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.     

Genetic diversity of coastal Northwest Atlantic herring populations: implications for management

Analysis of nine tetranucleotide microsatellite loci for Atlantic herring at five locations in the Northwest Atlantic including the Bras d'Or Lakes shows considerable genetic variation and significant population structure within the Coastal Nova Scotia management component, and among coastal populations and herring collected from Georges Bank. However, results are also consistent with gene flow across the Gulf of Maine. The magnitude of differentiation between the Bras d'Or Lakes sample and all others considered was sufficient to warrant further investigation. These data support the precautionary spawning-ground based management approach implemented in this area.     

Palm heart harvesting in the Brazilian Atlantic forest: changes in industry structure and the illegal trade

1. Until the late 1960s, Euterpe edulis was the most important edible palm species in the Brazilian markets. Since then, overharvesting of natural stands and the limited scope of plantations have caused the industry to shift to the multistemmed E. oleracea from the Amazon river estuary.
2. As a result of the relocation of the industry, the structure of the palm harvesting industry has changed and illegal trade has continued to exploit the remaining natural stands of E. edulis .
3. It is suggested that, to avoid the total harvesting of E. edulis and to achieve sustainable management of the palm heart, it will be necessary to diversify the local economy, create incentives for small land owners to improve their management practices, while keeping their competitiveness against the illegal trade, create the incentive of new sources of palm hearts and create a 'green stamping' for management palms.
4. Transformation of the illegal structure of the palm heart industry is probably the only solution to avoid the total depletion of the wild stands of E. edulis .     

An mtDNA analysis in ancient Basque populations: implications for haplogroup V as a marker for a major paleolithic expansion from southwestern europe.

mtDNA sequence variation was studied in 121 dental samples from four Basque prehistoric sites, by high-resolution RFLP analysis. The results of this study are corroborated by (1) parallel analysis of 92 bone samples, (2) the use of controls during extraction and amplification, and (3) typing by both positive and negative restriction of the linked sites that characterize each haplogroup. The absence of haplogroup V in the prehistoric samples analyzed conflicts with the hypothesis proposed by Torroni et al., in which haplogroup V is considered as an mtDNA marker for a major Paleolithic population expansion from southwestern Europe, occurring approximately 10,000-15,000 years before the present (YBP). Our samples from the Basque Country provide a valuable tool for checking the previous hypothesis, which is based on genetic data from present-day populations. In light of the available data, the most realistic scenario to explain the origin and distribution of haplogroup V suggests that the mutation defining that haplogroup (4577 NlaIII) appeared at a time when the effective population size was small enough to allow genetic drift to act-and that such drift is responsible for the heterogeneity observed in Basques, with regard to the frequency of haplogroup V (0%-20%). This is compatible with the attributed date for the origin of that mutation (10,000-15, 000 YBP), because during the postglacial period (the Mesolithic, approximately 11,000 YBP) there was a major demographic change in the Basque Country, which minimized the effect of genetic drift. This interpretation does not rely on migratory movements to explain the distribution of haplogroup V in present-day Indo-European populations.     

Microsatellite multiplex assay for the analysis of Atlantic sturgeon populations

We have developed a multiplex assay covering 16 microsatellite loci, amplified in four polymerase chain reaction (PCR) assays, and loaded on the ABI DNA Analyzer in two separate panels. The assay was tested on 603 individuals originating from wild populations and hatchery stocks of Atlantic sturgeon. The assay was also tested on 12 individuals of European sturgeon and appeared to be almost equally useful. The multiplex assay designed in this study can be successfully applied in studies requiring high genetic resolution, such as relatedness analysis, selective breeding programs, and stock identification of Atlantic sturgeon.     

Diversity distribution and floristic differentiation of the coastal lowland vegetation: implications for the conservation of the Brazilian Atlantic Forest

Floristic differentiation and vegetation definition is an important step to recognize biome distribution and for biodiversity conservation. Here, we aim to verify if the distribution of the costal lowland vegetation in Brazilian littoral is congruent with climatic gradient and the previous vegetation definitions. Additionally we discussed the importance of terms for the Atlantic Forest conservation. Our study was based on floristic and geo-climatic data from 58 published surveys. We generate a checklist of 1088 woody species and verified species distribution according to environmental gradient using a Detrended Correspondence Analysis (DCA). We compared DCA??s groups with the a priori vegetation definition and generate an a posteriori classification using TWINSPAN. DCA and TWINSPAN resulted in groups determined mainly by rainfall (r = ?0.65) and soil sandiness (r = ?0.71). Those groups were not congruent with both the previous vegetation definitions. The coastal lowland vegetation comprises two distinctive floristic groups representing forests and scrubs that occur in wetter climates (Ombrophilous lowland forests) in the Brazilian states of Santa Catarina, Paraná and São Paulo and in drier climates of Espírito Santo, Rio de Janeiro (Restinga-Northern group) and Rio Grande do Sul (Restinga-Southern group) states. The floristic and historical relationships between Ombrophylous lowland forests and Restingas suggest that conservation initiatives should be more conservative and treat collectively all coastal lowland vegetation as a biodiversity hotspot.     

MtDNA haplogroups in the populations of Croatian Adriatic Islands

The number of previous anthropological studies pointed to very complex ethnohistorical processes that shaped the current genetic structure of Croatian island isolates. The scope of this study was limited to the general insight into their founding populations and the overall level of genetic diversity based on the study mtDNA variation. A total of 444 randomly chosen adult individuals from 32 rural communities of the islands of Krk, Brac, Hvar and Korcula were sampled. MtDNA HVS-I region together with RFLP sites diagnostic for main Eurasian and African mtDNA haplogroups were analysed in order to determine the haplogroup structure. The most frequent haplogroups were "H" (27.8-60.2%), "U" (10.2-24.1%), "J" (6.1-9.0%) and "T" (5.1-13.9%), which is similar to the other European and Near Eastern populations. The genetic drift could have been important aspect in history, as there were examples of excess frequencies of certain haplogroups (11.3% of "I" and 7.5% of "W" in Krk, 10.5% of "HV" in Brac, 13.9% of "J" in Hvar and 60.2% of "H" in Korcula). As the settlements on the islands were formed trough several immigratory episodes of genetically distant populations, this analysis (performed at the level of entire islands) showed greater genetic diversity (0.940-0.972) than expected at the level of particular settlements.     

MtDNA polymorphism in the Hungarians: comparison to three other Finno-Ugric-speaking populations

Mitochondrial DNA sequence variation as well as restriction site polymorphisms were examined in 437 individuals from four Finno-Ugric-speaking populations. These included the Hungarians (Budapest region and the Csángós from Hungary and Romania), the Finns and two Saami groups from northeastern Finland (Inari Saami and Skolt Saami), and the Erzas from central Russia. The mtDNA data obtained in this study were combined with our previous data on Y chromosomal variation for eight different loci in these populations. The genetic variation observed among the Hungarians resembled closely that found in other European populations. The Hungarians could not be distinguished from the neighboring populations (e.g., the Austrians) any more than from their Finno-Ugric linguistic relatives.     

The phylogeny of the four pan-American MtDNA haplogroups: implications for evolutionary and disease studies

Only a limited number of complete mitochondrial genome sequences belonging to Native American haplogroups were available until recently, which left America as the continent with the least amount of information about sequence variation of entire mitochondrial DNAs. In this study, a comprehensive overview of all available complete mitochondrial DNA (mtDNA) genomes of the four pan-American haplogroups A2, B2, C1, and D1 is provided by revising the information scattered throughout GenBank and the literature, and adding 14 novel mtDNA sequences. The phylogenies of haplogroups A2, B2, C1, and D1 reveal a large number of sub-haplogroups but suggest that the ancestral Beringian population(s) contributed only six (successful) founder haplotypes to these haplogroups. The derived clades are overall starlike with coalescence times ranging from 18,000 to 21,000 years (with one exception) using the conventional calibration. The average of about 19,000 years somewhat contrasts with the corresponding lower age of about 13,500 years that was recently proposed by employing a different calibration and estimation approach. Our estimate indicates a human entry and spread of the pan-American haplogroups into the Americas right after the peak of the Last Glacial Maximum and comfortably agrees with the undisputed ages of the earliest Paleoindians in South America. In addition, the phylogenetic approach also indicates that the pathogenic status proposed for various mtDNA mutations, which actually define branches of Native American haplogroups, was based on insufficient grounds.     

Native American Y chromosomes in Polynesia: the genetic impact of the Polynesian slave trade

Since Thor Heyerdahl asserted that Polynesia was first colonized from the Americas (Heyerdahl 1950), geneticists have sought--but have not found--any evidence to support his theories. Here, Native American Y chromosomes are detected on the Polynesian island of Rapa. However, this, together with other odd features of the island's Y-chromosomal gene pool, is best explained as the genetic impact of a 19th century Peruvian slave trade in Polynesia. These findings underscore the need to account for history before turning to prehistory and the value of archival research to understanding modern genetic diversity. Although the impact of the Atlantic slave trade on the distribution of modern genetic diversity has been well appreciated, this represents the first study investigating the impact of this underappreciated episode on genetic diversity in the Pacific.     

Essential oil analysis of 10 Piperaceae species from the Brazilian Atlantic forest

Three new quercetin 3,3',4'-tri-O-beta-D-glucopyranosides isolated from leaves of Eruca sativa (Mill.) were identified as quercetin 3,3',4'-tri-O-beta-D-glucopyranoside, quercetin 3'-(6-sinapoyl-O-beta-D-glucopyranosyl)-3,4'-di-O-beta-D-glucopyranoside and quercetin 3-(2-sinapoyl-O-beta-D-glucopyranosyl)-3'-(6-sinapoyl-O-beta-D-glucopyranosyl)-4'-O-beta-D-glucopyranoside. The structures were established by one- and two-dimensional 1H and 13C NMR spectra as well as b     

MtDNA of Fulani nomads and their genetic relationships to neighboring sedentary populations

Despite the large size of the contemporary nomadic Fulani population (roughly 13 million people), the genetic diversity and degree of differentiation of Fulanis compared to other sub-Saharan populations remain unknown. We sampled four Fulani nomad populations (n = 186) in three countries of sub-Saharan Africa (Chad, Cameroon, and Burkina Faso) and analyzed sequences of the first hypervariable segment of the mitochondrial DNA. Most of the haplotypes belong to haplogroups of West African origin, such as L1b, L3b, L3d, L2b, L2c, and L2d (79.6% in total), which are all well represented in each of the four geographically separated samples. The haplogroups of Western Eurasian origin, such as J1b, U5, H, and V, were also detected but in rather low frequencies (8.1% in total). As in African hunter-gatherers (Pygmies and Khoisan) and some populations from central Tunisia (Kesra and Zriba), three of the Fulani nomad samples do not reveal significant negative values of Fu's selective neutrality test. The multidimensional scaling of FST genetic distances of related sub-Saharan populations and the analysis of molecular variance (AMOVA) show clear and close relationships between all pairs of the four Fulani nomad samples, irrespective of their geographic origin. The only group of nomadic Fulani that manifests some similarities with geographically related agricultural populations (from Guinea-Bissau and Nigeria) comes from Tcheboua in northern Cameroon.     

Phenological variation within and among populations of Plathymenia reticulata in Brazilian Cerrado, the Atlantic Forest and transitional sites

BACKGROUND AND AIMS: Plathymenia reticulata (Leguminosae) is a Brazilian tree that occurs in two biomes: Cerrado, a woody savanna vegetation, and the Atlantic Forest, a tropical forest. In this study, phenological patterns and their variability within and among populations located in these biomes and in transitional zones between them were assessed. METHODS: During a 15-month period, individuals from two populations in Cerrado, two in the Atlantic Forest, and six in transitional zones (three in a cerrado-like environment and three in forest fragments) were evaluated in Minas Gerais State, Brazil. The individuals were evaluated monthly according to the proportion of the canopy in each vegetative phenophase (leaf fall, leaf flush and mature leaves) and each reproductive phenophase (floral buds, flowers, immature fruits and mature fruit/seed dispersal). In order to assess the phenological variability within and among populations, habitats and biomes, the Shannon-Wiener diversity index, the Morisita-Horn similarity index and genetic population approach of partitioning diversity were used. KEY RESULTS: Populations of P. reticulata, in general, showed similar phenology; the main differences were related to leaf fall, a process that starts months earlier in the Cerrado than in transitional sites, and even later in forest areas. Considerable synchrony was observed for reproductive phenology among populations and between biomes. Most phenological diversity was due to differences among individuals within populations. CONCLUSION: In spite of environmental differences, P. reticulata from the Atlantic Forest and Cerrado showed similar phenological behavior with only about 10% of the total diversity being attributed to differences between biomes.     

History and structure of sub-Saharan populations of Drosophila melanogaster

Drosophila melanogaster is an important model organism in evolutionary genetics, yet little is known about the population structure and the demographic history of this species within sub-Saharan Africa, which is thought to contain its ancestral range. We surveyed nucleotide variation at four 1-kb fragments in 240 individual lines representing 21 sub-Saharan and 4 Palearctic population samples of D. melanogaster. In agreement with recent studies, we find a small but significant level of genetic differentiation within sub-Saharan Africa. A clear geographic pattern is observed, with eastern and western African populations composing two genetically distinct groups. This pattern may have resulted from a relatively recent establishment of D. melanogaster in western Africa. Eastern populations show greater evidence for long-term stability, consistent with the hypothesis that eastern Africa contains the ancestral range of the species. Three sub-Saharan populations show evidence for cosmopolitan introgression. Apart from those cases, the closest relationships between Palearctic and sub-Saharan populations involve a sample from the rift zone (Uganda), suggesting that the progenitors of Palearctic D. melanogaster might have come from this region. Finally, we find a large excess of singleton polymorphisms in the full data set, which is best explained by a combination of population growth and purifying selection.     

Microsatellite analysis of genetic variation in black bear populations

Measuring levels of genetic variation is an important aspect of conservation genetics The informativeness of such measurements is related to the variability of the genetic markers used; a particular concern in species, such as bears, which are characterized by low levels of genetic variation resulting from low population densities and small effective population sizes We describe the development of microsatellite analysis in bears and its use in assessing interpopulation differences in genetic variation in black bears from three Canadian National Parks These markers are highly variable and allowed identification of dramatic differences in both distribution and amount of variation between populations Low levels of variation were observed in a population from the Island of Newfoundland The significance of interpopulation differences in variability was tested using a likelihood ratio test of estimates of θ= 4 N_eu.     

Reassessing the impact of North Atlantic Oscillation on the sub-Saharan vegetation productivity

The Northern Atlantic Oscillation (NAO) has been shown to have a significant impact on the terrestrial ecosystem in the Sahelian region of Africa during the 1980s, and it has been strongly suggested that NAO may be a reliable predictor for the response of the Sahelian ecosystem to global climate variability. Using data from an extended period, we provide a reassessment for the impact of NAO on the Sahelian climate and ecosystem, and show that there is no consistent relationship between NAO and the ecosystem over Sahel. Statistical analysis on the NAO, vegetation, and precipitation data indicates that NAO influences the Sahelian vegetation productivity exclusively through its impact on precipitation. However, the relationship between the NAO index and Sahelian precipitation varies substantially with time. The correlation coefficient fluctuates between positive and negative values, and does not pass the 5% significance test during most of the twentieth century. The NAO system, although documented to govern the ecosystem dynamics over many other regions, does not have a consistent impact on the ecosystem over the Sahel. Therefore, the NAO index cannot produce a useful prediction on the ecosystem variability and changes in this region. This study provides an example that correlations based on short climate and ecological records (less than 20 years in this case) can be spurious and potentially misleading.     

Genetic structure of Heliofungia actiniformis (Scleractinia: Fungiidae) populations in the Indo-Malay Archipelago: implications for live coral trade management efforts

The fungiid Heliofungia actiniformis is one of the most popular scleractinian coral species in the growing live aquarium trade, with the majority of specimens originating in Indonesia. Details on population connectivity may potentially provide important information with regards to harvest management efforts. Genetic structure was examined, using ribosomal ITS1, 5.8S and partial ITS2 sequences on a small scale among populations in the Spermonde Archipelago, South Sulawesi (up to 65 km distance, Φ_st = 0.09), and on a large scale throughout the Indo-Malay Archipelago (up to 2,900 km distance, Φ_st = 0.26). Significant genetic structuring was found at both scales. Within the Spermonde Archipelago isolation by distance as well as local oceanographic features shaped patterns of genetic connectivity. On the large scale, the data revealed genetically distinct populations in Tomini Bay, New Guinea and the Thousand Islands near Jakarta, and a lack of genetic differentiation among populations lying close to or directly in the path of the Indonesian throughflow: from the central Visayas to the Flores Sea (Φ_ct = 0.32). Whilst the influence of both historical and present day processes on genetic structuring of H. actiniformis populations was revealed, large scale results further emphasised the importance of oceanographic dynamics on larval dispersal patterns in this species. Potential for larval input from surrounding populations, and the increased vulnerability of upstream as well as isolated populations should be taken into consideration when setting future harvest quotas.     

Variation of female and male lineages in sub-Saharan populations: the importance of sociocultural factors

In this paper, we present a study of genetic variation in sub-Saharan Africa, which is based on published and unpublished data on fast-evolving (hypervariable region 1 of mitochondrial DNA and six microsatellites of Y chromosome) and slow-evolving (haplogroup frequencies) polymorphisms of mtDNA and Y chromosome. Our study reveals a striking difference in the genetic structure of food-producer (Bantu and Sudanic speakers) and hunter-gatherer populations (Pygmies, Kung, and Hadza). In fact, the ratio of mtDNA to Y-chromosome Nupsilon is substantially higher in food producers than in hunter-gatherers as determined by fast-evolving polymorphisms (1.76 versus 0.11). This finding indicates that the two population groups differ substantially in female and male migration rate and/or effective size. The difference also persists when linguistically homogeneous populations are used and outlier populations are eliminated (1.78 vs 0.19) or when the jacknife procedure is applied to a paired population data set (1.32 to 7.84 versus 0.14 to 0.66). The higher ratio of mtDNA to Y-chromosome Nnu in food producers than in hunter-gatherers is further confirmed by the use of slow-evolving polymorphisms (1.59 to 7.91 versus 0.12 to 0.35). To explain these results, we propose a model that integrates demographic and genetic aspects and incorporates ethnographic knowledge. In such a model, the asymmetric gene flow, polyginy, and patrilocality play an important role in differentiating the genetic structure of sub-Saharan populations. The existence of an asymmetric gene flow is supported by the phylogeographic features of mtDNA and Y-chromosome haplogroups found in the two population groups. The role of polyginy and patrilocality is sustained by the evidence of a differential pressure of genetic drift and gene flow on maternal and paternal lineages of food producers and hunter-gatherers that is revealed through the analysis of mitochondrial and Y-chromosomal intrapopulational variation.