Biology subjects

Balakrishnan, C. N.

Publications and source records attributed to Balakrishnan, C. N..

7 recordsLinked to original sources

bioRxiv2025

Evolutionary diversity and function of odorant receptors in birds

Abstract: Odorant receptors (ORs) form among the largest gene families in vertebrates; most mammals have hundreds of intact OR genes. Although birds display diverse behavior and ecology, they were long thought to rely minimally on olfaction. We reexamine this idea by using genomic data to uncover diverse and variable OR repertoires in birds, including the nocturnal kiwi (Apteryx mantelli), which possesses the largest number of ORs known (3,750). We reveal that widespread gene conversion is shaping the evolution of bird ORs, reflecting a novel mechanism for generating functional diversity. We show that ORs are expressed in avian olfactory sensory neurons and show responses to defined, ecologically relevant odorants. Our results demonstrate the importance and functional mechanisms underlying olfaction in birds.

evolutionary biology↗

bioRxiv2025

Genomic resources for comparative analyses of obligate avian brood parasitism

Examples of convergent evolution, wherein distantly related organisms evolve similar traits, including behaviors, underscore the adaptive power of natural selection. In birds, obligate brood parasitism, and the associated loss of parental care behaviors, has evolved independently in seven different lineages, though little is known about the genetic basis of the complex suite of traits associated with this rare life history strategy. We generated genome assemblies for ten brood parasitic species plus eight species representatives of their parental/nesting outgroups. This includes nine long-read chromosome-level assemblies, with scaffold N50 sizes ranging from 38.1 to 72.6 MB, and gene representation completeness measures >97%. Leveraging this new catalog of avian genomes, we constructed clade-level alignments that reveal variation in chromosomal synteny, provide first-time or improved annotations of protein-coding and non-coding genes, and define cross-species ortholog reference sets. We also refine estimates for the timing of the seven independent origins of brood parasitism, ranging from recent events such as 1.6 to 4.5 million years ago in Molothrus cowbirds to much earlier origins over 30 million years ago in two of the three cuckoo lineages. These genomic resources lay the foundation for investigating the genetic and genomic underpinnings of brood parasitism, including the loss of parental care, shifts in mating systems, perhaps resulting in heightened sperm competition, elevated annual fecundity, improved spatial cognition related to nest-finding, and the diverse adaptations shaped by intense coevolution with host species.

genomics↗

bioRxiv2025

Comparative population genomics reveals convergent adaptation across independent origins of avian obligate brood parasitism

Parental care evolved as a strategy to enhance offspring survival at the cost of reduced fecundity. While most birds provide parental care, obligate brood parasites circumvent this tradeoff by exploiting the parental behavior of other species. This radical life history shift has occurred independently seven times in birds, offering an outstanding opportunity to test for convergent patterns of adaptation in the genome. To investigate genomic adaptations underlying this transition, we analyzed population resequencing data from five brood-parasitic species across three independent origins of brood parasitism -- three parasitic finches (family Viduidae), a honeyguide, and a cowbird -- alongside related non-parasitic (parental) outgroups. Using the McDonald-Kreitman framework, we found evidence for repeated adaptation in genes involved in spermatogenesis and sperm function in multiple parasitic clades, but not in the matched outgroup parental species. This is consistent with evidence for increased male-male competition in parasitic lineages as a result of the loss of parental care. In addition, we detected selective sweeps near genes associated with nervous system development in parasitic lineages, perhaps associated with improved spatial cognition that aids brood parasites in locating, monitoring, and laying eggs in host nests. Finally, we found more selective sweeps in host-specific brood parasites as compared to parental outgroups, perhaps reflecting ongoing host-parasite coevolutionary arms races.

evolutionary biology↗

bioRxiv2022

Neurogenomic landscape of social status-dependent cooperative display behavior

The neurogenomic mechanisms mediating male-male reproductive cooperative behaviors are unknown. We leveraged extensive transcriptomic and behavioral data on a neotropical bird (Pipra filicauda) that perform cooperative courtship displays to understand these mechanisms. Cooperative display is modulated by testosterone, it promotes cooperation in non-territorial birds, but suppresses cooperation in territory holders. We sought to understand the neurogenomic underpinnings of these three related traits: social status, cooperative behavior, and testosterone phenotype. To do this, we profiled gene expression in 10 brain nuclei spanning the social decision-making network (SDMN), and two key endocrine tissues that regulate social behavior. We associated gene expression with each birds behavioral and endocrine profile derived from three years of repeated measures taken from free-living birds in the Ecuadorian Amazon. We found distinct landscapes of constitutive gene expression were associated with social status, testosterone phenotype, and cooperation, reflecting the modular organization and engagement of neuroendocrine tissues. Sex-steroid and neuropeptide signaling appeared to be important in mediating status-specific relationships between testosterone and cooperation, suggesting shared regulatory mechanisms with male aggressive and sexual behaviors. We also identified differentially regulated genes involved in cellular activity and synaptic potentiation, suggesting multiple mechanisms underpin these genomic states. Finally, we identified SDMN-wide gene expression differences between territorial and floater males that could form the basis of "status-specific" neurophysiological phenotypes, potentially mediated by testosterone and growth hormone. Overall, our findings provide new, systems-level insights into the mechanisms of cooperative behavior and suggest that differences in neurogenomic state are the basis for individual differences in social behavior.

evolutionary biology↗

bioRxiv2018

Co-regulation of hormone receptors, neuropeptides, and steroidogenic enzymes across the vertebrate social behavior network

The vertebrate basal forebrain and midbrain contain a set of interconnected nuclei that control social behavior. Conserved anatomical structures and functions of these nuclei have now been documented among fish, amphibians, reptiles, birds and mammals, and these brain regions have come to be known as the vertebrate social behavior network (SBN). While it is known that nuclei (nodes) of the SBN are rich in steroid and neuropeptide activity linked to behavior, simultaneous variation in the expression of neuroendocrine genes among several SBN nuclei has not yet been described in detail. In this study, we use RNA-seq to profile gene expression across seven brain regions representing five nodes of the vertebrate SBN in a passerine bird, the wire-tailed manakin Pipra filicauda. Using weighted gene co-expression network analysis (WGCNA), we reconstructed sets of coregulated genes, revealing striking patterns of variation in neuroendocrine gene expression across the SBN. We describe regional expression variation networks comprising a broad set of hormone receptors, neuropeptides, steroidogenic enzymes, catecholamines, and other neuroendocrine signaling molecules. Our findings highlight how heterogeneity of brain gene expression across the SBN can provide functional insights into the neuroendocrine and genetic mechanisms that underlie vertebrate social behavior.

neuroscience↗

bioRxiv2018

The variability of song variability in wild and domesticated zebra finches Taeniopygia guttata

Birdsong is a classic example of a learned social behavior. Like many traits of interest, however, song production is also influenced by genetic factors and understanding the relative contributions of genetic and environmental influences remains a major research goal. In this study we take advantage of genetic variation among captive zebra finch populations to examine variation in a population-level song trait: song variability. We find that zebra finch populations differ in levels of song variability. Domesticated T. g. castanotis populations displayed higher song diversity than more recently wild-derived populations of both zebra finch subspecies T. g. castanotis and T. g. guttata, the Timor zebra finch. To determine whether these differences could have a genetic basis, we cross-fostered domesticated T. g. castanotis and Timor zebra finches to Bengalese finches Lonchura striata domestica. Following cross-fostering, domesticated T. g. castanotis maintained a higher level of song diversity than T. g. guttata. We suggest that the high song variability of domesticated zebra finches may be a consequence of reduced purifying selection acting on song traits. Intraspecific differences in the mechanisms underlying song variability therefore represent an untapped opportunity for probing the mechanisms of song learning and production.

animal behavior and cognition↗

bioRxiv2017

Transcriptional response to West Nile virus infection in the zebra finch (Taeniopygia guttata), a songbird model for immune function

West Nile Virus (WNV) is the one of most widespread arboviruses worldwide. WNV exists in a bird-mosquito transmission cycle where passerine birds act as the primary reservoir host. As a public health concern, the mammalian immune response to WNV has been studied in detail. Little, however, is known about the avian immune response to WNV. Avian taxa show variable susceptibility to WNV and what drives this variation is unknown. Thus, to study the immune response to WNV in birds, we experimentally infected captive zebra finches (Taeniopygia guttata). Zebra finches provide a useful model, as like many natural avian hosts they are moderately susceptible to WNV and thus provide sufficient viremia to infect mosquitoes. We performed splenic RNAseq during peak viremia to provide an overview of the transcriptional response. In general, we find strong parallels with the mammalian immune response to WNV, including up-regulation of five genes in the Rig-I-like receptor signaling pathway, and offer insights into avian specific responses. Together with complementary immunological assays, we provide a model of the avian immune response to WNV and set the stage for future comparative studies among variably susceptible populations and species.

genomics↗