Publications

Abstract

Tropical ecosystems are known for high species diversity. Adaptations permitting niche differentiation enable species to coexist. Historically, research focused primarily on morphological and behavioral adaptations for foraging, roosting, and other basic ecological factors. Another important factor, however, is differences in sensory capabilities. So far, studies mainly have focused on the output of behavioral strategies of predators and their prey preference. Understanding the coexistence of different foraging strategies, however, requires understanding underlying cognitive and neural mechanisms. In this study, we investigate hearing in bats and how it shapes bat species coexistence. We present the hearing thresholds and echolocation calls of 12 different gleaning bats from the ecologically diverse Phyllostomid family. We measured their auditory brainstem responses to assess their hearing sensitivity. The audiograms of these species had similar overall shapes but differed substantially for frequencies below 9 kHz and in the frequency range of their echolocation calls. Our results suggest that differences among bats in hearing abilities contribute to the diversity in foraging strategies of gleaning bats. We argue that differences in auditory sensitivity could be important mechanisms shaping diversity in sensory niches and coexistence of species.

Abstract

Comparative studies of vocal learning and vocal non-learning animals can increase our understanding of the neurobiology and evolution of vocal learning and human speech. Mammalian vocal learning is understudied: most research has either focused on vocal learning in songbirds or its absence in non-human primates. Here we focus on a highly promising model species for the neurobiology of vocal learning: grey seals. We provide a neuroanatomical atlas (based on dissected brain slices and magnetic resonance images), a labelled MRI template, a 3D model with volumetric measurements of brain regions, and histological cortical stainings. Four main features of the grey seal brain stand out. (1) It is relatively big and highly convoluted. (2) It hosts a relatively large temporal lobe and cerebellum, structures which could support developed timing abilities and acoustic processing. (3) The cortex is similar to humans in thickness and shows the expected six-layered mammalian structure. (4) Expression of FoxP2 - a gene involved in vocal learning and spoken language - is present in deeper layers of the cortex. Our results could facilitate future studies targeting the neural and genetic underpinnings of mammalian vocal learning, thus bridging the research gap from songbirds to humans and non-human primates.Competing Interest StatementThe authors have declared no competing interest.

Abstract

During vocal communication, the spectro‑temporal structure of vocalizations conveys important
contextual information. Bats excel in the use of sounds for echolocation by meticulous encoding of
signals in the temporal domain. We therefore hypothesized that for social communication as well,
bats would excel at detecting minute distortions in the spectro‑temporal structure of calls. To test
this hypothesis, we systematically introduced spectro‑temporal distortion to communication calls of
Phyllostomus discolor bats. We broke down each call into windows of the same length and randomized
the phase spectrum inside each window. The overall degree of spectro‑temporal distortion in
communication calls increased with window length. Modelling the bat auditory periphery revealed
that cochlear mechanisms allow discrimination of fast spectro‑temporal envelopes. We evaluated
model predictions with experimental psychophysical and neurophysiological data. We first assessed
bats’ performance in discriminating original versions of calls from increasingly distorted versions of
the same calls. We further examined cortical responses to determine additional specializations for
call discrimination at the cortical level. Psychophysical and cortical responses concurred with model
predictions, revealing discrimination thresholds in the range of 8–15 ms randomization‑window
length. Our data suggest that specialized cortical areas are not necessary to impart psychophysical
resilience to temporal distortion in communication calls.

Abstract

Vocal production learning (VPL) is the capacity to learn to produce new vocalizations, which is a rare ability in the animal kingdom and thus far has only been identified in a handful of mammalian taxa and three groups of birds. Over the last few decades, approaches to the demonstration of VPL have varied among taxa, sound production systems and functions. These discrepancies strongly impede direct comparisons between studies. In the light of the growing number of experimental studies reporting VPL, the need for comparability is becoming more and more pressing. The comparative evaluation of VPL across studies would be facilitated by unified and generalized reporting standards, which would allow a better positioning of species on any proposed VPL continuum. In this paper, we specifically highlight five factors influencing the comparability of VPL assessments: (i) comparison to an acoustic baseline, (ii) comprehensive reporting of acoustic parameters, (iii) extended reporting of training conditions and durations, (iv) investigating VPL function via behavioural, perception-based experiments and (v) validation of findings on a neuronal level. These guidelines emphasize the importance of comparability between studies in order to unify the field of vocal learning.

Abstract

Human vocal development and speech learning require acoustic feedback, and
humans who are born deaf do not acquire a normal adult speech capacity. Most
other mammals display a largely innate vocal repertoire. Like humans, bats are
thought to be one of the few taxa capable of vocal learning as they can acquire
new vocalizations by modifying vocalizations according to auditory experiences.
We investigated the effect of acoustic deafening on the vocal development of the
pale spear-nosed bat. Three juvenile pale spear-nosed bats were deafened, and
their vocal development was studied in comparison with an age-matched, hear-
ing control group. The results show that during development the deafened bats
increased their vocal activity, and their vocalizations were substantially altered,
being much shorter, higher in pitch, and more aperiodic than the vocalizations
of the control animals. The pale spear-nosed bat relies on auditory feedback
for vocal development and, in the absence of auditory input, species-atypical
vocalizations are acquired. This work serves as a basis for further research
using the pale spear-nosed bat as a mammalian model for vocal learning, and
contributes to comparative studies on hearing impairment across species.
This article is part of the theme issue ‘Vocal learning in animals and
humans’.

Abstract

Differences in auditory perception between species are influenced by phylogenetic origin and the perceptual challenges imposed by the natural environment, such as detecting prey- or predator-generated sounds and communication signals. Bats are well suited for comparative studies on auditory perception since they predominantly rely on echolocation to perceive the world, while their social calls and most environmental sounds have low frequencies. We tested if hearing sensitivity and stimulus level coding in bats differ between high and low-frequency ranges by measuring auditory brainstem responses (ABRs) of 86 bats belonging to 11 species. In most species, auditory sensitivity was equally good at both high- and low-frequency ranges, while amplitude was more finely coded for higher frequency ranges. Additionally, we conducted a phylogenetic comparative analysis by combining our ABR data with published data on 27 species. Species-specific peaks in hearing sensitivity correlated with peak frequencies of echolocation calls and pup isolation calls, suggesting that changes in hearing sensitivity evolved in response to frequency changes of echolocation and social calls. Overall, our study provides the most comprehensive comparative assessment of bat hearing capacities to date and highlights the evolutionary pressures acting on their sensory perception.

Abstract

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 scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species, one generated in this study, encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune and metabolic genes. 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.

Abstract

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1,2,3,4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Abstract

Background

Heterozygous variants in CNTNAP2 have been implicated in a wide range of neurological phenotypes, including intellectual disability (ID), epilepsy, autistic spectrum disorder (ASD), and impaired language. However, heterozygous variants can also be found in unaffected individuals. Biallelic CNTNAP2 variants are rarer and cause a well-defined genetic syndrome known as CASPR2 deficiency disorder, a condition characterised by ID, early-onset refractory epilepsy, language impairment, and autistic features.
Case-report

A 7-year-old boy presented with hyperkinetic stereotyped movements that started during early infancy and persisted over childhood. Abnormal movements consisted of rhythmic and repetitive shaking of the four limbs, with evident stereotypic features. Additional clinical features included ID, attention deficit-hyperactivity disorder (ADHD), ASD, and speech impairment, consistent with CASPR2 deficiency disorder. Whole-genome array comparative genomic hybridization detected a maternally inherited 0.402 Mb duplication, which involved intron 1, exon 2, and intron 2 of CNTNAP2 (c.97 +?_209-?dup). The affected region in intron 1 contains a binding site for the transcription factor FOXP2, potentially leading to abnormal CNTNAP2 expression regulation. Sanger sequencing of the coding region of CNTNAP2 also identified a paternally-inherited missense variant c.2752C > T, p.(Leu918Phe).
Conclusion

This case expands the molecular and phenotypic spectrum of CASPR2 deficiency disorder, suggesting that Hyperkinetic stereotyped movements may be a rare, yet significant, clinical feature of this complex neurological disorder. Furthermore, the identification of an in-frame, largely non-coding duplication in CNTNAP2 points to a sophisticated underlying molecular mechanism, likely involving impaired FOXP2 binding.

Abstract

How learning affects vocalizations is a key question in the study of animal
communication and human language. Parallel efforts in birds and humans
have taught us much about how vocal learning works on a behavioural
and neurobiological level. Subsequent efforts have revealed a variety of
cases among mammals in which experience also has a major influence on
vocal repertoires. Janik and Slater (Anim. Behav. 60, 1–11. (doi:10.1006/
anbe.2000.1410)) introduced the distinction between vocal usage and pro-
duction learning, providing a general framework to categorize how
different types of learning influence vocalizations. This idea was built on
by Petkov and Jarvis (Front. Evol. Neurosci. 4, 12. (doi:10.3389/fnevo.2012.
00012)) to emphasize a more continuous distribution between limited and
more complex vocal production learners. Yet, with more studies providing
empirical data, the limits of the initial frameworks become apparent.
We build on these frameworks to refine the categorization of vocal learning
in light of advances made since their publication and widespread agreement
that vocal learning is not a binary trait. We propose a novel classification
system, based on the definitions by Janik and Slater, that deconstructs
vocal learning into key dimensions to aid in understanding the mechanisms
involved in this complex behaviour. We consider how vocalizations can
change without learning, and a usage learning framework that considers
context specificity and timing. We identify dimensions of vocal production
learning, including the copying of auditory models (convergence/
divergence on model sounds, accuracy of copying), the degree of change
(type and breadth of learning) and timing (when learning takes place, the
length of time it takes and how long it is retained). We consider grey
areas of classification and current mechanistic understanding of these beha-
viours. Our framework identifies research needs and will help to inform
neurobiological and evolutionary studies endeavouring to uncover the
multi-dimensional nature of vocal learning.
This article is part of the theme issue ‘Vocal learning in animals and
humans’.

Abstract

Exceptionally long-lived species, including many bats, rarely show overt signs of aging, making it difficult to determine why species differ in lifespan. Here, we use DNA methylation (DNAm) profiles from 712 known-age bats, representing 26 species, to identify epigenetic changes associated with age and longevity. We demonstrate that DNAm accurately predicts chronological age. Across species, longevity is negatively associated with the rate of DNAm change at age-associated sites. Furthermore, analysis of several bat genomes reveals that hypermethylated age- and longevity-associated sites are disproportionately located in promoter regions of key transcription factors (TF) and enriched for histone and chromatin features associated with transcriptional regulation. Predicted TF binding site motifs and enrichment analyses indicate that age-related methylation change is influenced by developmental processes, while longevity-related DNAm change is associated with innate immunity or tumorigenesis genes, suggesting that bat longevity results from augmented immune response and cancer suppression.

Abstract

Mutations of the FOXP2 gene cause a severe speech and language disorder, providing a molecular window into the neurobiology of language. Individuals with FOXP2 mutations have structural and functional alterations affecting brain circuits that overlap with sites of FOXP2 expression, including regions of the cortex, striatum, and cerebellum. FOXP2 displays complex patterns of expression in the brain, as well as in non-neuronal tissues, suggesting that sophisticated regulatory mechanisms control its spatio-temporal expression. However, to date, little is known about the regulation of FOXP2 or the genomic elements that control its expression. Using chromatin conformation capture (3C), we mapped the human FOXP2 locus to identify putative enhancer regions that engage in long-range interactions with the promoter of this gene. We demonstrate the ability of the identified enhancer regions to drive gene expression. We also show regulation of the FOXP2 promoter and enhancer regions by candidate regulators – FOXP family and TBR1 transcription factors. These data point to regulatory elements that may contribute to the temporal- or tissue-specific expression patterns of human FOXP2. Understanding the upstream regulatory pathways controlling FOXP2 expression will bring new insight into the molecular networks contributing to human language and related disorders.

Abstract

Intellectual disability (ID) is a severe neurodevelopmental disorder with genetically heterogeneous causes. Large-scale sequencing has led to the identification of many gene-disrupting mutations; however, a substantial proportion of cases lack a molecular diagnosis. As such, there remains much to uncover for a complete understanding of the genetic underpinnings of ID. Genetic variants present in non-coding regions of the genome have been highlighted as potential contributors to neurodevelopmental disorders given their role in regulating gene expression. Nevertheless the functional characterization of non-coding variants remains challenging. We describe the identification and characterization of de novo non-coding variation in 3′UTR regulatory regions within an ID cohort of 50 patients. This cohort was previously screened for structural and coding pathogenic variants via CNV, whole exome and whole genome analysis. We identified 44 high-confidence single nucleotide non-coding variants within the 3′UTR regions of these 50 genomes. Four of these variants were located within predicted miRNA binding sites and were thus hypothesised to have regulatory consequences. Functional testing showed that two of the variants interfered with miRNA-mediated regulation of their target genes, AMD1 and FAIM. Both these variants were found in the same individual and their functional consequences may point to a potential role for such variants in intellectual disability.

Abstract

Understanding the genetic factors underlying neurodevelopmental and neuropsychiatric disorders is a major challenge given their prevalence and potential severity for quality of life. While large-scale genomic screens have made major advances in this area, for many disorders the genetic underpinnings are complex and poorly understood. To date the field has focused predominantly on protein coding variation, but given the importance of tightly controlled gene expression for normal brain development and disorder, variation that affects non-coding regulatory regions of the genome is likely to play an important role in these phenotypes. Herein we show the importance of 3 prime untranslated region (3'UTR) non-coding regulatory variants across neurodevelopmental and neuropsychiatric disorders. We devised a pipeline for identifying and functionally validating putatively pathogenic variants from next generation sequencing (NGS) data. We applied this pipeline to a cohort of children with severe specific language impairment (SLI) and identified a functional, SLI-associated variant affecting gene regulation in cells and post-mortem human brain. This variant and the affected gene (ARHGEF39) represent new putative risk factors for SLI. Furthermore, we identified 3′UTR regulatory variants across autism, schizophrenia and bipolar disorder NGS cohorts demonstrating their impact on neurodevelopmental and neuropsychiatric disorders. Our findings show the importance of investigating non-coding regulatory variants when determining risk factors contributing to neurodevelopmental and neuropsychiatric disorders. In the future, integration of such regulatory variation with protein coding changes will be essential for uncovering the genetic causes of complex neurological disorders and the fundamental mechanisms underlying health and disease

Abstract

Sensory systems experience a trade-off between maximizing the
detail and amount of sampled information. Thistrade-off is particularly
pronounced in sensorysystemsthat are highlyspecialised fora single
task and thus experience limitations in other tasks. We hypothesised
that combining sensory input from multiple streams of information
may resolve this trade-off and improve detection and sensing
reliability. Specifically, we predicted that perceptive limitations
experienced by animals reliant on specialised active echolocation
can be compensated for by the phylogenetically older and less
specialised process of passive hearing. We tested this hypothesis in
greater horseshoe bats, which possess morphological and neural
specialisations allowing them to identify fluttering prey in dense
vegetation using echolocation only. At the same time, their
echolocation system is both spatially and temporally severely
limited. Here, we show that greater horseshoe bats employ passive
hearing to initially detect and localise prey-generated and other
environmental sounds, and then raise vocalisation level and
concentrate the scanning movements of their sonar beam on the
sound source for further investigation with echolocation. These
specialised echolocators thus supplement echo-acoustic information
with environmental acoustic cues, enlarging perceived space beyond
their biosonar range. Contrary to our predictions, we did not find
consistent preferences for prey-related acoustic stimuli, indicating the
use of passive acoustic cues also for detection of non-prey objects.
Our findings suggest that even specialised echolocators exploit a
wide range of environmental information, and that phylogenetically
older sensory systems can support the evolution of sensory
specialisations by compensating for their limitations.

Abstract

Although humans are unmatched in their capacity to produce
speech and learn language, comparative approaches in diverse
animalmodelsareabletoshedlightonthebiologicalunderpinnings
of language-relevant traits. In the study of vocal learning, a trait
crucial for spoken language, passerine birds have been the
dominant models, driving invaluable progress in understanding the
neurobiology and genetics of vocal learning despite being only
distantly related to humans. To date, there is sparse evidence that
our closest relatives, nonhuman primates have the capability to
learn new vocalisations. However, a number of other mammals
have shown the capacity for vocal learning, such as some
cetaceans, pinnipeds, elephants, and bats, and we anticipate that
with further study more species will gain membership to this
(currently) select club. A broad, cross-species comparison of vocal
learning, coupled with careful consideration of the components
underlying this trait, is crucial to determine how human speech and
spoken language is biologically encoded and how it evolved. We
emphasise the need to draw on the pool of promising species that
havethusfarbeenunderstudiedorneglected.Thisisbynomeansa
call for fewer studies in songbirds, or an unfocused treasure-hunt,
but rather an appeal for structured comparisons across a range of
species, considering phylogenetic relationships, ecological and
morphological constrains, developmental and social factors, and
neurogenetic underpinnings. Herein, we promote a comparative
approachhighlightingtheimportanceofstudyingvocallearningina
broad range of model species, and describe a common framework
for targeted cross-taxon studies to shed light on the biology and
evolution of vocal learning.

Abstract

Bats are gregarious, highly vocal animals that possess a broad repertoire of social vocalisations. For in-depth studies of their vocal behaviours, including vocal flexibility and vocal learning, it is necessary to gather repeatable evidence from controlled laboratory experiments on isolated individuals. However, such studies are rare for one simple reason: eliciting social calls in isolation and under operant control is challenging and has rarely been achieved. To overcome this limitation, we designed an automated setup that allows conditioning of social vocalisations in a new context, and tracks spectro-temporal changes in the recorded calls over time. Using this setup, we were able to reliably evoke social calls from temporarily isolated lesser spear-nosed bats (Phyllostomus discolor). When we adjusted the call criteria that could result in food reward, bats responded by adjusting temporal and spectral call parameters. This was achieved without the help of an auditory template or social context to direct the bats. Our results demonstrate vocal flexibility and vocal usage learning in bats. Our setup provides a new paradigm that allows the controlled study of the production and learning of social vocalisations in isolated bats, overcoming limitations that have, until now, prevented in-depth studies of these behaviours.

Abstract

Language, humans’ most distinctive trait, still remains a ‘mystery’ for evolutionary theory. It is underpinned by a universal infrastructure—cooperative turn-taking—which has been suggested as an ancient mechanism bridging the existing gap between the articulate human species and their inarticulate primate cousins. However, we know remarkably little about turn-taking systems of non-human animals, and methodological confounds have often prevented meaningful cross-species comparisons. Thus, the extent to which cooperative turn-taking is uniquely human or represents a homologous and/or analogous trait is currently unknown. The present paper draws attention to this promising research avenue by providing an overview of the state of the art of turn-taking in four animal taxa—birds, mammals, insects and anurans. It concludes with a new comparative framework to spur more research into this research domain and to test which elements of the human turn-taking system are shared across species and taxa.

Abstract

Genes including FOXP2, FOXP1 and CNTNAP2, have been implicated in human speech and language phenotypes, pointing to a role in the development of normal language-related circuitry in the brain. Although speech and language are unique human phenotypes, a comparative approach is possible by addressing language-relevant traits in animal model systems. One such trait, vocal learning, represents an essential component of human spoken language, and is shared by cetaceans, pinnipeds, elephants, some birds and bats. Given their vocal learning abilities, gregarious nature, and reliance on vocalisations for social communication and navigation, bats represent an intriguing mammalian system in which to explore language-relevant genes. We used immunohistochemistry to detail the distribution of FoxP2, FoxP1 and Cntnap2 proteins, accompanied by detailed cytoarchitectural histology in the brains of two vocal learning bat species; Phyllostomus discolor and Rousettus aegyptiacus. We show widespread expression of these genes, similar to what has been previously observed in other species, including humans. A striking difference was observed in the adult Phyllostomus discolor bat, which showed low levels of FoxP2 expression in the cortex, contrasting with patterns found in rodents and non-human primates. We created an online, open-access database within which all data can be browsed, searched, and high resolution images viewed to single cell resolution. The data presented herein reveal regions of interest in the bat brain and provide new opportunities to address the role of these language-related genes in complex vocal-motor and vocal learning behaviours in a mammalian model system.

Abstract

Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>132 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.

Abstract

Heterozygous mutations of the Forkhead-box protein 2 (FOXP2) gene in humans cause childhood apraxia of speech. Loss of Foxp2 in mice is known to affect striatal development and impair motor skills. However, it is unknown if striatal excitatory/inhibitory balance is affected during development and if the imbalance persists into adulthood. We investigated the effect of reduced Foxp2 expression, via a loss-of-function mutation, on striatal medium spiny neurons (MSNs). Our data show that heterozygous loss of Foxp2 decreases excitatory (AMPA receptor-mediated) and increases inhibitory (GABA receptor-mediated) currents in D1 dopamine receptor positive MSNs of juvenile and adult mice. Furthermore, reduced Foxp2 expression increases GAD67 expression, leading to both increased presynaptic content and release of GABA. Finally, pharmacological blockade of inhibitory activity in vivo partially rescues motor skill learning deficits in heterozygous Foxp2 mice. Our results suggest a novel role for Foxp2 in the regulation of striatal direct pathway activity through managing inhibitory drive.

Abstract

Neurodevelopmental disorders have a strong genetic component, but despite widespread efforts, the specific genetic factors underlying these disorders remain undefined for a large proportion of affected individuals. Given the accessibility of exome-sequencing, this problem has thus far been addressed from a protein-centric standpoint; however, protein-coding regions only make up ∼1-2% of the human genome. With the advent of whole-genome sequencing we are in the midst of a paradigm shift as it is now possible to interrogate the entire sequence of the human genome (coding and non-coding) to fill in the missing heritability of complex disorders. These new technologies bring new challenges, as the number of non-coding variants identified per individual can be overwhelming, making it prudent to focus on non-coding regions of known function, for which the effects of variation can be predicted and directly tested to assess pathogenicity. The 3’UTRome is a region of the non-coding genome that perfectly fulfils these criteria and is of high interest when searching for pathogenic variation related to complex neurodevelopmental disorders. Herein, we review the regulatory roles of the 3’UTRome as binding sites for microRNAs, RNA binding proteins or during alternative polyadenylation. We detail existing evidence that these regions contribute to neurodevelopmental disorders and outline strategies for identification and validation of novel putatively pathogenic variation in these regions. This evidence suggests that studying the 3’UTRome will lead to the identification of new risk factors, new candidate disease genes and a better understanding of the molecular mechanisms contributing to NDDs.