Biology subjects

Kandlikar, G.

Publications and source records attributed to Kandlikar, G..

5 recordsLinked to original sources

bioRxiv2026

Urban Environments Reshape Reproductive Phenology in Plants Across the Tropics

Plant phenological responses to global change phenomena like urbanization remain understudied in the tropics, hindering predictions regarding the dynamics of tropical ecosystems amid rapid land use changes. Studies of tropical phenology are limited by complexities, like the limited availability of phenological data, especially in urbanized landscapes. Observations recorded on citizen science platforms can overcome this limitation by providing vast, spatially distributed data. In this study, we utilize iNaturalist data to evaluate plant reproductive phenology in tropical urban vs. rural habitats. We first compare iNaturalist data (111533 records) to herbarium collections (217991 records) in order to validate their use, and we then investigate urban-rural phenology differences within 25-km spatial grids for 238 species. Data from iNaturalist and herbaria yield complementary insights, with the former being uniformly distributed between urban and rural settings, and the latter biased towards rural observations. On average, we found species to have significantly longer reproductive duration ({beta} = 11.79 {+/-} 2.83 SE, t = 4.16, p < 10^4), and correspondingly weaker strength of seasonality in urban settings than in nearby rural localities. We also find trait-mediated variation, with seasonal, annual, and herbaceous plants showing more pronounced differences in reproductive duration and seasonality strength. These results suggest that urbanization in tropical landscapes might have important implications for plant demography, with potential consequences for community and ecosystem dynamics. Our work also points to the value of integrating insights from natural history collections with data from citizen science platforms for enabling broad-scale insights into ecological dynamics in tropical urban landscapes.

ecology↗

bioRxiv2020

Functional traits predict species responses to environmental variation in a California grassland annual plant community

O_LITurnover in species composition and community-wide functional traits across environmental gradients is a ubiquitous pattern in ecology, and is generally assumed to reflect shifts in trait optima across these gradients. However, the demographic processes that give rise to these trait turnover patterns at the community level remain unclear. C_LIO_LIWe asked whether shifts in the community-weighted means of three key functional traits across an environmental gradient in a southern California grassland reflect variation in the trait-performance relationship across the landscape. C_LIO_LIWe planted seeds of 17 annual plant species in cleared patches with no competitors, and quantified the lifetime seed production of 1360 individuals. We then asked whether models that included trait-environment interactions help explain interspecific variation in demographic responses to the environment. This allowed us to evaluate whether observed shifts in community-weighted mean traits matched the direction of any trait-environment interactions detected in the plant performance experiment. C_LIO_LIOur results indicate that commonly-measured plant functional traits help explain variation in species responses to the environment - for example, high-SLA species had a demographic advantage in soils with high soil Ca:Mg levels, while low-SLA species had an advantage in low Ca:Mg soils. We also found that shifts in community-weighted mean traits often reflect the direction of these trait-environment interactions, though not all trait-environment relationships at the community level reflect interactive effects of traits and environment on species performance. C_LIO_LIOur results support the value of plant functional traits for predicting species responses to environmental variation, and highlight a need for more detailed evaluation of how trait-performance relationships change across environments to improve such predictions. C_LI

ecology↗

bioRxiv2020

Quantifying microbially mediated fitness differences reveals the tendency for plant-soil feedbacks to drive species exclusion among California annual plants

Soil microorganisms influence a variety of processes in plant communities. Many the-oretical and empirical studies have shown that dynamic feedbacks between plants and soil microbes can stabilize plant coexistence by generating negative frequency-dependent plant population dynamics. However, inferring the net effects of soil microbes on plant coexistence requires also quantifying the degree to which they provide one species an average fitness advantage, an effect that has received little empirical attention. We conducted a greenhouse study to quantify microbially mediated stabilization and fitness differences among fifteen pairs of annual plants that co-occur in southern California grasslands. We found that although soil microbes frequently generate negative frequency-dependent dynamics that stabilize plant interactions, they simultaneously mediate large average fitness differences between species. The net result is that if the plant species are otherwise competitively equivalent, the impact of plant-soil feedbacks is often to favor species exclusion over coexistence, a result that only becomes evident by quantifying the microbially mediated fitness difference. Our work highlights that comparing the stabilizing effects of plant-soil feedbacks to the fitness difference they generate is essential for understanding the influence of soil microbes on plant diversity.

ecology↗

bioRxiv2019

The California Environmental DNA \"CALeDNA\" Program

Global change is leading to habitat shifts that threaten species persistence throughout Californias unique ecosystems. Baseline biodiversity data provide opportunities for ecosystems to be managed for community complexity and connectivity. In 2017, the University of California Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program, a community science initiative monitoring Californias biodiversity through environmental DNA (eDNA)--DNA shed from organisms through fur, mucus, spores, pollen, etc. Community scientists collect soil and sediment samples, then researchers analyze the eDNA in the samples and share results with the public. The results are catalogues of thousands of organisms per sample, ranging from microbes to mammals. The CALeDNA website presents biodiversity inventories in a platform designed for the public and researchers alike, as well as user-friendly analysis tools and educational modules. Here, we present CALeDNA as a scalable community science framework that can harmonize with future biodiversity research and education initiatives.

scientific communication and education↗

bioRxiv2018

Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode datasets

1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable, and non-invasive. Longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high-throughput sequencing platforms, fast multilocus metabarcode processing, and accurate taxonomic assignment. As bioinformatics tools continue to improve, addressing each of these demands within a single bioinformatics toolkit is becoming a reality.\n\n2. We present the modular metabarcode sequence toolkit Anacapa (https://github.com/limey-bean/Anacapa/), which addresses the above needs, allowing users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data A novel aspect of Anacapa is our database building module, Creating Reference libraries Using eXisting tools (CRUX), which generates comprehensive reference databases for specific user-defined metabarcode loci. The Quality Control and Dereplication module sorts and processes multiple metabarcode loci and processes merged, unmerged and unpaired reads maximizing recovered diversity. Followed by amplicon sequence variants (ASVs) detection using DADA2. The Anacapa Classifier module aligns these ASVs to CRUX-generated reference databases using Bowtie2. Taxonomy is assigned to ASVs with confidence scores using a Bayesian Lowest Common Ancestor (BLCA) method. The Anacapa Toolkit also includes an R package, ranacapa, for automated results exploration through standard biodiversity statistical analysis.\n\n3. We performed a series of benchmarking tests to verify that the Anacapa Toolkit generates comprehensive reference databases that capture wide taxonomic diversity and that it can assign high-quality taxonomy to both MiSeq-length and Hi-Seq length sequence data. We demonstrate the value of the Anacapa Toolkit to assigning taxonomy to eDNA sequences from seawater samples from southern California including capability of this tool kit to process multilocus metabarcoding data.\n\n4. The Anacapa Toolkit broadens the exploration of eDNA and assists in biodiversity assessment and management by generating metabarcode specific databases, processing multilocus data, retaining all read types, and expanding non-traditional eDNA targets. Anacapa software and source code are open and available in a virtual container to ease installation.

bioinformatics↗