registered lines and subjects by the end of 2012. METHODS Affected individuals were identified from a national register of hereditary eye diseases at the National Eye Clinic (NEC), a tertiary low vision rehabilitation center for the entire Danish population. The assembling of LHON pedigrees was based on the reconstruction of published families and newly diagnosed cases from 1980 to 2012 identified in the files of NEC. Genealogic follow-up on the maternal ancestry of all affected individuals was performed to identify a possible relation to an already known maternal line. A full genotypic characterization of the nation-based LHON cohort is provided. RESULTS Forty different lines were identified. The number of live affected individuals with a verified mitochondrial DNA mutation was 104 on January 1, 2013, which translates to a prevalence rate of 1:54,000 in the Danish population. CONCLUSIONS Haplogroup distribution as well as mutational spectrum of the Danish LHON cohort do not deviate from those of other European populations. The genealogic follow-up reveals a relatively high turnover among families with approximately 15 newly affected families per century and the dying out of earlier maternal lines.

Assignment of the locus order DXS28‐ DXS67‐DMD as a spin‐off from diagnostic DNA marker analysis in a family with Duchenne muscular dystrophy

During diagnostic segregation analysis for seven DNA markers, linked to and flanking the locus for Duchenne muscular dystrophy (DMD), a family was identified in which a boy with a recombinant X chromosome had inherited his maternal grandmothers alleles at the loci DXS43 (D2/Pvu II) and DXS28 (C7/Eco RV), and his maternal grandfathers alleles at DXS67 (B24/Msp I) and DXS84 (754/Pst 1).