Protein polymorphism and genetic distance in South American cricetid rodents of the genus Calomys

Allozymic variation in population samples of Calomys laucha, C. musculinus and C. venustus collected simultaneously from the province of Córdoba, Argentina, was analyzed by gel electrophoresis. These three species showed high levels of polymorphism: for C. laucha, the P value was 72.7% and the H value was 0.147 (19 loci); for C. musculinus, P=61.9% and H=0.149 (20 loci); for C. venustus, P=66.7% and H=0.146 (18 loci). These species are non-fossorial generalists, have a high reproductive rate and live in disturbed habitats. The similarity indices (S) range between 0.613 and 0.681. On the basis of genetic distance, D (between 0.354 and 0.476), divergence time was estimated to be from 6.3 to 8.5 million years (late Miocene). Even admitting some imprecision for this estimate, the remarkable differences at the structural gene level shown by the species analyzed, suggest they had an early origin.     

Species delimitation in the continental forms of the genus Epicrates (Serpentes, Boidae) integrating phylogenetics and environmental niche models

Until recently, the genus Epicrates (Boidae) presented only one continental species, Epicrates cenchria, distributed in Central and South America, but after a taxonomic revision using morphologic characters five species were recognized: E. cenchria, E. crassus, E. maurus, E. assisi, and E. alvarezi. We analyzed two independent data sets, environmental niche models and phylogeny based on molecular information, to explore species delimitation in the continental species of this genus. Our results indicated that the environmental requirements of the species are different; therefore there are not evidences of ecological interchangeability among them. There is a clear correlation between species distributions and the major biogeographic regions of Central and South America. Their overall distribution reveals that allopatry or parapatry is the general pattern. These evidences suggest that habitat isolation prevents or limits gene exchange among them. The phylogenetic reconstruction showed that the continental Epicrates are monophyletic, being E. alvarezi the sister species for the remaining two clades: E. crassus-E. assisi, and E. maurus-E. cenchria. The clade grouping the continental Epicrates is the sister taxon of the genus Eunectes and not of the Caribbean Epicrates clade, indicating that the genus is paraphyletic. There is a non-consistent pattern in niche evolution among continental Epicrates. On the contrary, a high variation and abrupt shifts in environmental variables are shown when ancestral character states were reconstructed on the sequence-based tree. The degree of genetic and ecological divergence among continental Epicrates and the phylogenetic analyses support the elevation to full species of E. cenchria, E. crassus, E. maurus, E. assisi, and E. alvarezi.     

Molecular identification and phylogenetic relationships among the species of the genus Oligoryzomys (Rodentia, Cricetidae) present in Argentina, putative reservoirs of hantaviruses

The systematics and geographical distribution of the species of Oligoryzomys present in Argentina are poorly known. From some of the species different hantavirus genotypes have been recovered. In order to contribute to the accurate identification of those species and to infer their phylogenetic relationships, we analysed data of restriction sites and sequences of the mtDNA d -loop region. The samples used represent almost all Oligoryzomys species known to occur in Argentina. The trees obtained with the two types of data were similar, showing high bootstrap values for the majority of the nodes. Our results support the idea that the specific name Oligoryzomys longicaudatus should be applied only to individuals from the south of Argentina and Chile and confirm that O. nigripes and O. delticola are conspecific. Specimens identified as O. flavescens conform three related clades, probably belonging to a species complex. This study also emphasises that the use of a DNA fragment characterised by a high evolutionary rate compare with other mitochondrial segments as the d -loop, was appropriate to infer the phylogenetic relationships in a group originated by a rapid speciation process. We also suggest the following modifications in the rodent–hantavirus relationships: the only viral genotype associated to O. longicaudatus would be Andes Sout, while O. chacoensis would be the natural host of the genotype Oran. One of the forms of the O. flavescens complex would be the natural host of the genotype Bermejo. Our data are consistent with the hypothesis that each hantavirus genotype is associated with a specific rodent host.     

Inheritance of random amplified polymorphic DNA (RAPD-PCR) markers and their use in population genetic studies of Calomys musculinus (Rodentia,Muridae), the reservoir of Argentine hemorrhagic fever

In order to assess the reliability of RAPD markers in the estimation of the genetic structure of natural populations of the murid rodent Calomys musculinus (reservoir of Junin virus, ethiological agent of Argentine Hemorrhagic Fever), we have analyzed the heritability of RAPD bands in 10 parents and their offspring (33 individuals). Fourteen out of a total of 119 bands obtained were absent in the parental patterns, but consistently amplified in offspring from some families. These bands can be eliminated from analyses. Overall degree of band sharing between individuals, including non-parental bands, correctly grouped members of a family in the same cluster in a UPGMA tree, with a high bootstrap percentage. Results support the usefulness of RAPDs as hereditable markers. One hundred polymorphic RAPD loci were identified in three natural populations of C. musculinus. Mean expected heterozygosity in three natural populations ranged from 0.206 to 0.220. Allele frequency based and phenotype based measures of genetic differentiation among natural populations of C. musculinus gave similar results (Weir and Cockerham's theta = 0.133; Excoffier et al.'s phi = 0.127). These values were considerably higher than those found previously using allozymes as genetic markers, and are compatible with moderate to low levels of gene flow among populations.     

Patterns of evolution in Graomys griseoflavus (Rodentia,Muridae). IV. A case of rapid speciation

The South American group of rodents known as Graomys griseoflavus comprises two sibling species differing only in diploid chromosomal complement: G. griseoflavus (2n = 36, 37 and 38) and G. centralis (2n=42). Reproductive barriers comprising postzygotic as well as precopulatory mechanisms prevent gene exchange between these species. We have studied genetic polymorphism in two populations of G. centralis and four of G. griseoflavus by means of gel electrophoresis of enzymes and other proteins giving information on a total of 30 loci. Values of interspecific genetic identity were similar to those obtained for conspecific populations, suggesting that fixation of Robertsonian fusions would have occurred without significant bottlenecks. It would also indicate that the cladogenetic process must be relatively recent. F_IS values showed no evidence of inbreeding. Fixation indices (F_ST) for the ancestral species showed a tendency to form demes with very low gene flow among them, while in the derived species such tendency was not shown. However, because of the characteristics of the region they occupy, populations are of moderate size, and genic flow is low. Lack of correlation between gene flow levels and geographical distance between population pairs would indicate a recent and fast colonization of its distribution areas by the derived species. It is possible that fixation of Robertsonian fusions occurred in a marginal deme of the ancestral species, e.g. in a parapatric geographical context.     

Distribution of genetic variability in populations of two chromosomal races of Dichroplus pratensis (Melanoplinae, Acrididae) and their hybrid zone

We examined, through allozyme electrophoresis, the genetic structure of populations of the acridid grasshopper Dichroplus pratensis from two chromosomal races (Northern and Southern) and their hybrid zone in Argentina. No fixed alleles for any particular race were found, although genetic differentiation among parental races was significant (0 = 0.044, 95% CI: 0.004-0.068). Hybrid populations are genetically more similar to the Southern race (0 = 0.008, 95% CI: -0.005-0.018) than to Northern ones (0 = 0.018, 95% CI: 0.002-0.030). Differential viability or fertility of hybrids, or asymmetry in mating preferences in favour of one particular cross would cause a higher proportion of matings between hybrid individuals and those from the Southern race. This would explain the high genetic similarity between those groups, in spite of their geographical vicinity with northern race populations.     

Phylogenetic relationships among populations of the Nacobbus aberrans (Nematoda,Pratylenchidae) complex reveal the existence of cryptic species

The plant‐parasitic nematode Nacobbus aberrans sensu lato is an agricultural pest of quarantine importance. Due to the morphometric, physiological and genetic variability observed within the species, there is no agreement on the taxonomy of this nematode. The objective of this study was to analyse the ITS rDNA region and the D2–D3 expansion segments of 28S rDNA in 10 Argentine populations and one from Ecuador and to establish their phylogenetic relationship with other known sequences from South and North America. Phylogenetic trees of the ITS gene showed seven statistically well‐supported clades; the high and significant F_st values obtained among these groups confirmed this partitioning. The Argentine populations here considered were separated into three clades: one comprising a population from the Andean region and two grouping nematodes from lower altitudes. Three other clades were distinguished for South American populations, which included known sequences of individuals from Peru, Bolivia and north of Argentina. The other clade included sequences from Mexico, Ecuador and two Argentine populations of unknown origin. The important degree of genetic divergence observed among Andean populations suggests that the Andes may have played a crucial role in speciation of Nacobbus, which would have originated in this region. Although D2–D3 segments exhibited lower variation, they were useful for establishing phylogenetic relationships among the Argentine populations considered in this work. As there are no other GenBank sequences available for these segments, it was not possible to make comparisons with other populations from South and North America. The considerable genetic differentiation observed in ITS rDNA region among Nacobbus populations showed evidence of cryptic species within the N. aberrans s.l. complex. Integration of morphological and morphometric studies and molecular analyses considering other genes may aid in the identification of species and their phylogenetic relationships within this genus.     

Co-amplification of mitochondrial pseudogenes in Calomys musculinus (Rodentia, Cricetidae): a source of error in phylogeographic studies.

In a previous phylogeographic study of the rodent Calomys musculinus, 24 haplotypes of the mitochondrial DNA D-loop region were detected using the restriction fragment length polymorphism technique (PCR-RFLP). Seven percent of the individuals showed patterns in which the sum of the sizes of the restriction fragments exceeded the size of the original PCR product. In the present paper we analyze possible causes of these atypical haplotypes. PCR products were cloned, and two or three different clones from a single individual were detected by their RFLP patterns. Nine clones with different restriction patterns were selected for sequence analyses. A maximum parsimony phylogenetic analysis revealed two well-supported paraphyletic groups. One group comprised sequences showing low nucleotide divergence compared with the most common haplotypes detected in the phylogeographic study. The other group was basal to the three species of Calomys other than C. musculinus included in the study; the mutations in the short portion of the cytochrome b gene amplified corresponded to 12 amino acid substitutions. The results suggest that two independent insertions of mtDNA sequences into the nucleus occurred; these sequences would co-amplify in the PCR procedure. Identification of pseudogenes is crucial to obtain reliable reconstruction of the intraspecific genealogy in phylogeographic studies.