The molecular phylogenetics of the genus Oligoryzomys (Rodentia: Cricetidae) clarifies rodent host-Hantavirus associations

Several species of the genus Oligoryzomys are natural hosts of different hantavirus genotypes affecting humans. The systematics of the genus is confusing, which complicates the identification of the rodent host and hence the potential endemic areas of hantavirus pulmonary syndrome. In this study, we analyse molecular data to infer phylogenetic relationships among Central and South American specimens of Oligoryzomys, and compare our results with previously published data on karyotypic, geographic distribution and host–virus associations to solve contradictory taxonomic reports. We identified 25 clades, each one corresponding to a different putative species. The phylogenetic trees show that Oligoryzomys longicaudatus is strongly related to the Oligoryzomys flavescens complex, which comprises four clades; Oligoryzomys nigripes is related to Oligoryzomys stramineus, Oligoryzomys vegetus is related to Oligoryzomys fulvescens from Central America, and Oligoryzomys brendae is the sister species of Oligoryzomys aff. destructor. We identified the following rodent host–hantavirus genotype relationships: O. longicaudatus–Andes; O. flavescens ‘West'–Bermejo; O. flavescens ‘East'–Lechiguanas; O. nigripes–Juquitiba; Oligoryzomys microtis–Rio Mamore and Rio Mamore-3; Oligoryzomys chacoensis–Oran; Oligoryzomys costaricencis–Choclo; Oligoryzomys delicatus–Maporal; Oligoryzomys utiaritensis–Castelo dos Sonhos; Oligoryzomys sp. RT2012–Rio Mamore-4; Oligoryzomys sp. (and not Oligoryzomys fornesi)–Anajatuba. This work, besides contributing to the development of prevention programmes for hantavirus epidemiology in Latin America, represents a comprehensive update of the systematics of the genus Oligoryzomys.Fil: González Ittig, Raúl Enrique. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Diversidad y Ecologia Animal; ArgentinaFil: Rivera, Paula Cecilia. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Diversidad y Ecologia Animal; ArgentinaFil: Levis, Silvana C.. Direccion Nacional de Instituto de Investigacion. Adm.nacional de Laboratorio E Instituto de Salud "dr.c.g.malbran". Instituto Nacional de Enfermedades Virales Humanas; ArgentinaFil: Calderón, Gladys E.. Direccion Nacional de Instituto de Investigacion. Adm.nacional de Laboratorio E Instituto de Salud "dr.c.g.malbran". Instituto Nacional de Enfermedades Virales Humanas; ArgentinaFil: Gardenal, Cristina Noemi. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Diversidad y Ecologia Animal; Argentin

Caries and genetic variability of Streptococcus mutans.

In the last two decades, the increase in population genetics studies has contributed to elucidating important questions about the evolution of the pathogenesis of bacteria of clinical interest. The objective of this study is to revise and update the knowledge of the last fifteen years regarding the genetic variability of Streptococcus mutans and their association with dental caries. Streptococcus mutans, one of the most widely distributed bacteria in the world, are heavily associated with this condition. This research shows the results of numerous studies carried out in various countries that, using molecular and biochemical methods, revealed associations between different serotypes and caries activity. In addition, it is reported that the population genetics structure of Streptococcus mutans in Argentina is highly recombinant, which reflects the largest waves of human immigration that occurred in the 19th and 20th centuries. On the other hand, demographic analysis suggests that these bacteria experienced a population expansion that coincided with the beginning of agricultural development.En las últimas dos décadas el incremento de los estudios de genética de poblaciones ha contribuido a dilucidar cuestiones importantes sobre la evolución de la patogénesis de bacterias de interés clínico. El objetivo de este trabajo es realizar una actualización sobre los conocimientos de los últimos quince años referidos a la variabilidad genética de Streptococcus mutansy su relación con la caries dental. Streptococcus mutans, de amplia distribución mundial, es una de las bacterias más fuertemente asociada a dicha enfermedad. En este trabajo se muestran resultados de numerosos estudios realizados en diferentes países que utilizando métodos moleculares y bioquímicos revelaron asociaciones entre diferentes serotipos y la actividad de caries. Además, se reporta que la estructura genética poblacional de Streptococcus mutans de Argentina es de alto nivel recombinante, lo que reflejaría las grandes oleadas inmigratorias humanas ocurridas en los siglos 19th y 20th. Por otra parte, los análisis demográficos sugieren que esta bacteria experimentó una expansión poblacional coincidente con el comienzo del desarrollo de la agricultura

The disjunct pattern of the Neotropical harvestman Discocyrtus dilatatus (Gonyleptidae) explained by climate-driven range shifts in the Quaternary: Paleodistributional and molecular evidence.

The disjunct distribution of the harvestman Discocyrtus dilatatus (Opiliones, Gonyleptidae) is used as a case study to test the hypothesis of a trans-Chaco Pleistocene paleobridge during range expansion stages. This would have temporarily connected humid regions ('Mesopotamia' in northeastern Argentina, and the 'Yungas' in the northwest, NWA) in the subtropical and temperate South American lowlands. The present study combines two independent approaches: paleodistributional reconstruction, using the Species Distribution Modeling method MaxEnt and projection onto Quaternary paleoclimates (6 kya, 21 kya, 130 kya), and phylogeographic analyses based on the cytochrome oxidase subunit I molecular marker. Models predict a maximal shrinkage during the warm Last Interglacial (130 kya), and the rise of the hypothesized paleobridge in the Last Glacial Maximum (21 kya), revealing that cold-dry stages (not warm-humid ones, as supposed) enabled the range expansion of this species. The disjunction was formed in the mid-Holocene (6 kya) and is intensified under current conditions. The median-joining network shows that NWA haplotypes are peripherally related to different Mesopotamian lineages; haplotypes from Santa Fe and Córdoba Provinces consistently occupy central positions in the network. According to the dated phylogeny, Mesopotamia-NWA expansion events would have occurred in the last glacial period, in many cases closely associated to the Last Glacial Maximum, with most divergence events occurring shortly thereafter. Only two (out of nine) NWA haplotypes are shared with Mesopotamian localities. A single, presumably relictual NWA haplotype was found to have diverged much earlier, suggesting an ancient expansion event not recoverable by the paleodistributional models. Different measures of sequence statistics, genetic diversity, population structure and history of demographic changes are provided. This research offers the first available evidence for the historical origin of NWA disjunct populations of a Mesopotamian harvestman

Population genetic structure and demographic history of the scallop Argopecten purpuratus from Peru and Northern Chile: implications for management and conservation of natural beds

The scallop Argopecten purpuratus is a heavily exploited resource along the coasts of Peru and north-central Chile, especially after El Niño events, when the species undergoes high increases in abundance. Little is known about its genetic structure or demographic history, two important factors to ensure sustainable exploitation. We sequenced the cytochrome oxidase I and cytochrome b genes of 116 individuals from six localities (between 05°44′S 80°53′W and 23°31′S 70°33′W). We found high levels of genetic diversity in the analyzed populations. No geographical structuring was observed in the haplotype network, which consisted of a few central, widely distributed haplotypes, and many derived population-specific haplotypes separated by few mutations. This pattern suggests a recent population expansion and moderate to low current gene flow among populations. Mismatch analysis, neutrality tests, and a Bayesian skyline analysis confirmed the occurrence of a past event of population expansion approximately 5,000 years ago, which coincides with increasingly stronger and more frequent El Niño events

COI polymorphism in <i>Discocyrtus dilatatus</i> for the complete data set and two data partitions.

<p>COI polymorphism in <i>Discocyrtus dilatatus</i> for the complete data set and two data partitions.</p

Hierarchical partition of the variance components for haplotypes of <i>Discocyrtus dilatatus</i> under different hypotheses.

<p>Hierarchical partition of the variance components for haplotypes of <i>Discocyrtus dilatatus</i> under different hypotheses.</p

Bayesian skyline plot, depicting the demographic history of <i>Discocyrtus dilatatus</i>.

<p>The y axis represents the increase of the effective population size and the x axis represents the time in million years. The solid line indicates the mean value of the population size over time; the shaded area displays the 95% confidence interval.</p

Calibrated maximum-clade-credibility tree obtained with beast.

<p>Estimated ages (large numbers) are given only for nodes with posterior probability >0.67 (indicated with open dots; the higher support, the larger dots); small numbers display the 95% credibility interval. Supported clades are identified by letters (A to G). Color squares refer to the geographical areas predefined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187983#pone.0187983.g005" target="_blank">Fig 5</a>, and circles point out the ancestral haplotypes, as recognized by their position in the median-joining network; their chronological span in the tree is indicated with a distinct color in branches (grey, blue, brown). Stars indicate presumed expansion events affecting NWA haplotypes. Crosses at some nodes display the position in the phylogeny of the hypothetical nodes recovered in the haplotype network. Pleistocene glacial-interglacial cycles, with ages in kya, are represented by vertical stripes; Last Glacial Maximum (LGM) in darker blue.</p

Presence records of <i>Discocyrtus dilatatus</i> plotted over relevant ecoregions in subtropical and temperate South America.

<p>Yellow dots: records used to calibrate the models; white dots (in Paraguay): three pre-1950 records excluded in this research. Dashed line: Tropic of Capricorn (Trop. Capr, 23°26’14”S). Nomenclature of ecoregions [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187983#pone.0187983.ref014" target="_blank">14</a>]: HCh: Humid Chaco, DCh: Dry Chaco, Yu: Southern Andean Yungas, FS: Paraná flooded savanna, Es: Espinal, HP: Humid Pampas, MS: Southern Cone Mesopotamian savanna, UrS: Uruguayan savanna, APAF: Alto Paraná Atlantic forests, AMF: Araucaria moist forests, SM: Serra do Mar coastal forests, Pa: Pantanal, Ce: Cerrado. Inset: sector represented in South America, displaying the ecoregions that form the ‘dry diagonal’ of open vegetation (Dry Chaco-yellow, Cerrado-grey, Caatinga-blue). Maps were designed using free spatial data available at <a href="http://www.diva-gis.org/Data" target="_blank">http://www.diva-gis.org/Data</a>, and <a href="https://www.worldwildlife.org/publications/terrestrial-ecoregions-of-the-world" target="_blank">https://www.worldwildlife.org/publications/terrestrial-ecoregions-of-the-world</a>.</p

Major biogeographical scenarios proposed for the Upper Quaternary history of <i>Discocyrtus dilatatus</i>, based on the integrated molecular and paleodistributional evidence.

<p>Major biogeographical scenarios proposed for the Upper Quaternary history of <i>Discocyrtus dilatatus</i>, based on the integrated molecular and paleodistributional evidence.</p