Molecular parallelism in fast-twitch muscle proteins in echolocating mammals

Abstract

Detecting associations between genomic changes and phenotypic differences is fundamental to understanding how phenotypes evolved. By developing a method to systematically screen for parallel amino acid substitutions, we discovered that echolocating bats and dolphins exhibit more parallel substitutions than expected in fast-twitch but in not slow-twitch muscle fiber proteins. Both bats and dolphins rely on specialized superfast muscles to produce an extremely rapid call rate when homing in on their prey. We show that these genes with parallel substitutions are expressed in the superfast call-producing muscle of bats and demonstrate that the calcium storage protein calsequestrin 1 of bats and dolphins form calcium-sequestering polymers at lower calcium concentrations, consistent with adaptations to rapid calcium transients required for superfast muscle physiology. Our results provide molecular insights into the convergent evolution of vocalization in echolocating mammals and demonstrate the potential of systematic screens to uncover associations between genomic changes and phenotypic differences.

Synergism, Bifunctionality, and the Evolution of a Gradual Sensory Trade-off in Hummingbird Taste Receptors

“…In contrast to our previous study on hummingbirds, which specifically examined the Venus flytrap domain of T1R3 ( Baldwin et al 2014 ; Toda et al 2021b ), we used receptor chimeras of both T1R1 and T1R3 and investigated the role of different domains. To narrow down residues within a functionally relevant section of the VFT, we next explored the use of three criteria, and tested a multiple point-mutant chimera that contained residues that differed between ancestral pairs that were a) radical changes (following for instance Lee et al [2018] ), b ) had a BLOSUM62 ( Henikoff and Henikoff 1992 ) score of 0 or below (to examine amino acid substitutions that occur relatively infrequently), and c) were evolutionarily conserved between AR2 and all extant hummingbird sequences. To examine the role of radical changes or amino acids with low BLOSUM62 scores in T1R1, we synthesized TMDs containing residue subsets and generated receptor chimeras as described above.…”

A simple conceptual framework and nomenclature for studying repeated, parallel and convergent evolution

“…Second, vague or imprecise terms are likely to impact early career researchers and newcomers to the field, who are sedimenting their knowledge, creating a superfluous barrier to their understanding. For instance, in biodiversity genomics parallel evolution has been used to refer to 'parallel changes at the molecular sequence level' (Natarajan et al, 2015), 'parallel replacements/substitutions' (Natarajan et al, 2015;Mendes et al, 2016;Lee et al, 2018), 'parallel evolution and fixation of mutations' (Stern, 2013), 'parallel selection on standing genetic variation' (Pease et al, 2016), 'parallel adaptation' (Stoltzfus & McCandlish, 2017;Bohutínská et al, 2021;Konečná et al, 2021;Szukala et al, 2022), 'parallel evolution of phenotypes' (Colosimo et al, 2005;Szukala et al, 2022), among other terms. Third, because nuances in the terms are likely field-specific (when considering developmental biology, physiology, ecology, genomics as di erent fields within biology), they may obstruct multidisciplinary e orts.…”

Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits

“…But the function of candidate genes may also be described from other studies in the scientific literature. In this way, Forward Genomics identified new links between genomic changes in genes as well as regulatory elements and various phenotypic changes such as adaptations to fully aquatic lifestyles in cetaceans and manatees (Sharma et al 2018a), echolocation in bats and toothed whales (Lee et al 2018), reductions and losses of the mammalian vomeronasal system (Hecker et al 2019a), the evolution of body armour in pangolins and armadillos (Sharma et al 2018a), the absence of testicular descent (Sharma et al 2018b), and the reduction of eye sight in subterranean mammals (Roscito et al 2018;Langer et al 2018).…”