Ancestral Asian source(s) of new world Y-chromosome founder haplotypes

Haplotypes constructed from Y-chromosome markers were used to trace the origins of Native Americans. Our sample consisted of 2,198 males from 60 global populations, including 19 Native American and 15 indigenous North Asian groups. A set of 12 biallelic polymorphisms gave rise to 14 unique Y-chromosome haplotypes that were unevenly distributed among the populations. Combining multiallelic variation at two Y-linked microsatellites (DYS19 and DXYS156Y) with the unique haplotypes results in a total of 95 combination haplotypes. Contra previous findings based on Y- chromosome data, our new results suggest the possibility of more than one Native American paternal founder haplotype. We postulate that, of the nine unique haplotypes found in Native Americans, haplotypes 1C and 1F are the best candidates for major New World founder haplotypes, whereas haplotypes 1B, 1I, and 1U may either be founder haplotypes and/or have arrived in the New World via recent admixture. Two of the other four haplotypes (YAP+ haplotypes 4 and 5) are probably present because of post-Columbian admixture, whereas haplotype 1G may have originated in the New World, and the Old World source of the final New World haplotype (1D) remains unresolved. The contrasting distribution patterns of the two major candidate founder haplotypes in Asia and the New World, as well as the results of a nested cladistic analysis, suggest the possibility of more than one paternal migration from the general region of Lake Baikal to the Americas.     

mtDNA analysis of a prehistoric Oneota population: implications for the peopling of the New World.

mtDNA was successfully extracted from 108 individuals from the Norris Farms Oneota, a prehistoric Native American population, to compare the mtDNA diversity from a pre-Columbian population with contemporary Native American and Asian mtDNA lineages and to examine hypotheses about the peopling of the New World. Haplogroup and hypervariable region I sequence data indicate that the lineages from haplogroups A, B, C, and D are the most common among Native Americans but that they were not the only lineages brought into the New World from Asia. The mtDNA evidence does not support the three-wave hypothesis of migration into the New World but rather suggests a single "wave" of people with considerable mtDNA diversity that exhibits a signature of expansion 23,000-37,000 years ago.     

Herpesvirus saimiri strains from three DNA subgroups have different oncogenic potentials in New Zealand white rabbits

Herpesvirus saimiri is a primate tumor virus that induces acute T-cell lymphomas in New World monkeys. Strains of this virus have been previously classified into three groups on the basis of extreme DNA variability of the rightmost region of unique L-DNA. To compare the oncogenic potentials of various strains, we inoculated New Zealand White rabbits with viruses representing groups A, B, and C of herpesvirus saimiri. The results showed that a group C strain were highly oncogenic in New Zealand White rabbits; however, group A or B viruses were not oncogenic in these rabbits. Analysis of DNAs of tumor tissues and lymphoid cell lines established from tumors showed that the viral genome exists in circular episomal form. To identify which part of the genome of the group C strain is responsible for the highly oncogenic phenotype, group B-C recombinant strains were constructed by an efficient drug selection technique. Two group B recombinant strains in which the right-end 9.2 kilobase pairs of unique DNA is replaced by group C virus DNA were oncogenic in rabbits, indicating that the rightmost sequences contribute to the oncogenic properties of the group C strain. Oncogenicity of herpesvirus saimiri has been traditionally evaluated in New World monkeys; infection of rabbits with group C strain 484-77 offers a much more accessible animal model to study the mechanism of oncogenicity of this virus.     

mtDNA variation indicates Mongolia may have been the source for the founding population for the New World.

mtDNA RFLP variation was analyzed in 42 Mongolians from Ulan Bator. All four founding lineage types (A [4.76%], B [2.38%], C [11.9%], and D [19.04%]) identified by Torroni and colleagues were detected. Seven of the nine founding lineage types proposed by Bailliet and colleagues and Merriwether and Ferrell were detected (A2 [4.76%], B [2.38%], C1 [11.9%], D1 [7.14%], D2 [11.9%], X6 [16.7%], and X7 [9.5%]). Sixty-four percent of these 42 individuals had "Amerindian founding lineage" haplotypes. A survey of 24 restriction sites yielded 16 polymorphic sites and 21 different haplotypes. The presence of all four of the founding lineages identified by the Torroni group (and seven of Merriwether and Ferrell's nine founding lineages), combined with Mongolia's location with respect to the Bering Strait, indicates that Mongolia is a potential location for the origin of the founders of the New World. Since lineage B, which is widely distributed in the New World, is absent in Siberia, we conclude that Mongolia or a geographic location common to both contemporary Mongolians and American aboriginals is the more likely origin of the founders of the New World.     

Toward a molecular paleontology of primate genomes

KpnI restriction of anthropoid primate DNAs, from a New World monkey to man, releases a series of segments that are remarkable among all of the alphoid DNAs in the constancy of their relative amounts in the various primate genomes, in their long-range organization, and in their internal sequence structure. These segments are labeled the KpnI A, B, C and D segments. Cross-hybridization analysis by Southern filter-transfer hybridization indicates that the KpnI segments represent separate and distinct families of alphoid DNAs. These families are termed the KpnI A, B, C and D families of alphoid sequences, of which only the KpnI A and B families were studied in detail here. - Evidence is presented suggesting that the KpnI segments do not exist as long, tandemly repeated sequences in the primate genome: rather, they may occur interspersed among other, perhaps nonalphoid sequences. From the stained gel patterns and from Southern filter-transfer hybridization experiments, the KpnI families appear to be absent from the genomes of the two prosimians studied - the galago and the black lemur. The KpnI A and B families are found among all of the anthropoid primates, including the New World capuchin monkey. The KpnI C family was detected in the genomes of the Old World anthropoid primates whereas the KpnI D family was detected only among the great apes and man. - The results are in accord with the observation (Musich et al., 1980) that with the continued evolutionary development of the primate Order, there has been a parallel trend toward an increased number and variety of alphoid DNA sequences. The properties of the KpnI families suggest that these sequences, unique among the alphoid DNAs, have been conservatively maintained throughout primate phylogeny and that they are among the most ancient of all primate DNAs.     

Old World and New World Cupressus pollen: morphological and cytological remarks

The aim of this work was to collect new information about pollen morphology and pollen wall structure comparing Cupressus species from the Old World and New World. Cupressus is a nonmonophyletic genus that includes species that appear to be divided into Old World and New World clades. Observations in this study on cypress pollen indicate that grain size and composition of intine β-glucans are different between the considered Old World and New World species. Different from all the other American cypress species, pollen of C. macrocarpa reacted to dying in a similar manner to Old World species. Rehydrated pollen grains collected from 20 Asian, Afro-Mediterranean and American cypress species were measured under a light microscope. The size of the pollen grains and the percentage of intine in relation to the pollen grain diameter were significantly different between Old World and New World species. Pollen wall composition was tested after addition of different dyes to the hydration solution, and subsequent observations were carried out by light and fluorescence microscopy. Lugol and calcofluor staining showed differences in composition of the middle and inner intine layers between New World and Old World species.     

Iberian origins of New World horse breeds

Fossil records, archaeological proofs, and historical documents report that horses persisted continuously in the Iberian Peninsula since the Pleistocene and were taken to the American continent (New World) in the 15th century. To investigate the variation within the mitochondrial DNA (mtDNA) control region of Iberian and New World horse breeds, to analyze their relationships, and to test the historical origin of New World horses, a total of 153 samples, representing 30 Iberian and New World breeds, were analyzed by sequencing mtDNA control region fragments. Fifty-four haplotypes were found and assigned to seven haplogroups. Reduced levels of variation found for the Menorquina, Sorraia, and Sulphur Mustang breeds are consistent with experienced bottlenecks or limited number of founders. For all diversity indices, Iberian breeds showed higher diversity values than South American and North American breeds. Although, the results show that the Iberian and New World breeds stem from multiple origins, we present a set of genetic data revealing a high frequency of Iberian haplotypes in New World breeds, which is consistent with historical documentation.     

New World arenavirus clade C, but not clade A and B viruses, utilizes alpha-dystroglycan as its major receptor

Alpha-dystroglycan (alpha-DG) has been identified as a major receptor for lymphocytic choriomeningitis virus (LCMV) and Lassa virus, two Old World arenaviruses. The situation with New World arenaviruses is less clear: previous studies demonstrated that Oliveros virus also exhibited high-affinity binding to alpha-DG but that Guanarito virus did not. To extend these initial studies, several additional Old and New World arenaviruses were screened for entry into mouse embryonic stem cells possessing or lacking alpha-DG. In addition, representative viruses were further analyzed for direct binding to alpha-DG by means of a virus overlay protein blot assay technique. These studies indicate that Old World arenaviruses use alpha-DG as a major receptor, whereas, of the New World arenaviruses, only clade C viruses (i.e., Oliveros and Latino viruses) use alpha-DG as a major receptor. New World clade A and B arenaviruses, which include the highly pathogenic Machupo, Guanarito, Junin, and Sabia viruses, appear to use a different receptor or coreceptor for binding. Previous studies with LCMV have suggested the need for a small aliphatic amino acid at LCMV GP1 glycoprotein amino acid position 260 to allow high-affinity binding to alpha-DG. As reported herein, this requirement appears to be broadly applicable to the arenaviruses as determined by more extensive analysis of alpha-DG receptor usage and GP1 sequences of Old and New World arenaviruses. In addition, GP1 amino acid position 259 also appears to be important, since all arenaviruses showing high-affinity alpha-DG binding possess a bulky aromatic amino acid (tyrosine or phenylalanine) at this position.     

New world clade B arenaviruses can use transferrin receptor 1 (TfR1)-dependent and -independent entry pathways, and glycoproteins from human pathogenic strains are associated with the use of TfR1

Arenaviruses are rodent-borne viruses, with five members of the family capable of causing severe hemorrhagic fevers if transmitted to humans. To date, two distinct cellular receptors have been identified that are used by different pathogenic viruses, α-dystroglycan by Lassa fever virus and transferrin receptor 1 (TfR1) by certain New World clade B viruses. Our previous studies have suggested that other, as-yet-unknown receptors are involved in arenavirus entry. In the present study, we examined the use of TfR1 by the glycoproteins (GPs) from a panel of New World clade B arenaviruses comprising three pathogenic and two nonpathogenic strains. Interestingly, we found that TfR1 was only used by the GPs from the pathogenic viruses, with entry of the nonpathogenic strains being TfR1 independent. The pathogenic GPs could also direct entry into cells by TfR1-independent pathways, albeit less efficiently. A comparison of the abilities of TfR1 orthologs from different species to support arenavirus entry found that the human and feline receptors were able to enhance entry of the pathogenic strains, but that neither the murine or canine forms were functional. Since the ability to use TfR1 is a characteristic feature of the human pathogens, this interaction may represent an important target in the treatment of New World hemorrhagic fevers. In addition, the ability to use TfR1 may be a useful tool to predict the likelihood that any existing or newly discovered viruses in this family could infect humans.     

Ancestry of SINE-R.C2 a human-specific retroposon

We have reported previously that a retroposon, containing a variable number of tandemly repeated nucleotide sequences, is present in the third intron of the human C2 gene. This element, termed SINE-R.C2, is a member of a large retroposon family derived from the endogenous retrovirus HERV-K10 and estimated to include a few thousand copies per haploid human genome. In the present study we analyzed genomic DNA from 175 humans from several ethnic groups including Americans of European and African descent, Chinese, Africans, Australians, Pacific Islanders, Japanese, and Koreans. They all contained SINE-R.C2, as indicated by Southern blotting. However, SINE-R.C2 was absent from the genome of nonhuman primates, although SINE-R-type elements were present in chimpanzees and gorillas and the HERV-K10 genome was apparently present in all primates except for New World monkeys. These results indicate that HERV-K10 was inserted into the genome after the divergence of New World monkeys; the prototype SINE-R element, after divergence of orangutans; and SINE-R.C2, after the split between humans and chimpanzees.     

Endogenous type C RNA virus of Odocoileus hemionus, a mammalian species of New World origin.

Type C RNA viruses have been isolated from several Old World vertebrates, and an even larger number of Old World species have been shown to contain endogenous viral genetic sequences. The present report describes the first isolation of type C virus endogenous to a species originating in the New World. This virus, isolated from cells of the Columbian black-tailed deer, Odocoileus hemionus, is shown to possess genetic sequences in common with DNA of its species of origin. While it shares biochemical and immunologic characteristics with other mammalian type C viruses, its immunologic properties readily distinguish it from known endogenous viruses.     

Comparative anatomy of brain monoaminergic neurons in New World and Old World monkeys

A comparison of the distribution of brain monoamine neurons in several New World and Old World monkeys was undertaken using the Falck-Hillarp formaldehyde histofluorescence technique. The overall organization of the monoamine neurons was very similar in all species, although subtle variations were found. Catecholamine (noradrenaline and dopamine) and indoleamine (serotonin) cell bodies corresponding to groups A1–A7, A8–A10, and B1–B9, respectively were found throughout the brainstem. A few catecholamine (dopamine) cells equivalent to groups All and A12 in the diencephalon were also observed. Noradrenaline neurons, rather than those of the dopamine and serotonin systems, tended to be less numerous in the New World monkeys. Ascending catecholamine and indoleamine fiber bundles were observed in most monkeys. It is interesting that fibers corresponding to the “ventral noradrenaline bundle” appeared to be much finer in the common marmoset and tamarin than in other species. In addition, a substantial catecholamine (noradrenaline) innervation of the diencephalon was noted in all the Old World monkeys, while a much lower overall terminal density was apparent in the New World forms.     

Grooved Stones from Zawi Chemi Shanidar, a Protoneolithic Site in Northern Iraq

Grooved stones appear as a new cultural element in Epipaleolithic-Protoneolithic sites (dating from ca. 9000–6000 B.C.) in a broad geographic zone from Southwest Asia to North Africa. Similar objects have been recorded from archeological and ethnographic contexts in both the Old World and the New World. Ethnographic and other evidence has shown that the several types of grooved stones are associated with a variety of functions, mainly related to the manufacture and use of arrows and arrow shafts. It is suggested that these tools may be associated with the discovery and diffusion of the bow and arrow .     

Wolbachia infection dynamics in experimental laboratory populations of Metaseiulus occidentalis

The present study examined the acceptability and suitability of Old World stemborers (Chilo partellus and C. orichalcociliellus) for the development of New World parasitoids (Apanteles deplanatus and A. minator) and New World stemborers (Diatraea saccharalis and D. grandiosella) for the development of Old World parasitoids (Cotesia sesamiae, C. flavipes and C. chilonis). Results revealed that acceptance and suitability were high in old associations. In new associations, parasitoids accepted about 60% of the new association hosts. In addition, 10 out of 17 new associations were successful. Apanteles species appeared to be more physiologically host specific than Cotesia species. For example, two of four new association hosts were accepted by A. deplanatus and only one (D. saccharalis) was partially suitable for progeny development. Among the Cotesia species, Cotesia flavipes appeared to have a wider host range than the two other species. It attacked all hosts offered and successfully parasitized all but one (D. grandiosella). Diatraea saccharalis was accepted and was a suitable host for the development of all parasitoid species tested, whereas D. grandiosella was unsuitable for the development of four out of five parasitoid species tested. No clear pattern was observed as behavioral acceptance did not always agree with the pattern of physiological suitability. Implications of these findings for importation biological control of stemborers are discussed.     

Identification of a novel family of human endogenous retroviruses and characterization of one family member, HERV-K(C4), located in the complement C4 gene cluster.

We have identified a novel family of about 10-50 human endogenous retrovirus elements (HERVs) and have characterized one family member (HERV-KC4). This retrovirus element is integrated within intron 9 of and complement C4A genes and also in some C4B genes, and is a principal contribution to interlocus and interallelic length heterogeneity of C4 genes. The HERV-K(C4) sequence has a typical retrovirus structure with elements of gag, pol and env domains, flanked by two long terminal repeats (LTRs) and is similar to type A, B and D retroviruses. Multiple termination codons preclude the existence of long open reading frames, suggesting that the HERV-K(C4) sequence is no longer functional. Zoo blot hybridization reveals that New World monkeys appear to lack sequences similar to HERV-K(C4), suggesting that integration has occurred after the divergence of Old and New World monkeys. Retrotransposition of prototype viruses is presumed to have led to the amplification and integration of the members of the family in different loci, which in humans, appear to be dispersed over several chromosomes. The absence of the HERV-K(C4) element in some C4B genes in both humans and orangutangs indicate that the retrovirus inserted into the C4A gene after the duplication of the cluster. Subsequent spread of the HERV-K(C4) sequence to C4B genes presumably occurred by interlocus sequence exchange mechanisms, such as unequal crossover and gene conversion-like mechanisms.     

Mitochondrial sequence variation in the Guahibo Amerindian population from Venezuela

New data were obtained on mitochondrial DNA (mtDNA) from Guahibo from Venezuela, a group so far not studied using molecular data. A population sample (n = 59) was analyzed for mtDNA variation in two control-region hypervariable segments (HV1 and HV2) by sequencing. The presence or absence of a 9-bp polymorphism in the COII/tRNA(Lys) region was studied by direct amplification and electrophoretic identification. Thirty-eight variable sites were detected in regions HV1 and HV2, defining 26 mtDNA lineages; 23.7% of these were present in a single individual. The 9-bp deletion was found in 3.39% of individuals. Nucleotide and haplotype diversities were relatively high compared with other New World populations. The identified sequence haplotypes were classified into four major haplogroups (A-D) according to previous studies, with high frequencies for A (47.46%) and C (49.15%), low frequency for B (3.39%), and an absence of D.     

Hepatocellular carcinoma in a free‐living marmoset (Callithrix sp.) with concomitant biliary trematodiasis

Hepatocellular carcinoma (HCC) is rare in New World primates. We report the gross, microscopical, and immunocytochemical features of a spontaneous HCC in a free‐living marmoset (Callithrix sp.). Hepatitis B and C virus and aflatoxin immunohistochemistry were negative; however, concomitant intra‐ and extrahepatic biliary trematodiasis could have played a role.     

The taxonomic significance of leaf micromorphology in the genus Eugenia L. (Myrtaceae)

Leaf micromorphological features of both the Old and New World representatives of Eugenia L. have been studied by light microscopy and scanning electron microscopy. The leaves are hypostomatic and, in the majority of species, the stomata are raised above the epidermis. Trichomes are usually present on the abaxial surface of the New World species. The patterns of abaxial surface sculpturing and arrangement of outer stomatal rims are unique in the New World species. The majority of the Old W'orld species showed different anticlinal wall patterns on the adaxial and abaxial epidermises. In the majority of the New World species the anticlinal wall patterns are more or less the same except in E. axillaris. The paracytic type of stomata, with a non-prominent T-piece cutinization at the poles of the guard cells, is a characteristic feature of the New World species. The taxonomic significance of these features in identification and elucidation of species from both areas is discussed.     

Bezzimyia— a genus of native New World Rhinophoridae (Insecta, Diptera)

The New World genus Bezzimyia Townsend, 1919 is revised and the following 15 new species are described: B. barbarista sp. n., B. bisecta sp. n., B. bulbosa sp. n., B. floridensis sp. n., B. hansoni sp. n., B. jamaica sp. n., B. lapidicina sp. n., B. orestes sp. n., B. pittieri sp. n., B. platina sp. n., B. ramicornis sp. n., B. setifax sp. n., B. sternothrix sp. n., B. thompsonorum sp. n. and B. yepezi sp. n. The oviposition, egg and first instar larva are described for Bezzimyia yepezi from Venezuela. It is argued that Bezzimyia is a member of the family Rhinophoridae, which was previously considered to be represented in the New World only through two immigrant Palaearctic species.     

What are the closest relatives of the hot-spring snakes (Colubridae, Thermophis), the relict species endemic to the Tibetan Plateau?

We conducted phylogenetic analyses to identify the closest related living relatives of the Xizang and Sichuan hot-spring snakes (T. baileyi and T. zhaoermii) endemic to the Tibetan Plateau, using mitochondrial DNA sequences (cyt b, ND4) from eight specimens, together with sequences from 95 additional caenophidian and five henophidian genera that were downloaded from GenBank. Phylogenetic trees were obtained using Bayesian Inference and Maximum likelihood methods. Results suggest that hot-spring snakes, which are adapted to high and cold environments, were clustered in the monophyletic Xenodontinae. Xenodontinae is one of the largest subfamilies of colubrid snakes, with about 90 genera and more than 500 species known, and are primarily tropical snakes previously thought to be restricted to the New World. Our data failed to provide any evidence that the New World xenodontines diverged from Thermophis and dispersed into the New World, also failed to suggest a colonization of Asia by New World xenodontines by dispersal from the New World. An alternative plausible scenario may be that Thermophis and the New World xenodontines evolved independently in Asia and America, respectively, after the divergence of their common ancestor. The divergence of the two species in Thermophis was caused by the barrier of the Hengduan Mountains, and the speciation had almost occurred when Tibetan Plateau attained present elevation.