Gene Loss

Publication Details

Identifier: JB_KZN2KH

Curator: M. Lopes-Marques

DOI: 10.1016/j.ympev.2022.107463

PMID: 35358696

Title:

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 postnatal 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 at ancestral nodes. 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.

Last update:

21-01-2025

Associated Glosses (130 results)

GlossID	Species	Symbol	Gene Loss Mechanism	Loss Type	Lineage Specific	Citation
GL_NFKMDX	Balaenoptera acutorostrata	ENAM	LOF (frameshift, premature stop, ss)	Full	No	10.1016/j.ympev.2022.107463
GL_NIHGI8	Eschrichtius robustus	ODAPH	Gene deletion	Full	No	10.1016/j.ympev.2022.107463
GL_O8UXSL	Balaenoptera bonaerensis	AMTN	LOF (frameshift, premature stop, ss)	Full	No	10.1016/j.ympev.2022.107463
GL_OIHSWW	Balaenoptera edeni	ODAPH	Gene deletion	Full	No	10.1016/j.ympev.2022.107463
GL_OQY4IN	Kogia breviceps	AMELX	LOF (frameshift, premature stop, ss)	Full	No	10.1016/j.ympev.2022.107463
GL_OUZQT4	Orcinus orca	ENAM	LOF (frameshift, premature stop, ss)	Full	No	10.1016/j.ympev.2022.107463
GL_P1YVMZ	Balaenoptera musculus	KLK4	LOF (frameshift, premature stop, ss)	Full	Mysticeti	10.1016/j.ympev.2022.107463
GL_PUM294	Kogia breviceps	KLK4	Exon(s) deletion	Full	No	10.1016/j.ympev.2022.107463
GL_QD0FHI	Caperea marginata	AMELX	LOF (frameshift, premature stop, ss)	Full	No	10.1016/j.ympev.2022.107463
GL_QG1KID	Balaenoptera physalus	AMBN	LOF (frameshift, premature stop, ss)	Full	No	10.1016/j.ympev.2022.107463