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Thread: SMBE 2019 abstracts

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    SMBE 2019 abstracts

    SMBE 2019 programme with abstracts is available: http://smbe2019.org/programme/interactive-programme/

    Some interesting asbtracts:

    [OR-041] The Origins of Taurine Cattle: An Ancient Genomic Tale - Victoria Mullin

    2:00 PM–2:15 PM Jul 22, 2019

    V. E. Mullin 1 2,*, M. Pereira Verdugo 2, A. Scheu 3, D. G. Bradley 2

    Topic: Genomic perspectives on plant and animal domestication

    The domestication of taurine cattle (Bos taurus) marks a significant period of time in human prehistory. Taurine cattle were domesticated in the Near East from their wild progenitor, Bos primigenius (aurochs), approximately 10,000 yrBP. Human mediated migration of taurine cattle into Europe started to occur c. 8,400 yrBP. Until now, the study of modern nuclear genomes and ancient mitogenomes have contributed to our understanding of the domestication of taurine cattle, subsequent migrations and admixture events. We have sequenced ~70 ancient cattle nuclear genomes from the Neolithic to the Middle Ages originating from the South West Asia and Europe. These ancient genomes provide a snapshot of the genetic diversity present in the past, allowing the timing of population events such as admixture and migration, that have shaped the genome of a globally important domesticate.


    [OR-042] Ancient genomic structure of domestic dogs - Anders Bergström

    2:15 PM–2:30 PM Jul 22, 2019

    A. Bergström 1,*, L. Frantz 2, R. Schmidt 3, E. Ersmark 4, L. Girdland-Flink 5, S. Amiri 6, G. Bar-Oz 7, J. Bulatović 8, S. Fedorov 9, I. Fiore 10, M. Germonpré 11, L. K. Horwitz 12, L. Janssens 13, Y. Kuzmin 14, R. Losey 15, M. Mashkour 16, V. Onar 17, D. Orton 18, M. Radivojević 19, M. Sablin 20, S. M. San José Santamaria 21, I. Stojanović 22, J. Storĺ 23, A. Tagliacozzo 10, K. Trantalidou 24, A. Villaluenga 25, A. Carmagnini 2, J. Haile 26, E. Irving-Pease 27, A. Linderholm 28, A. Götherström 23, L. Dalén 4, R. Pinhasi 29, G. Larson 27, P. Skoglund 1

    Topic: Genomic perspectives on plant and animal domestication

    The dog was the first animal to be domesticated, and has accompanied humans through major lifestyle changes and population movements. Yet very little is known about the population history of dogs and to what extent it reflects that of associated human populations. We sequenced 27 ancient dog genomes from the last 10,000 years to a median depth of 1.5-fold, including samples from the Near East, Siberia and across Europe. We find that the major lineages of dog ancestry cannot be related without invoking admixture events. Ancient West Eurasian dog genomes display a cline of dual affinities to early Near Eastern dogs and early Siberian dogs. Present-day African dogs share the majority of their ancestry with early Neolithic Near Eastern dogs. Modern European breeds display a remarkably uniform ancestry with structure among breeds uncorrelated to early European population structure, suggesting that they derive from a single, homogeneous source population. By co-analysing the dog genomes with ancient human genomes matched in time and space, we uncover several features of dog ancestry relationships that mirror known human population history, but also features where dogs display opposing trends. Overall, our ancient genomic data reveals that the divergent ancestries observed in European, Near Eastern, African, Siberian, East Asian, Oceanian, and American dog populations must have diversified already by 10,000 years ago.


    [OR-133] Population genomics of Ice Age gray wolves - Pontus Skoglund

    10:15 AM–10:30 AM Jul 24, 2019

    A. Bergström 1, U. Talon 2, L. Frantz 3, M.-H. S. Sinding 4, E. Ersmark 5, V. Schuenemann 6, T. Davy 1, L. Girdland-Flink 7, S. Gopalakrishnan 4, J. Ramos-Madrigal 4, T. Feuerborn 4 8, S. Münzel 9, S. Pfrengle 8, N. Conard 8, C. Carře 4, J. Haile 10, A. Linderholm 10, D. Stanton 5, N. Benecke 11, H. Bocherens 8 12, R. F. Carden 13, S. Fedorov 14, M. Lázničková-Galetová 15, M. Germonpré 16, V. V. Ivanova 17, R. P. Jennings 7, A. K. Kasparov 18, I. V. Kirrilova 19, Y. Kuzmin 20, P. Nikolskiy 21, E. Y. Pavlova 22, V. V. Pitulko 18, M. Sablin 23, F. K. Shidlovskiy 19, J. Storĺ 24, J. A. Leonard 25, A. Götherström 24, M. Hofreiter 2, M. T. P. Gilbert 4, G. Larson 10, J. Krause 8 26, L. Dalén 5, P. Skoglund 1,*

    Topic: Understanding the genomics of climate change response

    The gray wolf is distributed across diverse environments in Eurasia and North America, and persisted as a species through dramatic periods of climate change, including the time around the Last Glacial Maximum when many other megafaunal populations went extinct. However, the fossil record has suggested the existence of distinct wolf ecomorph populations that may have gone extinct. To understand gray wolf population dynamics, history, and genomic adaptations, we sequenced 48 ancient wolf genomes from Europe, Siberia and Alaska spanning the last 50,000 years, to a median 1-fold depth. We find that all present-day Eurasian wolves trace their ancestry to a founding population emerging after the Last Glacial Maximum (LGM), with direct evidence for replacement of the Ice Age populations in both western and eastern Eurasia. Domestic dogs also trace their ancestry to the Eurasian wolf population emerging after the LGM, and we observe the first appearance of differentiation between the dog and present-day gray wolf lineages shortly after this time. We identify genomic regions that were highly differentiated in the Ice Age Eurasian wolf lineages, that may have had adaptations to the cold climates and prey niche of that period. Finally we use the deep time resolution of the dataset to reconstruct allele frequency trajectories through time, to identify genomic regions that may have conferred adaptations to the warming climate. This dataset thus provides the first direct genomic time transect of a natural mammal population and its evolution throughout the changing environmental conditions of the last 50,000 years, persisting through the last glacial maximum in the face of local extinctions and giving rise to a key domesticated animal.

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    [OR-029] Using patterns of introgressed archaic ancestry to detect adaptive evolution in modern humans - Beth Shapiro

    2:30 PM–3:00 PM Jul 22, 2019

    B. Shapiro*, N. Schaefer 1, R. E. Green 1

    An ancestral recombination graph (ARG) is a precise description of how every genome is related to every other genome across all variable positions in the genome. In this way, an ARG is a complete description of the relatedness of individuals and can be used to ask fundamental questions about demography and selection. We present a new heuristic, parsimonious, ARG inference algorithm called SARGE (Speedy Ancestral Recombination Graph Estimator), and use it to map segments of archaic ancestry across a panel of 279 modern human genomes from the Simons Genome Diversity Panel. We locate high-frequency Neanderthal and Denisovan variants present in moderns humans including sub-Saharan Africans, and show that Denisovan-like ancestry in modern humans may have arisen from multiple instances of admixture. Finally, we catalog genomic regions for which modern human and archaic hominin lineages are completely sorted and discuss how these may have played a role in the evolution of the modern human lineage.


    [OR-244] The population genomic legacy of the second plague pandemic in Trondheim, Norway - Shyam Gopalakrishnan

    4:00 PM–4:15 PM Jul 22, 2019

    S. Gopalakrishnan 1,*, I. Lundstrřm 1, S. S. Ebenesersdottir 2, L. van Dorp 3, P. Luisi 4, S. Piedrahita Abella 1, M. Martin 5, G. Turner-Walker 6, I. Moltke 1, M. Avila-Arcos 7, J. Samaniego Castruita 1, J. Schraiber 8, S. Rasmussen 1, D. Juan 9, P. Gelabert 9, L. Masatti 1, T. de-Dios 9, A. Margaryan 1, A. Fotakis 1, M. Orbegozo 1, Ĺ. Vĺgene 1, A. Christophersen 5, H. Stenřien 5, F. Vieira 1, S. Liu 10, T. Günther 11, T. Kivisild 12, B. Skar 5, M. Sandoval Velasco 1, N. Wales 13, H. Schroeder 1, P. Campos 1, V. Guđmundsdóttir 2, T. Sicheritz-Ponten 1, B. Petersen 1, J. Halgunset 14, T. F. Higham 15, E. Willerslev 1, J. Krause 16, F. Balloux 3, T. Marques-Bonet 9, C. Lalueza-Fox 9, K. Stefansson 2, R. Nielsen 17, A. Helgasson 2, M. T. P. Gilbert 1 5

    Human populations have been shaped by past catastrophes, some of which may have left long-lasting signatures in our genomes. The second plague pandemic represented the most important demographic collapse in historical Europe, with mortality rates estimated to possibly >50% of the population. It is widely assumed this must have significantly affected the genetic makeup of the populations. We explored its consequences on the Norwegian city of Trondheim, which like most European cities suffered a pandemic induced bottleneck, with estimates ranging from 50-70% reduction in census population size attributable to the second plague pandemic.
    To explore the genomic effects of the second plague pandemic in Trondheim, we collected 54 genomes spanning 3 time periods, specifically 11 samples from before 1349 AD, 13 samples from the 16-18th centuries, and 30 samples from modern Trondheim. Using whole genome sequencing on these samples, we examined the global genome-wide changes in the ancestry composition of the population, and identified regions of the genome which showed radical changes in allele freuquencies through the period of the second plague pandemic.
    Despite the relatively small sample sizes of our dataset, our results validate with the hypothesis that the second plague pandemic played a significant role in shaping the genomic diversity of Trondheim - something expected given the large estimated change in population size that occurred during this period. In particular, our data is compatible with a major decrease in migration from previous population sources (e.g. the British Isles) during this time, consistent with the decrease in Trondheim’s political and economic importance. The average proportion of ancestry derived from British Isles decreases from ~30-40% in the pre-1349 samples, to under 5% in the post-1349 samples.
    Additionally, we find allele frequency changes in genes that can be plausibly linked to resistance against bacterial infections. We note that it is impossible to pinpoint the pathogen Yersinia pestis as the driver of these changes - in theory other pathogens or even non pathogenic factors may have lead to the observed decreases in population diversity and shifts in allele frequencies at key genomic loci. Ultimately this leads us to propose that genetically encoded immune defense and ability to deal with septicemic states may have been a relevant factor for surviving bubonic plague.


    [OR-244A] Population continuity of a Pre-Hispanic Civilization from Central Mexico - Viridiana Villa-Islas

    4:15 PM–4:30 PM Jul 22, 2019

    V. Villa-Islas 1,*, M. Sandoval-Velasco 2, E. Mejía Pérez-Campos 3, A. Herrera-Muńóz 3, G. Zepeda García-Moreno 4, K. Sandoval-Mendoza 5, M. A. Nieves-Colón 5 6, M. C. Ávila-Arcos 7

    Toluquilla and Ranas are two archeological sites located at Sierra Gorda, Querétaro, Central Mexico. Interesting aspects about the culture that inhabited these sites are a larger occupation span compared to other major Pre-Columbian societies (300 BCE to 1,500 CE) and that they were located at the limits of two large cultural regions: Aridoamerica and Mesoamerica. At the end of the XI century, the climate underwent drastic fluctuations affecting the agricultural resources and inducing a shift in the perimeters of these cultural regions, leading to a hypothesized population replacement of the Sierra Gorda inhabitants by hunter-gatherers from Aridoamerica. However, Toluquilla site displays cultural continuity suggesting that this climatic phenomenon did not affect this side of Sierra Gorda with the same harshness compared to the central highlands. To assess both scenarios and gain insights into the population history and fine-scale regional demographic events of the inhabitants of Sierra Gorda region, we generated paleogenomic data from human remains of different time points spanning the time of the alleged replacement. We recovered complete mitochondrial genomes and low-coverage nuclear data for 9 individuals. When comparing these to paleogenomic data of 4 individuals from a Pre-Hispanic site at the neighboring State of Guanajuato, as well as to genome-wide data from present-day Native Mexicans, we identified a clear genetic affinity to present-day populations from Central-West Mexico and similar genetic structure for both time periods. Suggesting a genetic continuity between both periods leading to interesting insights about adaptation strategies by these population in response to drastic climate shifts.

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    [OR-248] Whole genome sequence analysis of the Aeta, a First Sundaland people from the Philippines - Timothy Jinam

    5:45 PM–6:00 PM Jul 22, 2019

    T. A. Jinam 1,*, N. Saitou 1

    The First Sundaland people (negritos) of Southeast Asia encompasses various groups from Peninsular Malaysia, Andaman Islands and the Philippines who share common phenotypes including dark skin, frizzy hair, and short stature. We sequenced the whole genomes of 10 Aeta individuals (Philippine negritos), whose samples were collected in 1985 by Keiichi Omoto, at high coverage. Comparison with other published genomes reveal that these Aeta individuals had substantially higher proportion of archaic human introgressed regions. Their effective population size showed signals of gradual decrease until approximately 5 thousand years ago (kya), and they split from other Southeast Asians approximately 20 kya. A more in-depth analysis of these genomes will hopefully shed more light into the complexities of human movements out of Africa.


    [OR-115] Relatives from the Iron Age: Combining Ancient and Modern Genomes in the Genealogy - Ruoyun Hui

    5:45 PM–6:00 PM Jul 23, 2019

    R. Hui 1,*, C. Scheib 2, S. Inskip 1, C. Cessford 3, J. Robb 4, T. Kivisild 5

    Parallel to the explosive growth in sequencing of modern human genomes, developments in the field of ancient DNA has also revealed an increasing number of genomes from past populations. These ancient genomes benefit from large modern reference panels to mitigate limitations in data quality largely caused by preservation issues; at the same time, the temporal dimension these genomes provide adds new excitement to the genetic history of populations and individuals. Here we study the relatedness and population history of 20 individuals from a Late Iron Age to Early Romano-British enclosed burial ground at Duxford, a site lying on a chalk knoll close to a crossing point on River Granta, England. We interpret the results in the context of a time series of sites around Cambridge. The Haplotype Reference Consortium panel enabled us to accurately impute common variants, even in low-coverage genomes. We report four pairs of close relatives, including a family trio that allows us to fine-map identity-by-descent (IBD) segments and de novo mutations. We further construct genome-wide genealogies of the newly-reported samples together with published ancient and modern European genomes. Aided by the pattern of rare allele and IBD sharing, the result allows us to examine genetic relationship across space and time on a finer scale. Finally, we also predict height and health-related traits using polygenic risk scores and estimated the correlation with local ancestry. Our results demonstrate that combining ancient and modern genomes into the same framework greatly enhances clarity and resolution in the study of population history.


    [OR-179] The genetic landscape of Ethiopia: diversity, intermixing and the association with culture - Garrett Hellenthal

    4:45 PM–5:00 PM Jul 24, 2019

    G. Hellenthal 1,*, S. Lopez 1, A. Tarekegn 2, N. Bradman 3, M. Thomas 1, E. Bekele 2

    The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with -- and shape -- genetic structure. Here we report results from analyses of new genome-wide autosomal DNA from >1100 Ethiopians representing 69 different ethnic groups. Using novel statistical approaches, we report the extent to which genetic similarity among Ethiopians correlates with birthplace, ethnic identity, shared language and the sharing of 31 cultural practices. We demonstrate significant associations between genetic similarity and each of geographic and elevation distance, both among present-day Ethiopians as expected and, more surprisingly, between present-day Ethiopians and a 4,500-year-old Ethiopian. We also show how ethnic groups that reported engaging in particular cultural practices are more genetically similar than expectations based on language and spatial distance. Furthermore, we give examples of how social behaviours have directly -- and strongly -- increased genetic differences among groups, though also providing evidence of recent intermixing among peoples from different language groups and religious affiliations.

    In addition, we describe the ancestral history of different Ethiopian groups, revealing a southwest-northeast cline across Ethiopia defined by ancestry related to Central and West African groups versus Egyptian groups. We date distinct admixture events that show correlations with major language classifications and geography, including events dated to ~1600-2800 years ago involving sources carrying DNA similar to present-day Egyptians versus events starting ~1,450 years ago involving sources carrying DNA related to western Sub-Saharan Africans. Overall these results showcase the ability of genetics to help shed light on the ancestral histories of different ethnic groups, for example corroborating oral traditions. They also illustrate the necessity of accounting for ethnicity, geography, and sometimes even occupation, when designing sampling strategies (e.g. for genome-wide association studies, GWAS) to study Ethiopians.

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    Quote Originally Posted by rozenfeld View Post
    [B][OR-029]
    [OR-244] The population genomic legacy of the second plague pandemic in Trondheim, Norway - Shyam Gopalakrishnan

    4:00 PM–4:15 PM Jul 22, 2019

    S. Gopalakrishnan 1,*, I. Lundstrřm 1, S. S. Ebenesersdottir 2, L. van Dorp 3, P. Luisi 4, S. Piedrahita Abella 1, M. Martin 5, G. Turner-Walker 6, I. Moltke 1, M. Avila-Arcos 7, J. Samaniego Castruita 1, J. Schraiber 8, S. Rasmussen 1, D. Juan 9, P. Gelabert 9, L. Masatti 1, T. de-Dios 9, A. Margaryan 1, A. Fotakis 1, M. Orbegozo 1, Ĺ. Vĺgene 1, A. Christophersen 5, H. Stenřien 5, F. Vieira 1, S. Liu 10, T. Günther 11, T. Kivisild 12, B. Skar 5, M. Sandoval Velasco 1, N. Wales 13, H. Schroeder 1, P. Campos 1, V. Guđmundsdóttir 2, T. Sicheritz-Ponten 1, B. Petersen 1, J. Halgunset 14, T. F. Higham 15, E. Willerslev 1, J. Krause 16, F. Balloux 3, T. Marques-Bonet 9, C. Lalueza-Fox 9, K. Stefansson 2, R. Nielsen 17, A. Helgasson 2, M. T. P. Gilbert 1 5

    Human populations have been shaped by past catastrophes, some of which may have left long-lasting signatures in our genomes. The second plague pandemic represented the most important demographic collapse in historical Europe, with mortality rates estimated to possibly >50% of the population. It is widely assumed this must have significantly affected the genetic makeup of the populations. We explored its consequences on the Norwegian city of Trondheim, which like most European cities suffered a pandemic induced bottleneck, with estimates ranging from 50-70% reduction in census population size attributable to the second plague pandemic.
    To explore the genomic effects of the second plague pandemic in Trondheim, we collected 54 genomes spanning 3 time periods, specifically 11 samples from before 1349 AD, 13 samples from the 16-18th centuries, and 30 samples from modern Trondheim. Using whole genome sequencing on these samples, we examined the global genome-wide changes in the ancestry composition of the population, and identified regions of the genome which showed radical changes in allele freuquencies through the period of the second plague pandemic.
    Despite the relatively small sample sizes of our dataset, our results validate with the hypothesis that the second plague pandemic played a significant role in shaping the genomic diversity of Trondheim - something expected given the large estimated change in population size that occurred during this period. In particular, our data is compatible with a major decrease in migration from previous population sources (e.g. the British Isles) during this time, consistent with the decrease in Trondheim’s political and economic importance. The average proportion of ancestry derived from British Isles decreases from ~30-40% in the pre-1349 samples, to under 5% in the post-1349 samples.
    Additionally, we find allele frequency changes in genes that can be plausibly linked to resistance against bacterial infections. We note that it is impossible to pinpoint the pathogen Yersinia pestis as the driver of these changes - in theory other pathogens or even non pathogenic factors may have lead to the observed decreases in population diversity and shifts in allele frequencies at key genomic loci. Ultimately this leads us to propose that genetically encoded immune defense and ability to deal with septicemic states may have been a relevant factor for surviving bubonic plague.
    .
    This looks very interesting, especially since my great grandmother was born in Trondheim (although her parents were from near Rřros, which is south of Trondheim).. I doubt the British % is correct, I think they might have fallen into the same pit that most commercial DNA companies have with regards to mislabeling German and Nordic ancestry as British..

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    [OR-027] Inferring the selection history of Europe over the last 10,000 years using a novel statistical approach - Louise Ormond
    2:00 PM–2:15 PM Jul 22, 2019

    We describe an efficient new Bayesian statistical model to identify selection in admixed populations using allele counts from Single Nucleotide Polymorphisms (SNPs) in low and/or high coverage ancient and/or modern genome data. This novel approach accounts for demography and variation in coverage across loci and samples, and also infers proportions of ancestry relating populations (e.g. due to admixture) and levels of genetic differentiation among groups. The program can provide both selection probabilities for individual SNPs and/or jointly test sets of SNPs (e.g.in pathways) for selection effects. We demonstrate the model’s utility through simulations, and we showcase its ability to identify previous targets of selection using DNA from prehistoric and modern humans. We apply our method to a large dataset of ancient and modern genomes, including 75 previously unpublished data from ancient genomes, that span hunter-gatherer and Neolithic early farmer populations from 12,000 years BC through until the late Bronze Age. We identify the time periods over which individual SNPs have experienced selection, and we assess the evidence for selection in sets of SNPs associated with diet, immunity, skin pigmentation and the metabolic syndrome, illustrating the evolutionary constraints on populations at critical periods throughout the history of Europe.


    ============

    [OR-178] Isolation in the Fortunate Isles: genetic composition and migration patterns of the Canary Islands indigenous population - Rosa Fregel
    4:30 PM–4:45 PM Jul 24, 2019

    The Canaries consist of seven main islands situated in the Atlantic Ocean, near the western Saharan coast of Africa. Although it is thought Plinio the Elder (23 - 79 AD) wrote about the Canary Islands in his Natural History, they were forgotten until re-discovered by European sailors in the 13th century and eventually conquered and colonized by the kingdom of Castile in the 15th century. The crushing of the resistance, and new diseases brought in by the conquerors, resulted in a high mortality rate among the native population, and the subsequent admixture with the European colonizers led to the loss of the indigenous culture and language.

    Multidisciplinary research, including the analysis of ancient DNA, places the origin of the indigenous population in North Africa, mostly related to Berber communities, and radiocarbon dates on short-lived samples point to the 1st millennia for the peopling of the islands. Apart from the interest that the indigenous population of the Canary Islands raises by itself, they also represent an open window to the Prehistory of North Africa, a region that has been understudied from a paleogenomic perspective. The analysis of the Canarian indigenous population also offers a unique opportunity to understand how human populations are affected by isolation, migration and/or adaptation to a new environment. To provide detailed paleogenomic data on the Canary Islands indigenous population, we analyzed 48 ancient samples from 25 different archaeological sites from all seven islands.

    Some mtDNA lineages present in the indigenous population of the Canary Islands have a clear North African adscription, pointing to a Berber origin. However, most indigenous lineages have a wider Mediterranean distribution, corroborating recent evidences of Neolithic dispersions in North Africa. Comparisons between islands indicate that the genetic composition of the indigenous population was variable, with some populations having high genetic diversity, while others were probably affected by genetic drift and/or bottlenecks. This result implies that, after the peopling of the archipelago, every island experienced its own evolutionary path, determined by the environmental conditions and limitations of insularity. We also observe an asymmetrical distribution of mtDNA haplogroups in the ancient population, with certain haplogroups appearing exclusively in the islands closer to the continent, implying the existence of more than one migration event. Although results are still preliminary, low-coverage whole-genome data starts to provide support to the conclusions reached using mtDNA, and suggests that the European Neolithic impact in North Africa was
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