Phylogenetic relationships among the phyllotini (rodentia: Sigmodontinae) using morphological characters

Thirty-three species representing all 14 genera of the South American rodent tribe Phyllotini and 5 problematic genera are surveyed for 96 multistate and binary dental, cranial, skeletal, external, and male reproductive tract characters. Wagner parsimony analysis confirmsCalomys as the most basal phyllotine genus, and as currently constituted it is likely paraphyletic. The results are consistent with the exclusion ofPseudoryzomys from the phyllotines and the separation ofReithrodon andNeotomys fromHolochilus at the tribal level. Several highly differentiated generic groups that include a radiation of altiplano endemics centered onAuliscomys and the largely southern Andean/PatagonianReithrodon group appear to form a clade. AGraomys generic group that includesAndalgalomys andEligmodontia is also apparent, but its relationships to other phyllotines are obscured by poorly resolved internal nodes in the more species-rich and probably paraphyletic genusPhyllotis. The significance and consequences of more intensive taxonomic sampling are discussed. The taxonomic consequences of the phylogeny are presented.     

Evolutionary relationships among eight species of South American phyllotine rodents (Rodentia: Muridae) based on allozymic data

Rodents of the tribe Phyllotini represents one of the main radiations of South American Sigmodontini. Phylogenetic relationships among species of this highly diversified group are poorly known. In this paper we analyse evolutionary relationships among eight phyllotine species belonging to the genera Calomys , Graomys , Phyllotis and Eligmodontia , on the basis of allozymic polymorphisms. Most of the differences among species were in allele frequencies and not of allele class. Neighbour-joining and maximum likelihood methods place P. xanthopygus in the same group as E. typus and G. griseoflavus , in agreement with results obtained by several authors on the basis of morphological characters. Parsimony analysis of 0–9 coded data suggest that the genus Calomys is paraphyletic, but with a low bootstrap support. In the tree based on genetic distance data, the genus also appears as paraphyletic. The maximum likelihood method yields a tree where Calomys is monophyletic, but this phylogeny is supported by only two out of 78 alleles analysed. Calomys hummelincki and C. venustus occupy a basal position among Calomys species. Calomys musculinus and C. lepidus are the most closely related species of the genus, with C. laucha as sister to them. These relationships are strongly supported by bootstrap percentages.     

Genetic structure of populations of Calomys laucha (muridae, sigmodontinae) from central Argentina

The genetic structure of populations of the Sigmodontinae rodent Calomys laucha was studied by means of allozyme electrophoresis. This highly opportunistic species is found preferably in periodically perturbed habitats of crop fields in central Argentina, where it can attain very high densities. A total of 17 enzymatic proteins assayed gave information on 25 loci; only four were monomorphic in the seven populations studied. Levels of genetic variability (H_o from 0.144 to 0.171; P_95% from 44% to 56%) were higher than mean values reported for mammals and rodents. These high levels of heterozygosity could be maintained by large populations that do not experience great fluctuations in size, or by a social structure consistent in many small breeding groups that are formed and dissappear every breeding season. Genetic differentiation at a macrogeographical scale (θ=0.018) was low but statistically significant, and showed no correlation with geographic distance between pairs of populations. The pattern of population differentiation found is compatible with a relatively recent range expansion.     

The Scotch broom,Cytisus scoparius (Fabaceae), a paradox in Denmark – an invasive plant or endangered native species?

Scotch broom, Cytisus scoparius, spreads rapidly in parts of Denmark and is considered an invasive species by some authors. However, the species has been present in the Danish flora for centuries and is therefore considered native to Denmark. In the present study we explore whether Danish Scotch broom consists of one or two gene pools with potential differences in phenotype and invasiveness. One plastid and five nuclear microsatellite markers were used to reveal potential substructuring of Danish Scotch broom. Nine populations were included representing populations exhibiting invasive behaviour and populations showing non‐invasive behaviour. An Italian population was used as reference. Bayesian analysis based on genetic markers indicated that the sampled populations form two distinct gene pools, and this pattern was supported by neighbour‐joining trees. Measurements of height and width of the analysed plants showed that the two gene pools correspond to populations exhibiting either a horizontal habit and non‐invasive behaviour or an erect habit and, in some cases, invasive behaviour. The Italian population clustered with the erect ones. We discuss the origin and taxonomic status of the two gene pools and conclude that Danish horizontal Scotch broom should be given a formal taxonomic status in order to initiate conservation activities for its protection. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ●● , ●●–●●.     

Enzyme polymorphism in a population of Calomys musculinus (Rodentia,Cricetidae)

NAD-linked lactate, malate, glycerophosphate, alcohol and nonspecific dehydrogenases, aspartate aminotransferases, and soluble esterases from extracts of tissues of individuals from a wild population of Calomys musculinus (Rodentia, Cricetidae) have been analyzed by means of starch gel electrophoresis and specific staining. Allelic frequencies and heterozygosity have been determined. Mendelian inheritance of some of the variants detected was confirmed by breeding experiments. Ten out of fifteen (66.6%) of the genetic loci investigated presented polymorphism. Mean heterozygosity per locus was very high (H=0.2014, se 0.046).This work has been supported, in part, by grants from the Secretaria de Ciencia y Tecnología de la Nación (National Program for Endemic Diseases) and from the Fundación Emilio Ocampo. C. N. G. is a Fellow and A. B. a Career Investigator of the Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina.     

Gene Flow Among Calomys Musculinus (Rodentia, Muridae) Populations in Argentina

Calomys musculinus is a Sigmodontinae rodent inhabiting periodically disturbed habitats in the central eastern plains of Argentina. It is the natural reservoir host of Junin virus, the etiological agent of Argentine Hemorrhagic Fever (AHF). In order to analyze the levels of gene flow among populations of this species, allozymic variability at 26 loci was studied in 291 individuals from the endemic zone of AHF and localities outside it. All populations showed high levels of polymorphism (H _e between 0.107 and 0.144; P_95% between 38 and 54%). Individual loci f values were in most cases negative, although not significantly different from zero. Mean genetic differentiation among populations was low, but statistically significant (=0.020; P<0.01). There was no correlation between genetic and geographic distances between pairs of populations, and scatter of the pairwise points suggests that, at the regional scale, genetic drift is more influential than gene flow. This result can be interpreted as indicative of a relatively recent expansion of C. musculinus habitat and restricted on-going gene flow, which would be compatible with a relatively slow expansion rate of AHF.     

Structural evaluation of the effects of chronic ethanol ingestion on the testis of Calomys callosus

Chronic exposure to ethanol may results in pathophysiologic changes in cellular function. The present work was designed to investigate the morphology of testis submitted to experimental ethanol ingestion. Experimental animals were divided into two groups. The control group (n = 23) received a solid diet and tap water and the alcoholic group (n = 23) received the same solid diet and ethanol P.A. diluted 20% in water (v/v). After 120 days of treatment, all animals were anesthetized, weighed and sacrificed. Testosterone and luteinizing hormone levels in serum were lower in the alcoholic group than in the control group. Histological and ultrastructural alterations were observed in the testicular alcoholic germinative cells like enormous spaces, lipid droplets accumulation, digestive vacuoles, irregular diameter of the seminiferous tubules and interstitial dilated blood vessels. It was concluded that 20% ethanol provokes lesions on the testis germinative epithelium probably inducing gonadal dysfunction.     

Multiple refugia and glacial expansions in the Tucumane–Bolivian Yungas: The phylogeography and potential distribution modeling of Calomys fecundus (Thomas, 1926) (Rodentia: Cricetidae)

The Yungas, a subtropical mountain rainforest of South America, has been little studied in relation to the evolutionary history of the large-bodied species of the genus Calomys. Particularly, two species have been synonymized: C. boliviae and C. fecundus; the first is only known from its type locality in the northern Bolivian Yungas, whereas the second is known along the Tucumane–Bolivian Yungas shared by Bolivia and Argentina. In this study, we combined a phylogeographic approach with ecological niche modeling, with samples covering most of the geographic range of C. fecundus. One mitochondrial and two nuclear genes were used for population genetic analyses. Current and paleoclimatic models were obtained. Nuclear genes resulted uninformative by retention of ancestral polymorphism with other species of Calomys. The mitochondrial marker revealed a complex network showing signals of several population expansions. Three genetic clusters in a latitudinal sense were detected, which are coincident with the three stable climatic zones estimated by current and paleoclimatic models. We determined a pattern of expansion during glacial cycles and ancestral refugia during interglacial cycles. None of the potential distribution models predicted the presence of C. fecundus in the type locality of C. boliviae. Therefore, we recommend making integrative taxonomic studies in the Bolivian Yungas, to determine whether or not C. fecundus and C. boliviae correspond to the same species.     

Isolation and characterization of eight microsatellite loci from the longheaded eagle ray, Aetobatus flagellum (Elasmobranchii, Myliobatidae)

The longheaded eagle ray, Aetobatus flagellum feeds mainly on bivalves, and there have been some indications that the current reduction in the bivalve population in southern Japan may be due to an increase in the number of longheaded eagle rays. Consequently, the 'predator control programme' for reducing the longheaded eagle ray population was established in 2001 in Japan. For studying the population genetics of the longheaded eagle ray, we isolated eight polymorphic microsatellite loci (two to six alleles per locus; expected heterozygosity, 0.172-0.700) from this species.     

Characterization of five new bovine dinucleotide repeats

Five new bovine (TG)n microsatellite sequences were characterized. During the screening procedure, one-third of the clones had essentially the same flanking sequences. A fast technique was devised to eliminate these clones.     

Genetic characterization of Uruguayan Pampa Rocha pigs with microsatellite markers

In this study, we genetically characterized the Uruguayan pig breed Pampa Rocha. Genetic variability was assessed by analyzing a panel of 25 microsatellite markers from a sample of 39 individuals. Pampa Rocha pigs showed high genetic variability with observed and expected heterozygosities of 0.583 and 0.603, respectively. The mean number of alleles was 5.72. Twenty-four markers were polymorphic, with 95.8% of them in Hardy Weinberg equilibrium. The level of endogamy was low (F_IS = 0.0475). A factorial analysis of correspondence was used to assess the genetic differences between Pampa Rocha and other pig breeds; genetic distances were calculated, and a tree was designed to reflect the distance matrix. Individuals were also allocated into clusters. This analysis showed that the Pampa Rocha breed was separated from the other breeds along the first and second axes. The neighbour-joining tree generated by the genetic distances D_A showed clustering of Pampa Rocha with the Meishan breed. The allocation of individuals to clusters showed a clear separation of Pampa Rocha pigs. These results provide insights into the genetic variability of Pampa Rocha pigs and indicate that this breed is a well-defined genetic entity.     

Testing the role of genetic factors across multiple independent invasions of the shrub Scotch broom (Cytisus scoparius)

Knowledge of the introduction history of invasive plants informs on theories of invasiveness and assists in the invasives management. For the highly successful invasive shrub Scotch broom, Cytisus scoparius, we analysed a combination of nuclear and chloroplast microsatellites for eight native source regions and eight independent invasion events in four countries across three continents. We found that two exotic Australian populations came from different sources, one of which was derived from multiple native populations, as was an invasive sample from California. An invasive population from New Zealand appeared to be predominantly sourced from a single population, either from the native or exotic ranges. Four invasive populations from Chile were genetically differentiated from the native range samples analysed here and so their source of introduction could not be confirmed, but high levels of differentiation between the Chilean populations suggested a combination of different sources. This extensive global data set of replicated introductions also enabled tests of key theories of invasiveness in relation to genetic diversity. We conclude that invasive populations have similar levels of high genetic diversity to native ranges; levels of admixture may vary across invasive populations so admixture does not appear to have been an essential requirement for invasion; invasive and native populations exhibit similar level of genetic structure indicating similar gene flow dynamics for both types of populations. High levels of diversity and multiple source populations for invasive populations observed here discount founder effects or drift as likely explanations for previously observed seed size differences between ranges. The high levels of genetic diversity, differential and source admixture identified for most exotic populations are likely to limit the ability to source biocontrol agents from the native region of origin of invasive populations.     

Isolation and characterization of microsatellites from the canine genome

Microsatellite sequences comprising (dC-dA)_n.(dG-dT)_n repeats have been isolated from canine libraries and sequenced. Oligonucleotide primers have been synthesized to the micro-satellite flanking sequences and used in the polymerase chain reaction to amplify those loci from genomic DNA. The degree of polymorphism of each microsatellite was estimated in a set of unrelated dogs. It is concluded that of the 10 loci studied, nine are sufficiently polymorphic to be useful in genetic studies.