Molecular Evolutionary Analyses of Tooth Genes Support Sequential Loss of Enamel and Teeth in Baleen Whales (Mysticeti)

Abstract

The loss of teeth and evolution of baleen racks in Mysticeti was a profound transformation that permitted baleen whales to radiate and diversify into a previously underutilized ecological niche of bulk filter-feeding on zooplankton and other small prey. Ancestral state reconstructions suggest that teeth were lost in the common ancestor of crown Mysticeti. Genomic studies provide some support for this hypothesis and suggest that the genetic toolkit for enamel production was inactivated in the common ancestor of living baleen whales. However, molecular studies to date have not provided direct evidence for the complete loss of teeth, including their dentin component, on the stem mysticete branch. Given these results, several questions remain unanswered: (1) Were teeth lost in a single step or did enamel loss precede dentin loss? (2) Was enamel lost early or late on the stem mysticete branch? (3) If enamel and dentin/tooth loss were decoupled in the ancestry of baleen whales, did dentin loss occur on the stem mysticete branch or independently in different crown mysticete lineages? To address these outstanding questions, we compiled and analyzed complete protein-coding sequences for nine tooth-related genes from cetaceans with available genome data. Seven of these genes are associated with enamel formation (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) whereas two other genes are either dentin-specific (DSPP) or tooth-specific (ODAPH) but not enamel-specific. Molecular evolutionary analyses indicate that all seven enamel-specific genes have inactivating mutations that are scattered across branches of the mysticete tree. Three of the enamel genes (ACP4, KLK4, MMP20) have inactivating mutations that are shared by all mysticetes. The two genes that are dentin-specific (DSPP) or tooth-specific (ODAPH) do not have any inactivating mutations that are shared by all mysticetes, but there are shared mutations in Balaenidae as well as in Plicogulae (Neobalaenidae + Balaenopteroidea). These shared mutations suggest that teeth were lost at most two times. Shared inactivating mutations and dN/dS analyses, in combination with cetacean divergence times, were used to estimate inactivation times of genes and by proxy enamel and tooth phenotypes. The results of these analyses are most compatible with a two-step model for the loss of teeth in the ancestry of living baleen whales: enamel was lost very early on the stem Mysticeti branch followed by the independent loss of dentin (and teeth) in the common ancestors of Balaenidae and Plicogulae, respectively. These results imply that some stem mysticetes, and even early crown mysticetes, may have had vestigial teeth comprised of dentin with no enamel. Our results also demonstrate that all odontocete species (in our study) with absent or degenerative enamel have inactivating mutations in one or more of their enamel genes.

Evolution of ion channels in cetaceans: A natural experiment in the Tree of life

“…Interestingly, on average, cetaceans possess fewer annotated ion channels than the non-cetacean mammals in our sampling (187.56 ± 7.32 vs. 197.56 ± 13.00, unpaired one-tailed t-test with d.f.=12.605; t-statistic = -2.011 and p-value = 0.033). This result is consistent with other studies in which a reduction in gene copy number in cetaceans, and other groups, are associated with evolutionary innovations (Feng et al 2014;Nery et al 2014;Sun et al 2017;Huelsmann et al 2019;Helsen et al 2020a;McGowen et al 2020;Cabrera et al 2021;Randall et al 2022;Zheng et al 2022;Osipova et al 2023;Pinto et al 2023).…”

“…2). This result is consistent with other studies in which a reduction in gene copy number in cetaceans and other groups is associated with evolutionary innovations (Feng et al 2014;Nery et al 2014;Sun et al 2017;Huelsmann et al 2019;Helsen et al 2020a;McGowen et al 2020;Cabrera et al 2021;Randall et al 2022;Zheng et al 2022;Osipova et al 2023;Pinto et al 2023). We annotated, on average, 192.56 ion channels in the genomes of the species included in our taxonomic sampling, representing 0.96% of the protein-coding genes (Fig.…”

“…Support for this idea has been widely documented in the literature for cetaceans and other groups (Feng et al 2014;Nery et al 2014;Sun et al 2017;Huelsmann et al 2019;Helsen et al 2020;McGowen et al 2020;Randall et al 2022;Zheng et al 2022;Osipova et al 2023;Pinto et al 2023).…”

“…Taking advantage of the advancement of genomic tools, these adaptations have been investigated from the molecular perspective to expand further our knowledge about the evolutionary process behind the conquest of an aquatic lifestyle (McGowen et al 2011;McGowen et al 2012;Nery, González, et al 2013;Nery, Arroyo, et al 2013;Sun et al 2013;Nery et al 2014;McGowen et al 2020). Interestingly, several studies have reported the loss of genes as a strategy of phenotypic evolution (Feng et al 2014;Nery et al 2014;Sun et al 2017;Huelsmann et al 2019;Helsen et al 2020a;McGowen et al 2020;Randall et al 2022;Zheng et al 2022;Osipova et al 2023;Pinto et al 2023).…”

Genomic data suggest parallel dental vestigialization within the xenarthran radiation

“…Xenarthran dental genes point to a third path towards this phenotype, with discrete events of enamel loss followed by tooth loss in the evolution of anteaters, based on shared and distinct pseudogenization signals in vermilinguans and sloths. This dental regression scenario was also recently inferred in a study on the evolution of baleen whales (Mysticeti) based on a similar comparison of dental genes (Randall et al, 2022).…”