Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

Árnason, Úlfur; Lammers, Fritjof; Kumar, Vikas; Nilsson, Maria A.; Janke, Axel

doi:10.1126/sciadv.aap9873

Cited by 124 publications

(158 citation statements)

References 56 publications

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“…The basal split among balaenopteroids is between minke whale and the other five balaenopteroids. Consistent with previous molecular studies (e.g., Rychel et al 2004;Sasaki et al 2005;Nikaido et al 2006;Deméré et al 2008;McGowen et al 2009;Árnason et al 2018), fin whale and humpback whale are sister taxa, and blue whale is closely related to sei whale. The gray whale is positioned as the sister taxon to fin whale + humpback whale.…”

Section: Laurasiatheria Retroposonssupporting

confidence: 90%

“…The gray whale is positioned as the sister taxon to fin whale + humpback whale. This coalescence-based retroposon tree matches a neighbor-joining distance analysis and a Bayesian inference tree for the same data (Lammers et al 2019) as well as earlier molecular and total evidence work (McGowen et al 2009;Marx and Fordyce, 2015;Árnason et al 2018). The branch that unites gray whale with the fin whale + humpback whale clade is very short (0.0182 CUs) on the ASTRAL tree, although there is moderately high bootstrap support (89%) and local PP (0.88) for this clade which is resistant to collapse following removal of many gene trees from ASTRAL analysis.…”

Section: Laurasiatheria Retroposonssupporting

confidence: 81%

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An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

Ms¹,

Gatesy

2019

Preprint

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DNA sequence alignments provide the majority of data for inferring phylogenetic relationships with both concatenation and coalescence methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroposon insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free.In addition, retroposon insertions satisfy the 'no intralocus recombination' assumption of summary coalescence methods because they are singular events and better approximate neutrality relative to DNA sequences commonly applied in phylogenomic work.Retroposons have traditionally been analyzed with phylogenetic methods that ignore incomplete lineage sorting (ILS). Here, we analyze three retroposon data sets for mammals (Placentalia, Laurasiatheria, Balaenopteroidea) with two different ILS-aware methods. The first approach constructs a species tree from retroposon bipartitions with ASTRAL, and the second is a modification of SVD-Quartets. We also develop a χ 2 Quartet-Asymmetry Test to detect hybridization using retroposon data. Both coalescence methods recovered the same topology for each of the three data sets. The ASTRAL species tree for Laurasiatheria has consecutive short branch lengths that are consistent with an anomaly zone situation. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both coalescence methods recovered a topology that supports the paraphyly of Balaenopteridae. Application of the χ 2 Quartet-Asymmetry Test to this data set detected 16 different quartets of species for which historical hybridization may be inferred, but significant asymmetry was not detected in the placental root and Laurasiatheria analyses.

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Section: Laurasiatheria Retroposonssupporting

confidence: 90%

Section: Laurasiatheria Retroposonssupporting

confidence: 81%

An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

Ms¹,

Gatesy

2019

Preprint

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“…In summary, the global data set of genomes analysed here contributes further to the emerging consensus (Árnason, Lammers, Kumar, Nilsson, & Janke, 2018;Arnold, 2016;Gopalakrishnan et al, 2018;Malinsky et al, 2018;Sinding et al, 2018;Tusso et al, 2018) that the relationship among natural populations is rarely well represented as a bifurcating tree. The evolutionary history of natural populations can include episodic long-range dispersal, population replacement and admixture which greatly transform the distribution of global genetic variation.…”

Section: Discussionmentioning

confidence: 65%

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

et al. 2019

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Reconstruction 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 data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman 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 postglacial 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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“…To detect those genes that were inactivated during the transition from land to water in the cetacean stem lineage, we next excluded all genes that have inactivating mutations in the hippopotamus lineage. To this end, we first aligned the genome of the common hippopotamus (40) to the human hg38 assembly using lastz (parameters K = 2400, L = 3000 and default scoring matrix), axtChain, chainCleaner, and chainNet (all with default parameters) (135,137,138), and used our approach to detect inactivating mutations in the common hippopotamus.…”

Section: Excluding Genes With Inactivating Mutations In the Hippopotamentioning

confidence: 99%

Genes lost during the transition from land to water in cetaceans highlight genomic changes involved in aquatic adaptations

Huelsmann

Hecker

Springer

et al. 2019

Preprint

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The transition from land to water in whales and dolphins (cetaceans) was accompanied by remarkable anatomical, physiological and behavioral adaptations. To better understand the genomic changes that occurred during this transition, we systematically screened for protein-coding genes that were inactivated in the ancestral cetacean lineage. We discovered genes whose loss is likely beneficial for cetaceans by reducing the risk of thrombus formation during diving (F12, KLKB1), improving the fidelity of oxidative DNA damage repair (POLM), and protecting from oxidative stress-induced lung inflammation (MAP3K19). Additional gene losses may reflect other diving-related adaptations, such as enhanced vasoconstriction during the diving response (mediated by SLC6A18) and altered pulmonary surfactant composition (SEC14L3), while loss of SLC4A9 relates to a reduced need for saliva in aquatic environments. Finally, the complete loss of melatonin synthesis and receptor genes (AANAT, ASMT, MTNR1A/B) may have been a precondition for the evolution of unihemispheric sleep. Our findings suggest that some genes lost in the ancestral cetacean lineage may have been involved in adapting to a fully-aquatic lifestyle.

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Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

Abstract: Network-like evolution suggests sympatric speciation of baleen whales.

Cited by 124 publications

References 56 publications

An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

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

Genes lost during the transition from land to water in cetaceans highlight genomic changes involved in aquatic adaptations

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