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The nominal species Oligoryzomys flavescens (yellow pygmy rice rat) appears in different phylogenetic reconstructions as paraphyletic, forming a complex together with Oligoryzomys fornesi (Fornes' pygmy rice rat) or Oligoryzomys sp. B. To test if O. flavescens includes cryptic species, we used a phylogenetic and a phylogeographic approach to analyze the evolutionary relationships among the lineages of this complex and estimated their geographical distributions using niche modeling analysis. We analyzed a portion of the mitochondrial cytochrome b (Cytb), exon 1 of the Interphotoreceptor Retinoid Binding Protein (Rhp3), and intron 7 of the beta fibrinogen (Fgb) genes and estimated divergence times among lineages using a fossil-calibrated molecular clock. The Cytb phylogenetic tree shows 2 main clades: 1 clustering individuals distributed predominantly in the east of the study area and the other grouping individuals from the west, which would correspond to the subspecies O. f. occidentalis. The eastern clade includes 5 lineages: Oligoryzomys sp. B, O. fornesi, and 3 clades named O. flavescens (O. flavescens Uruguay and southeastern Brazil, O. flavescens eastern Brazil, and O. f. flavescens). The phylogenetic break between these 2 main clades occurred about 0.89 million years ago. These clades were not recovered when nuclear markers were evaluated, revealing incomplete lineage sorting and retention of ancestral polymorphisms. The spatial distributions of the ecological niche of the clades obtained in the Cytb phylogenetic reconstructions were predominantly parapatric; narrow overlapping zones between some of them were detected. Phylogeographic analyses in O. f. flavescens revealed a population expansion about 100,000 years ago, and conformed to an isolation by distance pattern. Our results, together with morphological differences previously described between populations belonging to the east and the samples referable to O. f. occidentalis, suggest that the latter should be recognized as a full species. Fil: Rivera, Paula Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina Fil: González Ittig, Raúl Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina Fil: Robainas Barcia, Aymée. Pierre Fabre Iberica; España Fil: Trimarchi, Laura Inés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina Fil: Levis, Silvana. Instituto Nacional de Enfermedades Virales Humanas Dr Julio I. Maiztegui; Argentina Fil: Calderon, Gladys. Instituto Nacional de Enfermedades Virales Humanas Dr Julio I. Maiztegui; Argentina Fil: Gardenal, Cristina Noemi. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina

The population genetic structure of Oligoryzomys longicaudatus colilargo was examined at two geographical scales: (a) regional, including five populations of the Argentinean Patagonia separated by 60–315 km and (b) landscape scale, using five populations from different valleys of the locality of Cholila in the subantarctic forest separated by 6–27 km, and a nearby locality of the Patagonian steppe, with an average distance from Cholila of 33 km. Eight microsatellite loci specific for O. longicaudatus were used as genetic markers. At the regional scale, four genetic clusters were detected by the Geneland software. The genetic structure was found to follow a latitudinal pattern. This result was supported by the FST statistic, indicating low levels of current gene flow within the region. At the landscape level, genetic differentiation among the five populations was also found. Estimated migration rates were, in general, low and asymmetrical between nearby populations. Using a causal modeling approach, we detected that the combination of landscape features such as lakes, rivers, urban settlements and roads appear to constrain the dispersal of O. longicaudatus at this scale. This result would explain why nearby populations were so different in their genetic composition. The information about geographic features limiting rodent dispersal provided here could help to design more accurate prevention measures against the expansion of hantavirus pulmonary syndrome. Fil: Ortiz, N.. Universidad Nacional de Córdoba; Argentina Fil: Polop, Francisco Jose. Universidad Nacional de Río Cuarto; Argentina Fil: Andreo, Verónica Carolina. Universidad Nacional de Río Cuarto; Argentina Fil: Provensal, María Cecilia. Universidad Nacional de Río Cuarto; Argentina Fil: Polop, Jaime Jose. Universidad Nacional de Río Cuarto; Argentina Fil: Gardenal, Cristina Noemi. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina Fil: González Ittig, Raúl Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina

The long-tailed pygmy rice rat Oligoryzomys longicaudatus (Rodentia, Cricetidae) experiences marked population density fluctuations. This species is the major reservoir of the Andes orthohantavirus associated with the hantavirus pulmonary syndrome in southern Argentina, and information on dispersal patterns at different population densities, or differences in dispersal between the sexes during those periods, could contribute to understanding risk of viral transmission among individuals. We examined the spatial genetic structure of O. longicaudatus at a local scale to elucidate how variation in population density influences dispersal patterns. Effective dispersal levels were estimated through spatial genetic autocorrelation (SGA) analyses in periods of different density, and for females and males separately, within an area of 510 × 180 m, using seven microsatellite loci. In autumn (high-intermediate and intermediate densities), SGA was primarily determined by females, which show philopatric behavior in defense of their nests and newborns. In summer (low density), neither sex showed SGA, which could be due to spacing behavior combined with high recruitment rates among adjacent environments. At high-intermediate densities, females remained close to each other, contracting their home ranges. These established individuals would “fence” the area, preventing the immigration of individuals from proximate areas, until population density declines again. We detected differential patterns of effective dispersal for both sexes in different stages of the annual and inter-annual population phases of O. longicaudatus. Since high levels of gene flow were reported for both sexes in summer and for males in all analyzed seasons, the transmission risk of diseases such as hantavirus pulmonary syndrome would be high at a local scale.La densidad poblacional del ratón “colilargo” Oligoryzomys longicaudatus (Rodentia, Cricetidae) experimenta marcadas fluctuaciones. Esta especie es el principal reservorio del ortohantavirus Andes, asociado con el síndrome pulmonar por hantavirus en el sur de Argentina. El conocimiento sobre los patrones de dispersión a diferentes densidades poblacionales y entre los sexos durante esos períodos, podría contribuir a evaluar el riesgo de transmisión viral entre individuos. Examinamos la estructura genética espacial de O. longicaudatus a escala local para determinar de qué manera las variaciones en la densidad poblacional influyen sobre los patrones de dispersión del roedor. Los niveles de dispersión efectiva se estimaron mediante análisis de autocorrelación genética espacial (AGE) utilizando siete loci de microsatélites, dentro de un área de 510 × 180 m. Los análisis se hicieron en distintos períodos de densidad para la población general y para hembras y machos por separado. En otoño (densidad alta-intermedia e intermedia), la AGE estuvo determinada principalmente por las hembras, lo que podría explicarse por su comportamiento filopátrico en relación a la defensa de sus nidos y crías. En verano (baja densidad), ninguno de los sexos mostró AGE, debido a un comportamiento de espaciamiento combinado con altas tasas de reclutamiento entre ambientes adyacentes con diferentes recursos. A densidades altas-intermedias, las hembras permanecieron cerca una de la otra, contrayendo su área de acción. Estos individuos cercarían el área, evitando la inmigración de individuos de áreas cercanas, hasta que la densidad poblacional disminuya nuevamente. Detectamos patrones diferenciales de dispersión efectiva para ambos sexos en cada una de las fases de densidad poblacional (anual e interanual) de O. longicaudatus. El riesgo de transmisión del síndrome pulmonar por hantavirus sería elevado a escala local, dado que se detectaron altos niveles de flujo génico para ambos sexos en verano y para los machos en todas las estaciones analizadas.

In the present study, we analysed the genetic structure of Triatoma infestans populations with a phylogeographical approach using sequences of the mitochondrial NADH dehydrogenase subunit 5 (ND5) and the nuclear elongation factor-1 alpha (EF-1α) genes of bugs obtained from Argentina and Bolivia. Spatially circumscribed haplogroups were distinguished from the ND5 gene sequences, one distributed exclusively to the south of the studied area and, in agreement with the results from the EF-1α gene, one haplogroup limited to Bolivia and another to Morajú located in the Chaco region of Argentina. In both the ND5 and EF-1α networks, the most widespread haplogroup or allele group showed a star-like topology, which is compatible with a recent demographic expansion. The asymmetric historical gene flow detected from a population of the Chaco region towards Bolivia and the spatiotemporal phylogeographical reconstruction of lineage dispersal would support the hypothesis that postulates the Chaco biogeographical region as the area of origin for the species. However, additional studies with a broader sampling in the Andean region are needed to define with certainty whether the origin of T. infestans is Chacoan or Andean.

The nominal species Calomys tener (Winge, 1887) ranges broadly in open lands of the Caatinga, Cerrado, Pantanal and Mata Atlântica of Brazil, and was recently reported from the Pampas of southern Brazil, and in the Selva Paranaense of eastern Paraguay and northeastern Argentina. This rodent can be infected with the pathogenic Araraquara hantavirus in Brazil. Given that most epidemiological studies have not taken into account updated taxonomic findings of their rodent hosts, in this study, we obtained sequence data of the Cyt-b and COI genes of specimens of C. tener from 22 different geographical localities from throughout the currently known distribution of the species (including individuals from Argentina, Paraguay, Bolivia, and Brazil) to test if it constitutes a single genetic unit or if it presents genetic discontinuities that may represent different evolutionary lineages. Phylogenetic analyses including several species of Calomys recovered several clades with strong support. Regarding C. tener, it is recovered as sister to the node that cluster C. laucha (Fischer, 1814) sensu lato, C. expulsus (Lund, 1841) and species in the C. callosus (Rengger, 1830) species complex. At the intraspecific level there are no genetic gaps among haplotypes of C. tener that could suggest more than one species. The recent captures in the Pampas of southern Brazil and in the Selva Paranaense suggest that the species may be colonizing new geographic areas. Fil: González Ittig, Raúl Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina Fil: Kandel, Narayan P.. Texas Tech University. Department Of Biological Sciences; Estados Unidos Fil: Bonvicino, Cibele R.. Instituto Nacional de Cáncer. División de Genetica; Brasil Fil: Salazar-Bravo, Jorge. Texas Tech University. Department Of Biological Sciences; Estados Unidos

To identify and predict situations of increased risk of orthohantavirus infection in humans, it is necessary to study the relationships between the virus and its rodent hosts. The present study investigated orthohantavirus infection in an assemblage of wild Sigmodontinae rodents of the Paraná Delta, Argentina, and providing new evidence of host-switching events. Rodents belonging to the species Oxymycterus rufus (n=187), Akodon azarae (n=82), Oligoryzomys flavescens (n=80), Oligoryzomys nigripes (n=47), Scapteromys aquaticus (n=38), Deltamys kempi (n=7) and Holochilus brasiliensis (n=2) were captured at 4 sampling sites during 20 trapping sessions. Blood sampleswere analyzed by IgG ELISA and livers by a nested reverse transcription PCR for the diagnosis of orthohantavirus infection. The amplified products of the S and M orthohantavirus genomes were sequenced and analyzed to determine similarities with species of the Orthohantavirus genus. The species of the Oligoryzomys positive to the virus were confirmed by amplifying and sequencing thecomplete cyt b gene. Of the 443 serum samples analyzed by IgG ELISA, A. azarae presented the highest host-specific prevalence value (10/82, 12.2%) followed by Ol. nigripes (4/47, 8.5 %) and Ox. rufus (1/187, 0.5%). All the sero-positive Ol. nigripes (n= 4) were positive to the amplification of the S and M segments of the Lechiguanas genotype (98% nucleotide identity for both segments).This is surprising given that Ol. nigripes has been previously associated with Juquitiba genotype, not Lechiguanas. The latter is generally associated with Ol. flavescens, which in our study were all sero-negative. In addition, the association Ox. rufus ? Pergamino genotype found here is, to ourknowledge, novel and another potential evidence of host-switching considering that Pergamino has been originally associated with A. azarae. These findings contribute to the building evidence that contradicts the one-genotype-one-reservoir species premise in the association betweenrodent reservoirs and orthohantaviruses, and supports the hypothesis that the community structure of sympatric host species may contribute to orthohantavirus dynamics. Fil: Colombo, Valeria Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Santa Fe. Instituto de Ciencias Veterinarias del Litoral; Argentina. Laboratorio de Ecología de Enfermedades; Argentina Fil: Brignone, Juan Jeronimo. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; Argentina Fil: Sen, Carina. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; Argentina Fil: Previtali, Maria Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Martin, María Laura. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; Argentina Fil: Levis, Silvana del Carmen. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; Argentina Fil: Monje, Lucas Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Santa Fe. Instituto de Ciencias Veterinarias del Litoral; Argentina. Laboratorio de Ecología de Enfermedades; Argentina Fil: González Ittig, Raúl Enrique. Universidad Nacional del Litoral. Facultad de Humanidades y Ciencias; Argentina Fil: Beldomenico, Pablo Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Santa Fe. Instituto de Ciencias Veterinarias del Litoral; Argentina. Laboratorio de Ecología de Enfermedades; Argentina

The population genetics of Triatoma dimidiata haplogroups was analyzed at landscape and sub-regional scales in Chiapas and regional level across the Mexican Neotropics, and phylogeography of the complex was re-analyzed across its complete geographic range. Two contiguous fragments of the ND4 gene were analyzed due to bias from differential haplogroup specificity using a previously designed sequence. At both landscape (anthropic modification gradient) and regional (demographic, fragmentation, biogeographic, climate) scales, lowest T. dimidiata genetic diversity occurs where there is greatest historical anthropic modification, and where T. cruzi infection prevalence is significantly highest. Trypanosoma cruzi prevalence was significantly higher than expected in haplogroups 1 and 3, while lower than expected in haplogroup 2. There was also a significant difference of DTUI and DTUVI infection frequencies in both haplogroups 1 and 3, while no difference of either in haplogroup 2. All haplogroups from the Mexican Neotropics had moderate to high haplotype diversity, while greatest genetic differentiation was between haplogroups 1 and 3 (above FST = 0.868, p < 0.0001). Divergence of the complex from the MRCA was estimated between 0.97 MYA (95% HPD interval = 0.55–1.53 MYA) and 0.85 MYA (95% HPD interval = 0.42–1.5 MYA) for ND4A and both concatenated fragments, respectively, with primary divergence from the MRCA of haplogroups 2 and 3. Effective population size for Mexican haplogroups 1 and 2 increased between 0.02 and 0.03 MYA. This study supports previous ecological niche evidence for the complex´s origin surrounding the Tehuantepec Isthmus, and provides evidence for recent divergence of three primary dimidiata haplogroups, with differential T. cruzi infection frequency and DTU specificity, important components of vector capacity., Author summary Triatoma dimidiata is one of the broadest distributed triatomine species´ complexes transmitting Trypanosoma cruzi. In Mexico, three haplogroups of the T. dimidiata complex have been reported and all are primary vectors of Chagas disease south of the Tehuantepec Isthmus. Given their epidemiological importance, the question arises whether haplogroups have similar genetic diversity in domestic/modified landscapes, as well as infection characteristics and parasite DTU associations, key components of vector capacity. The aim of the present study was to analyze Triatoma dimidiata population genetics across landscapes, sub-regional, regional, and global Neotropical realm scales, using two contiguous fragments of the ND4 gene. Our results support previous evidence for the complex´s origin surrounding the Tehuantepec Isthmus, and provides evidence for recent divergence of three principal dimidiata haplogroups and significant secondary divergence within each. Differential T. cruzi prevalence and Discrete Typing Unit (DTU) specificity for individual haplogroups provide evidence for potential differential vector capacity within the complex in Mexico.

Background The Lutzomyia longipalpis complex has a wide but discontinuous distribution in Latin America, extending throughout the Neotropical realm between Mexico and northern Argentina and Uruguay. In the Americas, this sandfly is the main vector of Leishmania infantum, the parasite responsible for Visceral Leishmaniasis (VL). The Lu. longipalpis complex consists of at least four sibling species, however, there is no current consensus on the number of haplogroups, or on their divergence. Particularly in Argentina, there have been few genetic analyses of Lu. longipalpis, despite its southern expansion and recent colonization of urban environments. The aim of this study was to analyze the genetic diversity and structure of Lu. longipalpis from Argentina, and to integrate these data to re-evaluate the phylogeography of the Lu. longipalpis complex using mitochondrial markers at a Latin American scale. Methodology/Principal findings Genetic diversity was estimated from six sites in Argentina, using a fragment of the ND4 and the 3´ extreme of the cyt b genes. Greatest genetic diversity was found in Tartagal, Santo Tomé and San Ignacio. There was high genetic differentiation of Lu. longipalpis in Argentina using both markers: ND4 (FST = 0.452, p < 0.0001), cyt b (FST = 0.201, p < 0.0001). Genetic and spatial Geneland analyses reveal the existence of two primary genetic clusters in Argentina, cluster 1: Tartagal, Santo Tomé, and San Ignacio; cluster 2: Puerto Iguazú, Clorinda, and Corrientes city. Phylogeographic analyses using ND4 and cyt b gene sequences available in GenBank from diverse geographic sites suggest greater divergence than previously reported. At least eight haplogroups (three of these identified in Argentina), each separated by multiple mutational steps using the ND4, are differentiated across the Neotropical realm. The divergence of the Lu. longipalpis complex from its most recent common ancestor (MRCA) was estimated to have occurred 0.70 MYA (95% HPD interval = 0.48–0.99 MYA). Conclusions/Significance This study provides new evidence supporting two Lu. longipalpis genetic clusters and three of the total eight haplogroups circulating in Argentina. There was a high level of phylogeographic divergence among the eight haplogroups of the Lu. longipalpis complex across the Neotropical realm. These findings suggest the need to analyze vector competence, among other parameters intrinsic to a zoonosis, according to vector haplogroup, and to consider these in the design and surveillance of vector and transmission control strategies., Author summary The Lutzomyia longipalpis complex has a wide but discontinuous distribution in Latin America, extending throughout the Neotropical realm between Mexico and northern Argentina and Uruguay. In the Americas, this sandfly is the main vector of Leishmania infantum, the parasite responsible for Visceral Leishmaniasis (VL). The Lu. longipalpis complex is composed of at least four sibling species, although there is no current consensus on the number of haplogroups, or their divergence. In Argentina, little is known about the complex population structure. Therefore, the aim of this study was to analyze the diversity and genetic structure of Lu. longipalpis from Argentina and subsequently to analyze the complex phylogeography at a Latin American scale, using two mitochondrial markers. Greatest genetic diversity was found in Tartagal, Santo Tomé and San Ignacio. Two genetic clusters and three Lu. longipalpis haplogroups were identified from the six sites in Argentina. Phylogeographic analyzes using ND4 and cyt b gene sequences and those from across the Neotropical realm registered in GenBank, suggest greater divergence than previously reported. At least eight haplogroups are differentiated using the ND4, each separated by multiple mutational steps. Lu. longipalpis complex divergence from its most recent common ancestor (MRCA) was estimated at mid Pleistocene, 0.70 MYA (95% HPD interval = 0.48–0.99 MYA).

Population genetic studies can contribute to current knowledge about the epidemiology of pathogens such as Streptococcus mutans, which is one of the most widely distributed bacteria in the world to be associated with human dental caries. In the present study, we investigated whether the population genetic structure of the species is clonal or recombinant, and we also evaluated the current levels of gene flow, admixed ancestry, and the hypothesis of an expansion of the bacteria within the last 10 000 years. Strains of S. mutans from Córdoba (Argentina) were obtained, with sequences of the genes aroE, gltA, gyrA, and lepC genes being aligned with those of strains from Japan, Thailand, and Finland. Most of our statistical analyses performed on the DNA matrix of 193 strains supported the existence of recombination at the intergene level. We also estimated the number of genetic clusters via Bayesian analyses, with three genetic clusters being detected in the four countries at different frequencies, as well as the number of strains with pure or admixed ancestry varying among countries. Argentina revealed 50% admixed strains, whereas these types of strains were present in only 8-19% of the other three countries analyzed. This result could be associated with the important human migration waves that Argentina has experienced, which may have mixed strains of S. mutans of different geographical origins. The demographic history was obtained using Extended Bayesian Skyline Plot anslysis, which showed important growth in the effective population size approximately 5000 years ago, coincident with the beginning of the dispersion of agriculture and a change to a diet rich in carbohydrates. Fil: González Ittig, Raúl Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina Fil: Carletto Korber, Fabiana Pia Marina. Universidad Nacional de Córdoba. Facultad de Odontología. Cátedra de Biología Celular; Argentina Fil: Vera, Noelia Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina Fil: Jimenez, Maria Graciela. Universidad Nacional de Córdoba. Facultad de Ciencias Médicas. Hospital Universitario de Maternidad y Neonatología; Argentina Fil: Cornejo, Lila Susana. Universidad Nacional de Córdoba. Facultad de Odontología. Cátedra de Biología Celular; Argentina