Comparative assessment of the effective population size and linkage disequilibrium of Karan fries composite cattle revealed viable population dynamics.

Objective: Karan Fries (KF), a high-producing composite cattle was developed through crossing indicine Tharparkar cows with taurine bulls (Holstein Friesian, Brown Swiss, and Jersey), to increase the milk yield across India. This composite cattle population must maintain sufficient genetic diversity for long-term development and breed improvement in the coming years. The level of Linkage disequilibrium (LD) measures the influence of population genetic forces on the genomic structure and provides insights into the evolutionary history of populations, while the decay of LD is important in understanding the limits of genome-wide association studies for a population. Effective population size (Ne) which is genomically based on LD accumulated over the course of previous generations, is a valuable tool for evaluation of the genetic diversity and level of inbreeding. The present study was undertaken to understand KF population dynamics through the estimation of Ne and LD for the long-term sustainability of these breeds. Methods: The present study included 96 KF samples genotyped using Illumina HDBovine array to estimate the effective population and examine the LD pattern. The genotype data were also obtained for other crossbreds (Santa Gertrudis, Brangus, and Beefmaster) and Holstein Friesian cattle for comparison purposes. Results: The average LD between SNPs was r2 = 0.13 in the present study. LD decay (r2 = 0.2) was observed at 40 kb inter-marker distance, indicating a panel with 62765 SNPs was sufficient for genomic breeding value estimation in KF cattle. The pedigree-based effective population size (Ne) of KF was determined to be 78, while the Ne estimates obtained using LD-based methods were 52 (SNeP) and 219 (Genetic Optimization for Ne Estimation - GONE), respectively. Conclusion: KF cattle have an effective population size (Ne) exceeding the FAO's minimum recommended level of 50, which was desirable. The study also revealed significant population dynamics of KF cattle and increased our understanding of devising suitable breeding strategies for long-term sustainable development.

Deciphering local adaptation of native Indian cattle (Bos indicus) breeds using landscape genomics and in-silico prediction of deleterious SNP effects on protein structure and function.

India has 50 registered breeds of native cattle (Bos indicus) which are locally adapted to diverse environmental conditions. This study aimed to investigate the genomic basis of adaptation of native Indian cattle and to predict the impact of key SNPs on the amino acid changes that affect protein function. The Illumina 777 K BovineHD BeadChip was used to genotype 178 native cattle belonging to contrasting landscapes and agro-climatic conditions. The genotype-environment association was investigated with R. SamBada, using 5,74,382 QC passed SNPs and 11 predictor variables (10 multi-collinearity controlled environmental variables and 1 variable as "score of PCA" on ancestry coefficients of individuals). In total, 1,12,780 models were selected as significant (q < 0.05) based on G score. The pathway ontology of the annotated genes revealed many important pathways and genes having a direct and indirect role in cold and hot adaptation. Only ten SNP variants had a SIFT score of < 0.05 (deleterious), and only two of them, each lying in the genes CRYBA1 and USP18, were predicted to be deleterious with high confidence. RaptorX predicted the tertiary structures of proteins encoded by wild and mutant variants of these genes. The quality of the models was determined using Ramachandran plots and RaptorX parameters, indicating that they are accurate. RaptorX and I-Mutant 2.0 softwares revealed significant differences among wild and mutant proteins. Adaptive alleles identified in the present investigation might be responsible for the local adaptation of these cattle breeds. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03493-3.

Machine learned hybrid Gaussian analysis of COVID-19 pandemic in India.

This article discusses short term forecasting of the Novel Corona Virus (COVID -19) data for infected, recovered and active cases using the Machine learned hybrid Gaussian and ARIMA method for the spread in India. The Covid-19 data is obtained from the World meter and MOH (Ministry of Health, India). The data is analyzed for the period from January 30, 2020 (the first case reported) to October 15, 2020. Using ARIMA (2, 1, 0), we obtain the short forecast up to October 31, 2020. The several statistics parameters have tested for the goodness of fit to evaluate the forecasting methods but the results show that ARIMA (2, 1, 0) gives better forecast for the data system. It is observed that COVID 19 data follows quadratic behavior and in long run it spreads with high peak roughly estimated in September 18, 2020. Also, using nonlinear regression it is observed that the trend in long run follows the Gaussian mixture model. It is concluded that COVID 19 will follow secondary shock wave in the month of November 2020. In India we are approaching towards herd immunity. Also, it is observed that the impact of pandemic will be about 441 to 465 days and the pandemic will end in between April-May 2021. It is concluded that primary peak observed in September 2020 and the secondary shock wave to be around November 2020 with sharp peak. Thus, it is concluded that the people should follow precautionary measures and it is better to maintain social distancing with all safety measures as the pandemic situation is not in control due to non-availability of medicines.

Novel Doublesex Duplication Associated with Sexually Dimorphic Development of Dogface Butterfly Wings.

Sexually dimorphic development is responsible for some of the most remarkable phenotypic variation found in nature. Alternative splicing of the transcription factor gene doublesex (dsx) is a highly conserved developmental switch controlling the expression of sex-specific pathways. Here, we leverage sex-specific differences in butterfly wing color pattern to characterize the genetic basis of sexually dimorphic development. We use RNA-seq, immunolocalization, and motif binding site analysis to test specific predictions about the role of dsx in the development of structurally based ultraviolet (UV) wing patterns in Zerene cesonia (Southern Dogface). Unexpectedly, we discover a novel duplication of dsx that shows a sex-specific burst of expression associated with the sexually dimorphic UV coloration. The derived copy consists of a single exon that encodes a DNA binding but no protein-binding domain and has experienced rapid amino-acid divergence. We propose the novel dsx paralog may suppress UV scale differentiation in females, which is supported by an excess of Dsx-binding sites at cytoskeletal and chitin-related genes with sex-biased expression. These findings illustrate the molecular flexibility of the dsx gene in mediating the differentiation of secondary sexual characteristics.

Origin of the mechanism of phenotypic plasticity in satyrid butterfly eyespots.

Plasticity is often regarded as a derived adaptation to help organisms survive in variable but predictable environments, however, we currently lack a rigorous, mechanistic examination of how plasticity evolves in a large comparative framework. Here, we show that phenotypic plasticity in eyespot size in response to environmental temperature observed in Bicyclus anynana satyrid butterflies is a complex derived adaptation of this lineage. By reconstructing the evolution of known physiological and molecular components of eyespot size plasticity in a comparative framework, we showed that 20E titer plasticity in response to temperature is a pre-adaptation shared by all butterfly species examined, whereas expression of EcR in eyespot centers, and eyespot sensitivity to 20E, are both derived traits found only in a subset of species with eyespots.

A well-known family of butterflies have circular patterns on their wings that look like eyes. These eye-like markings help deflect predators away from the butterfly's body so they attack the outer edges of their wings. However, in certain seasons, such as the dry season in Africa, the best way for this family to survive is by not drawing any attention to their bodies. Thus, butterflies born during this season shrink the size of their eyespots so they can hide among the dry leaves. How this family of butterflies are able to change the size of these eye-like spots has only been studied in the species Bicyclus anynana. During development low temperatures, which signify the beginning of the dry season, reduce the amount of a hormone called 20E circulating in the blood of this species. This changes the behavior of hormone-sensitive cells in the eyespots making them smaller in size. But it remains unclear how B. anynana evolved this remarkable tactic and whether its relatives have similar abilities. Now, Bhardwaj et al. show that B. anynana is the only one of its relatives that can amend the size of its eyespots in response to temperature changes. In the experiments, 13 different species of butterflies, mostly from the family that has eyespots, were developed under two different temperatures. Low temperatures caused 20E hormone levels to decrease in all 13 species. However, most of these species did not develop smaller eyespots in response to this temperature change. This includes species that are known to have larger and smaller eyespots depending on the season. Like B. anynana, four of the species studied have receptors for the 20E hormone at the center of their eyespots. However, changing 20E hormone levels in these species did not reduce eyespot size. These results show that although temperature changes alter hormone levels in a number of species, only B. anynana have taken advantage of this mechanism to regulate eyespot size. In addition, Bhardwaj et al. found that this unique mechanism evolved from several genetic changes over millions of years. Other species likely use other environmental cues to trigger seasonal changes in the size of their eyespots.

Differential Regulation of Innate and Learned Behavior by Creb1/Crh-1 in Caenorhabditis elegans.

Memory formation is crucial for the survival of animals. Here, we study the effect of different crh-1 [Caenorhabditis elegans homolog of mammalian cAMP response element binding protein 1 (CREB1)] isoforms on the ability of C. elegans to form long-term memory (LTM). Null mutants in creb1/crh-1 are defective in LTM formation across phyla. We show that a specific isoform of CREB1/CRH-1, CRH-1e, is primarily responsible for memory related functions of the transcription factor in C. elegans Silencing of CRH-1e-expressing neurons during training for LTM formation abolishes the LTM of the animal. Further, CRH-1e expression in RIM neurons is sufficient to rescue LTM defects of creb1/crh-1-null mutants. We go on to show that apart from being LTM defective, creb1/crh-1-null animals show defects in innate chemotaxis behavior. We further characterize the amino acids K247 and K266 as responsible for the LTM related functions of CREB1/CRH-1 while being dispensable for its innate chemotaxis behavior. These findings provide insight into the spatial and temporal workings of a crucial transcription factor that can be further exploited to find CREB1 targets involved in the process of memory formation.SIGNIFICANCE STATEMENT This study elucidates the role of a specific isoform of CREB1/CRH-1, CRH-1e, in Caenorhabditis elegans memory formation and chemosensation. Removal of this single isoform of creb1/crh-1 shows defects in long-term memory formation in the animal and expression of CREB1/CRH-1e in a single pair of neurons is sufficient to rescue the memory defects seen in the mutant animals. We further show that two specific amino acids of CRH-1 are required for the process of memory formation in the animal.

Male Bicyclus anynana Butterflies Choose Females on the Basis of Their Ventral UV-Reflective Eyespot Centers.

Butterflies often use their dorsal and ventral wing color patterns for distinct signaling functions. Color patterns on hidden dorsal wing surfaces are often used in sexual signaling, while exposed ventral patterns are often used to ward off predator attacks. At rest, however, part of the ventral forewings are often hidden by the hindwings, allowing individuals to also use the patterns on this wing surface for sexual signaling. Here, we test this hypothesis in Bicyclus anynana (Butler, Lepidoptera, Nymphalidae) butterflies by first determining the degree of sexual dimorphism in ventral forewing patterns, focusing on the eyespots, from both wet and dry season forms, and then testing the role of the larger ventral forewing eyespots of dry season females in male mate choice. We also test male investment in reproduction. We show that ventral forewing UV-reflective eyespot centers, in addition to dorsal forewing eyespot centers previously examined in this species, play a role in sexual signaling as males preferentially mated with females with their ventral eyespot centers intact instead of blocked with black paint. This male preference, however, did not translate into a detectable higher reproductive investment via a single mating toward ornamented females. This study provides an example of how ventral forewing patterns, often hidden by hindwings, are used in sexual communication, in this case by females to attract males.

Sex Differences in 20-Hydroxyecdysone Hormone Levels Control Sexual Dimorphism in Bicyclus anynana Wing Patterns.

In contrast to the important role of hormones in the development of sexual traits in vertebrates (Cox RM, Stenquist DS, Calsbeek R. 2009. Testosterone, growth and the evolution of sexual size dimorphism. J Evol Biol. 22(8):1586-1598.), the differentiation of these traits in insects is attributed almost exclusively to cell-autonomous mechanisms controlled by members of the sex determination pathway (Verhulst EC, van de Zande L. 2015. Double nexus - doublesex is the connecting element in sex determination. Brief Funct Genomics 14(6):396-406.), such as doublesex. Although hormones can shape the development of sexual traits in insects, variation in hormone levels are not conclusively known to cause dimorphism in these traits (Prakash A, Monteiro A. 2016. Molecular mechanisms of secondary sexual trait development in insects. Curr Opin Insect Sci. 17:40-48.). Here, we show that butterflies use sex-specific differences in 20-hydroxyecdysone hormone titers to create sexually dimorphic wing ornaments. Females of the dry season (DS) form of Bicyclus anynana display a larger sexual ornament on their wings than males, whereas in the wet season form both sexes have similarly sized ornaments (Prudic KL, Jeon C, Cao H, Monteiro A. 2011. Developmental plasticity in sexual roles of butterfly species drives mutual sexual ornamentation. Science 331(6013):73-75.). High levels of circulating 20-hydroxyecdysone during larval development in DS females and wet season forms cause proliferation of the cells fated to give rise to this wing ornament, and results in sexual dimorphism in the DS forms. This study advances our understanding of how the environment regulates sex-specific patterns of plasticity of sexual ornaments and conclusively shows that hormones can play a role in the development of secondary sexual traits in insects, just like they do in vertebrates.

Males Become Choosier in Response to Manipulations of Female Wing Ornaments in Dry Season Bicyclus anynana Butterflies.

Male investment towards reproduction is substantial in some species, and this leads to the evolution of choosy males. Male choice is often directed towards female phenotypes that are good indicators of fecundity such as body size, age, or virgin status, and often acts in the same direction as fecundity selection. In insects, only a few examples exist where male choice is directed towards female ornaments as proxies Butler of female quality. Here, we use dry season males of the sex-role reversed butterfly species Bicyclus anynana to test for differences in male choosiness and investment towards females of varying attractiveness using ornament-manipulations. Male reproductive investment in this species is in the form of a nuptial gift, a spermatophore, given to females upon mating. Males were placed in cages with either wild-type ornamented females or with nonornamented females (center of the dorsal forewing eyespots painted over), and time to mating, duration of mating, and longevity of males and females after a single mating were measured. Ornament manipulations consisted of blocking the UV-reflective scales in the center of the dorsal forewing eyespots of females, a known sexual ornament. Males displayed lower latency to mate and longer mating durations with ornamented females. The longer mating duration did not, however, translate in the transfer of a nuptial gift that increased female longevity or reduced male longevity. Instead, we propose that longer mating durations with ornamented females may represent increased mate guarding behavior or increased sperm transfer.

Differential Expression of Ecdysone Receptor Leads to Variation in Phenotypic Plasticity across Serial Homologs.

Bodies are often made of repeated units, or serial homologs, that develop using the same core gene regulatory network. Local inputs and modifications to this network allow serial homologs to evolve different morphologies, but currently we do not understand which modifications allow these repeated traits to evolve different levels of phenotypic plasticity. Here we describe variation in phenotypic plasticity across serial homologous eyespots of the butterfly Bicyclus anynana, hypothesized to be under selection for similar or different functions in the wet and dry seasonal forms. Specifically, we document the presence of eyespot size and scale brightness plasticity in hindwing eyespots hypothesized to vary in function across seasons, and reduced size plasticity and absence of brightness plasticity in forewing eyespots hypothesized to have the same function across seasons. By exploring the molecular and physiological causes of this variation in plasticity across fore and hindwing serial homologs we discover that: 1) temperature experienced during the wandering stages of larval development alters titers of an ecdysteroid hormone, 20-hydroxyecdysone (20E), in the hemolymph of wet and dry seasonal forms at that stage; 2) the 20E receptor (EcR) is differentially expressed in the forewing and hindwing eyespot centers of both seasonal forms during this critical developmental stage; and 3) manipulations of EcR signaling disproportionately affected hindwing eyespots relative to forewing eyespots. We propose that differential EcR expression across forewing and hindwing eyespots at a critical stage of development explains the variation in levels of phenotypic plasticity across these serial homologues. This finding provides a novel signaling pathway, 20E, and a novel molecular candidate, EcR, for the regulation of levels of phenotypic plasticity across body parts or serial homologs.