LANGEBIO, Irapuato, Guanajuato, Mexico
Program and Abstracts
Organizing committee
Andrés Moreno Estrada (LANGEBIO-IPN) Karla Sandoval Mendoza (LANGEBIO-IPN) Mitzi Flores Ponce (LANGEBIO-IPN) María C. Ávila Arcos (LIIGH-UNAM) Victor Acuña Alonzo (ENAH-INAH)
#mexpopgen3
Program
9:30-10:00 Registration
10:00 – 11:35 Session I
10:00 – 10:05 – Opening remarks Andrés Moreno-Estrada, LANGEBIO, México
10:05 – 10:35 “Genome Odyssey: Theatre as an effective way to teach scientific concepts to children” Guest Speaker: Anna-Sapfo Malaspinas, University of Lausanne, Switzerland
10:35 -10:55 “Genomics of Middle Neolithic farmers at the fringe of of Europe“ Federico Sánchez-Quinto, Uppsala University, Sweden
10:55-11:15 “Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans” J. Víctor Moreno-Mayar, Natural History Museum of Denmark, University of Copenhagen
11:15 – 11:35“Reconstructing Human Migrations from Genomic data across Latin America and the Pacific“ Andrés Moreno Estrada, LANGEBIO, Mexico
11:35 – 12:00 Coffee break
12:00 – 13:40 Session II
12:00 – 12:30 “Insights into human adaptation” Guest speaker: Emilia Huerta- Sanchez, University of California Merced, USA
12:30 – 12:50 “Imputation of Ancient Hominin ABO Haplotype Structure From Modern Populations” Keolu Fox. University of California, San Diego, USA
12:50 – 13:20 “Tracing the origins 19th century enslaved Africans” Guest speaker: Marcela Sandoval-Velasco, Natural History Museum of Denmark, University of Copenhagen.
13:20 – 13:40 "Phosphatidylcholine balance as a possible driver of maize adaptation to Mexican highlands" Rubén Rellán Álvarez, LANGEBIO, Mexico
13:40 – 15:00 Lunch
15:00 – 16:00 Session III Spark talks by Students - TBD
15:00 – 15:10 “Paleogenomic study of Serranos - a Pre-Hispanic Civilization from Sierra Gorda, Mexico.” Viridiana Villa-Islas, LIIGH-UNAM, Mexico
15:10 – 15:20 “Interspecies Bacterial Competitive Outcomes in C. elegans Intestine Reveal the Principles of Community Assembly in a Simple Animal Gut” Anthony Ortiz MIT, USA
15:20 – 15:30 “Genome-wide allele-specific expression of the transcriptional landscape associated to Capsicum domestication” Erik Omar Díaz Valenzela, LANGEBIO-CINVESTAV, Mexico
15:30 – 15:40 "Change in the population structure of maize landraces associated to the introgression from inbreed lines " Idalia Rojas, Instituto de Ecología, UNAM, Mexico
15:40 – 15:50 "Domestication of the open-pollinated scarlet runner bean (Phaseolus coccineus L.)" Azalea Guerra García, Instituto de Ecología, UNAM, Mexico
15:50 – 16:00 "Análisis de asociación de fenotipos de pigmentación en población mexicana del Proyecto CANDELA-México." Paola Everardo Martínez, Instituto de Investigaciones Antropológicas, UNAM Mexico.
16:00 – 17:30 Poster Session
Poster presentations
1. “Efecto de las variantes alélicas CYP2C9*2 y CYP2C9*3 en la respuesta terapéutica y farmacocinética de la glibenclamida en población Maya de Yucatán” Barbara I. de la Peña Espinoza et al.
2. “Genomic Insights into the Origin and Diversification of Late Maritime Hunter- Gatherers from the Chilean Patagonia” Constanza de la Fuente et al.
3. “Genetic structure of blue-eyed shags in the Kerguelen and Crozet archipelagos” Juan C. Guevara López et al.
4. “Reconstructing admixture and migration dynamics of Post-Columbian Mexico” Juan E. Rodríguez Rodríguez et al.
5. “Genetic diversity of Afro-descendant communities from the Lesser Antilles.” María A. Nieves et al.
6. Late and gradual domestication of ancient Tehuacan maize Miguel Vallebueno-Estrada et al.
7. “Paleogenomic study of ancient pathogens in Pre-Hispanic indigenous individuals from Central Mexico” Miriam Bravo López et al.
8. Population and evolutionary genomics in non-model mammals Sergio Nigenda-Morales et al.
ABSTRACTS
Oral presentations
1. Presenter: Anna-Sapfo Malaspinas University of Lausanne, Switzerland [email protected]
Title: Genome Odyssey: theatre as an effective way to teach scientific concepts to children
Authors and affiliations: Anna-Sapfo Malaspinas, University of Lausanne, Switzerland.
Over the course of about eight months a team of roughly 30 professionals in the arts and science worked together to create a theatre play intended for children. The starting point of the play was a scientific publication about the peopling of Australia and the intention was to communicate some scientific results to children as young as 8 years old. The play covered population genetic concepts, was meant to raise awareness about Aboriginal Australians while also conveying the fact that science is fun and is meant for all. We surveyed about 450 children (incl. 200 that took part in a study) before and after the play asking them the same questions to assess how much they learned from it. We present the results in this talk.
2. Presenter: Federico Sánchez-Quinto Uppsala University [email protected]
Title: Genomics of Middle Neolithic farmers at the fringe of of Europe
Authors and affiliations: Federico Sanchez-Quinto1, Helena Malmström1, Magdalena Fraser1,3, Linus Girdland Flink4, Emma M. Svensson1, Jan Storå5, Anders Götherström2 and Mattias Jakobsson1
1 Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 75236, Uppsala, Sweden 2 Department of Archaeology and Classical Studies, Stockholm University, Wallenberglaboratoriet, 10691 Stockholm, Sweden 3 Department of Archaeology and Ancient History, Uppsala University-Campus Gotland, SE-621 67 Visby, Sweden 4 Research Centre in Evolutionary Anthropology and Palaeoecology, School of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF. 5 Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm
Agriculture emerged in the Fertile Crescent around 11,000 years before present (BP) and then spread, reaching central Europe some 7,500 years ago (ya.) and eventually Scandinavia by 6,000 years ya. Recent paleogenomic studies have shown that the spread of agriculture from the Fertile Crescent into Europe was due mainly to a demic process. Such event reshaped the genetic makeup of European populations since incoming farmers displaced and admixed with local hunter-gatherers. The Middle Neolithic period in Europe is precisely characterized by such interaction, and a time where a resurgence of hunter- gatherer ancestry has been documented. While most research has been focused on the genetic origin and admixture dynamics with hunter-gatherers of farmers from Central Europe, the Iberian Peninsula, and Anatolia, data from farmers at the North-Western edges Europe remains scarce. Here, we investigate genetic data from Middle Neolithic from Ireland, Scotland, and Scandinavia and compare it to genomic data from hunter-gatherers, Early and Middle Neolithic farmers across Europe. We note affinities between the British Isles and Iberia, confirming previous reports. Moreover, we note some indications of interactions between Middle Neolithic Farmers of the British Isles and Scandinavia. Finally, our data together that of previous publications allow us to grasp a better understanding of the interactions between farmers and hunter-gatherers at the northwestern fringe of Europe.
3. Presenter: J. Víctor Moreno-Mayar Natural History Museum of Denmark, University of Copenhagen [email protected]
Title: Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans
Authors and affiliations: J. Víctor Moreno-Mayar (1) Ben A. Potter (2) Lasse Vinner (1) Matthias Steinrücken (3,4) Simon Rasmussen (5) Jonathan Terhorst (6,7) John A. Kamm (6,8) Anders Albrechtsen (9) Anna-Sapfo Malaspinas (1,10,11) Martin Sikora (1) Joshua D. Reuther (2) Joel D. Irish (12) Ripan S. Malhi (13,14) Ludovic Orlando (1) Yun S. Song (6,15,16) Rasmus Nielsen (1,6,17) David J. Meltzer (1,18) Eske Willerslev (1,8,19)
(1) Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen (2) Department of Anthropology, University of Alaska (3) Department of Biostatistics and Epidemiology, University of Massachusetts (4) Department of Ecology and Evolution, University of Chicago (5) Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark (6)Department of Statistics, University of California, Berkeley (7)Department of Statistics, University of Michigan (8) Wellcome Trust Sanger Institute, Wellcome Genome Campus. (9) The Bioinformatics Centre, Department of Biology, University of Copenhagen (10) Department of Computational Biology, University of Lausanne (11) Swiss Institute of Bioinformatics (12) Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University (13) Department of Anthropology, University of Illinois at Urbana-Champaign (14) Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign. (15) Computer Science Division, University of California, Berkeley (16) Chan Zuckerberg Biohub, San Francisco, California (17) Department of Integrative Biology, University of California (18) Department of Anthropology, Southern Methodist University. (19) Department of Zoology, University of Cambridge.
Recent studies of contemporary Native Americans have revealed a high degree of genetic structure, some of which is inferred to date back to the late Pleistocene arrival of the first Americans. However, evidence from archaeology, skeletal anatomy, linguistics and modern genetics has not resolved whether this early structure arose from a single or multiple migrations into the Americas. Specifically, it is not known whether that structure emerged in Siberia, Alaska, or south of the North American continental ice sheets. Ancient human remains from late Pleistocene Alaska, the entryway into the Americas, are key to this debate. We sequenced the ~17X genome of an ~11.5 kyo child skeleton (USR1), recovered in Alaska at the Upward Sun River (Xaasaa Na’) site. Genomic data revealed that USR1 belonged to a basal Native American population that diverged prior to the deep split between North and South Native Americans, thus supporting a single founding event. Based on this split pattern, we estimate a demographic model for Siberians, USR1 and other Native Americans using whole genome data. Finally, the USR1 genome allowed us to re-assess the source of the two Holocene migrations that likely gave rise to Na-Dene-speaking and Inuit populations in northern North America. These results provide additional detailed insight into the demographic history of the early peopling of the Americas.
4. Presenter: Andrés Moreno Estrada Head of Genomics Core Facility LANGEBIO – CINVESTAV , Mexico [email protected]
Title: Reconstructing Human Migrations from Genomic data across Latin America and the Pacific
Genetic data is transforming our understanding of the natural world and the diversity of our own species. Latin America is among the regions that concentrate most of the biodiversity of the planet, including ethnic, linguistic and cultural diversity of Latin American human populations. However, despite the globalization of biotechnologies to analyze the human genome, indigenous populations from the Americas remain underrepresented in large-scale genomic studies.
In this talk, I will discuss recent efforts to characterize the genetic profile of Native Americans throughout the continent and focus on regional approaches aimed at resolving finer scale population structure patterns and human migrations throughout Mexico, the Caribbean, South America, and the Pacific.
This topic poses challenges and opportunities to adequately study human diversity not only for the benefit of researchers and science, but also for the benefit of the local communities, which are bearers of a unique evolutionary history that has been recorded in their DNA. This rapidly evolving field also raises questions about the best practices when applying genomic approaches to promote a sustainable use of Latin American biodiversity in a modern and globalized world.
5. Presenter: Emilia Huerta-Sanchez University of California Merced, USA [email protected]
Title: Insights into human adaptation
Authors and affiliations: Emilia Huerta-Sanchez UC Merced, Fernando Racimo Centre for GeoGenetics in the Natural History Museum of the University of Copenhagen, Chenling Antelope, Computational Biology, UC Berkeley, Davide Marnetto, University of Turin
One of the central questions in evolutionary genetics is what proportion of genetic variation is non-neutral, i.e. under the force of natural selection. The field has mainly adopted a model-based paradigm for this question- that is, we construct a particular null model of no selection, or model of selection, and then compare real data to test deviations or similarity to the model predictions with an appropriate summary of the genetic variation. This approach has been applied in large number of studies, and as a result many genes have been identified as candidates for positive selection. Now that whole genome sequencing data sets are available across global populations, we argue that we need to revisit the candidate regions to re-examine the evolutionary models underlying these adaptations
6. Presenter: Keolu Fox University of California, San Diego Email: [email protected]
Title: Imputation of Ancient Hominin ABO Haplotype Structure From Modern Populations
Authors and affiliations: KEOLU FOX(1), IAN B. STANAWAY(2), EVAN EICHLER (3), JILL JOHNSEN(4) and DEBORAH A. NICKERSON(3)
1.) School of Medicine, University of California, San Diego 2.) Biomedical Informatics and Medical Education, University of Washington 3.) Department of Genome Sciences, University of Washington 4.) Blood Works Northwest, Seattle
Characterizing variation in the ABO gene is important in transfusion and transplantation medicine because variants in ABO have significant consequences with regard to recipient compatibility. While many believe that the genetics of the ABO locus is well understood, little is known about the impact of novel, rare variation in the ABO gene. Here, we analyze next-generation sequence derived coding variation in ~10,000 individuals from 30 populations, including two ancient hominins (Neanderthal and Denisovan). We hypothesize that imputed ABO types from the 1,000 Genomes Project, and the National Heart, Lung, and Blood Institutes, Exome Sequencing project will recapitulate previous estimates based on serologically derived ABO blood types (Cavalli-Sforza et al., 1994) and allow us to impute ABO haplotype structure in ancient hominins.
Through our analysis, we validated previous estimates of ABO blood type based on serology. We identified common variants known to influence ABO function, including those known to the common A and B haplotype as well as a common deletion that leads to the O genotype. We also identified rare population specific coding variants within ABO including single nucleotide/missense variants and insertion/deletions. We then used those haplotypes to impute ABO blood type for both ancient hominins.
These analyses are important for future studies of human blood group genes to (1) improve the specificity of blood typing at both the clinical and research level by identifying rare functional alleles that might result in atypical serological patterns, (2) illuminate ABO gene architecture on a global scale, and (3) assess the potential for introgression of ancient ABO haplotypes found in contemporary human populations.
7. Presenter: Alejandra Moreno Letelier Natural History Museum of Denmark, University of Copenhagen [email protected]
Title: “Tracing the origins 19th century enslaved Africans”
Abstract not available
8. Presenter: Rubén Rellán Álvarez LANGEBIO [email protected]
Title: Phosphatidylcholine balance as a possible driver of maize adaptation to Mexican highlands
Authors and affiliations: Karla Juarez-Nunez, Juan Estevez, Jeffrey Ross-Ibarra, Daniel Gates, Li Wang, Matthew Hufford, Ruairidh Sawers
Abstract: After domestication from lowland teosinte in the Mexican subtropics, maize colonized the highlands of Mexico and South America. In both Mexican and South American highlands maize encountered lower temperatures and in several volcanic area soils with low phosphorus availability. We hypothesize that these two abiotic stresses were major selective forces during maize adaptation to the highlands and shaped glycerolipid metabolism since low temperature and P deficiency have opposite effects on the relative content of glycerolipid species. We are using this system to explore how metabolic pathways change during the process of local adaptation and how we can use metabolic phenotyping together with quantitative and population genetics to identify loci that might have been under selection during the local adaptation events.
I will present data on a couple of common garden experiments in highland and lowland Mexican field sites where we grew a maize RIL mapping population made of a cross between B73, a temperate inbred and Palomero Toluqueno (PT3), a Mexican highland landrace; and a 120 landrace diversity panel composed of highland and lowland maize. From these plants we were able to identify around 125 glycerolipid species that we are using in different ways to identify loci involved in glycerolipid metabolism I will present these results and in particular on an interesting QTL in ch3 where a candidate phospholipase A1 gene seems to be responsible for phosphatidylcholine (PC) to lysophosphatidylcholine (lyso-PC) conversion. RILs with PT genotype at the QTL peak have high PC/lyso-PC ratios while RILs with B73 genotype have low PC/lyso-PC ratios. This phenotype is characteristic of highland landraces from Mexico. We sequenced the B73 and PT gene and identified a mutation in the flap/lid domain of the phospholipase domain that could explain the biochemical phenotype we observe. Using data from 30 genomes of highland and lowland maize across the Americas we observe that the PT allele of this mutation is conserved in highland Mexican, Guatemalan, and SW US maize but not in lowland or South American landraces. Finally using publicly available GBS data from 4,000 landraces we observe that the gene was under selection in Mexican highlands. We are now trying to understand to what extent balancing PC to lyso-PC species might be important to local adaptation in the highlands, the possible convergence of this phenotype in Mexican and South American highland maize and the possibility to apply this knowledge understand how maize adapts to different temperatures and phosphorus levels.
Student Ignite Talks
1. Presenter: Viridiana Villa Islas Laboratorio Internacional de Investigación sobre el Genoma Humano [email protected]
Title: Paleogenomic study of Serranos - a Pre-Hispanic Civilization from Sierra Gorda, Mexico.
Authors and affiliations: Viridiana Villa-Islas1, Marcela Sandoval-Velasco2, Elizabeth Mejía Pérez-Campos3, María C Ávila-Arcos1.
1.-International Laboratory for Human Genome Research, National Autonomous University of Mexico, Querétaro, Mexico. 2.-Center for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark. 3.- Instituto Nacional de Antropología e Historia, Querétaro, Mexico.
Abstract: Toluquilla and Ranas are two archeological sites located in the Sierra Gorda, in the State of Querétaro, Central Mexico. These sites were part of the limits of two large cultural regions of the pre-Hispanic period: Aridoamerica and Mesoamerica. The population who inhabited this area is referred to as “Serrana” culture, with a specialized economy oriented to cinnabar mining –a toxic mineral. It has been hypothesized that Toluquilla and Ranas area was occupied first by groups belonging to Mesoamerican-like civilizations, and subsequently by Chichimecas due to climatic fluctuations around 800 AD. Despite this, Toluquilla and Ranas display striking cultural continuity, which opens the question of whether the populations that inhabited them were continuous, or if there were replacements as a consequence of the expansion of Aridoamerica into the south. To approach this, we generated paleogenomic data from six individuals, four from Toluquilla and two from Ranas, from different time points spanning the time of the shift. We determined mitochondria and Y chromosome haplogroups, and used autosomal data to contrast past and present-day Native Mexican genetic diversity. Of notice, we identify that samples post-dating the shift have a clear genetic affinity and genetic structure similar to present-day populations from Central-West Mexico, while one of the samples that pre-dates it (1,200 YBP), falls outside known present-day genetic variation and shows a genetic structure mostly from northern Native Mexican ancestry.
2. Presenter: Anthony Ortiz [email protected] MIT
Title: Interspecies Bacterial Competitive Outcomes in C. elegans Intestine Reveal the Principles of Community Assembly in a Simple Animal Gut
Authors and affiliations: Anthony Ortiz Lopez (1,2,3), Nicole M. Vega (3), Jeff Gore (3)
1. Licenciatura en Ciencias Genómicas, UNAM 2. Microbiology Graduate Program, MIT 3. Physics of Living Systems, Department of Physics, MIT
Animals throughout the tree of life contain complex multi-species gut communities that play an important role in health and disease. However, the complexity of these gut microbiomes often constrains our ability to gain a mechanistic understanding of how these communities assemble and function. We colonize the gut of the worm C. elegans, a tractable experimental system, with 11 bacterial species in singles, all possible pairs, and selected trios. We find a mixture of coexistence and competitive exclusion with a hierarchical structure lacking any rock-paperscissors interactions. With the intention of associating the characteristics of these one, two, and three species microbiomes, we find a correlation between the monoculture colonization capacity of a bacteria and its average fraction at pairwise competition, and we encounter that the fractions of pairwise competitions possess good predictive power of trio outcomes. We further show that the C. elegans gut environment changes the outcome a pair of species would have outside of the host, with the low intestinal pH being one of the causes. These results highlight that a bottom-up approach to microbiome community assembly may provide valuable insight into the structure and function of complex microbial communities.
3. Presenter: Erik Omar Díaz Valenzela LANGEBIO UGA [email protected]
Title: Genome-wide allele-specific expression of the transcriptional landscape associated to Capsicum domestication
Authors and affiliations: Erik Díaz-Valenzuela1, Ruairidh Sawers2, Salvador Montes-Hernández3 & Angélica Cibrián-Jaramillo1
1- Ecological and Evolutionary Genomics Group. Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Irapuato Guanajuato, México. 2- Maize Genetics and Genomics Group. Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Irapuato Guanajuato, México. 3- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Bajío, Celaya, 38010, México.
Abstract: Plants have inhabited the earth since ca. 470 Mya and through that time they have evolved an ample diversity of morphologies. Most of this morphological diversity often correlates with changes in gene expression driven by the rewiring of ancient gene regulatory networks (GRN), rather than changes in the sequence of structural or enzymatic protein-coding genes. GRNs control the expression patterns of genes downstream by means of interactions between cis (promoters) and trans (transcription factors) regulatory elements. Thus, genetic variation associated to morphology evolution and expression divergence, should be contained in cis and trans regulatory elements. Short timeframe morphological divergences, as plant domestication, are ideal scenarios to understand how transcriptional landscapes are shaped during rapid phenotypic divergences, but also to understand what regulatory changes accompany them. In this study, we utilized the fruit of Capsicum annnuum as a model to investigate what transcriptional changes were derived from human-mediated domestication, and what their underlying genetics are. We used RNA-seq technology to: 1) characterize the genome-wide transcriptional divergence between wild (W) and cultivated (C) C. annuum fruits, and 2) dissect the regulatory mechanisms underlying expression divergence by means of Allele Specific Expression Analyses (ASE) in F1 hybrids derived from crosses between C and W. We found that 51% of the shared genes between C and W show differential expression. This expression divergence appears to be biased towards overexpression in cultivated chilies, and loaded into biological processes such as response to biotic and abiotic stresses as well as fruit development. Also, by means of a custom-made bioinformatic pipeline to perform ASE, we discovered that, 66% of the genes with expression divergence between W and C showed evidence of trans-regulatory variation, 44% of cis- acting variation, and 41% of both. Also, we found that most of the trans- regulatory changes appear to have arisen from recessive loss of function (LOF) mutations. In addition to the above-mentioned evidence, we found that, the biological processes reproduction and fruit development, were exclusively loaded into genes that showed trans-only variation. Which led us to hypothesize that changes in fruit morphology during human-mediated domestication could be underlaid by recessive LOF mutations at trans-acting regulatory elements. However, whether the mutations are in the coding sequence of the trans-acting elements or upstream, is not possible to know without reconstructing the whole GRN that controls fruit morphology. Despite of all the ongoing work needed to fully characterize fruit morphology evolution, this study provides important findings that contribute to the overall understanding of genomic mechanisms driving plant phenotypic evolution.
4. Presenter: Idalia Rojas [email protected] Instituto de Ecología, UNAM
Title: Change in the population structure of maize landraces associated to the introgression from inbreed lines
Authors and affiliations: Rojas I (1), Wegier A (2), Sánchez J (3), Owens G (4), Rieseberg L(4), Piñero D(1). (1) Laboratorio de Genética y Ecología, Instituto de Ecología, UNAM (2)Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, UNAM (3) Departamento de Producción Agrícola, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara (4) Department of Botany, British Columbia University
The study of gene flow in domesticated plants has been mainly focused on the genetic exchange with their wild relatives (WR) or genetically modified organisms, and less frequently with modern inbreed lines (IL). In this work, we assessed the short-term changes in the genomes of seven maize landraces (LR) native to Mexico and two WR subspecies, associated with the gene flow from IL. We took advantage of the historical collections of maize and teosintes available in Mexico. We compared the genotypes obtained by Genotyping-by-Sequencing (GBS) for the LR and WR, before and after the introduction of IL. Our results showed that the paired divergence index (Fst) between LR-IL and WR-IL has decreased across time. In addition, the population structure of the tested LR has been modified in the evaluated period by the introgression from IL into four of the seven LR. Our findings agree with previous works that have evaluated short- term evolution in cultivated plants; and allowed us to identify ongoing changes in the genetic pool of maize. We think this kind of works can be used as a tool to design strategies for the coexistence of different types of agriculture.
5. Presenter: Azalea Guerra [email protected] Instituto de Ecología, UNAM
Title: Domestication of the open-pollinated scarlet runner bean (Phaseolus coccineus L.)
Authors and affiliations: Azalea Guerra-García, Posgrado en Ciencias Biológicas, UNAM Marco Suárez-Atilano, Instituto de Ecología, UNAM Alicia Mastretta-Yanes, CONACYT-CONABIO Alfonso Delgado-Salinas, Instituto de Biología, UNAM Daniel Piñero, Instituto de Ecología, UNAM
The runner bean is a legume species from Mesoamerica closely related to common bean (Phaseolus vulgaris). It is a perennial species, but it is usually cultivated in small-scale agriculture as an annual crop for its dry seeds and edible immature pods. Unlike the common bean, P. coccineus has received little attention from a genetic standpoint. In this work we aim to (1) provide information about the domestication history and domestication events of P. coccineus; (2) examine the distribution and level of genetic diversity in wild and cultivated Mexican populations of this species; and, (3) identify candidate loci to natural and artificial selection. For this, we generated genotyping by sequencing data (42,548 SNPs) from 242 individuals of P. coccineus and the domesticated forms of the closely related species P. vulgaris and P. dumosus. Eight genetic clusters were detected, of which half corresponds to wild populations and the rest to domesticated plants. The cultivated populations conform a monophyletic clade, suggesting that only one domestication event occurred in Mexico, and that it took place around populations of the Trans- Mexican Volcanic Belt. No difference between wild and domesticated levels of genetic diversity was detected and effective population sizes are relatively high, supporting a weak genetic bottleneck during domestication. Most populations presented an excess of heterozygotes, probably due to inbreeding depression. One population of P. coccineus subsp. striatus had the greatest excess and seems to be genetically isolated despite being geographically close to other wild populations. Based on outlier detection methods, we identified 24 domestication-related SNPs, 13 related to cultivar diversification and eight under natural selection. Few of these SNPs fell within annotated loci, but the annotated domestication-related SNPs are highly expressed in flowers and pods.
6. Presenter: Paola Everardo Martínez [email protected] Instituto de Investigaciones Antropológicas, UNAM
Title: Análisis de asociación de fenotipos de pigmentación en población mexicana del Proyecto CANDELA-México
Los fenotipos de pigmentación de la piel se han asociado a una gran cantidad de variantes de genes involucrados en las vías de producción y distribución de la melanina (Beleza et al. 2012, Donelly et al. 2012, Caliebe et al. 2016), el pigmento principal. Las frecuencias de algunas de estas variantes muestran patrones que evidencian la ocurrencia de selección positiva (Soejima et al. 2006, Lao et al. 2007, Wilde et al. 2014), así como de convergencia evolutiva (Yang et al. 2016) en poblaciones que se han expuesto a distintos niveles de radiación UV. Este escenario, aunado a los mecanismos de interacción génica, plantea una mayor complejidad para la asociación de estas variantes en poblaciones mestizas, como la muestra de México colectada en el marco del Proyecto CANDELA (Consorcio para el Análisis de la Diversidad y Evolución de Latinoamérica). Latinoamérica resulta de gran interés debido a que producto de diversos eventos demográficos conjunta poblaciones que en el pasado evolucionaron en ambientes con exposición a radiación diferenciada, incluida la población nativa, de la cual se tienen pocos datos. Se llevaron a cabo análisis de asociación a un número aproximado de 1300 participantes, de entre 18 y 50 años, de ambos sexos, provenientes de distintas partes de la República Mexicana. Se cuenta con los datos correspondientes al índice de melanina (IM) obtenidos con un colorímetro digital DSM II Color Meter y con los genotipos individuales para 22 variantes distribuidas a lo largo del genoma y previamente reportadas como asociadas a los fenotipos de pigmentación. Como parte de los resultados se encontró asociación con variantes previamente reportadas en la poblaciones parentales de la población mestiza, así como asociaciones no reportadas para población mestiza mexicana pero asociadas a pigmentación en poblaciones de la India (Sarkar et al. 2017). Esto puede ser reflejo de las dinámicas demográficas como el mestizaje, pero también de procesos evolutivos particulares en la región, para comprobar esta hipótesis es necesario analizar los datos provenientes de otros países latinoamericanos así como refinar las pruebas estadísticas.
Poster presentations 1. Presenter: Bárbara Itzel Peña Espinoza [email protected] Laboratorio de Genómica de la Diabetes, UNAM
Title: Efecto de las variantes alélicas CYP2C9*2 y CYP2C9*3 en la respuesta terapéutica y farmacocinética de la glibenclamida en población Maya de Yucatán
Authors and affiliations: 1Rivera-Santiago Carolina, 2Sánchez-Pozos Katy, 2 Peña-Espinoza Bárbara Itzel, 3Ortiz-López María Guadalupe, 1Granados- Silvestre María de los Ángeles, 1,2Menjivar Marta
1Laboratorio de Diabetes, Facultad de Química-Universidad Nacional Autónoma de México, 2Laboratorio de Genómica de la Diabetes, Facultad de Química- Unidad Académica de Ciencia y Tecnología de la UNAM en Yucatán 3Laboratorio de Endocrinología Molecular, Hospital Juárez de México
El CYP2C9 es la enzima responsable de metabolizar aproximadamente el 25% de los fármacos de importancia clínica entre ellos la glibenclamida1,2. Este fármaco es el medicamento de primera línea de prescripción, seguido de la metformina, para el control glicémico en pacientes con Diabetes Tipo 2 (DT2)3. El gen CYP2C9, es altamente polimórfico4. La frecuencia de las variantes CYP2C9*2 y CYP2C9*3 han sido estudiadas en diversas poblaciones, sin embargo poco se sabe del efecto biológico que pudieran tener esta variantes en poblaciones indígenas mexicanas5. El objetivo del trabajo fue evaluar la farmacocinética de la glibenclamida en población indígena maya en voluntarios sanos y la respuesta al tratamiento en pacientes con DT2, considerando su genotipo CYP2C9 (*1/*1, *1/*2 y *1/*3). La metodología se dividió en dos etapas, en la primera se llevó a cabo la identificación de sujetos diabéticos portadores de variantes en los genes involucrados en el metabolismo de hipoglucemiantes orales. En la segunda etapa se llevó a cabo la evaluación del fenotipo metabólico. Los resultados mostraron que la presencia de las variantes CYP2C9*2 y CYP2C9*3 modifican el efecto funcional de la enzima CYP2C9 disminuyendo el aclaramiento y aumentando el tiempo medio de residencia de la glibenclamida en voluntarios sanos indígenas maya. De acuerdo con las concentraciones de glibenclamida en el estado estacionario, los pacientes maya con DT2 de ambos genotipos requieren un ajuste de dosis del medicamento. La farmacogenética permitirá proporcionar al paciente un tratamiento personalizado para un adecuado régimen farmacológico. Lo que nos lleva a concluir que el monitoreo individualizado durante la terapia farmacológica es importante para un mejor control glicémico en los pacientes con DT2, específicamente en aquellos sujetos portadores de estas variantes genéticas.
2. Presenter: Constanza de la Fuente [email protected] University of Copenhagen
Title: Genomic Insights into the Origin and Diversification of Late Maritime Hunter-Gatherers from the Chilean Patagonia
Authors and affiliations: de la Fuente, Constanza1, 2; Ávila-Arcos, Maria C.3; Galimany, Jacqueline1; Carpenter, Meredith L.4,5; Homburger, Julian6; Blanco, Alejandro1; Contreras, Paloma1; Cruz Dávalos, Diana7; Reyes, Omar8; San Roman, Manuel8; Moreno-Estrada, Andrés9; F. Campos, Paula2,10; Eng, Celeste11; Huntsman, Scott11; Burchard, Esteban G.12; Malaspinas, Anna- Sapfo13; Bustamante, Carlosd4,6; Willerslev, Eske2,14,15; Llop, Elena1; Verdugo, Ricardo1; Moraga, Mauricio1
1 Human Genetics Program, ICBM, Faculty of Medicine, University of Chile 2 Centre for GeoGenetics, University of Copenhagen 3 Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México 4 Center for Computational, Evolutionary and Human Genomics, Stanford University 5 Arc Bio, LLC 6 Department of Genetics, Stanford University 7 Institute of Ecology and Evolution, University of Bern 8 Centro de Estudios del Hombre Austral, Instituto de la Patagonia, Universidad de Magallanes 9 National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico 10 CIIMAR Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Portugal 11 Department of Medicine, University of California, San Francisco 12 Department of Bioengineering and Therapeutic Science, University of California, San Francisco 13 Department of Computational Biology, University of Lausanne, Switzerland. 14 Department of Zoology, University of Cambridge 15 Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge.
Patagonia was the last region of the Americas reached by humans who entered the continent from Siberia ca. 15–20,000 years ago. Despite recent genomic approaches to reconstruct the continental evolutionary history, regional characterization of ancient and modern genomes remains understudied. Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation. Here we present genome data from four modern populations from Central Southern Chile and Patagonia and four ancient maritime individuals from Patagonia (ca. 1,000-year-old). Both the modern and ancient individuals studied in this work have a greater genetic affinity with other modern Native Americans than to any non-American population, showing within South America a clear structure between major geographical regions. Native modern Patagonian showed the highest genetic affinity with the ancient individuals, indicating genetic continuity in the region during the past 1000 years before present, together with an important agreement between the ethnic affiliation and historical distribution of both groups. Lastly, the affinities of the ancient individuals within Patagonia supports a model with an initial separation of a common ancestral group to both maritime populations from a terrestrial population, with a later diversification of the maritime groups.
3. Presenter: Juan Carlos Guevara López [email protected] Laboratorio de Genética Molecular, Escuela Nacional de Antropología e Historia
Title: Genetic structure of blue-eyed shags in the Kerguelen and Crozet archipelagos
Authors and affiliations: Juan Carlos Guevara-López, Escuela Nacional de Antropología e Historia, Mexico, Theresa M Burg, University of Lethbridge, Alberta, Canada, Charles-Andre Bost Centre d’Études Biologiques de Chizé, France.
Studying the population genetic structure of marine birds could show evidence of selective pressures that affect the gene flow. Differences can be due geographical and non-geographical barriers; for example, the food availability and the foraging patterns that keep bird colonies isolated despite nesting in close proximity. The blue-eyed shags that inhabit the Kerguelen and Crozet archipelagos provide a good model to observe the genetic structure resulting from foraging patterns and differences in the body size. We genotyped 56 blood samples of blue-eyed shags from 4 colonies using 10 microsatellite markers. We observed significant genetic structure between Crozet and Kerguelen colonies and within Kerguelen populations, corresponding to in-shore and open sea shag colonies. These results might support the hypothesis of selective pressures originated by food availability and foraging patterns.
4. Presenter: Juan Esteban Rodríguez Rodríguez LANGEBIO [email protected]
Title: Reconstructing admixture and migration dynamics of Post- Columbian Mexico
Authors and affiliations: Juan Esteban Rodriguez Rodriguez, Alexander Ioannidis, Javier Blanco Portillo, Andres Moreno Estrada. Human Population Genetics Lab, LANGEBIO-CINVESTAV, GTO, Mexico. Department of Genetics, Stanford University, CA, USA.
Mexico has a considerable population substructure due to historical events and different amounts of admixture between diverse human groups, predominately Native Americans, Europeans, Sub-Saharan Africans and, to a lesser extent, East Asians. Using genome-wide SNP array data from indigenous and admixed Mexican populations, we explored the ancestry tract length distribution from 7 different states across Mexico to infer the timing of admixture in each region, as well as the number of migratory pulses. We observed older admixture timings in the earliest colonial cities, in agreement with historical records. Moreover, we show for the first time a second pulse of combined European/Native American origin in the states of Guanajuato and Guerrero.
On the other hand, we identified some individuals from Guerrero with more than 5% of Asian ancestry. To trace the origin of this understudied heritage, we compared the Asian-derived Mexican haplotypes with a reference panel of Southeast and East Asian populations. These individuals, particularly from the Pacific Coastal port of Acapulco, clustered with Indonesian and non-Negrito Filipino populations, suggesting a historical genetic record from the Manila Galleon trade between Philippines and Mexico.
5. Presenter: Maria A Nieves-Colón [email protected] LANGEBIO-Cinvestav
Title: Genetic diversity of Afro-descendant communities from the Lesser Antilles.
Authors and affiliations: Maria A. Nieves-Colón1,2, Jada Benn-Torres3, Andrés Moreno-Estrada2 and Anne C. Stone1
1School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 2 Laboratorio de Genómica para la Biodiversidad, Unidad de Genómica Avanzada CINVESTAV, Irapuato, Guanajuato, MX 3Department of Anthropology, Vanderbilt University, Nashville, TN
Afro-Caribbean populations remain underrepresented in population genetics research. This sampling gap precludes understanding of how the African diaspora has shaped the genomic and cultural variation of Caribbean islanders. Here we address this gap by examining high-density nuclear SNP genotypes from 73 self-identified Afro-Caribbean communities across five Lesser Antilles: St. Kitts, St. Lucia, St. Vincent, Grenada, and Trinidad. Our findings indicate that all islanders have large components of African ancestry and low proportions of Native American ancestry; a significantly different pattern from that observed among admixed Latinos from the Greater Antilles. We further found variation in admixture patterns between island communities. Trinidadian Afro-Caribbeans for instance, carry large components of East and South Asian ancestry which were likely contributed by Indian and Chinese migrants during the colonial indentureship period. Overall, our findings underscore the large impact of post- colonial demographic processes in shaping the genomes of afro-descendant islanders. In addition to its anthropological or historical importance, such knowledge is also essential for informing the identification of functional or medically relevant genetic variation in these populations.
6. Presenter's name: Miguel Vallebueno-Estrada LANGEBIO [email protected]
Title: Late and gradual domestication of ancient Tehuacan maize
Authors and affiliations: Miguel Vallebueno-Estrada1,2; Javier Martínez3; Ángel García-Cook3; Rafael Montiel 1; Jean-Philippe Vielle Calzada 2
1 Laboratorio de Interacción Núcleo Mitocondrial y Paleogenomica, 2 Grupo de Desarrollo Reproductivo y Apomixis; Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y estudios avanzados del Instituto politécnico Nacional. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México.3 Instituto Nacional de Antropología e Historia, México DF.
Humans have contributed to the domestication of many animal and plant species around the planet since the early Holocene, with important consequences for the processes that shape genomic structure in relatively fast evolutionary context. The origins of maize can be traced back to a single domestication event originating from populations of Zea mays ssp. parviglumis of the Balsas region around 9000 years ago. Although the significant reduction in nucleotide variability that affects ~4% of maize genome could be associated with a domestication bottleneck (Yamasaki et al 2007), a clear understanding of genetic function, ancient allelic variability, and time for selection remains to be elucidated for most of the corresponding loci. Under the guidance of the Instituto Nacional de Antropología e Historia (INAH), we initiated the exploration of previously discovered or unreported rock shelters potentially containing paleobotanic plant samples in central and southeast Mexico. The first season in Tehuacan valley yielded more than 30 non-manipulated maize samples that were morphologically characterized and carbon dated using accelerator mass spectrometry (AMS). Their age spans several thousand years, with specific strata yielding equivalent age at distinct geographic locations. Using paleogenomic approaches, DNA was extracted from samples spanning between 1,000 - 5,100 BP, with total yields allowing multiple library construction for next-generation sequencing technologies, with or without maize DNA enrichment. Their initial alignment to sequences coalescing around previously identified domestication loci suggests recovery of informative segments corresponding to ancient allelic variants. We identified different levels of diversity thru time allowing a glimpse of gradual impact exerted by ancient maize later than previously reported
7. Presenter: Miriam Bravo López International Laboratory for Human Genome Research, UNAM [email protected]
Title: Paleogenomic study of ancient pathogens in Pre-Hispanic indigenous individuals from Central Mexico
Authors and affiliations: Miriam Bravo López1, Erick Ramírez1, Viridiana Villa Islas1, Elizabeth Pérez-Campos2, María Ávila Arcos1.
1.International Laboratory for Human Genome Research, UNAM 2. Instituto Nacional de Antropología e Historia, Querétaro.
Recent advances in paleogenomics have allowed the identification of pathogens responsible of past human infectious diseases. However, many of the most devastating pathogenic agents in Pre-Hispanic indigenous individuals from Mexico, for which we have record, remain unknown. We characterized the metagenome from six teeth belonging to Pre-Hispanic indigenous individuals excavated in Toluquilla and Ranas archeological sites, located in the state of Queretaro, Mexico. These individuals belonged to the “Serrana” culture which occupation lasted from 400 BC through 1550 AD, which is lengthier than other major Pre-Hispanic societies. Here we report the identification of three ancient pathogens: Tannerella forsythia, Porphyromonas gingivalis, and Treponema denticola. These bacteria belong to the so-called “red-complex”, which is associated with periodontal disease and the progression of cardiovascular disease, when untreated. The presence of red-complex bacteria was identified just in one individual, a high-ranking male adult, which could have influenced the type of diet and promoted the development of periodontal disease. Our study represents a first step towards a molecular understanding of infectious diseases in the pre-contact period in Mexico and opens up questions regarding past lifestyle, diet and genetic makeup of pathogens and hosts in that time period.
8. Presenter's name: Sergio F. Nigenda-Morales LANGEBIO [email protected]
Title: Population and evolutionary genomics in non-model mammals
Authors and affiliations: Sergio F. Nigenda-Morales1,2. Andrés Moreno- Estrada2, Cei Abreu-Goodger1.
1.Laboratorio de Genómica Computacional de RNAs / Laboratorio de Genómica Humana, LANGEBIO-CINVESTAV. 2. Laboratorio de Genómica Humana, LANGEBIO-CINVESTAV
Mexico is the third country with more diversity of mammal species in the world, many of these are of conservation concerns due to their low population numbers, economic value or adaptive potential to new environments. Surprisingly, these taxonomic group has been mostly neglected in genomic studies in our country, which may be due to the challenges to obtain large sample collections to perform population studies and to work with organisms with limited or null genomic resources. We are applying multiple genomic techniques to explore the evolutionary and demographic history of three species of non-model mammal species that are distributed in Mexico. We are studying two marine mammal species, the fin whale (Balaenoptera physalus) and the sea otter (Enhydra lutris). The Gulf of California fin whale population is small, resident and genetically isolated from other populations in the Eastern North Pacific, we are sequencing a reference genome for the species and using capture arrays to sequence genomic and neutral regions to estimate critical population parameters (i.e. Ne, m, divergence time) in six populations in the North and South Pacific to compare with the GOC population. The sea otter was thought to be extinct in the Mexican Pacific, recent sightings in Baja California may suggest the California population is expanding its range southwards or the presence of a relict population, we are applying capture arrays and mitochondrial genome sequencing to determine the origin of the few Baja samples that have been collected. We are also studying a marsupial species, the Virginia opossum (Didelphis virginiana), which is widely distributed in Central and North America. Using Genotyping-by-Sequencing (GBS) we found high population structure throughout the range of this species. Populations in the U.S. are highly divergent from Mexican ones and the Cozumel Island population is separated from others in the Yucatan Peninsula. Our research will encourage and advance the genomic research of mammal species in Mexico, but more importantly, will help to develop better management and conservation plans for these species in our country.