Killer whale genomes reveal a complex history of recurrent admixture and vicariance

AbstractReconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global dataset of killer whale genomes in a rare attempt to elucidate global population structure in a non-human species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species’ range, likely associated with founder effects and allelic surfing during post-glacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

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Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians

Science Advances ◽

10.1126/sciadv.abe4414 ◽

2021 ◽

Vol 7 (13) ◽

pp. eabe4414

Author(s):

Guido Alberto Gnecchi-Ruscone ◽

Elmira Khussainova ◽

Nurzhibek Kahbatkyzy ◽

Lyazzat Musralina ◽

Maria A. Spyrou ◽

...

Keyword(s):

Bronze Age ◽

Iron Age ◽

Gene Pools ◽

Social Rules ◽

Eurasian Steppe ◽

Central Asian ◽

Genome Wide ◽

Genome Wide Data ◽

History Of ◽

First Millennium

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.

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Genetic legacy of state centralization in the Kuba Kingdom of the Democratic Republic of the Congo

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1811211115 ◽

2018 ◽

Vol 116 (2) ◽

pp. 593-598 ◽

Cited By ~ 4

Author(s):

Lucy van Dorp ◽

Sara Lowes ◽

Jonathan L. Weigel ◽

Naser Ansari-Pour ◽

Saioa López ◽

...

Keyword(s):

Large Scale ◽

Democratic Republic ◽

Central Province ◽

Genome Wide ◽

Genetic Patterns ◽

Genetic Impact ◽

Genome Wide Data ◽

Republic Of The Congo ◽

History Of ◽

State Centralization

Few phenomena have had as profound or long-lasting consequences in human history as the emergence of large-scale centralized states in the place of smaller scale and more local societies. This study examines a fundamental, and yet unexplored, consequence of state formation: its genetic legacy. We studied the genetic impact of state centralization during the formation of the eminent precolonial Kuba Kingdom of the Democratic Republic of the Congo (DRC) in the 17th century. We analyzed genome-wide data from over 690 individuals sampled from 27 different ethnic groups from the Kasai Central Province of the DRC. By comparing genetic patterns in the present-day Kuba, whose ancestors were part of the Kuba Kingdom, with those in neighboring non-Kuba groups, we show that the Kuba today are more genetically diverse and more similar to other groups in the region than expected, consistent with the historical unification of distinct subgroups during state centralization. We also found evidence of genetic mixing dating to the time of the Kingdom at its most prominent. Using this unique dataset, we characterize the genetic history of the Kasai Central Province and describe the historic late wave of migrations into the region that contributed to a Bantu-like ancestry component found across large parts of Africa today. Taken together, we show the power of genetics to evidence events of sociopolitical importance and highlight how DNA can be used to better understand the behaviors of both people and institutions in the past.

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Evolutionary History of Mammalian Transposons Determined by Genome-wide Defragmentation

PLoS Computational Biology ◽

10.1371/journal.pcbi.0030137.eor ◽

2005 ◽

Vol preprint (2007) ◽

pp. e137

Author(s):

Joti Giordano ◽

Yongchao Ge ◽

Yevgeniy Gelfand ◽

Gyorgy Abrusan ◽

Gary Benson ◽

...

Keyword(s):

Evolutionary History ◽

Genome Wide ◽

History Of

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Early diversification and permeable species boundaries in the Mediterranean firs

Annals of Botany ◽

10.1093/aob/mcz186 ◽

2019 ◽

Vol 125 (3) ◽

pp. 495-507 ◽

Cited By ~ 2

Author(s):

Francisco Balao ◽

María Teresa Lorenzo ◽

José Manuel Sánchez-Robles ◽

Ovidiu Paun ◽

Juan Luis García-Castaño ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Evolutionary History ◽

Taxonomic Status ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Early Diversification ◽

Genome Wide ◽

History Of ◽

The Mediterranean ◽

Independent Species

Abstract Background and Aims Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate. Methods We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status. Key Results Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene–Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. Conclusions Our phylogenomic results contribute to shed light on conifers’ diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.

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Predicting the Landscape of Recombination Using Deep Learning

Molecular Biology and Evolution ◽

10.1093/molbev/msaa038 ◽

2020 ◽

Vol 37 (6) ◽

pp. 1790-1808 ◽

Cited By ~ 13

Author(s):

Jeffrey R Adrion ◽

Jared G Galloway ◽

Andrew D Kern

Keyword(s):

Deep Learning ◽

Evolutionary History ◽

Model Misspecification ◽

Natural Populations ◽

High Accuracy ◽

Demographic Model ◽

Recombination Rates ◽

Genome Wide ◽

A Genome ◽

The Face

Abstract Accurately inferring the genome-wide landscape of recombination rates in natural populations is a central aim in genomics, as patterns of linkage influence everything from genetic mapping to understanding evolutionary history. Here, we describe recombination landscape estimation using recurrent neural networks (ReLERNN), a deep learning method for estimating a genome-wide recombination map that is accurate even with small numbers of pooled or individually sequenced genomes. Rather than use summaries of linkage disequilibrium as its input, ReLERNN takes columns from a genotype alignment, which are then modeled as a sequence across the genome using a recurrent neural network. We demonstrate that ReLERNN improves accuracy and reduces bias relative to existing methods and maintains high accuracy in the face of demographic model misspecification, missing genotype calls, and genome inaccessibility. We apply ReLERNN to natural populations of African Drosophila melanogaster and show that genome-wide recombination landscapes, although largely correlated among populations, exhibit important population-specific differences. Lastly, we connect the inferred patterns of recombination with the frequencies of major inversions segregating in natural Drosophila populations.

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Phylogenomic Reconstruction of the Neotropical Poison Frogs (Dendrobatidae) and Their Conservation

Diversity ◽

10.3390/d11080126 ◽

2019 ◽

Vol 11 (8) ◽

pp. 126 ◽

Cited By ~ 5

Author(s):

Wilson X. Guillory ◽

Morgan R. Muell ◽

Kyle Summers ◽

Jason L. Brown

Keyword(s):

Bayesian Methods ◽

Evolutionary History ◽

Conservation Status ◽

Nuclear Data ◽

Nuclear Markers ◽

Poison Frog ◽

Sequence Capture ◽

Genome Wide ◽

Frog Species ◽

History Of

The evolutionary history of the Dendrobatidae, the charismatic Neotropical poison frog family, remains in flux, even after a half-century of intensive research. Understanding the evolutionary relationships between dendrobatid genera and the larger-order groups within Dendrobatidae is critical for making accurate assessments of all aspects of their biology and evolution. In this study, we provide the first phylogenomic reconstruction of Dendrobatidae with genome-wide nuclear markers known as ultraconserved elements. We performed sequence capture on 61 samples representing 33 species across 13 of the 16 dendrobatid genera, aiming for a broadly representative taxon sample. We compare topologies generated using maximum likelihood and coalescent methods and estimate divergence times using Bayesian methods. We find most of our dendrobatid tree to be consistent with previously published results based on mitochondrial and low-count nuclear data, with notable exceptions regarding the placement of Hyloxalinae and certain genera within Dendrobatinae. We also characterize how the evolutionary history and geographic distributions of the 285 poison frog species impact their conservation status. We hope that our phylogeny will serve as a backbone for future evolutionary studies and that our characterizations of conservation status inform conservation practices while highlighting taxa in need of further study.

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The genomic history of the Iberian Peninsula over the past 8000 years

Science ◽

10.1126/science.aav4040 ◽

2019 ◽

Vol 363 (6432) ◽

pp. 1230-1234 ◽

Cited By ~ 84

Author(s):

Iñigo Olalde ◽

Swapan Mallick ◽

Nick Patterson ◽

Nadin Rohland ◽

Vanessa Villalba-Mouco ◽

...

Keyword(s):

Iberian Peninsula ◽

Iron Age ◽

North Africa ◽

Eastern Mediterranean ◽

Hunter Gatherers ◽

Y Chromosomes ◽

Genome Wide ◽

Genome Wide Data ◽

History Of ◽

Genetic Substructure

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European–speaking regions but also into non-Indo-European–speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.

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Blockwise Site Frequency Spectra for Inferring Complex Population Histories and Recombination

10.1101/077958 ◽

2016 ◽

Cited By ~ 3

Author(s):

Champak R. Beeravolu ◽

Michael J. Hickerson ◽

Laurent A.F. Frantz ◽

Konrad Lohse

Keyword(s):

Demographic History ◽

Composite Likelihood ◽

Model Organisms ◽

Secondary Contact ◽

Parameter Estimates ◽

Genome Sequences ◽

Frequency Spectra ◽

Genome Wide ◽

Complex Population ◽

History Of

AbstractWe introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel composite likelihood framework based on a recently introduced summary of sequence variation: the blockwise site frequency spectrum (bSFS). This simulation-based framework uses the the frequencies of bSFS configurations to jointly model demographic history and recombination and is explicitly designed to make inference using multiple whole genomes or genome-wide multi-locus data (e.g. RADSeq) catering to the needs of researchers studying model or non-model organisms respectively. The flexible nature of our method further allows for arbitrarily complex population histories using unphased and unpolarized whole genome sequences. In silico experiments demonstrate accurate parameter estimates across a range of divergence models with increasing complexity, and as a proof of principle, we infer the demographic history of the two species of orangutan from multiple genome sequences (over 160 Mbp in length) from each species. Our results indicate that the two orangutan species split approximately 650-950 thousand years ago but experienced a pulse of secondary contact much more recently, most likely during a period of low sea-level South East Asia (∼300,000 years ago). Unlike previous analyses we can reject a history of continuous gene flow and co-estimate genome-wide recombination. ABLE is available for download at https://github.com/champost/ABLE.

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A dynamic 6,000-year genetic history of Eurasia’s Eastern Steppe

10.1101/2020.03.25.008078 ◽

2020 ◽

Cited By ~ 4

Author(s):

Choongwon Jeong ◽

Ke Wang ◽

Shevan Wilkin ◽

William Timothy Treal Taylor ◽

Bryan K. Miller ◽

...

Keyword(s):

Bronze Age ◽

Population History ◽

Complex Interplay ◽

Cultural Changes ◽

Genetic History ◽

Nomadic Pastoralists ◽

Eurasian Steppe ◽

Genome Wide ◽

Genome Wide Data ◽

History Of

SummaryThe Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region’s population history. Here we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher Eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.

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Towards a new history and geography of human genes informed by ancient DNA

10.1101/003517 ◽

2014 ◽

Cited By ~ 1

Author(s):

Joseph Pickrell ◽

David Reich

Keyword(s):

Natural Selection ◽

Ancient Dna ◽

Population Replacement ◽

Local Conditions ◽

Geographic Locations ◽

Technological Advances ◽

Genome Wide ◽

Human Genes ◽

Genome Wide Data ◽

History Of

Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture and population replacement have been the rule rather than the exception in human history. In light of this, we argue that it is time to critically re-evaluate current views of the peopling of the globe and the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically-known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.

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