Alfredo Coppa

The Role of Selection in the Evolution of Human Mitochondrial Genomes

High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (P < 0.01) excess of rRNA and nonsynonymous base substitutions among hotspots of recurrent mutation. Most hotspots involved transitions from guanine to adenine that, with thymine-to-cytosine transitions, illustrate the asymmetric bias in codon usage at synonymous sites on the heavy-strand DNA. The mitochondrion-encoded tRNAThr varied significantly more than any other tRNA gene. Threonine and valine codons were involved in 259 of the 414 amino acid replacements observed. The ratio of nonsynonymous changes from and to threonine and valine differed significantly (P = 0.003) between populations with neutral (22/58) and populations with significantly negative Tajimas D values (70/76), independent of their geographic location. In contrast to a recent suggestion that the excess of nonsilent mutations is characteristic of Arctic populations, implying their role in cold adaptation, we demonstrate that the surplus of nonsynonymous mutations is a general feature of the young branches of the phylogenetic tree, affecting also those that are found only in Africa. We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups.

Where West Meets East: The Complex mtDNA Landscape of the Southwest and Central Asian Corridor

The southwestern and Central Asian corridor has played a pivotal role in the history of humankind, witnessing numerous waves of migration of different peoples at different times. To evaluate the effects of these population movements on the current genetic landscape of the Iranian plateau, the Indus Valley, and Central Asia, we have analyzed 910 mitochondrial DNAs (mtDNAs) from 23 populations of the region. This study has allowed a refinement of the phylogenetic relationships of some lineages and the identification of new haplogroups in the southwestern and Central Asian mtDNA tree. Both lineage geographical distribution and spatial analysis of molecular variance showed that populations located west of the Indus Valley mainly harbor mtDNAs of western Eurasian origin, whereas those inhabiting the Indo-Gangetic region and Central Asia present substantial proportions of lineages that can be allocated to three different genetic components of western Eurasian, eastern Eurasian, and south Asian origin. In addition to the overall composite picture of lineage clusters of different origin, we observed a number of deep-rooting lineages, whose relative clustering and coalescent ages suggest an autochthonous origin in the southwestern Asian corridor during the Pleistocene. The comparison with Y-chromosome data revealed a highly complex genetic and demographic history of the region, which includes sexually asymmetrical mating patterns, founder effects, and female-specific traces of the East African slave trade.

The African Diaspora: Mitochondrial DNA and the Atlantic Slave Trade

Between the 15th and 19th centuries ad, the Atlantic slave trade resulted in the forced movement of approximately 13 million people from Africa, mainly to the Americas. Only approximately 11 million survived the passage, and many more died in the early years of captivity. We have studied 481 mitochondrial DNAs (mtDNAs) of recent African ancestry in the Americas and in Eurasia, in an attempt to trace them back to particular regions of Africa. Our results show that mtDNAs in America and Eurasia can, in many cases, be traced to broad geographical regions within Africa, largely in accordance with historical evidence, and raise the possibility that a greater resolution may be possible in the future. However, they also indicate that, at least for the moment, considerable caution is warranted when assessing claims to be able to trace the ancestry of particular lineages to a particular locality within modern-day Africa.

Do the four clades of the mtDNA haplogroup L2 evolve at different rates

Forty-seven mtDNAs collected in the Dominican Republic and belonging to the African-specific haplogroup L2 were studied by high-resolution RFLP and control-region sequence analyses. Four sets of diagnostic markers that subdivide L2 into four clades (L2a-L2d) were identified, and a survey of published African data sets appears to indicate that these clades encompass all L2 mtDNAs and harbor very different geographic/ethnic distributions. One mtDNA from each of the four clades was completely sequenced by means of a new sequencing protocol that minimizes time and expense. The phylogeny of the L2 complete sequences showed that the two mtDNAs from L2b and L2d seem disproportionately derived, compared with those from L2a and L2c. This result is not consistent with a simple model of neutral evolution with a uniform molecular clock. The pattern of nonsynonymous versus synonymous substitutions hints at a role for selection in the evolution of human mtDNA. Regardless of whether selection is shaping the evolution of modern human mtDNAs, the population screening of L2 mtDNAs for the mutations identified by our complete sequence study should allow the identification of marker motifs of younger age with more restricted geographic distributions, thus providing new clues about African prehistory and the origin and relationships of African ethnic groups.

Adiabatic light transfer via dressed states in optical waveguide arrays

We report on the experimental demonstration of adiabatic light transfer between the outer waveguides in a finite array of evanescently coupled optical waveguides with negligible excitation of all the intermediate waveguides. Such a counterintuitive light transfer scheme is an optical analogue of stimulated Raman adiabatic passage via an auxiliary dressed state proposed in atomic physics for multilevel systems.

Dental anthropology of central-southern, iron age Italy: The evidence of metric versus nonmetric traits

Discrete and metric dental traits are used to assess biological similarities and differences among 13 bioarchaeological populations located on each side of the Apennine mountains in central-southern Italy and dated to the first millennium BC. An initial hypothesis, that the mountain chain might provide a significant geographical barrier for population movement (resulting in greater biological affinities among those groups on the same side), is not supported. Instead, the samples appear to cluster more on the basis of time than geography. Archaeological evidence, however, supports an association between populations on opposite sides of the mountains and thus is in accord with the dental data. As anticipated, discrete dental traits appear to be more useful than metric dental traits in assessing such population affinities. This research represents a beginning to a better comprehension of the complexity of the biological and cultural dynamics of Italian populations during recent millennia.

First European Exposure to Syphilis: The Dominican Republic at the Time of Columbian Contact

Recognition of syphilis in Europe in the late 15th century and its prior absence suggest New World origin. Skeletal populations were examined from sites with documented Columbian contact in the Dominican Republic. Examination of 536 skeletal remains revealed periosteal reaction characteristic of treponemal disease in 6%-14% of the afflicted population. Findings were identical to that previously noted in confirmed syphilis-affected populations and distinctive from those associated with yaws and bejel: it was a low population frequency phenomenon, affecting an average of 1.7-2.6 bone groups, often asymmetric and sparing hands and feet, but associated with significant tibial remodeling. While findings diagnostic of syphilis have been reported in the New World, actual demonstration of syphilis in areas where Columbus actually had contact was missing, until now. The evidence is consistent with this site as the point of initial contact of syphilis and of its subsequent spread from the New World to the Old.

Beeswax as dental filling on a Neolithic human tooth

Evidence of prehistoric dentistry has been limited to a few cases, the most ancient dating back to the Neolithic. Here we report a 6500-year-old human mandible from Slovenia whose left canine crown bears the traces of a filling with beeswax. The use of different analytical techniques, including synchrotron radiation computed micro-tomography (micro-CT), Accelerator Mass Spectrometry (AMS) radiocarbon dating, Infrared (IR) Spectroscopy and Scanning Electron Microscopy (SEM), has shown that the exposed area of dentine resulting from occlusal wear and the upper part of a vertical crack affecting enamel and dentin tissues were filled with beeswax shortly before or after the individual’s death. If the filling was done when the person was still alive, the intervention was likely aimed to relieve tooth sensitivity derived from either exposed dentine and/or the pain resulting from chewing on a cracked tooth: this would provide the earliest known direct evidence of therapeutic-palliative dental filling.

Phylogeographic refinement and large scale genotyping of human Y chromosome haplogroup E provide new insights into the dispersal of early pastoralists in the African continent.

Haplogroup E, defined by mutation M40, is the most common human Y chromosome clade within Africa. To increase the level of resolution of haplogroup E, we disclosed the phylogenetic relationships among 729 mutations found in 33 haplogroup DE Y-chromosomes sequenced at high coverage in previous studies. Additionally, we dissected the E-M35 subclade by genotyping 62 informative markers in 5,222 samples from 118 worldwide populations. The phylogeny of haplogroup E showed novel features compared with the previous topology, including a new basal dichotomy. Within haplogroup E-M35, we resolved all the previously known polytomies and assigned all the E-M35* chromosomes to five new different clades, all belonging to a newly identified subhaplogroup (E-V1515), which accounts for almost half of the E-M35 chromosomes from the Horn of Africa. Moreover, using a Bayesian phylogeographic analysis and a single nucleotide polymorphism-based approach we localized and dated the origin of this new lineage in the northern part of the Horn, about 12 ka. Time frames, phylogenetic structuring, and sociogeographic distribution of E-V1515 and its subclades are consistent with a multistep demic spread of pastoralism within north-eastern Africa and its subsequent diffusion to subequatorial areas. In addition, our results increase the discriminative power of the E-M35 haplogroup for use in forensic genetics through the identification of new ancestry-informative markers.

Dental evidence of biological affinity and environmental conditions in prehistoric Trentino (Italy) samples from the Neolithic to the Early Bronze Age

The use of teeth in anthropological analyses has always provided valuable information on the subsistence patterns of human communities, as well as the biological relationships among them. The present study analyses the permanent dentition of several diachronically continuing samples from the Trentino alpine region of Italy from the Neolithic to the Early Bronze Age. The study of both metric and non-metric dental traits show a strong level of homogeneity from the earlier to the later samples, indicating little external biological influence from surrounding areas. However, the evidence of oral pathology and linear enamel hypoplasia highlights a trend of increase in defects, particularly between the Neolithic and the Copper Age. This has been ascribed to a shift towards more intense agricultural activities and pastoralism, that led to a change in diet and to an increased sedentism. Copyright