Mammalian vocal communication as a model for human language; from genes and brains to behaviour

Lead Research Organisation: University of St Andrews
Department Name: Biology

Abstract

Our ability to communicate via spoken language requires a complex skill set built upon cognitive and physiological processes. I aim to discover the biological bases of language related skills and understand how they unite to create the sophisticated social communication system that is language. Bats present a unique opportunity to shed light on these issues because they are an extraordinary group of animals with intricate social structures and communication abilities. They feature speech and language relevant traits such as vocal learning - the ability to learn new vocalisations, a crucial component of how we learn to speak. However this potential has rarely been exploited. My goal is to use bat models to understand the biological encoding of social-vocal communication abilities. By comparing these findings with other mammals and with humans, it will be possible to shed light on mechanisms by which human language evolved.

Specifically, I will explore the behavioural abilities that bats have to learn new vocalisations in a social context, and compare this with other vocal learning mammals (e.g. seals, dolphins). I will investigate the neurobiological, genetic, and genomic factors contributing to these abilities. And I will integrate findings from human language disorder studies to identify parallels between the mechanisms that allow these social-vocal communicative behaviours in bats and other mammals, to those that underscore human language abilities and evolution.

Planned Impact

The fellowship will study vocal learning in bats, using leading-edge techniques to drive understanding of the genomics, genetics, neurobiology and behaviour of this trait. This will provide the first model for studying the neurobiology and genetics of language relevant traits in a non-human mammal. This new approach will ultimately shed light on the biological underpinnings of human speech and language and associated disorders, and resolve unanswered questions about how speech and language may have evolved.

Goal 1. Foster partnerships for knowledge exchange with industry/technology development. Beneficiaries: Industry/technology partners.
Being at the forefront of genomic sequencing with the Bat1K consortium, I will work with Industrial/technology development partners to exchange knowledge about the implementation and utilization of their rapidly developing genomic technologies. As 'super users' of these technologies, we will provide feedback throughout the fellowship about what works well and what is problematic about the technology and help them focus their improvement and development efforts to improve the technology hardware and software that is available. This has knock-on effects to accelerate technology development as well as industry and research output.

Goal 2. Engage and encourage the next generation of scientists, particularly minority and disadvantaged students. Beneficiaries: Students
Education of the next generation of scientists, as well as promoting equality in science is a high priority. These activities engage with student education and actively encourage students from minorities or less advantaged backgrounds to interact with ongoing research and understand the reality of being a scientist. Giving hands on experience with scientific research can demystify science as a higher education option or career path, therefore increasing opportunities for minority or disadvantaged students to succeed.

Goal 3. Increase the public understanding of science, promote conservation of bats, and involve patient groups. Beneficiaries: Charitable partners, museums, general public, students, patient groups.
Bats are fascinating creatures with special skills such as being able to 'see in the dark' via echolocation, living to extraordinarily old ages, and avoiding otherwise deadly diseases like ebola. Furthermore, bats are vital to our ecosystems and crops as they pollinate plants, disperse seeds and consume harmful insect pests. The goal will be to work with museums, galleries and local artists to generate exhibitions and installations that engage different audiences to learn about bats. By working with charitable partners such as bat conservation charities, local artists, students and patient groups (children with speech/language disorders, autism, etc., given bats relevance for human language, and blindness given their ability to navigate via sound) we will facilitate community driven exhibitions and installations. These activities will benefit the general public and students by teaching them about the special features of bats and their protection, and will benefit UK agriculture and ecosystems by encouraging bat conservation. They will benefit patient groups by finding new ways to engage patients and families. These exhibitions will also benefit museums, local artists and conservation organisations by bringing new audiences to them.

In addition to these activities, we will actively engage with conservation groups to help them make use of the genomic resources we generate for conservation efforts, and with the media to promote our work and bats via print, web, radio and television.

Publications

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Description In the past year we have been able to sequence the genomes of multiple vocal learning relevant bat species and produce transcriptomic data to profile the expression of genes across these bats. This data will be released to the public for use in understanding vocal learning in bats, as well as a range of other specialised phenotypes associated with bats.
We have not been able to make as much progress as initially planned due to delays and interruptions caused by COVID, but are in a much better position to make progress given the measures we put in place this year to ameliorate these delays.
Exploitation Route Our genomic and transcriptomic data generated is being publicly released so that it may be used across multiple research areas.
Sectors Environment,Pharmaceuticals and Medical Biotechnology

 
Title Data for "Learning how to call: the vocal development of the pale spear-nosed bat is dependent on auditory feedback" 
Description Acoustic call parameters, auditory brainstem responses, and data analysis programs for Lattenkamp et al., "Learning how to call: the vocal development of the pale spear-nosed bat is dependent on auditory feedback". 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Acoustic parameters of P. discolor vocalisations, auditory brainstem responses, and data analysis programs for Lattenkamp et al., 2021. 
URL https://doi.gin.g-node.org/10.12751/g-node.lrqd92
 
Title Large-scale genome sampling reveals unique immunity and metabolic adaptations in bats 
Description Comprising more than 1,400 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 lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune system and metabolic genes. Genomes were obtained from public repositories and one genome (Phyllostomus hastatus) was assembled de novo. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defense receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defense response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance anti-viral immune response while dampening inflammatory signaling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact This repository contains the scripts used to generate data for the article "Large-scale genome sampling reveals unique immunity and metabolic adaptations in bats" from Molecular Ecology. These include the commands used for the assembly of genomes and transcriptomes, the construction of an ultrametric phylogenetic tree with the MCMCtree bioinformatics tool, the scripts used to run selection analysis with CODEML as well as the files used to perform gene family evolution analysis with CAFE. The dataset has been viewed 69 times, downloaded 16 times and cited by 1 research article. 
URL http://datadryad.org/stash/dataset/doi:10.5061/dryad.59zw3r265