Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation

Abstract

BackgroundBaleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious. In particular, reconstructing the phylogenetic position of the gray whales (Eschrichtiidae) has been complicated by evolutionary processes such as gene flow and incomplete lineage sorting (ILS). Here, whole-genome sequencing data of the extant baleen whale radiation allowed us to identify transposable element (TE) insertions in order to perform phylogenomic analyses and measure germline insertion rates of TEs. Baleen whales exhibit the slowest nucleotide substitution rate among mammals, hence we additionally examined the evolutionary insertion rates of TE insertions across the genomes.ResultsIn eleven whole-genome sequences representing the extant radiation of baleen whales, we identified 91,859 CHR-SINE insertions that were used to reconstruct the phylogeny with different approaches as well as perform evolutionary network analyses and a quantification of conflicting phylogenetic signals. Our results indicate that the radiation of rorquals and gray whales might not be bifurcating. The morphologically derived gray whales are placed inside the rorqual group, as the sister-species to humpback and fin whales. Detailed investigation of TE insertion rates confirm that a mutational slow down in the whale lineage is present but less pronounced for TEs than for nucleotide substitutions.ConclusionsWhole genome sequencing based detection of TE insertions showed that the speciation processes in baleen whales represent a rapid radiation. Large genome-scale TE data sets in addition allow to understand retrotransposition rates in non-model organisms and show the potential for TE calling methods to study the evolutionary history of species.Electronic supplementary materialThe online version of this article (10.1186/s13100-018-0143-2) contains supplementary material, which is available to authorized users.

An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

“…Retroposon insertions have commonly been analyzed using one or more variants of parsimony (e.g., Camin-Sokal parsimony [Nikaido et al 1999]; polymorphism parsimony [Suh et al 2015]; Dollo parsimony [Lammers et al 2019]), distance methods (e.g., neighbor joining [Lammers et al 2019]), or networks (e.g., Doronina et al, 2017a;Lammers et al 2019). More recently, Springer and Gatesy (2019) suggested that retroposons have several properties that are well matched to the assumptions of summary coalescent methods such as ASTRAL (Mirarab and Warnow 2015).…”

“…Individual retroposon insertions typically occur at unlinked sites and are more appropriate than gene sequences for analysis with single-site coalescent methods. Finally, as is the case for any new mutation, a retroposon insertion is polymorphic when it first appears in a population (e.g., Lammers et al 2019) as is required for any marker that is subject to ILS.…”

“…Here, we construct species trees for three retroposon data sets (Nishihara et al 2009;Doronina et al 2017a;Lammers et al 2019) using two coalescent methods that account for ILS. Then, we develop a general χ 2 ABBA-BABA test (Green et al 2010) for retroposon insertions.…”

Retroposon Insertions within a Multispecies Coalescent Framework Suggest that Ratite Phylogeny is not in the ‘Anomaly Zone’

“…Retroposon insertions provide an important alternative to sequence-based analyses for reconstructing species trees, and have been widely employed to investigate difficult phylogenetic problems within Mammalia (Nikaido et al, 1999(Nikaido et al, , 2001Nishihara et al, 2006Nishihara et al, , 2009Churakov et al, 2010;Nilsson et al, 2012;Hartig et al, 2013;Doronina et al, 2015Doronina et al, , 2017aDoronina et al, , 2017bDoronina et al, , 2019Gallus et al, 5 2015;Lammers et al, 2019). The same approach increasingly has been applied to additional taxonomic groups including birds (Suh et al, 2011(Suh et al, , 2015bMatzke et al, 2012;Sackton et al, 2019) and crocodilians (Suh et al, 2015a).…”

“…The same approach increasingly has been applied to additional taxonomic groups including birds (Suh et al, 2011(Suh et al, , 2015bMatzke et al, 2012;Sackton et al, 2019) and crocodilians (Suh et al, 2015a). Although retroposon insertions have been analyzed using variants of parsimony (e.g., Nikaido et al, 1999;Suh et al, 2015b), distance methods (e.g., Lammers et al, 2019), or networks (e.g., Doronina et al, 2017a), they have several properties that are well matched to the assumptions of summary coalescence methods, with the caveat that these methods must permit polytomies in gene trees, because each retroposon insertion only provides information for a single bipartition of taxa. First, the presence/absence property of an individual retroposon insertion represents a single evolutionary event and is not subject to intralocus recombination.…”