Singhal Lab

Singhal Lab

Publications

2024

  • Brennan IG, S Singhal, and ZA Bkhetan. pipesnake: Generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci. Bioinformatics, btae195. (pdf)
  • Title PO*, S Singhal*, MC Grundler, GC Costa, RA Pyron, TJ Colston, MR Grundler, I Prates, N Stepanova, MEH Jones, LBQ Cavalcanti, GR Colli, N Di-Poi, SC Donnellan, C Mortiz, DO Mesquita, ER Pianka, SA Smith, LJ Vitt, and DL Rabosky. The macroevolutionary singularity in snakes. Science, 383: 918-923. (*co-first author) (pdf and SI and repo)
  • Singhal S, K Kram, J Valliere, F Wang, B Heckel, S Leigh, K Theiss, C McCord, A Soroosh, T Taylor, S Zamora, and B. Sato. Integration of inquiry-based experiences department-wide: an example from biology curriculum. Experiential Learning and Teaching in Higher Education, 7:1. (pdf)
  • Stankowski S, 43 co-authors including S Singhal, and J Kulmuni. Towards the integration of speciation research. Evolutionary Journal of the Linnean Society, 3: kzae001. (pdf and SI)
  • Leaché AD, HR Davis, CR Feldman, MK Fujita, and S Singhal. Repeated patterns of reptile diversification in Western North America supported by the Northern Alligator Lizard (Elgaria coerulea). Journal of Heredity, 115: 57-71. (pdf and SI)

2023

  • Prates I, MN Hutchinson, S Singhal, C Moritz and DL Rabosky. Notes from the taxonomic disaster zone: Evolutionary drivers of intractable species boundaries in an Australian lizard clade (Scincidae: Ctenotus). Molecular Ecology, in press. (pdf and SI).

2022

  • Singhal S, J Wrath, and DL Rabosky. Genetic variability and the ecology of geographic range: a test of the central‐marginal hypothesis in Australian scincid lizards. Molecular Ecology, 31: 4242-4253. (pdf and SI and repo)
  • Singhal S, E Solis, and DL Rabosky. World Heritage lizard: population genetics and species status of the range-restricted Hamelin skink, Ctenotus zastictus. Bulletin of the Society of Systematic Biologists, 1: 86942. (pdf and SI and repo)
  • Singhal S, GR Colli, MR Grundler, GC Costa, I Prates, and DL Rabosky. No link between population isolation and speciation rate in squamate reptiles. Proceedings of the National Academy of Sciences, 119: e2113388119. (pdf and SI and repo)
  • Pereira RJ and S Singhal. A lizard with two tales: What diversification within Sceloporus occidentalis teaches us about species formation. Molecular Ecology, 31: 407-410. (pdf)
  • Prates I, S Singhal, M Marchán-Rivadeneira, MR Grundler, C Moritz, S Donnellan, DL Rabosky (2021). Genetic and Ecogeographic Controls on Species Cohesion in Australia’s Most Diverse Lizard Radiation. The American Naturalist, 199: E57-E75. (pdf and SI)

2021

  • Singhal S, GE Derryberry, GA Bravo, EP Derryberry, RT Brumfield, and MG Harvey. (2021). The dynamics of introgression across an avian radiation. Evolution Letters, 5: 568-581. (pdf and SI and repo)
  • Leaché AD, HR Davis, S Singhal, MK Fujita, ME Lahti, and KR Zamudio. (2021). Phylogenomic assessment of biodiversity using a reference-based taxonomy: an example with Horned Lizards (Phrynosoma). Frontiers in Ecology and Evolution, 437. (pdf and SI)
  • Melville J, DG Chapple, JS Keogh, J Sumner, A Amey, P Bowles, IG Brennan, P Couper, SC Donnellan, P Doughty, DL Edwards, RJ Ellis, D Esquerré, J Fenker, MG Gardner, A Georges, ML Haines, CJ Hoskin, M Hutchinson, C Moritz, J Nankivell, P Oliver, CJ Pavón-Vázquez, M Pepper, DL Rabosky, K Sanders, G Shea, S Singhal, JW Wilmer, R Tingley (2021). A return-on-investment approach for prioritization of rigorous taxonomic research needed to inform responses to the biodiversity crisis. PLoS Biology, 19: e3001210. (pdf)
  • Singhal S., A.B. Roddy, C. DiVittorio, A. Sanchez-Amaya, C. Henriquez, C.R. Brodersen, S. Fehlberg, and F. Zapata (2021). Diversification, disparification, and hybridization in the desert shrubs Encelia. New Phytologist, 230: 1228 - 1241. (pdf and SI and repo)
  • Singhal S., T.J. Colston, M.R. Grundler, S.A. Smith, G.C. Costa, G.R. Colli, C. Moritz, R.A. Pyron, and D.L. Rabosky (2021). Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective. Systematic Biology, 70: 542 - 557. (pdf and SI and repo)

2020

  • DiVittorio CD, S. Singhal, A.B. Roddy, F. Zapata, D.D. Ackerly, B. Baldwin, C.R. Brodersen, A. Burquez, P.V.A. Fine, M. Padilla Flores, E. Solis, J. Morales-Villavicencio, D. Morales-Arce, D. Kyhos (2020). Natural selection maintains species despite frequent hybridization in the desert shrub Encelia. Proceedings of the National Academy of Sciences, 117: 33373 - 33383. (pdf and SI and repo)
  • Fujita M., S. Singhal, T.O. Brunes, and J.A. Maldonado (2020). Evolutionary dynamics and consequences of parthenogenesis in vertebrates. AREES, 51: 191 - 214. (pdf)
  • Prates I. and S. Singhal (2020). Predicting speciation probability from replicated population histories. Molecular Ecology, 29: 2954 – 2956. (pdf)
  • McEntee J.P., J.G. Burleigh, and S. Singhal (2020). Dispersal predicts hybrid zone widths across animal diversity: Implications for species borders under incomplete reproductive isolation. The American Naturalist, 196: 9 - 28. (pdf and Appendix and SI and repo)
  • Zeng Y., C. O’Malley, S. Singhal, F. Rahim, S. Park, X. Hen, and R. Dudley (2020). A tale of winglets: evolution of flight morphology in stick insects. Frontiers in Ecology & Evolution, 8: 1 - 15. (pdf)

2019

  • Bi K., T. Linderoth, S. Singhal, D. Vanderpool, J.L. Patton, R. Nielsen, C. Moritz, and J.M. Good (2019) Temporal genomic contrasts reveal heterogeneous evolutionary responses within and among montane chipmunk species during recent climate change. PLoS Genetics, 15: e1008119. (pdf)
  • Harvey M.G., S. Singhal, and D.L. Rabosky (2019). Beyond Reproductive Isolation: Demographic Controls on the Speciation Process. AREES, 50: 75 - 95. (pdf)
  • Grundler M.R., S. Singhal, M.A. Cowan, and D.L. Rabosky (2019). Is genomic diversity a useful proxy for census population size? Evidence from a species-rich community of desert lizards. Molecular Ecology, 28: 1664 - 1674. (pdf)

2018

  • Singhal S., H. Huang, M. R. Grundler, M. R. Marchan-Rivadeneira, I. Holmes, P. O. Title, S. C. Connellan, and D.L. Rabosky (2018). Does Population Structure Predict the Rate of Speciation? A Comparative Test across Australia’s Most Diverse Vertebrate Radiation. The American Naturalist, 192: 432 - 447. (pdf and SI and repo)
  • Singhal S., C. J. Hoskin, P. Couper, S. Potter, and C. Moritz (2018). A Framework for Resolving Cryptic Species: A Case Study from the Lizards of the Australian Wet Tropics. Systematic Biology, 67: 1061 - 1075. (pdf and SI and appendix and repo)

2017

  • Singhal S., M. Grundler, G. Colli, and D.L. Rabosky (2017). SqCL: a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles. Molecular Ecology Resources, 17: e12 - e24. (pdf and SI and repo)
  • Singhal S. and K. Bi (2017). History cleans up messes: The impact of time in driving divergence and introgression in a tropical suture zone. Evolution 71: 1888-1899. (pdf and SI and repo)
  • Singhal S., H. Huang, P. Title, I. Holmes, S. Donnellan, and D. L. Rabosky (2017). Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards. Proceedings of Royal Society B 284: 20162588. (pdf and SI and repo)

2015 and earlier

  • Brandley M. C., J. G. Bragg, S. Singhal, D. G. Chapple, C. K. Jennings, A. R. Lemmon, E. M. Lemmon, M. B. Thompson, and C. Moritz (2015). Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards. BMC Evolutionary Biology 15: 62. (pdf)
  • *Singhal S., *E. M. Leffler, K. Sannareddy, I. Turner, O. Venn, D. M. Hooper, A. I. Strand, Q. Li, B. Raney, C. N. Balakrishnan, et al. (2015). Stable recombination hotspots in birds. Science 350: 928–932. (*co-first author) (pdf and SI and repo)
  • Singhal S. (2013). De novo transcriptome analyses for non-model organisms: an evaluation of methods across a multi-species data set. Molecular Ecology Resources, 13: 403–416. (pdf and SI)
  • Singhal S. and C. Moritz (2013). Reproductive isolation between phylogeographic lineages scales with divergence. Proceedings of the Royal Society B 280: 20132246. (pdf and SI)
  • Bi K., D. Vanderpool, S. Singhal, T. Linderoth, C. Moritz, and J. Good (2012). Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics 13: 403. (pdf)
  • Singhal S. and C. Moritz (2012). Strong selection maintains a narrow hybrid zone between morphologically cryptic lineages in a rainforest lizard. Evolution 66: 1474–1489. (pdf and SI)
  • Singhal S. and C. Moritz (2012). Testing hypotheses of genealogical discordance in a rainforest lizard. Molecular Ecology 21: 5059–5072. (pdf and SI)
  • Rowe K., S. Singhal, M. Macmanes, J. Ayroles, T. Morelli, E. Rubidge, K. Bi, and C. Moritz (2011). Museum genomics: a low cost and high accuracy approach for accessing genetic data from historical specimens. Molecular Ecology Resources 11: 1082–1092. (pdf)
  • Leung W. et al. (2010). A comparative study of the genomic sequences of the D. melanogaster and D. virilis dot chromosomes demonstrates a distinct evolutionary domain in the Drosophila genome. Genetics 185: 1519–1534. (pdf)
  • Singhal S., M. Johnson, and J. Ladner (2007). The behavioral ecology of sleep: natural sleeping site in three Anolis lizard species. Behaviour 144: 1033–1052. (pdf)
  • Schaal B., A. Bashir, S. Jamjod, W. Leverich, J. Londo, C. Maneechote, S. Nirantraiyakun, B. Rerkasem, and S. Singhal (2006). Introgression and gene flow in Asian rice. Proceedings of the 9th International Symposium on Biosafety of Genetically Modified Organisms 1: 127–130.