Biology subjects

Balakrishnan, C.

Publications and source records attributed to Balakrishnan, C..

5 recordsLinked to original sources

bioRxiv2025

Inbreeding depression and tuberculosis susceptibility in the critically endangered white-winged wood duck Asarcornis scutulata

Captive breeding can be a key component of species conservation strategies, but also exposes these rare species to novel environments including the pathogen landscape. The critically endangered white-winged wood duck (WWWD) Asarcornis scutulata has experienced substantial population declines, local extirpations and fragmentation of its former range in South-East Asia, making it one of the rarest birds in the world. Like other rare species, WWWD declines have led to the initiation of captive breeding programs, but these have been hampered by the WWWDs high susceptibility to Mycobacterium avium, avian tuberculosis (TB). In this study we describe genome-wide patterns of diversity to understand the WWWDs demographic and phylogeographic history, inbreeding in the wild and in captivity, and the causes of TB susceptibility. Captive birds, which originated from northeast India, are genetically differentiated from wild birds sampled in Sumatra, Indonesia, likely reflecting long-standing phylogeographic structure. Demographic analyses revealed that long-term (Pleistocene) population declines preceded anthropogenic declines, a pattern shared with other codistributed, forest-dependent species. All sampled WWWD populations had extremely low genetic diversity but wild-sampled birds retained higher Major Histocompatibility Complex (MHC) diversity, reflecting important functional diversity in the wild. Genetic diversity has eroded over time in captivity and importantly, birds with higher levels of inbreeding succumb earlier to TB infections, suggesting inbreeding depression. Finally, by comparing gene expression between susceptible WWWD and resistant redhead ducks Aythya americana we identify possible mechanisms of TB susceptibility in WWWD. Altogether our study provides genomically-guided objectives for future management and a cautionary tale for ex-situ conservation.

evolutionary biology↗

bioRxiv2020

Towards complete and error-free genome assemblies of all vertebrate species

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species1-4. 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 the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). 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 error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.

genomics↗

bioRxiv2019

Shared transcriptional responses to con- and heterospecific behavioral antagonists in a wild songbird

The recognition of and differential responses to salient stimuli are among the main drivers of behavioral plasticity, yet, how animals evolve and modulate functional responses to novel classes of antagonistic stimuli remain poorly understood. We studied free-living male red-winged blackbirds (Agelaius phoeniceus) to test whether gene expression responses in blood are distinct or shared between patterns of aggressive behavioral responses directed at simulated conspecific versus heterospecific intruders. In this species, males defend territories against conspecific males and respond aggressively to female brown-headed cowbirds (Molothrus ater), a brood parasite that commonly lays eggs in blackbird nests. Both conspecific songs and parasitic calls elicited aggressive responses from focal subjects and caused a downregulation in genes associated with immune system response, relative to control calls of a second, harmless heterospecific species. In turn, only the conspecific song treatment elicited an increase in singing behavior and an upregulation of genes associated with metabolic processes relative to the two heterospecific calls. Our results suggest that aspects of antagonistic responses to both conspecifics and brood parasites can be based on similar physiological responses, suggestive of shared molecular and behavioral pathways involved in the recognition and reaction to both evolutionarily old and new enemies.

animal behavior and cognition↗

bioRxiv2018

Parent and offspring genotypes influence gene expression in early life

Parents can have profound effects on offspring fitness. Little, however, is known about the mechanisms through which parental care variation influences offspring physiology in natural systems. White-throated sparrows Zonotrichia albicollis (WTSPs) exist in two genetic morphs, tan and white, controlled by a large polymorphic supergene. Morphs mate disassortatively, resulting in two pair types: tan male x white female (TxW) pairs, which provide biparental care and white male x tan female (WxT) pairs, which provide female-biased care. To investigate the effects of parental care variation, we performed RNA-seq on WTSP nestlings sampled from nests of both pair types. Pair type had the largest effect on nestling gene expression, with 881 genes differentially expressed (DE) and seven correlated gene co-expression modules. The DE genes and modules up-regulated in nests with female-biased parental care primarily function in metabolism and stress-related pathways resulting from the overrepresentation of stress response and proteolysis genes. These results show that parental genotypes, a proxy for parental care in this system, alter nestling physiology and highlight avenues of further research investigating the ultimate implications of alternative parental care strategies. Nestlings also exhibited morph-specific gene expression, driven by innate immunity genes and co-expression of genes located in the supergene. Remarkably, we identified the same regulatory hub genes in these blood-derived expression networks as were previously identified in WTSP brains (EPM2A, BPNT1, TAF5L). These hub genes were located within the supergene, highlighting the importance of this gene complex in structuring regulatory networks across diverse tissues.

genomics↗

bioRxiv2018

Losing maternal care: Neotenic gene expression in the preoptic area of avian brood parasites

Parental care for is critical for offspring survival in many species. However, parental behaviors have been lost in roughly 1% of avian species known as the obligate brood parasites. To shed light on molecular and neurobiological mechanisms mediating brood parasitic behavior, brain gene expression patterns between two brood parasitic species and one closely related non-parasitic Icterid (blackbird) species were compared. Our analyses focused on gene expression changes specifically in the preoptic area (POA), a brain region known to play a critical role in maternal behavior across vertebrates. Using comparative transcriptomic approaches, we identified gene expression patterns associated with brood parasitism and evaluated two alternative explanations for the evolution of brood parasitism: reduced expression of parental-related genes in the POA versus retention of juvenile (neotenic) gene expression. While we did not find evidence for large scale gene downregulation, expression patterns did reflect substantial evidence for neotenic POA gene expression in parasitic birds. Differentially expressed genes with previously established roles in parental care were identified. Targeted examination of these selected candidate genes in additional hypothalamic regions revealed species differences in gene expression patterns is not POA-specific. Together, these results provide new insights into neurogenomics underlying maternal behavior loss in avian brood parasites.

animal behavior and cognition↗