Evolution of CHR-2 SINEs in cetartiodactyl genomes: possible evidence for the monophyletic origin of toothed whales

Nikaido, Masato; Matsuno, Fumio; Abe, Hideaki; Shimamura, Mitsuru; Hamilton, Healy; Matsubayashi, Hisashi; Okada, Norihiro

doi:10.1007/s0033501-1015-4

Cited by 33 publications

(10 citation statements)

References 27 publications

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“…Indeed, analyses of a substantial diversity of molecular data repeatedly pointed out that cetaceans should be included among artiodactyls, most probably as the sister group of the Hippopotamidae (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). The independence of those results provides a strong support to the clade Cetartiodactyla (cetaceans plus artiodactyls, ref.…”

mentioning

confidence: 70%

The position of Hippopotamidae within Cetartiodactyla

Boisserie

Lihoreau

Brunet

2005

Proc. Natl. Acad. Sci. U.S.A.

105

171

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The origin of late Neogene Hippopotamidae (Artiodactyla) involves one of the most serious conflicts between comparative anatomy and molecular biology: is Artiodactyla paraphyletic? Molecular comparisons indicate that Cetacea should be the modern sister group of hippos. This finding implies the existence of a fossil lineage linking cetaceans (first known in the early Eocene) to hippos (first known in the middle Miocene). The relationships of hippos within Artiodactyla are challenging, and the immediate affinities of Hippopotamidae have been studied by biologists for almost two centuries without resolution. Here, we compare opposing hypotheses implicating several ''suiform'' families. This morphological analysis of a comprehensive set of taxa and characters offers a robust solution to the origins of Hippopotamidae. This family appears to be deeply nested within the otherwise extinct artiodactyl family Anthracotheriidae, most precisely within the most advanced selenodont forms. The proposed sister group of hippos is the middle to late Miocene African semiaquatic Libycosaurus. Any close relationships of hippos with suoids, particularly with Tayassuidae, are rejected. Furthermore, the clade (Hippopotamidae, Anthracotheriidae) is proposed as the sister group of the Cetacea, offering broad morphological support for a molecular phylogeny, such support being also consistent with the fossil record. Corroboration of this relationship requires an exploration of anthracothere affinities with other Paleogene artiodactyls. Among those, the position of Ruminantia is a central question, still to be solved. Further progress in this debate is likely to come from morphological studies of paleontological data, whether known or still to be discovered.hippo origin ͉ phylogeny ͉ Anthracotheriidae ͉ suoids ͉ archaeocetes

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mentioning

confidence: 70%

The position of Hippopotamidae within Cetartiodactyla

Boisserie

Lihoreau

Brunet

2005

Proc. Natl. Acad. Sci. U.S.A.

105

171

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“…The name of the SINE family as well as its subfamily is indicated in a bold box (CD, Cetacean deletions; CDO, Cetacean deletion Odontoceti; MDI, Middle deletion type I) [16]. The dots indicate nucleotides identical to the consensus sequence at the top.…”

Section: Methodsmentioning

confidence: 99%

“…[16,22,23,31,32,37-47]. They have been successfully applied to resolve phylogenetic relationships among various groups at different taxonomic ranks [31,32,37,39-42,44].…”

Section: Introductionmentioning

confidence: 99%

“…Nikaido and his colleagues pioneered the use of SINE insertions to address the relationships among cetaceans and other orders of mammals as well as to address relationships among both mysticetes and odontocetes [16,22,31,32,44]. For example, they examined 25 informative SINE insertions to support the monophyly of toothed whales and the paraphyly of river dolphins [31].…”

Section: Introductionmentioning

confidence: 99%

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Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences

Chen

Zhou

et al. 2011

BMC Evol Biol

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BackgroundA diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales), and great progress has been made in the past two decades. However, there is still some controversy concerning relationships among certain cetacean taxa such as river dolphins and delphinoid species, which needs to be further addressed with more markers in an effort to address unresolved portions of the phylogeny.ResultsAn analysis of additional SINE insertions and SINE-flanking sequences supported the monophyly of the order Cetacea as well as Odontocete, Delphinoidea (Delphinidae + Phocoenidae + Mondontidae), and Delphinidae. A sister relationship between Delphinidae and Phocoenidae + Mondontidae was supported, and members of classical river dolphins and the genera Tursiops and Stenella were found to be paraphyletic. Estimates of divergence times revealed rapid divergences of basal Odontocete lineages in the Oligocene and Early Miocene, and a recent rapid diversification of Delphinidae in the Middle-Late Miocene and Pliocene within a narrow time frame.ConclusionsSeveral novel SINEs were found to differentiate Delphinidae from the other two families (Monodontidae and Phocoenidae), whereas the sister grouping of the latter two families with exclusion of Delphinidae was further revealed using the SINE-flanking sequences. Interestingly, some anomalous PCR amplification patterns of SINE insertions were detected, which can be explained as the result of potential ancestral SINE polymorphisms and incomplete lineage sorting. Although a few loci were potentially anomalous, this study demonstrated that the SINE-based approach is a powerful tool in phylogenetic studies. Identifying additional SINE elements that resolve the relationships in the superfamily Delphinoidea and family Delphinidae will be important steps forward in completely resolving cetacean phylogenetic relationships in the future.

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“…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).…”

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confidence: 99%

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

Ms¹,

Gatesy

2019

Preprint

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coalescence methods were developed to address the negative impacts of incomplete lineage sorting on species tree estimation with concatenation. Coalescence methods are statistically consistent if certain requirements are met including no intralocus recombination, neutral evolution, and no gene tree reconstruction error. However, the assumption of no intralocus recombination may not hold for many DNA sequence data sets, and neutral evolution is not the rule for genetic markers that are commonly employed in phylogenomic coalescence analyses. Most importantly, the assumption of no gene tree reconstruction error is routinely violated, especially for rapid radiations that are deep in the Tree of Life. With the sequencing of complete genomes and novel pipelines, phylogenetic analysis of retroposon insertions has emerged as a valuable alternative to sequence-based phylogenetic analysis.Retroposon insertions avoid or reduce several problems that beset analysis of sequence data with summary coalescence methods: 1) intralocus recombination is avoided because retroposon insertions are singular evolutionary events, 2) neutral evolution is approximated in many cases, and 3) gene tree reconstruction errors are rare because retroposons have low rates of homoplasy. However, the analysis of retroposons within a multispecies coalescent framework has not been realized. Here, we propose a simple workaround in which a retroposon insertion matrix is first transformed into a series of incompletely resolved gene trees. Next, the program ASTRAL is used to estimate a species tree in the statistically consistent framework of the multispecies coalescent. The inferred species tree includes support scores at all nodes and internal branch lengths in coalescent units. As a test case, we analyzed a retroposon dataset for palaeognath birds (ratites and tinamous) with ASTRAL and compared the resulting species tree to an MP-EST species tree for the same clade derived from thousands of sequence-based gene trees. The MP-EST species tree suggests an empirical case of the 'anomaly zone' with three very short internal branches at the base of Palaeognathae, and as predicted for anomaly zone conditions, the MP-EST species tree differs from the most common gene tree. Although identical in topology to the MP-EST tree, the ASTRAL species tree based on retroposons shows branch lengths that are much longer and incompatible with anomaly zone conditions. Simulation of gene trees from the retroposon-based species tree reveals that the most common gene tree matches the species tree. We contend that the wide discrepancies in branch lengths between sequence-based and retroposon-based species trees are explained by the greater accuracy of retroposon gene trees (bipartitions) relative to sequence-based gene trees. Coalescence analysis of retroposon data provides a promising alternative to the status quo by reducing gene tree reconstruction error that can have large impacts on both branch length estimates and evolutionary interpretations.

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Evolution of CHR-2 SINEs in cetartiodactyl genomes: possible evidence for the monophyletic origin of toothed whales

Cited by 33 publications

References 27 publications

The position of Hippopotamidae within Cetartiodactyla

The position of Hippopotamidae within Cetartiodactyla

Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences

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

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