Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Frantz, Laurent; Schraiber, Joshua G.; Madsen, Ole; Megens, Hendrik‐Jan; Bosse, Mirte; Paudel, Yogesh; Semiadi, Gono; Meijaard, Erik; Li, Ning; Crooijmans, R.P.M.A.; Archibald, Alan; Slatkin, Montgomery; Schook, Lawrence B.; Larson, Greger; Groenen, Martien A. M.

doi:10.1186/gb-2013-14-9-r107

Cited by 153 publications

(317 citation statements)

References 54 publications

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“…Previous research indicated that SMALT is appropriate for mapping paired end reads when the reference genome is distantly related to the sampled species (Frantz et al, 2013 ). Furthermore, preliminary analyses showed that this soft ware produces the best results compared to other mapping soft ware (Fig.…”

Section: Processing Sequencesmentioning

confidence: 99%

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Ottenburghs

Megens

Kraus

et al. 2016

Molecular Phylogenetics and Evolution

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a b s t r a c tPhylogenetic incongruence can be caused by analytical shortcomings or can be the result of biological processes, such as hybridization, incomplete lineage sorting and gene duplication. Differentiation between these causes of incongruence is essential to unravel complex speciation and diversification events. The phylogeny of the True Geese (tribe Anserini, Anatidae, Anseriformes) was, until now, con tentious, i.e., the phylogenetic relationships and the timing of divergence between the different goose species could not be fully resolved. We sequenced nineteen goose genomes (representing seventeen spe cies of which three subspecies of the Brent Goose, Branta bernicla) and used an exon based phylogenomic approach (41,736 exons, representing 5887 genes) to unravel the evolutionary history of this bird group. We thereby provide general guidance on the combination of whole genome evolutionary analyses and analytical tools for such cases where previous attempts to resolve the phylogenetic history of several taxa could not be unravelled. Identical topologies were obtained using either a concatenation (based upon an alignment of 6,630,626 base pairs) or a coalescent based consensus method. Two major lineages, corre sponding to the genera Anser and Branta, were strongly supported. Within the Branta lineage, the White cheeked Geese form a well supported sub lineage that is sister to the Red breasted Goose (Branta ruficol lis). In addition, two main clades of Anser species could be identified, the White Geese and the Grey Geese. The results from the consensus method suggest that the diversification of the genus Anser is heavily influ enced by rapid speciation and by hybridization, which may explain the failure of previous studies to resolve the phylogenetic relationships within this genus. The majority of speciation events took place in the late Pliocene and early Pleistocene (between 4 and 2 million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of tem perate grasslands. Our approach will be a fruitful strategy for resolving many other complex evolutionary histories at the level of genera, species, and subspecies.

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Section: Processing Sequencesmentioning

confidence: 99%

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Ottenburghs

Megens

Kraus

et al. 2016

Molecular Phylogenetics and Evolution

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“…As we will discuss later, the spatial and temporal coexistence of these suid species involved frequent hybridization events . This circumstance complicates the reconstruction of the evolutionary history of the genus Sus and calls into question whether species such as Sus celebensis, which currently live in the wild but may have been domesticated in the past, could have contributed to the gene pool of Asian pigs (Albarella et al, 2006;Larson et al, 2011;Frantz et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

“…There is a general consensus that the Eurasian wild boar (Sus scrofa) and other sister species, such as Sus celebensis (Celebes warty pig), Sus verrucosus (Java warty pig), Sus cebifrons (Visayan warty pig), Sus philippensis (Philippine warty pig) and Sus barbatus (Bornean bearded pig), emerged in Southeast Asia in the early Pliocene (Figure 1), approximately 5.3-3.5 Myr ago (Larson et al, 2007a(Larson et al, , 2011Frantz et al, 2013). As we will discuss later, the spatial and temporal coexistence of these suid species involved frequent hybridization events .…”

Section: Introductionmentioning

confidence: 99%

Mining the pig genome to investigate the domestication process

et al. 2014

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Pig domestication began around 9000 YBP in the Fertile Crescent and Far East, involving marked morphological and genetic changes that occurred in a relatively short window of time. Identifying the alleles that drove the behavioural and physiological transformation of wild boars into pigs through artificial selection constitutes a formidable challenge that can only be faced from an interdisciplinary perspective. Indeed, although basic facts regarding the demography of pig domestication and dispersal have been uncovered, the biological substrate of these processes remains enigmatic. Considerable hope has been placed on new approaches, based on next-generation sequencing, which allow whole-genome variation to be analyzed at the population level. In this review, we provide an outline of the current knowledge on pig domestication by considering both archaeological and genetic data. Moreover, we discuss several potential scenarios of genome evolution under the complex mixture of demography and selection forces at play during domestication. Finally, we highlight several technical and methodological approaches that may represent significant advances in resolving the conundrum of livestock domestication.

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“…The significant D-statistics varied from 0.07 to 0.17, which is slightly higher compared to analyses on recent radiations, such as Darwin's Finches (0.004 -0.092; Lamichhaney et al, 2015) and butterflies of the genera Heliconius (0.04; Dasmahapatra et al, 2012) and Papilio (0.04; Zhang et al, 2013). These values do fall within the range of studies on other hybridizing species, such as pigs (0.11 -0.23; Frantz et al, 2013), bears (0.04 -0.46; Liu et al, 2014, Cahill et al, 2015 and Xiphophorus fish (0.03 -0.56; Cui et al, 2013). A significant D-statistic does not necessarily indicate introgression between the species from which the genomes are being compared.…”

Section: General Patterns Of Introgressionmentioning

confidence: 50%

“…Previous research indicated that SMALT is appropriate for mapping paired-end reads when the reference genome is distantly related to the sampled species (Frantz et al, 2013). Furthermore, preliminary analyses showed that this software produces the best results compared to other mapping software ( Figure S7.1).…”

Section: Processing Sequencesmentioning

confidence: 93%

Crossing species boundaries : the hybrid histories of the true geese

Ottenburghs¹

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. Crossing Species Boundaries: The Hybrid Histories of the True Geese. PhD thesis, Wageningen University, the Netherlands. Hybridization, the interbreeding of different species, is a common phenomenon in birds: about 16% of bird species is known to have hybridized with at least one other species. Numerous avian hybrid zones have been studied from a morphological or genetic perspective, often documenting the interspecific exchange of genetic material by hybridization and backcrossing (i.e. introgression). The incidence of hybridization varies among bird orders with the Anseriformes (waterfowl: ducks, geese and swans) showing the highest propensity to hybridize. In this thesis, I provide a genomic perspective on the role of hybridization in the evolutionary history of one particular anseriform tribe, the Anserini or "True Geese", which comprises 17 species divided over two genera: Anser and Branta . The diversification of this bird group took place in the late Pliocene and the early Pleistocene (between four and two million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of temperate grasslands. Most species show a steady population increase during this period, followed by population subdivision during the Last Glacial Maximum about 110,000 to 12,000 years ago. The combination of large effective population sizes and occasional range shifts facilitated contact between the diverging goose species, resulting in high levels of interspecific gene flow. Introgressive hybridization might have enabled these goose populations to quickly adapt to changing environments by transferring of advantageous alleles across species boundaries, increasing standing genetic variation or expanding phenotypic variation of certain traits (e.g., beak morphology). Hybridization seems to be a common and integral component in the evolution and diversification of geese. The pervasiveness of rapid speciation and hybridization in geese complicates the attempt to capture their evolutionary history in a phylogenetic tree, therefore I advocate a phylogenetic network approach. Indeed, trying to capture the complex diversification of the True Geese in a branching tree can be regarded as a wild goose chase. Abstract TABLE OF CONTENTS

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Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Cited by 153 publications

References 54 publications

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Mining the pig genome to investigate the domestication process

Crossing species boundaries : the hybrid histories of the true geese

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