Genomic differentiation of Neanderthals and anatomically modern man allows a fossil-DNA-based classification of morphologically indistinguishable hominid bones

Southern blot hybridizations of genomic DNA were introduced as a relatively simple fossil-DNA-based approach to classify remains of Neanderthals. When hybridized with genomic DNA of either human or Neanderthal origin, DNA extracted from two Neanderthal finds-the Os parietale, from Warendorf-Neuwarendorf, Germany, and a clavicula, from Krapina, Croatia-was shown to yield hybridization signals that differ by at least a factor of two compared to the signals obtained with the use of fossil DNA of an early Homo sapiens from the Vogelherd cave (Stetten I), Germany. When labeled chimpanzee DNA was used as a probe, Neanderthal and human DNA, however, revealed hybridization signals of similar intensity. Thus, the genome of Neanderthals is expected to differ significantly from the genome of anatomically modern man, because of the contrasting composition of repetitive DNA. These data support the hypothesis that Neanderthals were not ancestors of anatomically modern man.     

Fractionation of nucleic acids with special regard to rapidly labeled RNA.

Fractionation of nucleic acids with potassium acetate is useful for studying the synthesis of ribosomal RNA and messenger RNA. By quantitative removal of 4 and 5 s RNA and of DNA, the detection of messenger RNA is facilitated.     

Citrus in West Africa,with special reference to Liberia

Although ample evidence has been gathered to show that citrus can be grown in many parts of West Africa, relatively little of it is cultivated there at present because of difficulties in transportation and communication. Shifting agriculture is still characteristic of the region, and tradition makes the growing of any introduced tree crop difficult.     

The oldest anatomically modern humans from far southeast Europe: direct dating, culture and behavior

Background

Anatomically Modern Humans (AMHs) are known to have spread across Europe during the period coinciding with the Middle to Upper Paleolithic transition. Whereas their dispersal into Western Europe is relatively well established, evidence of an early settlement of Eastern Europe by modern humans are comparatively scarce.

Methodology/Principal Finding

Based on a multidisciplinary approach for the study of human and faunal remains, we describe here the oldest AMH remains from the extreme southeast Europe, in conjunction with their associated cultural and paleoecological background. We applied taxonomy, paleoecology, and taphonomy combined with geomorphology, stratigraphy, archeology and radiocarbon dating. More than 160 human bone remains have been discovered. They originate from a well documented Upper Paleolithic archeological layer (Gravettian cultural tradition) from the site of Buran-Kaya III located in Crimea (Ukraine). The combination of non-metric dental traits and the morphology of the occipital bones allow us to attribute the human remains to Anatomically Modern Humans. A set of human and faunal remains from this layer has been radiocarbon dated by Accelerator Mass Spectrometry. The direct-dating results of human bone establish a secure presence of AMHs at 31,900+240/−220 BP in this region. They are the oldest direct evidence of the presence of AMHs in a well documented archeological context. Based on taphonomical observations (cut marks and distribution of skeletal elements), they represent the oldest Upper Paleolithic modern humans from Eastern Europe, showing post-mortem treatment of the dead as well.

Conclusion/Significance

These findings are essential for the debate on the spread of modern humans in Europe during the Upper Paleolithic, as well as their cultural behaviors.     

Eco‐morphological differentiation in Lake Magadi tilapia,an extremophile cichlid fish living in hot,alkaline and hypersaline lakes in East Africa

Ecological diversification through divergent selection is thought to be a major force during the process of adaptive radiations. However, the large sizes and complexity of most radiations such as those of the cichlids in the African Great Lakes make it impossible to infer the exact evolutionary history of any population divergence event. The genus Alcolapia, a small cichlid lineage endemic to Lakes Magadi and Natron in East Africa, exhibits phenotypes similar to some of those found in cichlids of the radiations of the African Great Lakes. The simplicity within Alcolapia makes it an excellent model system to investigate ecological diversification and speciation. We used an integrated approach including population genomics based on RAD‐seq data, geometric morphometrics and stable isotope analyses to investigate the eco‐morphological diversification of tilapia in Lake Magadi and its satellite lake Little Magadi. Additionally, we reconstructed the demographic history of the species using coalescent simulations based on the joint site frequency spectrum. The population in Little Magadi has a characteristically upturned mouth—possibly an adaptation to feeding on prey from the water surface. Eco‐morphological differences between populations within Lake Magadi are more subtle, but are consistent with known ecological differences between its lagoons such as high concentrations of nitrogen attributable to extensive guano deposits in Rest of Magadi relative to Fish Springs Lagoon. All populations diverged simultaneously only about 1100 generations ago. Differences in levels of gene flow between populations and the effective population sizes have likely resulted in the inferred heterogeneous patterns of genome‐wide differentiation.     

Ethnic differentiation at VNTR loci, with special reference to forensic applications.

Allele-rich VNTR loci provide valuable information for forensic inference. Interpretation of this information is complicated by measurement error, which renders discrete alleles difficult to distinguish. Two methods have been used to circumvent this difficulty--i.e., binning methods and direct evaluation of allele frequencies, the latter achieved by modeling the data as a mixture distribution. We use this modeling approach to estimate the allele frequency distributions for two loci--D17S79 and D2S44--for black, Caucasian, and Hispanic samples from the Lifecodes and FBI data bases. The data bases are differentiated by the restriction enzyme used: PstI (Lifecodes) and HaeIII (FBI). Our results show that alleles common in one ethnic group are almost always common in all ethnic groups, and likewise for rare alleles; this pattern holds for both loci. Gene diversity, or heterozygosity, measured as one minus the sum of the squared allele frequencies, is greater for D2S44 than for D17S79, in both data bases. The average gene diversity across ethnic groups when PstI (HaeIII) is used is .918 (.918) for D17S79 and is .985 (.983) for D2S44. The variance in gene diversity among ethnic groups is greater for D17S79 than for D2S44. The number of alleles, like the gene diversity, is greater for D2S44 than for D17S79. The mean numbers of alleles across ethnic groups, estimated from the PstI (HaeIII) data, are 40.25 (41.5) for D17S79 and 104 (103) for D2S44. The number of alleles is correlated with sample size. We use the estimated allele frequency distributions for each ethnic group to explore the effects of unwittingly mixing populations and thereby violating independence assumptions. We show that, even in extreme cases of mixture, the estimated genotype probabilities are good estimates of the true probabilities, contradicting recent claims. Because the binning methods currently used for forensic inference show even less differentiation among ethnic groups, we conclude that mixture has little or no impact on the use of VNTR loci for forensics.     

mtDNA polymorphism in East Asian Populations,with special reference to the peopling of Japan.

Nucleotide sequences of the major noncoding (D-loop) region of human mtDNA from five East Asian populations including mainland Japanese, Ainu, Ryukyuans, Koreans, and Chinese were analyzed. On the basis of a comparison of 482-bp sequences in 293 East Asians, 207 different sequence types were observed. Of these, 189 were unique to their respective populations, whereas 18 were shared between two or three populations. Among the shared types, eight were found in common between the mainland Japanese and Koreans, which is the largest number in the comparison. The intergenic COII/tRNA(Lys) 9-bp deletion was observed in every East Asian population with varying frequencies. The D-loop sequence variation suggests that the deletion event occurred only once in the ancestry of East Asians. Phylogenetic analysis revealed that East Asian lineages were classified into at least 18 monophyletic clusters, though lineages from the five populations were completely intermingled in the phylogenetic tree. However, we assigned 14 of the 18 clusters for their specificity on the basis of the population from which the maximum number of individuals in each cluster was derived. Of note is the finding that 50% of the mainland Japanese had continental specificity in which Chinese or Koreans were dominant, while < 20% of either Ryukyuans or Ainu possessed continental specificity. Phylogenetic analysis of the entire human population revealed the closest genetic affinity between the mainland Japanese and Koreans. Thus, the results of this study are compatible with the hybridization model on the origin of modern Japanese. It is suggested that approximately 65% of the gene pool in mainland Japanese was derived from the continental gene flow after the Yayoi Age.     

Lectin histochemical study of lipopigments with special regard to neuronal ceroid-lipofuscinosis

Summary Concanavalin A (ConA) binding to lipopigments (LPs) of the lipofuscin type was proved to be due to the high content of mannose. The nature of the mannose bearing compound was twofold. One part was soluble in modified chloroform-methanol-water mixture (10:10:3) corresponding possibly to the oligosaccharyl diphosphodolichol (oligo-PP-Dol) described to be increased in LPs especially of inherited types. The second part, most probably a glycoprotein (GP), was entirely resistant to various extraction procedures. The ratio of the two components varied. The deposition of the typical lipofuscin (age pigment) was dominated by the GP component. Its amount was greatest in neurolipofuscin (especially in the olivary nucleus) and in the myocardium but very little in hepatocytic lipofuscin. In human neuronal ceroid lipofuscinoses (of early juvenile, and juvenile types) both components were found in large quantities in the storage granules of the affected neurons. The protein type variant of the storage material (Elleder 1978) displayed the highest degree of lipid-bound mannose accumulation, the GP component being extremely low or entirely absent. In the late infantile, infantile and Kufs variants studied in paraffin sections only, the GP component was detetable, too as in the case of the secondary neuronal LP in mucopolysaccharidoses and gangliosidoses. In the dog model of NCL lipid bound mannose clearly predominated, the GP component being concentrated in the cytoplasm and on the periphery od some storage granules. The nature of the GP component, a new finding of LP analysis, is discussed. The metabolic relationship between the two components is uncertain. Neither could be identified as the component resposible for autofluorescence. However, both are most probably responsible for PAS positivity of lipofuscins. The ceroid-type histiocytic LP did not display any detectable increase in any of the mannose bearing components.Abbreviations NCL neuronal ceroid lipofuscinosis - HNCL human NCL - CNCL canine NCL - ONCL ovine NCL - LP lipopigment - GP glycoprotein     

Lectin histochemical study of lipopigments with special regard to neuronal ceroid-lipofuscinosis. Results with concanavalin A

Concanavalin A (ConA) binding to lipopigments (LPs) of the lipofuscin type was proved to be due to the high content of mannose. The nature of the mannose bearing compound was twofold. One part was soluble in modified chloroform-methanol-water mixture (10:10:3) corresponding possibly to the oligosaccharyl diphosphodolichol (oligo-PP-Dol) described to be increased in LPs especially of inherited types. The second part, most probably a glycoprotein (GP), was entirely resistant to various extraction procedures. The ratio of the two components varied. The deposition of the typical lipofuscin (age pigment) was dominated by the GP component. Its amount was greatest in neurolipofuscin (especially in the olivary nucleus) and in the myocardium but very little in hepatocytic lipofuscin. In human neuronal ceroid lipofuscinoses (of early juvenile, and juvenile types) both components were found in large quantities in the storage granules of the affected neurons. The "protein type variant" of the storage material (Elleder 1978) displayed the highest degree of lipid-bound mannose accumulation, the GP component being extremely low or entirely absent. In the late infantile, infantile and Kufs variants studied in paraffin sections only, the GP component was detectable, too as in the case of the secondary neuronal LP in mucopolysaccharidoses and gangliosidoses. In the dog model of NCL lipid bound mannose clearly predominated, the GP component being concentrated in the cytoplasm and on the periphery od some storage granules. The nature of the GP component, a new finding of LP analysis, is discussed. The metabolic relationship between the two components is uncertain. Neither could be identified as the component resposible for autofluorescence.(ABSTRACT TRUNCATED AT 250 WORDS)