Reassessment of Tantilla boipiranga (Serpentes: Colubrinae) and a preliminary approach to the phylogenetic affinities within Tantilla

Tantilla is one of the most diverse genera among colubrids, with 67 species arranged in six phenotypically recognized species groups. Tantilla boipiranga is the most recently described species within the T. melanocephala group, and it was described based on a small type series, collected in the rupestrian grasslands of south-eastern Brazil. The morphological diversity and the phylogenetic affinity of this species remain poorly known. Here, based on the assessment of recently collected specimens in combination with results of a molecular phylogenetic analysis, we evaluate the morphological variation within T. boipiranga and its phylogenetic position. Our analyses confirm T. boipiranga as genetically distinct from its generic counterparts, and diagnosable based on a combination of colour pattern, meristic counts, and hemipenial morphology. However, contrary to its original description, the hemipenial ornamentation does not differen-tiate T. boipiranga from the highly variable T. melanocephala. In our phylogenetic analysis, T. boipiranga is retrieved as a monophyletic group, nested within the diversity of T. melanocephala and sister to a clade composed by specimens from south-eastern Brazil. Tantilla melanocephala is recovered as a highly diverse lineage, indicating the possible presence of undescribed species. Additionally, our analysis indicates that the T. coronata and T. planiceps species group are mono-phyletic, while the T. taeniata species group is paraphyletic and the only sampled species for the T. calamarina group is nested within the T. melanocephala group. Our results suggest that the phenotypic evolution within the genus is probably more complex than previously recognized, and some colouration patterns used to define the groups can in fact represent phenotypical convergences. Moreover, our phylogenetic analysis suggests a strong signal of geographical structure in the tree topology. Three main geographical lineages were found, a North American, a South American and a Central Ameri-can. The first two lineages were recovered as monophyletic, while the latter is paraphyletic, with Central American species positioned as sister groups of both, the North American and the South American clades. Although a more comprehensive phylogenetic analysis is needed, our study strongly indicates the existence of hidden diversity within the T. melanocephala group and that Tantilla represents an ideal model to evaluate the validity of phenotypical groups in snake systematics and to study the driven mechanisms of morphological evolution.

Development of user-friendly functional molecular markers for VvDXS gene conferring muscat flavor in grapevine.

High fruit and wine quality combined with good climatic adaptation and disease resistance are essential objectives of grape breeding. While several molecular markers are available for pyramiding resistance to fungal pathogens, molecular tools for predicting fruit composition are still scarce. Muscat flavor, caused by the accumulation of monoterpenoids in the berry, is an important target trait for breeding, sought after in both table grapes and wine. Four missense mutations in the VvDXS gene in grape germplasm have been shown to be tightly linked to muscat flavor. Here we present highly reproducible and breeder-friendly functional markers for each of the targeted polymorphisms developed by using either the multiplexed minisequencing SNaPshot™ method, the high-resolution melting (HRM) assay or the cleaved amplified polymorphic sequence system. A total of 242 grapevine accessions were analyzed to optimize these different genotyping methods and to provide allele-specific markers for accurate selection of muscat flavor at early stages of grape breeding programs. The HRM and the minisequencing SNaPshot multiplex assays allow for high-throughput automated screening and are suitable for large-scale breeding programs and germplasm characterization.

Molecular variability of the 16p13.3 region in Amerindians and its anthropological significance.

A total of 1558 base pairs in the 16p13.3 region were investigated in 98 individuals of Mongolian, Northern Arctic and Amerindian affiliation, and the results compared with those obtained in a previous worldwide study of the same genomic region. Fifty-five polymorphic sites could be classified into thirty-five haplotypes from the total data. A median joining network based on the haplotypes revealed two distinct clusters: one with low diversity, with haplotypes found in all five geographic-ethnic categories; while the other, with the most divergent haplotypes, was composed mainly of Africans and a few Amerindians. Almost all neutrality parameters yielded significantly negative values. Demographic simulations with the exclusively Amerindian dataset rejected all scenarios, including a bottleneck beginning more than 12,000 years ago. The demographic scenarios tested considering population growth were similar among the Amerindian and worldwide or Eurasian data sets. The results suggest that Amerindians are a representative sample of Eurasian populations, preserving the signal of demographic growth from the out of Africa exodus and, together with data from uniparental markers, support a scenario of a bottleneck of moderate intensity during the peopling of the New World.

Mitochondrial DNA and Alu insertions in a genetically peculiar population: the Ayoreo Indians of Bolivia and Paraguay.

A total of 91 Ayoreo individuals previously studied for blood groups and protein markers, living in two Bolivian and one Paraguayan communities, were extensively investigated in relation to the hypervariable 1 segment of the control and eight coding regions of their mitochondrial DNA (mtDNA). They show an extremely reduced mtDNA variability, the observed haplotypes being classifiable in just two haplogroups (C and D). They were also variously studied in relation to six Alu insertions; in this case, however, the prevalences found did not depart markedly from those obtained in other populations of this ethnic group. To assess the Ayoreo position in relation to these populations, 11 other groups that had also been studied for these systems and for blood groups and proteins were selected. The dendrograms obtained with two of the three sets of markers showed distinct patterns, but the Ayoreo were placed in a central position in both the blood group + proteins and Alu insertions trees. Therefore, they are clearly distinct in relation to their mtDNA only, suggesting a strong founder effect and/or random loss of variability in this system.

Alu insertions versus blood group plus protein genetic variability in four Amerindian populations.

BACKGROUND: Do the population relationships obtained using DNA or blood group plus protein markers remain the same or do they reveal different patterns, indicating that the factors which influence genetic variation at these two levels of analysis are diverse? Can these markers shed light on the biological classification of the Aché, a Paraguayan tribe which only recently established more permanent contacts with non-Indians? SUBJECTS AND METHODS: To consider these questions we typed 193 individuals from four Amerindian tribes in relation to 12 Alu polymorphisms (five of them never studied in these populations), while 22 blood group plus protein systems were studied among the Aché. These data were then integrated with those previously available (blood groups plus proteins) for the three other populations. DNA extraction and amplification, as well as the other laboratory procedures, were performed using standard methods currently in use in our laboratory. The genetic relationships were obtained using the D(A) distance, and the trees were constructed by the neighbour-joining method, both developed by M. Nei and collaborators. Reliability of the trees was tested by bootstrap replications. Other population variability values were also determined using Nei's methods. RESULTS: Alu polymorphism was observed in all populations and for most of the loci; in the seven systems from which we could compare our results with those of other Amerindian groups agreement was satisfactory. Unusual findings on the blood group plus protein systems of the Aché were a very low (5%) HP*1 frequency and the presence of the C(W) phenotype in the Rh blood group. The intertribal patterns of relationship and other aspects of their variation were remarkably congruent in the two sets (Alu; blood group plus protein) of systems. CONCLUSIONS: The answer to the first question posed above is affirmative. However, the problem of whether the Aché derived from a Gê group that preceded the Guarani colonization of Paraguay, or are just a differentiated Guarani group, could not be answered with the genetic information available; the second hypothesis seems more likely at present, but the point to be emphasized is the striking genetic distinctiveness of the Aché as compared to other Amerindians.