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Kalina T. J. Davies

Kalina T. J. Davies

PhD

About

52
Publications
8,326
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564
Citations
Citations since 2017
23 Research Items
458 Citations
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2017201820192020202120222023020406080100120
2017201820192020202120222023020406080100120
2017201820192020202120222023020406080100120
Introduction
My research aims to understand how different species sense their environment, and to identify the molecular changes that have taken place as species move into novel ecological niches. By using genomic data it is possible to identify molecular adaptations (e.g., positive selection, gene duplication and loss), and how these might affect sensory perception. I am also fascinated by parallel evolution as this highlights how evolution is shaped by both innovation and constraint.

Publications

Publications (52)
Article
Full-text available
Changes in behaviour may initiate shifts to new adaptive zones, with physical adaptations for novel environments evolving later. While new mutations are commonly considered engines of adaptive change, sensory evolution enabling access to new resources might also arise from standing genetic diversity, and even gene loss. We examine the relative cont...
Article
Full-text available
The loss of previously adaptive traits is typically linked to relaxation in selection, yet the molecular steps leading to such repeated losses are rarely known. Molecular studies of loss have tended to focus on gene sequences alone, but overlooking other aspects of protein expression might underestimate phenotypic diversity. Insights based almost s...
Article
Full-text available
Among mammals, several lineages have independently adapted to a subterranean niche, and possess similar phenotypic traits for burrowing (e.g. cylindrical bodies, short limbs and absent pinnae). Previous research on mole-rats has revealed molecular adaptations for coping with reduced oxygen, elevated carbon dioxide, and the absence of light. In cont...
Article
Full-text available
During their evolutionary radiation, mammals have colonized diverse habitats. Arguably the subterranean niche is the most inhospitable of these, characterized by reduced oxygen, elevated carbon dioxide, absence of light, scarcity of food, and a substrate that is energetically costly to burrow through. Of all lineages to have transitioned to a subte...
Article
Full-text available
Introduction Many mammals have evolved highly adapted hearing associated with ecological specialisation. Of these, bats possess the widest frequency range of vocalisations and associated hearing sensitivities, with frequencies of above 200 kHz in some lineages that use laryngeal echolocation. High frequency hearing in bats appears to have evolved v...
Article
While evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness‐related resources, and thus the underlying genomic architecture and morphology must cope with...
Preprint
Full-text available
While evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with...
Article
In most vertebrates, the demand for glucose as the primary substrate for cellular respiration is met by the breakdown of complex carbohydrates, or energy is obtained by protein and lipid catabolism. In contrast, a few bat and bird species have convergently evolved to subsist on nectar, a sugar-rich mixture of glucose, fructose, and sucrose.1-4 How...
Article
Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the...
Article
The role of mechanical morphologies in the exploitation of novel niche space is well characterized, however, the role of sensory structures in unlocking new niches is less clear. Here we investigate the relationship between the evolution of sensory structures and diet during the radiation of noctilionoid bats. With a broad range of foraging ecologi...
Article
Full-text available
Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sourc...
Preprint
Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent l...
Preprint
Full-text available
Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent l...
Preprint
Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent l...
Article
Full-text available
Diversification and adaptive radiations are tied to evolvability, which in turn is linked to morphological integration. Tightly integrated structures typically evolve in unison, whereas loosely integrated structures evolve separately. Highly integrated structures are therefore thought to constrain evolutionary change by limiting morphological dispa...
Article
Full-text available
Multigene families evolve from single‐copy ancestral genes via duplication, and typically encode proteins critical to key biological processes. Molecular analyses of these gene families require high‐confidence sequences, but the high sequence similarity of the members can create challenges for sequencing and downstream analyses. Focusing on the com...
Article
Full-text available
In mammals, social and reproductive behaviors are mediated by chemical cues encoded by hyperdiverse families of receptors expressed in the vomeronasal organ. Between species, the number of intact receptors can vary by orders of magnitude. However, the evolutionary processes behind variation in receptor number, and its link to fitness-related behavi...
Preprint
Full-text available
Multigene families evolve from single-copy ancestral genes via duplication, and typically encode proteins critical to key biological processes. Molecular analyses of these gene families require high-confidence sequences, but the high sequence similarity of the members can create challenges for both sequencing and downstream analyses. Focusing on th...
Article
Full-text available
The increased accessibility of soft-tissue data through diffusible iodine-based contrast-enhanced computed tomography (diceCT) enables comparative biologists to increase the taxonomic breadth of their studies with museum specimens. However, it is still unclear how soft-tissue measurements from preserved specimens reflect values from freshly collect...
Preprint
Full-text available
Studies of opsin genes offer insights into the evolutionary history and molecular basis of vertebrate color vision, but most assume intact open reading frames equate to functional phenotypes. Despite known variation in opsin repertoires and associated visual phenotypes, the genetic basis of such patterns has not been examined at each step of the ce...
Preprint
Full-text available
In mammals, social and reproductive behaviors are mediated by chemical cues encoded by hyperdiverse families of receptors expressed in the vomeronasal organ. Between species, the number of intact receptors can vary by orders of magnitude. However, the evolutionary processes behind variation in receptor number, and also its link to fitness-related b...
Article
The repeated independent evolution of similar features in divergent lineages, a process known as convergent evolution, has long been a source of fascination for both naturalists and evolutionary biologists. Until recently, this active area of research had been focused principally on the evolution of physical characteristics associated with novel tr...
Data
Full-text available
Figure S1. Protein-protein interaction networks for 105 protein-coding gene products tested in both cetaceans and the hippo that were found to be under positive selection in the cetaceans. Inset: protein-protein interaction networks for 20 protein-coding genes found to be under positive selection in the hippo. Nodes are labelled with the standard p...
Data
Table S8. Separate .xls file with results of GO enrichment analysis for the five branches tested for selection for the three GO domains: A. Biological Process; B. Cellular Component; C. Molecular Function.
Article
Full-text available
Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. Here, we obtained new transcript...
Article
The naked mole-rat (NMR) Heterocephalus glaber is a unique and fascinating mammal exhibiting many unusual adaptations to a subterranean lifestyle. The recent discovery of their resistance to cancer and exceptional longevity has opened up new and important avenues of research. Part of this resistance to cancer has been attributed to the fact that NM...
Article
Full-text available
Background The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and thus assumed to be under strong sel...
Article
Full-text available
The vestibular system maintains the body's sense of balance and, therefore, was probably subject to strong selection during evolutionary transitions in locomotion. Among mammals, bats possess unique traits that place unusual demands on their vestibular systems. First, bats are capable of powered flight, which in birds is associated with enlarged se...
Data
A Semicircular canal shape, as quantified by eigenshape analysis, versus relative cochlea size. For each semicircular canal the relationship between cochlea size and the first three eigenshape axes were investigated; the percentage of the total sample shape variance expressed by each axes was as follows: anterior ES1 28.73%, ES2 18.60% and ES3 9.32...
Data
Micro-computed tomography scan slice through four bat skulls, displaying the relative position of the three semicircular canals within the skull. Scans are from the following species: (A) Pteropus rodricensis (BMNH.76.3.15.14); (B) Myotis lucifugus (BMNH.7.7.7.3359); (C) Rhinolophus ferrumequinum (58.20697) and (D) Cloeotis percivali (BMNH.66.5456)...
Data
A Reconstructed inner ear volume of Trachops cirrhosus (BMNH.1924.3.1.33) indicating the orientation of each semicircular canal for outline collection. Starting points (white arrows) for each canal outline (red lines) were as follows: anterior semicircular canal (top left) - point of inflection of the ampullae; posterior semicircular canal (top rig...
Data
The relationship between log semicircular canal size and log WTS across a sample of echolocating Yinpterochiroptera (black circles). The measured points for Rhinolophus philippinensis small morph (white circle) falls beneath the 95% PI calculated for the remaining species for (A) anterior, (B) lateral and (C) posterior semicircular canals. (TIF)
Article
Full-text available
Hereditary deafness affects 0.1% of individuals globally and is considered as one of the most debilitating diseases of man. Despite recent advances, the molecular basis of normal auditory function is not fully understood and little is known about the contribution of single-nucleotide variations to the disease. Using cross-species comparisons of 11...
Data
Full-text available
The vestibular system maintains the body's sense of balance and, therefore, was probably subject to strong selection during evolutionary transitions in locomotion. Among mammals, bats possess unique traits that place unusual demands on their vestibular systems. First, bats are capable of powered flight, which in birds is associated with enlarged se...
Data
Full-text available
Measuring basilar membrane length from reconstructed inner ear endocasts. (A) Left: Medial view of the right cochlear endocast of Craseonycteris thonglongyai (specimen number HZM.1.34982, ref. Table S1). A representation of the path of the basilar membrane measured by this study is shown by the dotted line. Right upper: Apical view of the right coc...
Data
Full-text available
Multiple regression plots of echolocation call parameters, basilar membrane length, number of cochlear turns and body mass. Stepwise multiple regressions suggest that equations with only inner ear parameters were the best fitting models: log maximum frequency = -0.96 log basilar membrane + 1.58 log turns + 2.22, multiple R2= 0.26, F = 9.01 (2, 51 d...
Data
Full-text available
Maximum likelihood ancestral reconstructions of bat inner ears - (A) relative basilar membrane length and (B) number of cochlear turns. Phylogenies and character values are depicted as ‘Traitgrams’, whereby the position along the y-axis corresponds to node age in millions of years and position along the x-axis corresponds to the reconstructed chara...
Data
Morphological parameters versus echolocation call frequency in Rhinolophus species. Published values for species taken from literature (black points), the three Rhinolophus philippinensis size morphs measured by this study: small (red), medium (orange), large (yellow) and values published for one R. philippinensis values taken from [28] (blue). (A)...
Article
Full-text available
Recent findings of sequence convergence in the Prestin gene among some bats and cetaceans suggest that parallel adaptations for high-frequency hearing have taken place during the evolution of echolocation. To determine if this gene is an exception, or instead similar processes have occurred in other hearing genes, we have examined Tmc1 and Pjvk, bo...

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Project (1)
Project
All animals must sense their environment and other organisms to find food, avoid threats, and find partners. The ability of some individuals to locate food and mates more effectively than others can open opportunities for them to leave many more descendants. And yet, multiple advanced sensory systems seldom evolve in the same species despite the advantages they may confer, suggesting there are physical limits to developing several specialized senses. This project focuses on a diverse group of tropical bats in which various species evolved acute, specialized hearing, supersensitive eyes, the ability to smell subtle plant chemicals, or highly developed vomeronasal systems (thought to contribute to mating and social hierarchy). This project will compare approximately 2000 genes involved in vision, hearing, olfaction and the vomeronasal system in more than 150 bat species. To find out how some of these genes contribute to developing distinct sensory systems, their actions will be studied in the lab. This research will uncover the role of specific genes in the acquisition of specialized senses, test whether the size of the head limits the number of specialized sensory structures a species can have, and discover how sensory adaptations contribute to the diversity of species through time.