Biology subjects

Singh, N. D.

Publications and source records attributed to Singh, N. D..

6 recordsLinked to original sources

bioRxiv2024

Taxonomy and nomenclature of the giant hummingbirds (Patagona spp.) (Aves: Trochilidae)

Giant hummingbirds (Patagona spp.) are extraordinarily large hummingbirds whose taxonomy has been muddled for two centuries. Patagona systematics were recently redefined in a study of migration, physiology, and genomics, revealing two species: the Southern Giant Hummingbird and Northern Giant Hummingbird. Here, we re-evaluate taxonomy and nomenclature of the genus in light of its newly-clarified biology and species limits, analyzing data from 608 specimens and wild-caught individuals spanning 1864-2023. The forms gigas and peruviana were both described based on multiple syntypes. No adequate syntypes for P. gigas are extant, so we designate a neotype for this taxon. We then critically consider the identity and usage of gigas and peruviana, respectively, and examine identification challenges that have fostered taxonomic uncertainty. We endorse the names Patagona gigas for the Southern Giant Hummingbird and P. peruviana for the Northern Giant Hummingbird. The genetic identity of the peruviana lectotype remains untested, but its plumage appears to match the northern species. We found that [~]33% of Patagona gigas specimens in major museum collections are misidentified as peruviana; we provide this list to correct the historical record. To facilitate identification and future study of these two cryptic species, we provide comprehensive information on plumage, measurements, and seasonal ranges.

zoology↗

bioRxiv2023

Pathogen infection alters the gene expression landscape of transposable elements in Drosophila melanogaster: A meta-analysis

Transposable elements (TEs) are remnants of ancient viral infections and make up substantial proportions of eukaryotic genomes. Current research has begun to highlight the role TEs can play in the immune system response to infections. However, most of our knowledge about TE expression during infection is limited by the specific host and pathogen factors from each study, making it difficult to compare studies and develop broader patterns regarding the role of TEs during infection. Here, we use the tools and resources available in the model, Drosophila melanogaster, to analyze multiple RNAseq datasets of flies subject to bacterial, fungal, and viral infections. We analyzed differences in pathogen species, host genotype, host tissue, and sex to understand how these factors impact TE expression during infection. Our results highlight both shared and unique TE expression patterns between pathogens and suggest a larger effect of pathogen factors over host factors for influencing TE expression. AUTHOR SUMMARYTransposable elements (TEs) are short, repetitive genetic elements that make up substantial proportions of the genomes of all eukaryotic species. These TEs can become expressed during infections, either as a by-product of the infection itself or as a part of the defense mechanism of the immune system. Many studies have investigated TE activity during infection, often focusing on a single pathogen species, one specific host species and genotype, or even a small number of specific TEs. Though these studies provide important detail on these particular cases, less is known about broader patterns of TE activity during infections. Is TE expression the same across different types of infections, and how does the host affect these expression patterns? Here, we analyzed multiple gene expression datasets from infected flies to uncover these broader patterns in TE expression. We found that the type of infection, whether bacterial, fungal, or viral, has a large effect on TE expression. We also found that host factors, like sex, tissue, or genotype, have a much smaller effect on TE expression during infection compared to infection type. Our results offer a broader perspective on how TEs are activated during infections in flies.

genetics↗

bioRxiv2022

Candidate Genes Underlying Wolbachia-Associated Plastic Recombination Revealed by Ovarian Transcriptomics of D. melanogaster

Phenotypic plasticity is prevalent in nature and can facilitate the acclimation of organisms to changing environments. Recombination rate is plastic in a diversity of organisms and under a variety of stressful conditions. However, the recent finding that Wolbachia pipientis induces plastic recombination in Drosophila melanogaster was surprising because Wolbachia is not strictly considered a stressor to this host. We investigate the molecular mechanisms of Wolbachia-associated plastic recombination by comparing the ovarian transcriptomes of D. melanogaster infected and uninfected with Wolbachia. Our data suggest that infection explains a small amount of transcriptional variation but specifically affects genes related to cell cycle, translation, and metabolism. We also find enrichment of cell division and recombination processes among genes with infection-associated differential expression. Broadly, the transcriptomic changes identified in this study provide insight for the mechanisms of microbe-mediated plastic recombination, an important but poorly understood facet of host-microbe dynamics. Significance StatementThough it is documented that Wolbachia is associated with increased recombination in D. melanogaster, the underlying mechanisms remain unknown. Here we use ovarian transcriptomics in Wolbachia-infected and uninfected flies to identify candidate genes underlying Wolbachia-associated plastic recombination. We find that infection alters ovarian gene expression in subtle ways, and also identify exciting candidate genes for functional analysis in subsequent work. These candidate genes may be the first step in determining the molecular mechanisms underlying Wolbachia-associated plastic recombination. Moreover, our data contribute to the growing body of knowledge surrounding how Wolbachia affects host gene expression, and highlights how context-dependent these effects are.

evolutionary biology↗

bioRxiv2022

Variation in fine scale recombination rate in temperature-evolved Drosophila melanogaster populations in response to selection.

Meiotic recombination plays a critical evolutionary role in maintaining fitness in response to selective pressures due to changing environments. Variation in recombination rate has been observed amongst and between species and populations and within genomes across numerous taxa. Studies have demonstrated a link between changes in recombination rate and selection but the extent to which fine scale recombination rate varies between evolved populations during the evolutionary period in response to selection is under active research. Here we utilize a set of three temperature-evolved Drosophila melanogaster populations that were shown to have diverged in several phenotypes including recombination rate based on the temperature regime in which they evolved. Using whole genome sequencing data of these populations, we generated fine scale recombination maps of the three populations. We compare recombination rates and patterns among the three populations and show that they have diverged at fine scales but are conserved at broader scales. We further demonstrate a correlation between recombination rates and genomic variation in the three populations and observe variation in putative warm-spots between the populations with these enhanced areas and associated genes overlapping areas previously shown to have diverged in the three populations due to selection. These data support the existence of recombination modifiers in these populations which are subject to selection during evolutionary change.

evolutionary biology↗

bioRxiv2021

Diet effects on mouse sperm: a warning for recombination studies

Meiotic recombination is a critical process for sexually reproducing organisms. This exchange of genetic information between homologous chromosomes during meiosis is important not only because it generates genetic diversity, but also because it is often required for proper chromosome segregation. Consequently, the frequency and distribution of crossovers are tightly controlled to ensure fertility and offspring viability. However, in many systems it has been shown that environmental factors can alter the frequency of crossover events. Two studies in flies and yeast point to nutritional status affecting the frequency of crossing over. However, this question remains unexplored in mammals. Here we test how crossover frequency varies in response to diet in Mus musculus males. We use immunohistochemistry to estimate crossover frequency in multiple genotypes under two diet treatments. Our results indicate that while crossover frequency was unaffected by diet in some strains, other strains were sensitive even to small composition changes between two common laboratory chows. Therefore, recombination is both resistant and sensitive to certain dietary changes in a strain-dependent manner and, hence, this response is genetically determined. Our study is the first to report a nutrition effect on genome-wide levels of recombination. Moreover, our work highlights the importance of controlling diet in recombination studies and may point to diet as a potential source of variability among studies, which is relevant for reproducibility.

genetics↗

bioRxiv2021

Diet-induced changes in titer support a threshold effect of Wolbachia-associated plastic recombination in Drosophila melanogaster

Plastic recombination in Drosophila melanogaster has been associated with a variety of extrinsic and intrinsic factors such as temperature, starvation, and parasite infection. The bacterial endosymbiont Wolbachia pipientis has also been associated with plastic recombination in D. melanogaster. Wolbachia infection is pervasive in arthropods and this infection induces a variety of phenotypes in its hosts, the strength of which can depend on bacterial concentration, or titer. Here we test the hypothesis that the magnitude of Wolbachia-associated plastic recombination in D. melanogaster depends on titer. To manipulate titer, we raised Wolbachia-infected and uninfected flies on diets that have previously been shown to increase or decrease Wolbachia titer relative to controls. We measured recombination in treated and control individuals using a standard backcrossing scheme with two X-linked visible markers. Our results recapitulate previous findings that Wolbachia infection is associated with increased recombination rate across the yellow-vermillion interval of the X chromosome. Our data show no significant effect of diet or diet by Wolbachia interactions on recombination, suggesting that diet-induced changes in Wolbachia titer have no effect on the magnitude of plastic recombination. These findings represent the first step toward investigating the mechanisms behind Wolbachia-associated plastic recombination and demonstrate that the effect may be threshold-based as opposed to dose-dependent.

evolutionary biology↗