I. Phylogenomics and the reconstruction of the Spider Tree of Life with focus on miniaturization and web evolution in anapid spiders (Araneae, Araneoidea, “symphytognathoids”)
Araneae is an ancient clade dating back to the Devonian era whose evolutionary history has puzzled arachnologists for a long time. While the intra-family relationships are relatively well-resolved, hypotheses about the inter-family relationships have been contentious except a few. For example, the family relationships of the group of smallest spiders in the world and subsequently the evolution of their web is an unresolved question. I am using two advanced phylogenetic methods: transcriptomes and target capture (covering the ultra-conserved elements (UCEs)) to reconstruct the phylogeny of orb weaving spiders. This study will determine the timeline of speciation events and inter-relationships between the miniature orb-weaving spiders with their relative lineages. In the process, I am also reconstructing the Spider Tree of Life using UCEs that will establish an additional line of evidence laid by Sanger sequencing and transcriptomic studies.
II. Cracking the “missing data problem”: utility of Maximum Entropy principle in imputing missing nucleotide data
The resolution of relationships of any focal group is critical to understanding the evolutionary history of their respective clades (e.g., morphological, life history, biochemical etc.). Phylogenetic inferences using molecular datasets are affected by a range of factors like horizontal gene transfer, internal lineage sorting, missing data etc. Most, if not all empirical datasets contain missing or incomplete data. In evolutionary biology, the effects of missing data on tree topology have been debated for decades in the literature, as both—progressive and deleterious. The pro-side suggests that missing data can alleviate long-branch attraction by sub-dividing branches and adding characters with missing data can improve accuracy of results, i.e. deliver known, correct phylogeny. Another study indicated that missing data produces misleading tree topology and branch lengths. The recommended solutions were to select an alternative model or exclude either incomplete taxa, characters or both.
With an aim to overcome the influence of missing data, I wish to test the effects of the amount of missing data on tree topologies and test the efficiency of maximizing entropy from the distribution of available data to “correctly” impute missing data.
M.Sc., Zoology, Shivaji University, Kolhapur, India, 2014.
(Phylogenomics, Systematics, Biogeography, Methods, Taxonomy, Biodiversity policy making)
Robert Kallal, Siddharth Kulkarni, Dimitar Dimitrov, Ligia Benavides, Miquel Arnedo, Gonzalo Giribet & Gustavo Hormiga (in press) Converging on the orb: denser taxon sampling elucidates spider phylogeny and new analytical methods support repeated evolution of the orb web. Cladistics.
Siddharth Kulkarni, Robert Kallal, Hannah Wood, Dimitar Dimitrov, Gonzalo Giribet & Gustavo Hormiga (2020) Interrogating genomic-scale data to resolve recalcitrant nodes in the Spider Tree of Life. Molecular Biology and Evolution.
Christopher John Thorpe, Todd Lewis, Siddharth Kulkarni, Aparna Watve, David Pryce, Lewis Davies, Nikhil Gaitonde, David Bilton, Mairi Knight (2018) Micro-habitat distribution drives patch quality for sub-tropical rocky plateau amphibians in the northern Western Ghats, India. PLOSONE 13:3 e0194810.
Christopher John Thorpe, Todd Lewis, Matthew Fisher, Claudia Wierzbicki, Siddharth Kulkarni, Lewis Davies, David Pryce, Aparna Watve, Mairi Knight.(2018) Climate structuring of Batrachochytrium dendrobatidis infection in the threatened amphibians of the northern Western Ghats, India. Royal Society Open Science 5: 180211. http://dx.doi.org/10.1098/rsos.180211
Christopher John Thorpe, David Bilton, Siddharth Kulkarni, Jane Akerman, Aparna Watve, Mairi Knight (in press) Biogeographic patterns in the distribution of aquatic Coleoptera on the rocky plateaus in Western Maharashtra, India. Hydrobiologia.
Siddharth Kulkarni, Sameer Padhye (communicated). Biodiversity checklists and associated problems. Current Science.
Siddharth Kulkarni, Atul Vartak, Vishwas Deshpande, Dheeraj Halali (2017) The spiny theridiid genus Meotipa Simon, 1895 in India, with description of a strange new species with translucent abdomen and a phylogenetic analysis about the genus placement (Araneae, Theridiidae). Zootaxa 4291 (3): 504-520.
Hemant Ghate, Siddharth Kulkarni, Vijay Anand Ismvael (2017). Illustrated redescriptions of two large coreid bugs from Assam including the first Indian record of Schroederia feana (Distant, 1902) (Coreidae, Coreinae, Mictini). Entomon 42(2): 165-172.
Siddharth Kulkarni, Hemant Ghate (2016). A new cavernicolous assassin bug of the genus Bagauda Bergroth (Reduviidae, Emesinae) from Western Ghats, India. Zootaxa. 4127(2): 365-275.
David Pryce, C. John Thorpe, Siddharth Kulkarni, Todd Lewis (2016) Amphiesma stolatum (striped keelback): Habitat and reproduction. The Herpetological Bulletin. 136: 37-38.
Peter Jäger, Siddharth Kulkarni (2016) An unexpected new species of the genus Pseudopoda (Araneae, Sparassidae, Heteropodinae) from the Western Ghats in India. ZooKeys 577: 55-62. doi: 10.3897/zookeys.577.7848
Siddharth Kulkarni, Hemant Ghate (2016) First record of the thread-legged assassin bug Myiophanes greeni Distant, 1903 (Heteroptera: Reduviidae: Emesinae) from India. Biodiversity Data Journal 4: e7949. doi: 10.3897/BDJ.4.e7949
Sameer Padhye, Siddharth Kulkarni (2016). Regulated animal dissections in Indian academia as a measure to control invasive species. Current Science. 110 (2): 129-130.
Conference report: Siddharth Kulkarni, Peter Jäger (2016). 3rd Asian Society of Arachnology conference held at Amravati, India during Nov. 2015. Newsletter of the British Arachnological Society. 136: 3-6.