Evolutionary relationships, hybridization and diversification under domestication of the locoto chile (Capsicum pubescens) and its wild relatives.

Patterns of genetic variation in crops are the result of multiple processes that have occurred during their domestication and improvement, and are influenced by their wild progenitors that often remain understudied. The locoto chile, Capsicum pubescens, is a crop grown mainly in mid-highlands of South-Central America. This species is not known from the wild and exists only as a cultigen. The evolutionary affinities and exact origin of C. pubescens have still not been elucidated, with hypotheses suggesting its genetic relatedness and origin to two wild putative ancestral Capsicum species from the Central Andes, C. eximium and C. cardenasii. In the current study, RAD-sequencing was applied to obtain genome-wide data for 48 individuals of C. pubescens and its wild allies representing different geographical areas. Bayesian, Maximum Likelihood and coalescent-based analytical approaches were used to reconstruct population genetic patterns and phylogenetic relationships of the studied species. The results revealed that C. pubescens forms a well-defined monotypic lineage closely related to wild C. cardenasii and C. eximium, and also to C. eshbaughii. The primary lineages associated with the diversification under domestication of C. pubescens were also identified. Although direct ancestor-descendant relationship could not be inferred within this group of taxa, hybridization events were detected between C. pubescens and both C. cardenasii and C. eximium. Therefore, although hybrid origin of C. pubescens could not be inferred, gene flow involving its wild siblings was shown to be an important factor contributing to its contemporary genetic diversity. The data allowed for the inference of the center of origin of C. pubescens in central-western Bolivia highlands and for better understanding of the dynamics of its gene pool. The results of this study are essential for germplasm conservation and breeding purposes, and provide excellent basis for further research of the locoto chile and its wild relatives.

Ancestros de Helicobacter pylori de una zona de Nariño con alto riesgo de cáncer gástrico / Helicobacter pylori ancestors from an area of Nariño with high risk of gastric cancer

Objetivo: Determinar la ancestría de Helicobacter pylori aislado de pacientes provenientes de una zona de alto riesgo de cáncer gástrico del departamento de Nariño. Materiales y Métodos: Se incluyeron 16 pacientes con síntomas de dispepsia e infectados con Helicobacter pylori. Se utilizaron biopsias gástricas para el cultivo de Helicobacter pylori y subsecuente secuenciación del genoma total por Illumina MiSeq, 2x300 pb. El ensamblaje y anotación de los genomas se procedió mediante el uso de los algoritmos SPAdes y RASTtk. Las proporciones ancestrales de Helicobacter pylori se determinaron por STRUCTURE con el modelo de mezcla. Las diferencias entre estas proporciones se establecieron con las pruebas H de Kruskal Wallis y post hoc. Resultados: La estructura de la población de Helicobacter pylori deriva de cuatro poblaciones ancestrales: Ancestral Europa (AE) (61.2%), Ancestral Africa1 (AA1) (35.7%), Ancestral Este de Asia (AEA) (3%) y Ancestral Africa2 (AA2) (0.1%), siendo significativas las diferencias entre las proporciones de los ancestros de Helicobacter pylori (p<0.05). Se identificaron diferencias estadísticamente significativas entre: AA2 y AEA (p=0.022); AA2 y AA1 (p<0.05); AA2 y AE (p<0.05); AEA y AA1 (p=0.014) y AEA con AE (p<0.05), sin embargo, no se encontró diferencias significativas entre AA1 y AE (p=0.098), evaluadas por post hoc. Conclusión: Helicobacter pylori que coloniza la mucosa gástrica de una población de alto riesgo de cáncer gástrico en Nariño, deriva su acervo genético principalmente de ancestros europeos y africanos, confiriéndole a la bacteria alta capacidad competitiva asociada al desarrollo de lesiones severas en nichos gástricos amerindios.

Objective: To determine the ancestry of Helicobacter pylori isolated from patients from a high-risk area for gastric cancer in the department of Nariño. Materials and Methods: Sixteen patients with dyspepsia symptoms and infected with Helicobacter pylori were included. Gastric biopsies were used for Helicobacter pylori culture and subsequent whole genome sequencing by Illumina MiSeq, 2x300 bp. Genome assembly and annotation proceeded by using the SPAdes and RASTtk algorithms. The ancestral proportions of Helicobacter pylori were determined by STRUCTURE with the mixture model. Differences between these proportions were established with Kruskal Wallis and post hoc H-tests. Results: The population structure of Helicobacter pylori derived from four ancestral populations: Ancestral Europe (AE) (61.2%), Ancestral Africa1 (AA1) (35.7%), Ancestral East Asia (AEA) (3%) and Ancestral Africa2 (AA2) (0.1%), with differences between the proportions of Helicobacter pylori ancestors being significant (p<0.05). Statistically significant differences were identified between: AA2 and AEA (p=0.022); AA2 and AA1 (p<0.05); AA2 and AE (p<0.05); AEA and AA1 (p=0.014) and AEA with AE (p<0.05), however, no significant differences were found between AA1 and AE (p=0.098), evaluated by post hoc. Conclusion: Helicobacter pylori colonizing the gastric mucosa of a population at high risk of gastric cancer in Nariño, derives its gene pool mainly from European and African ancestors, giving the bacterium highly competitive capacity associated with the development of severe lesions in Amerindian gastric niches.

The multifaceted genomic history of Ashaninka from Amazonian Peru.

Despite its crucial location, the western side of Amazonia between the Andes and the source(s) of the Amazon River is still understudied from a genomic and archaeogenomic point of view, albeit possibly harboring essential information to clarify the complex genetic history of local Indigenous groups and their interactions with nearby regions,1,2,3,4,5,6,7,8 including central America and the Caribbean.9,10,11,12 Focusing on this key region, we analyzed the genome-wide profiles of 51 Ashaninka individuals from Amazonian Peru, observing an unexpected extent of genomic variation. We identified at least two Ashaninka subgroups with distinctive genomic makeups, which were differentially shaped by the degree and timing of external admixtures, especially with the Indigenous groups from the Andes and the Pacific coast. On a continental scale, Ashaninka ancestors probably derived from a south-north migration of Indigenous groups moving into the Amazonian rainforest from a southeastern area with contributions from the Southern Cone and the Atlantic coast. These ancestral populations diversified in the variegated geographic regions of interior South America, on the eastern side of the Andes, differentially interacting with surrounding coastal groups. In this complex scenario, we also revealed strict connections between the ancestors of present-day Ashaninka, who belong to the Arawakan language family,13 and those Indigenous groups that moved further north into the Caribbean, contributing to the early Ceramic (Saladoid) tradition in the islands.14,15.

Genetic divergence and evidence of human-mediated translocation of two-fingered sloths (Choloepus hoffmanni) in Costa Rica.

Sloths are notoriously slow and consequently have limited dispersal ability, which makes them particularly vulnerable to the effects of habitat fragmentation and degradation. Sloths in Costa Rica are considered of conservation concern due to habitat loss, livestock production and increasing urbanization. Reintroductions from rescue centres are commonplace across the country, yet their genetic diversity and population structure are unknown, and there is currently little consideration of the genetic background prior to intervention or releases. We used microsatellite analysis to undertake the first exploratory investigation into sloth population genetics in Costa Rica. Using data from 98 two-fingered sloths (Choloepus hoffmanni) from four different geographic regions, we determined the presence of four potential genetic groups, three of them with minimal population structuring despite the limited dispersal ability and presence of physical barriers. Sloths from the North appear to represent a highly distinct population that we propose may require management as a discrete unit for conservation. We stress the need for additional analyses to better understand the genetic structure and diversity of North andWest regions and suggest that rescue facilities in Costa Rica should consider the genetic background of rehabilitated sloths when planning future reintroductions. Our results also highlight the threat posed by physical isolation due to widespread urbanization and agriculture expansion for a species with a weak dispersal ability.

Genetic diversity in Mexican wild populations of the Great Curassow (Crax rubra) / Diversidad genética en poblaciones silvestres mexicanas del hocofaisán (Crax rubra)

Abstract The Great Curassow (Crax rubra) is a Neotropical bird with a wide distribution; it is classified under different threat categories and is listed as a vulnerable species by the IUCN. The Official Mexican Standard, the NOM-059-SEMARNAT-2010, indicates that the Great Curassow is a threatened species, and the subspecies Crax rubra griscomi, which is restricted to the island of Cozumel, is classified as critically endangered. Habitat loss and fragmentation, hunting, overexploitation, and illegal trade are among the main factors that have placed the bird at an endangered status. The objective of the present study was to determine the genetic structure and variation of the species within the Mexican populations of Crax rubra by using three mitochondrial markers, and one nuclear marker (COI, ND2, Cyt b, and MUSK). We used 47 samples obtained by noninvasive collection (feathers) including the two different color phases of the female plumage: dark brown and barred (rare in Mexico). Gene flow between the remaining populations is recent and extensive, even between the continental and the island population (C. r. griscomi). The results indicate that the subspecies C. r. rubra and C. r. griscomi do not present a marked genetic differentiation because the second exhibits an exclusive haplotype and a shared haplotype. With this study, we provide the first genetic-geographic approximation of the curassow in Mexico, where a gradual geographic differentiation is observed between the western and eastern populations of the Isthmus of Tehuantepec, and we provide a baseline for future studies. Finally, the information obtained indicates that important genetic diversity persists in the Mexican populations of the Great Curassow and that sufficient conservation within the ecosystems of these subspecies can be obtained by protecting them from overexploitation and by conserving and restoring their habitat.

Resumen El hocofaisán (Crax rubra) es un ave de la región Neotropical con amplia distribución, que se encuentra en diferentes categorías de riesgo, por la IUCN está catalogada como una especie Vulnerable. A nivel nacional, dentro de la NOM-059-SEMARNAT-2010 está considerada como una especie amenazada, y la subespecie Crax rubra griscomi restringida a la isla de Cozumel, está categorizada como en peligro de extinción. Entre los factores principales por los que se encuentra en grave riesgo, destacan la pérdida y fragmentación del hábitat, la cacería, la sobreexplotación, la extracción y el comercio ilegal. El objetivo del presente estudio es conocer la estructura y variación genética de la especie dentro de las poblaciones silvestres mexicanas de Crax rubra, mediante el uso de tres marcadores mitocondriales y uno nuclear (COI, ND2, Cyt b y MUSK). A partir de 47 muestras obtenidas mediante colecta no invasiva (plumas) que incluyen las dos fases de plumaje de la hembra: café oscura y barrada (rara en México). Se observó que el flujo génico entre las poblaciones remanentes es reciente y extenso, incluso entre las poblaciones continentales y la isleña (C. r. griscomi). Los resultados indican que las subespecies C. r. rubra y C. r. griscomi no presentan una marcada diferenciación genética dado que la segunda presentó un haplotipo exclusivo y uno compartido. Con el presente estudio brindamos la primera aproximación genético-geográfica del hocofaisán en México y una línea de base para futuros estudios, en el que se observa una diferenciación geográfica gradual entre las poblaciones del oeste y del este del Istmo de Tehuantepec. Finalmente, la información obtenida indica que en las poblaciones mexicanas del hocofaisán persiste una diversidad genética importante y que su conservación en los ecosistemas puede ser suficiente mediante la protección a la sobreexplotación, la conservación y restauración de su hábitat.

Mapping QTLs for drought tolerance in a SEA 5 x AND 277 common bean cross with SSRs and SNP markers

Abstract The common bean is characterized by high sensitivity to drought and low productivity. Breeding for drought resistance in this species involves genes of different genetic groups. In this work, we used a SEA 5 x AND 277 cross to map quantitative trait loci associated with drought tolerance in order to assess the factors that determine the magnitude of drought response in common beans. A total of 438 polymorphic markers were used to genotype the F8 mapping population. Phenotyping was done in two greenhouses, one used to simulate drought and the other to simulate irrigated conditions. Fourteen traits associated with drought tolerance were measured to identify the quantitative trait loci (QTLs). The map was constructed with 331 markers that covered all 11 chromosomes and had a total length of 1515 cM. Twenty-two QTLs were discovered for chlorophyll, leaf and stem fresh biomass, leaf biomass dry weight, leaf temperature, number of pods per plant, number of seeds per plant, seed weight, days to flowering, dry pod weight and total yield under well-watered and drought (stress) conditions. All the QTLs detected under drought conditions showed positive effects of the SEA 5 allele. This study provides a better understanding of the genetic inheritance of drought tolerance in common bean.

On the origins and genetic diversity of South American chickens: one step closer.

Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America. The obtained sequencing data from South American chickens indicate the presence of four haplogroups (A, B, E and D) that can be further subdivided into nine sub-haplogroups. Of these, four (B1, D1a, E1a(b), E1b) were absent from local Iberian Peninsula chickens and one (D1a) was present only on Easter Island. The presence of the sub-haplogroups A1a(b) and E1a(b) in South America, previously only observed in Eastern Asia, and the significant population differentiation between Iberian Peninsula and South American populations, suggest a second maternal source of the extant genetic pool in South American chickens.

Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012.

It remains unclear whether lineages of influenza A(H3N2) virus can persist in the tropics and seed temperate areas. We used viral gene sequence data sampled from Peru to test this source-sink model for a Latin American country. Viruses were obtained during 2010-2012 from influenza surveillance cohorts in Cusco, Tumbes, Puerto Maldonado, and Lima. Specimens positive for influenza A(H3N2) virus were randomly selected and underwent hemagglutinin sequencing and phylogeographic analyses. Analysis of 389 hemagglutinin sequences from Peru and 2,192 global sequences demonstrated interseasonal extinction of Peruvian lineages. Extensive mixing occurred with global clades, but some spatial structure was observed at all sites; this structure was weakest in Lima and Puerto Maldonado, indicating that these locations may experience greater viral traffic. The broad diversity and co-circulation of many simultaneous lineages of H3N2 virus in Peru suggests that this country should not be overlooked as a potential source for novel pandemic strains.

Genetic diversity within and between broodstocks of the white shrimp Litopenaeus vannamei (Boone, 1931) (Decapoda, Penaeidae) and its implication for the gene pool conservation

Genetic variation within and between fifteen closed broodstock lines of the Pacific white shrimp Litopenaeus vannamei, reared at different hatcheries in the Brazilian coast, was assessed by RAPD analysis. Fifty two polymorphic loci were identified when a set of five decamer primers was used in PCR. The genetic diversity analysis within lines evidenced genetic variation loss probably related to bottleneck effects and inbreeding. In addition, the genetic divergence values between the different samples appear to reflect the initial founder composition of such stocks, in some cases, sharing a common origin, suggesting a putative importance of interbreeding for the establishment of genetic improvement programs for these broodstocks. The genetic variation monitoring appears to be helpful to the gene pool conservation of this aquaculture species, mainly if considered its exotic status in Brazil and the current impossibility of new introduction of wild individuals.

A variação genética existente dentro e entre quinze linhagens fechadas de reprodutores do camarão branco Litopenaeus vannamei, mantidas em diferentes laboratórios de larvicultura na costa brasileira, foi estudada utilizando análises RAPD. Através de um conjunto de cinco iniciadores decâmeros em PCR, foram identificados 52 locos polimórficos. A análise da diversidade genética dentro de cada linhagem evidenciou perda da variação genética provavelmente devida a efeitos de bottleneck e endocruzamento. Em adição, os valores de divergência genética entre as diferentes linhagens parecem refletir a composição inicial de fundação desses estoques, em alguns casos, compartilhando uma origem comum, sugerindo uma importância potencial do exo-cruzamento para estabelecer programas de melhoramento genético baseado nessas linhagens reprodutoras. O monitoramento da variação genética será muito útil para a conservação do conjunto gênico desta espécie de aquacultura, especialmente se for considerado seu status exótico no Brasil e que atualmente é impossível a realização de novas introduções de indivíduos selvagens.

Genetic diversity within and between broodstocks of the white shrimp Litopenaeus vannamei (Boone, 1931) (Decapoda, Penaeidae) and its implication for the gene pool conservation

Genetic variation within and between fifteen closed broodstock lines of the Pacific white shrimp Litopenaeus vannamei, reared at different hatcheries in the Brazilian coast, was assessed by RAPD analysis. Fifty two polymorphic loci were identified when a set of five decamer primers was used in PCR. The genetic diversity analysis within lines evidenced genetic variation loss probably related to bottleneck effects and inbreeding. In addition, the genetic divergence values between the different samples appear to reflect the initial founder composition of such stocks, in some cases, sharing a common origin, suggesting a putative importance of interbreeding for the establishment of genetic improvement programs for these broodstocks. The genetic variation monitoring appears to be helpful to the gene pool conservation of this aquaculture species, mainly if considered its exotic status in Brazil and the current impossibility of new introduction of wild individuals.

A variação genética existente dentro e entre quinze linhagens fechadas de reprodutores do camarão branco Litopenaeus vannamei, mantidas em diferentes laboratórios de larvicultura na costa brasileira, foi estudada utilizando análises RAPD. Através de um conjunto de cinco iniciadores decâmeros em PCR, foram identificados 52 locos polimórficos. A análise da diversidade genética dentro de cada linhagem evidenciou perda da variação genética provavelmente devida a efeitos de bottleneck e endocruzamento. Em adição, os valores de divergência genética entre as diferentes linhagens parecem refletir a composição inicial de fundação desses estoques, em alguns casos, compartilhando uma origem comum, sugerindo uma importância potencial do exo-cruzamento para estabelecer programas de melhoramento genético baseado nessas linhagens reprodutoras. O monitoramento da variação genética será muito útil para a conservação do conjunto gênico desta espécie de aquacultura, especialmente se for considerado seu status exótico no Brasil e que atualmente é impossível a realização de novas introduções de indivíduos selvagens.

Genetic diversity within and between broodstocks of the white shrimp Litopenaeus vannamei (Boone, 1931) (Decapoda, Penaeidae) and its implication for the gene pool conservation

Genetic variation within and between fifteen closed broodstock lines of the Pacific white shrimp Litopenaeus vannamei, reared at different hatcheries in the Brazilian coast, was assessed by RAPD analysis. Fifty two polymorphic loci were identified when a set of five decamer primers was used in PCR. The genetic diversity analysis within lines evidenced genetic variation loss probably related to bottleneck effects and inbreeding. In addition, the genetic divergence values between the different samples appear to reflect the initial founder composition of such stocks, in some cases, sharing a common origin, suggesting a putative importance of interbreeding for the establishment of genetic improvement programs for these broodstocks. The genetic variation monitoring appears to be helpful to the gene pool conservation of this aquaculture species, mainly if considered its exotic status in Brazil and the current impossibility of new introduction of wild individuals.

A variação genética existente dentro e entre quinze linhagens fechadas de reprodutores do camarão branco Litopenaeus vannamei, mantidas em diferentes laboratórios de larvicultura na costa brasileira, foi estudada utilizando análises RAPD. Através de um conjunto de cinco iniciadores decâmeros em PCR, foram identificados 52 locos polimórficos. A análise da diversidade genética dentro de cada linhagem evidenciou perda da variação genética provavelmente devida a efeitos de bottleneck e endocruzamento. Em adição, os valores de divergência genética entre as diferentes linhagens parecem refletir a composição inicial de fundação desses estoques, em alguns casos, compartilhando uma origem comum, sugerindo uma importância potencial do exo-cruzamento para estabelecer programas de melhoramento genético baseado nessas linhagens reprodutoras. O monitoramento da variação genética será muito útil para a conservação do conjunto gênico desta espécie de aquacultura, especialmente se for considerado seu status exótico no Brasil e que atualmente é impossível a realização de novas introduções de indivíduos selvagens.

Allelic relationships of anthracnose (Colletotrichum lindemuthianum) resistance in the common bean (Phaseolus vulgaris L.) cultivar Michelite and the proposal of a new anthracnose resistance gene, Co-11

The genetic resistance of Phaseolus vulgaris L. cultivar Michelite to races 8 and 64 of Colletotrichum lindemuthianum, causal agent of bean anthracnose, was characterized. Crosses were made between Michelite and Mexico 222 cultivars and the F2 population was inoculated with race 64 in order to study the inheritance of resistance to anthracnose in Michelite. The segregation of F2 population fitted in a ratio of 3R:1S, showing the presence of a dominant gene in Michelite gene conditioning resistance to race 64. Allelism tests were conducted with F2 populations derived from crosses between Michelite and AB 136, AND 277, BAT 93, Cornell 49-242, G 2333, Kaboon, Mexico 222, Michigan Dark Red Kidney (MRDK), Ouro Negro, Perry Marrow, PI 207262, TO, TU, and Widusa. All the cultivars (except Mexico 222) were resistant to race 64. While F2 derived from the Michelite x Mexico 222 was inoculated with race 8. Additionally, allelism tests indicated that the gene present in Michelite is independent from Co-1, Co-2, Co-3, Co-4, Co-5, Co-6, Co-7, Co-9 and Co-10 genes. The monogenic inheritance observed in Michelite and the independence of this gene from those previously characterized allow the authors to propose that the anthracnose resistant gene in Michelite should be named Co-11.