Biology subjects

Gahr, M.

Publications and source records attributed to Gahr, M..

14 recordsLinked to original sources

bioRxiv2025

Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species

Bird genomes are among the most stable in terms of synteny and gene content across vertebrates. However, germline-restricted chromosomes (GRCs) represent a striking exception where programmed DNA elimination confines large-scale genomic changes to the germline. GRCs are known to occur in songbirds (oscines), but have been studied only in a few species of Passerides such as the zebra finch, the key model for passerine genomics. Their presence and evolutionary dynamics in most major passerine lineages remain largely unexplored, with suboscines entirely unexamined by cytogenetic or genomic methods. Here, we present the most comprehensive comparative analysis of GRCs to date, spanning 44 million years of passerine evolution. By generating the first germline reference genomes of an oscine and a suboscine, 22 novel germline draft genomes spanning nearly all major passerine lineages and a germline draft genome of a parrot outgroup, we show that the GRC is likely present in 6,700 passerine species. Our results reveal that the GRC evolves rapidly and distinctly from the standard A chromosomes (autosomes and sex chromosomes), yet retains functionally important, selectively maintained genes. We observed gene and repeat turnover occuring orders of magnitude faster than on the A chromosomes. Some GRC genes, such as cpeb1 and pim1, are widespread from an ancient duplication. In contrast, other GRC genes, like mfsd2b and bmp15, have been independently duplicated onto the GRC multiple times, suggesting adaptive constraints. The discovery of zglp1 on the zebra finch GRC, initially copied from chromosome 30 and subsequently lost from it, indicates functional replacement, where the GRC permits gene loss from the standard genome. As the GRC harbors the only zglp1 copy in most of the [~]4000 Passerides species, GRC loss would compromise essential germline functions. Our findings establish the GRC as a genomic innovator driving rapid germline evolution. This fact highlights its evolutionary significance for passerine diversification and suggests that programmed DNA elimination may be an overlooked yet phylogenetically widespread mechanism in many understudied animal lineages.

genomics↗

bioRxiv2024

Evolution of vocal production learning in parrots

Vocal production learning (VPL), the capacity to imitate sounds, is a crucial, but not exclusive component of human language. VPL is rare in animals but common in birds, where it evolved independently in songbirds, hummingbirds, and parrots. Parrots (Psittaciformes) learn new vocalizations throughout their lives and exhibit astonishing vocal flexibility and imitation capacity. They can copy allospecific sounds, e.g., human words and learn their associated meanings. Parrots, therefore, present an intriguing model to shed light on how VPL evolved and how it may relate to other language-relevant traits. How widely VPL is distributed across Psittaciformes and to what extent (qualitative) species differences exist, remains unknown. Here, we provide the first comprehensive overview of the phylogenetic distribution of (allospecific) VPL in this clade by conducting surveys of publicly available video footage. Out of the 398 currently recognized extant species, we found videos for 163, of which 136 showed evidence of VPL. Phylogenetic analyses suggest secondary losses and reacquisitions of VPL covarying with socioecological parameters (gregariousness), life-history (longevity), and morphological (body size) traits. This study provides the first insights into interspecific variation in vocal learning across all parrot species and reveals potential socio-ecological drivers of its evolution. SignificanceLittle is known about the selective forces that favor the evolution of vocal production learning (VPL), a rare trait in animals and a prerequisite for the evolution of human language. We provide the first insights into interspecific variation in VPL in the evolutionary history of parrots and uncover candidate evolutionary drivers. The current data suggest that the evolution of VPL within parrots has been highly dynamic, with multiple secondary losses and reacquisitions. Our model showed that VPL most likely was the ancestral state. Sociality, longevity and body size explain variation in VPL together with a highly uncertain effect of brain size. The findings may motivate comparative work in other taxa and contribute to research into the evolutionary origins of human language.

evolutionary biology↗

bioRxiv2024

Convergent and lineage-specific genomic changes contribute to adaptations in sugar-consuming birds

High-sugar diets cause human metabolic diseases, yet several bird lineages convergently adapted to feeding on sugar-rich nectar or fruits. We investigated the underlying molecular mechanisms in hummingbirds, parrots, honeyeaters, and sunbirds by generating nine new genomes and 90 tissue-specific transcriptomes. Comparative screens revealed an excess of repeated selection in both protein-coding and regulatory sequences in sugar-feeding birds, suggesting reuse of genetic elements. Sequence or expression changes in sugar-feeders affect genes involved in blood pressure regulation, lipid, amino acid and carbohydrate metabolism, with experiments showing functional changes in honeyeater hexokinase 3. MLXIPL, a key regulator of sugar and lipid homeostasis, showed convergent sequence and regulatory changes across all sugar-feeding clades; experiments revealed enhanced sugar-induced transcriptional activity of hummingbird MLXIPL, highlighting its adaptive role in high-sugar diets. Summary Figure: Our comparative screens across four independent sugar-feeding bird groups identified both repeated and lineage-specific targets of selection O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=65 SRC="FIGDIR/small/610474v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@148f5c8org.highwire.dtl.DTLVardef@1005dbaorg.highwire.dtl.DTLVardef@1097facorg.highwire.dtl.DTLVardef@9d365c_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2022

Extensive, transient, and long-lasting gene regulation in a song-controlling brain area during testosterone-induced song development in adult female canaries

Seasonal song production in canaries, influenced by gonadal hormones, is a well-documented phenomenon. We explored testosterone-induced song development in adult female canaries--a behavior rarely exhibited naturally. Gene regulatory networks in the song-controlling brain area HVC were compared at multiple time points (1 hour to 14 days) post-treatment with those of placebo-treated controls, paralleling HVC and song development. Females began vocalizing within four days of testosterone treatment, with song complexity and HVC volume increasing progressively over two weeks. Rapid transcriptional changes involving 2,739 genes preceded song initiation. Over two weeks, 9,913 genes--approximately 64% of the canarys protein-coding genome--were differentially expressed, with 98% being transiently regulated. These genes are linked to various biological functions, with early changes at the cellular level and later changes affecting the nervous system level after prolonged hormone exposure. Our findings suggest that testosterone-induced song development is accompanied by extensive and dynamic transcriptional changes in the HVC, implicating widespread neuronal involvement. The data reveal extensive transcriptomic changes, including alterations in steroid receptor expression and numerous transcription factors, coinciding with significant neural transformations. These changes underpin the gradual emergence of singing behavior, providing insights into the neural basis of seasonal behavioral patterns.

molecular biology↗

bioRxiv2022

The hidden structural variability in avian genomes

Structural variants (SVs) are DNA mutations that can have relevant effects at micro- and macro-evolutionary scales. The detection of SVs is largely limited by the type and quality of sequencing technologies adopted, therefore genetic variability linked to SVs may remain undiscovered, especially in complex repetitive genomic regions. In this study, we used a combination of long-read and linked-read genome assemblies to investigate the occurrence of insertions and deletions across the chromosomes of 14 species of birds-of-paradise and two species of estrildid finches including highly repetitive W chromosomes. The species sampling encompasses most genera and representatives from all major clades of birds-of-paradise, allowing comparisons between individuals of the same species, genus, and family. We found the highest densities of SVs to be located on the microchromosomes and on the female-specific W chromosome. Genome assemblies of multiple individuals from the same species allowed us to compare the levels of genetic variability linked to SVs and single nucleotide polymorphisms (SNPs) on the W and other chromosomes. Our results demonstrate that the avian W chromosome harbours more genetic variability than previously thought and that its structure is shaped by the continuous accumulation and turnover of transposable element insertions, especially endogenous retroviruses.

evolutionary biology↗

bioRxiv2021

The gene expression profile of the song control nucleus HVC shows sex specificity, hormone responsiveness, and species specificity among songbirds

Singing occurs in songbirds of both sexes, but some species show typical degrees of sex-specific performance. We studied the transcriptional sex differences in the HVC, a brain nucleus critical for song pattern generation, of the forest weaver (Ploceus bicolor), the blue-capped cordon-bleu (Uraeginthus cyanocephalus), and the canary (Serinus canaria), which are species that show low, medium, and high levels of sex-specific singing, respectively. We observed persistent sex differences in gene expression levels regardless of the species-specific sexual singing phenotypes. We further studied the HVC transcriptomes of defined phenotypes of canary, known for its testosterone-sensitive seasonal singing. By studying both sexes of canaries during both breeding and nonbreeding seasons, nonbreeding canaries treated with testosterone, and spontaneously singing females, we found that the circulating androgen levels and sex were the predominant variables associated with the variations in the HVC transcriptomes. The comparison of natural singing with testosterone-induced singing in canaries of the same sex revealed considerable differences in the HVC transcriptomes. Strong transcriptional changes in the HVC were detected during the transition from nonsinging to singing in canaries of both sexes. Although the sex-specific genes of singing females shared little resemblance with those of males, our analysis showed potential functional convergences. Thus, male and female songbirds achieve comparable singing behaviours with sex-specific transcriptomes.

molecular biology↗

bioRxiv2020

Functional differences in the hypothalamic-pituitary-gonadal axis are associated with alternative reproductive tactics based on an inversion polymorphism

The evolution of social behavior depends on genetic changes, yet, how genomic variation manifests itself in behavioral diversity is still largely unresolved. Chromosomal inversions can play a pivotal role in producing distinct behavioral phenotypes, in particular, when inversion genes are functionally associated with hormone synthesis and signaling. Male Ruffs exhibit alternative reproductive tactics (ARTs) with an autosomal inversion determining two alternative morphs with clear behavioral and hormonal differences to the ancestral morph. We investigated hormonal and transcriptomic differences in the pituitary and gonads. Using a GnRH challenge, we found that the ability to synthesize testosterone in inversion carriers is severely constrained, whereas the synthesis of androstenedione, a testosterone precursor, is not. Inversion morphs were able to produce a transient increase in androstenedione following the GnRH injection, supporting the view that pituitary sensitivity to GnRH is comparable to that of the ancestral morph. We then performed gene expression analyses in a second set of untreated birds and found no evidence of alterations to pituitary sensitivity, gonadotropin production or gonad sensitivity to luteinizing hormone or follicle-stimulating hormone across morphs. Inversion morphs also showed reduced progesterone receptor expression in the pituitary. Strikingly, in the gonads, inversion morphs over-expressed STAR, a gene that is located outside of the inversion and responsible for providing the cholesterol substrate required for the synthesis of sex hormones. In conclusion, our results suggest that the gonads determine morph-specific differences in hormonal regulation.

physiology↗

bioRxiv2020

Singing-related reorganization of the song motor circuit is accompanied by a shift in hormonal modulation of song

Sex hormones are essential modulators of birdsong. Testosterone, and its active androgenic and estrogenic metabolites, 5-dihydrotestosterone (DHT) and estradiol, can re-shape the brain circuits responsible for song learning and production. The differential mechanisms of action of these different hormones during song development and song maintenance are, nonetheless, not fully understood. Here we demonstrate that unlike testosterone, DHT treatment does not induce singing behavior in naive adult female canaries that have never previously produced song. However, in birds with previous testosterone-induced singing experience, DHT alone is enough to promote the re-acquisition of high quality songs, even after months of silence. In addition, we show that the synaptic reorganization that accompanies vocal motor skill development requires more than DHT-induced androgen receptor activation. These results indicate that vocal motor practice will persistently modify the hormone-sensitive brain circuit responsible for song production, suggesting a mechanistic differentiation in the hormone-dependent regulation of the initial vocal motor skill acquisition and later re-acquisition.

neuroscience↗

bioRxiv2020

Causal Understanding of the Stone Dropping Task in Two Species of Macaw

Causal understanding in animal cognition can be divided into two broad categories (Woodward, 2011): learned associations between cause and effect (Le Pelley et al., 2017) and understanding based on underlying mechanisms (Johnson and Ahn, 2017). One experiment that gives insight to animals use of causal mechanisms is the stone-dropping task. In this, subjects are given an opportunity to push a platform to make it collapse and are then required to innovate dropping a stone tool to recreate the platform collapsing (von Bayern et al., 2009). We describe how 16/18 subjects of two species of macaw (n=18; Ara ambiguus (n=9) & Ara glaucogularis (n=9)) were able to innovate the solution in this task. Many of the subjects were able to innovate the behaviour through exploratory object combination, but it is also possible that a mechanistic understanding of the necessity for contact with the platform influenced some subjects behaviour. All the successful subjects were able to recreate their novel stone-dropping behaviour in the first or second trial after innovation (and all trials thereafter) and they were also able to do the behaviour increasingly faster. This suggests they also rely on learned associations of cause and effect. However, in a transfer task in which subjects had to guide a stick tool to make it touch a differently positioned platform, all but one of the subjects failed. This would suggest that the majority of the subjects were not using an understanding of platform contact to solve the task, although the subjects difficulty with using stick tools may have also affected their performance in this transfer.

animal behavior and cognition↗

bioRxiv2020

Highly efficient genome modification of cultured primordial germ cells with lentiviral vectors to generate transgenic songbirds

SUMARYThe ability to genetically manipulate organisms has led to significant insights in functional genomics in many species. In birds, manipulation of the genome is hindered by the inaccessibility of the one-cell embryo. During embryonic development, avian primordial germ cells (PGCs) migrate through the blood stream and reach the gonadal anlage; where they develop into mature germ cells. Here, we explored the use of PGCs to produce transgenic offspring in the zebra finch, which is a major animal model for sexual brain differentiation, vocal learning and vocal communication. Zebra finch PGCs (zfPGCs) obtained from embryonic blood significantly proliferated when cultured in an optimized culture medium and conserved the expression of germ and stem cell markers. Transduction of cultured zfPGCs with lentiviral vectors was highly efficient leading to strong expression of the enhanced green fluorescent protein (eGFP). Transduced zfPGCs were injected into the host embryo and transgenic songbirds were successfully generated.

neuroscience↗

bioRxiv2020

Fast retrograde access to projection neuron circuits underlying vocal learning in songbirds

Understanding the structure and function of neural circuits underlying speech and language is a vital step towards better treatments for diseases of these systems. Songbirds, among the few animal orders that share with humans the ability to learn vocalizations from a conspecific, have provided many insights into the neural mechanisms of vocal development. However, research into vocal learning circuits has been hindered by a lack of tools for rapid genetic targeting of specific neuron populations to meet the quick pace of developmental learning. Here, we present a new viral tool that enables fast and efficient retrograde access to projection neuron populations. In zebra finches, Bengalese finches, canaries, and mice, we demonstrate fast retrograde labeling of cortical or dopaminergic neurons. We further demonstrate the suitability of our construct for detailed morphological analysis, for in vivo imaging of calcium activity, and for multicolor brainbow labeling.

neuroscience↗

bioRxiv2020

Morphological facilitators for vocal learning explored through the syrinx anatomy of a basal hummingbird

Vocal learning is a rare evolutionary trait that evolved independently in three avian clades: songbirds, parrots, and hummingbirds. Although the anatomy and mechanisms of sound production in songbirds are well understood, little is known about the hummingbirds vocal anatomy. We use high-resolution micro-computed tomography (CT) and microdissection to reveal the three-dimensional structure of the syrinx, the vocal organ of the black jacobin (Florisuga fusca), a phylogenetically basal hummingbird species. We identify three unique features of the black jacobins syrinx: (i) a shift in the position of the syrinx to the outside of the thoracic cavity and the related loss of the sterno-tracheal muscle, (ii) complex intrinsic musculature, oriented dorso-ventrally, and (iii) ossicles embedded in the medial vibratory membranes. Their syrinx morphology allows vibratory decoupling, precise control of complex acoustic parameters, and a large redundant acoustic space that may be key biomechanical factors facilitating the occurrence of vocal production learning.

evolutionary biology↗

bioRxiv2019

Collective singing dynamics in a competition context drive song plasticity

Singing by songbirds is a complex motor skill learnt during juvenile development or, in open-ended learners, before the onset of the breeding season. Outside of these specific periods, it is believed that birdsong does not change. Challenging this, here we demonstrate that in a seasonal songbird, social interactions during the breeding season induce a novel form of singing plasticity in naturalistic social environments. Using custom-made telemetric backpack technology to monitor song-based communication from freely-behaving canaries, we show that males temporally overlap their songs during aggressive duels. Singing duels induce an unexpected fast plasticity in song length, thereby enhancing singing performance and flexibility of a sexually-selected behavior. Remarkably, dueling canaries sing acoustically-similar songs, suggesting that competition within a specific song acoustic space drives dueling behavior. Overall, our findings reveal a previously unrecognized type of song plasticity different from the well-studied slow song plasticity as an imitation process for display purposes.

animal behavior and cognition↗

bioRxiv2018

Vocal motor experiences consolidate the vocal motor circuitry and accelerate future vocal skill development

Complex motor skills take considerable time and practice to learn. Without continued practice the level of skill performance quickly degrades, posing a problem for the timely utilization of skilled motor responses. Here we quantified the recurring development of vocal motor skills and the accompanying changes in synaptic connectivity in the brain of a songbird, while manipulating skill performance by consecutively administrating and withdrawing testosterone. We demonstrate that a songbird with prior singing experience can significantly accelerate the re-acquisition of vocal performance. We further demonstrate that an increase in vocal performance is accompanied by a pronounced synaptic pruning in the forebrain vocal motor area HVC, a reduction that is not reversed when birds stop singing. These results provide evidence that lasting synaptic changes in the motor circuitry are associated with the savings of motor skills, enabling a rapid recovery of motor performance under environmental time constraints.

animal behavior and cognition↗