Publications:

                                                                                                                                                                                                                                                                                                        Last Updated: 09/11/19

  1. Armstrong et al., Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection. BioRXiv
  2. Ghosh-Harihar M, An R, Athreya R, Borthakur U, Chanchani P, Chetry D, Datta A, Harihar A, Karanth KK, Mariyam, Ramakrishnan, U*….. (2019) Protected areas and biodiversity conservation in India. Biological Conservation. 237:114-24. 
  3. Alcala, N, Goldberg, A, Ramakrishnan, U and Rosenberg, NA (accepted, Molecular Biology and Evolution). Coalescent theory of migration network motifs. 2019 Oct 1;36(10):2358-2374. doi: 10.1093/molbev/msz136.
  4. Gupta P, Vishnudas CK, Ramakrishnan U, Robin VV, Dharmarajan G. (2019) Geographical and host species barriers differentially affect generalist and specialist parasite community structure in a tropical sky-island archipelago. Proceedings of the Royal Society B. 286(1904):20190439.
  5. Mukherjee S, Singh P, Silva AP, Ri C, Kakati K et al… Ramakrishnan, U (2019) Activity patterns of the small and medium felid (Mammalia: Carnivora: Felidae) guild in northeastern India. Journal of Threatened Taxa. 2019.11(4):13432-47.
  6. Agarwal I, Khandekar A, Giri VB, Ramakrishnan U, Karanth KP (2019) The hills are alive with geckos! A radiation of a dozen species on sky islands across peninsular India (Squamata: Gekkonidae, Hemiphyllodactylus) with the description of three new species. Organisms Diversity & Evolution. 19(2):341-361.
  7. Natesh, M*, Taylor, RW*, Truelove, N, Palumbi, SA, Hadly, EA, Petrov* and Ramakrishnan, U* (2019) Empowering conservation science and practice with efficient and economical genotyping from poor quality samples. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.13173
  8. Varudkar, A and Ramakrishnan, U (2018) Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus. Ecology and Evolution. 8(13): 6463-6472
  9. Nair, JN, Shanmugam, PV, Karpe, SD, Ramakrishnan, U and Olsson, S (2018) An optimized protocol for large‐scale in situ sampling and analysis of volatile organic compounds. Ecology and Evolution 8(11): 5924-5936
  10. Hsu, JL, Crawford, JC, Tammone, MN, Ramakrishnan, U, Lacey, EA and Hadly, EA (2018) Genomic data reveal a loss of diversity in two species of tuco-tucos (genus Ctenomys) following a volcanic eruption. Scientific Reports 7(1): 16227
  11. Agarwal, I, Khandekar, A, Ramakrishnan, U, Vyas, R, Giri, VB (2018) Two new species of the Ophisops microlepis (Squamata: Lacertidae) complex from northwestern India with a key to Indian Ophisops. Journal of Natural History, 1-29
  12. Thattai, P, Joshi, A, Vaidyanathan, S, Landguth, E, and Ramakrishnan, U (2018) Maintaining tiger connectivity and minimizing extinction into the next century: insights from landscape genetics and spatially-explicit simulations. Biological Conservation 218, 181-191
  13. Koparde, P, Mehta, P, Reddy, S, Ramakrishnan, U, Mukherjee, S and Robin, VV (2018) The critically endangered forest owlet Heteroglaux blewitti is nested within the currently recognized Athene clade: A century-old debate addressed. PLoS One, 13(2), e0192359.
  14. Garg, KM, Chattopadhya, B and Ramakrishnan, U (2018) Social structure of the harem-forming promiscuous fruit bat, Cynopterus sphinx, is the harem truly important? Royal Society Open Sciences 5(2): 172024\
  15. Natesh M, Atla G, Nigam P, Jhala YV, Zachariah A, Reddy AP, Borthakur U and Ramakrishnan U (2017) Conservation priorities for endangered Indian tigers through a genomic lens. Scientific Reports, 7 (1), 9614
  16. Garg, KM and Ramakrishnan, U (2017) Variance in Female Reproductive Success Differentially Impacts Effective Population Size in the Short-Nosed Fruit Bat, Cynopterus sphinx. Evolutionary Biology 44(3):366-373
  17. Wickramasinghe, N, Robin, VV, Ramakrishnan, U, Reddy, S and Seneviratn, SS (2017) Non-sister Sri Lankan white-eyes (genus Zosterops) are a result of independent colonizations. PLoS One 12 (8):e0181441
  18. Robin, VV, Vishnudas, CK, Gupta, P, Rheindt, FE, Hooper, DM, Ramakrishnan, U and Reddy, S (2017) Two new genera of songbirds represent endemic radiations from the Shola Sky Islands of the Western Ghats, India BMC evolutionary Biology, DOI: 10.1186/s12862-017-0882-6
  19. Suryawanshi, KR, Redpath, SM, Bhatnagar, YV, Ramakrishnan, U, Chaturvedi, V, Smout, SC and Mishra, C (2017) Impact of wild prey availability on livestock predation by snow leopards. Royal Society Open Science. 4: 170026. http://dx.doi.org/10.1098/rsos.170026
  20. Mani, RS, Dovih, DP, Ashwini, MA, Chattopadhyay, B, Harsha, PK, Garg, KM, Sudarshan, S, Puttaswamaiah, R, Ramakrishnan, U and Madhusudana, SN (2017) Serological Evidence of Lyssavirus Infection among Bats in Nagaland, a North-Eastern State in India. Epidemiology & Infection 145(8): 1635-1641
  21. Agarwal, I and Ramakrishnan, U (2017) A phylogeny of open-habitat lizards (Squamata: Lacertidae: Ophisops) supports the antiquity of Indian grassy biomes. Journal of Biogeography, DOI: 10.1111/jbi.12999
  22. Barnosky, A et al. (including Ramakrishnan, U) (2017) Merging paleobiology with conservation biology to guide the future of terrestrial ecosystems. Science 355(6325) DOI: 10.1126/science.aah4787
  23. Dahal, N., Lissovsky, AA, Lin, Z, Solari, K, Hadly, E A,  Zhan, X and Ramakrishnan, U (2017) Genetics, morphology and ecology reveal a cryptic pika lineage in the Sikkim Himalaya. Molecular Phylogenetics and Evolution. 106: 55–60
  24. Ramachandran, V., Robin, V.V., Tamma, K. and Ramakrishnan, U (2016) Climatic and geographic barriers drive distributional patterns of bird phenotypes within peninsular India. J Avian Biol. doi:10.1111/jav.01278
  25. Chattopadhyay, B, Garg, KM, Vinoth Kumar, AK, Swami Doss, DP, Rheindt, FE, Kandula, S and Ramakrishnan, U (2016). Genome-wide data reveal cryptic diversity and genetic introgression in an Oriental cynopterine fruit bat radiation. BMC Evolutionary Biology, 16:41
  26. Tamma, K, Marathe, A and Ramakrishnan, U (2016) Past influences present: Mammalian species from different biogeographic pools sort environmentally in the Indian subcontinent. Frontiers of Biogeography 8.1 
  27. Robin, VV, Vishnudas, CK, Gupta, P & Ramakrishnan, U. Deep and wide valleys drive nested phylogeographic impacts across a montane bird community (in press, Proceedings of the Royal Society B, Biological Sciences)
  28. Robin VV, Gupta P, Thatte P, Ramakrishnan U. Islands within islands: Two montane paleo-endemic birds impacted by recent anthropogenic fragmentation (in press, Molecular Ecology)
  29. Mondol S, Kumar S, Golpalaswamy A, Sunakar K, Karanth KU & Ramakrishnan U (2015) Identifying species, sex and individual tigers and leopards in the Malenad-Mysore landscape, Western ghats, India. Conservation Genetics Resources 7:353-361.
  30. Varudkar, A & Ramakrishnan, U (2015) Commensalism facilitates gene flow in mountains: A comparison between two Rattus species. Heredity 115:253-261. doi:10.1038/hdy.2015.34
  31. Garg, KM, Chattopadhyay, C, Vinoth Kumar, AK, Swami Doss, DP, Kandula, S & Ramakrishnan, U (2015) Males and females gain differentially from sociality in a promiscuous fruit bat Cynopterus sphinx. PLoS One 10(3):e0122180. DOI: 10.1371/journal.pone.0122180
  32. Tamma, K & Ramakrishnan, U (2015) Higher speciation and lower extinction rates influence mammal diversity gradients in Asia. BMC Evolutionary Biology 15:11  doi:10.1186/s12862-015-0289-1
  33. Savory, F & Ramakrishnan (2015) Cryptic diversity and habitat partitioning in an economically important aphid species complex Infection, Genetics and Evolution, 30:230-237.
  34.  Chattopadhyay, C, Garg, KM & Ramakrishnan, U (2014) Effect of diversity and missing data on genetic assignment with RAD-Seq markers. BMC research notes, 7:241.
  35. Chakraborty D, Sinha A, Ramakrishnan U (2014). Mixed fortunes: Ancient expansion and recent decline in population size of a subtropical montane primate, the Arunachal macaque Macaca munzala. PLoS ONE 9(7):  e97061.
  36. Chakraborty D, Ramakrishnan U, Sinha A (2014) Quaternary climate change and social behavior shaped the genetic differentiation of an endangered montane primate from the southern edge of the Tibetan Plateau. American Journal of Primatology DOI: 10.1002/ajp.22343
  37. Mondol, S, Sridhar, V, Yadav, P, Gubbi, S & Ramakrishnan, U (2014) Tracing the geographic origin of traded leopard body parts in the Indian subcontinent. Conservation Biology doi: 10.1111/cobi.12393.*
  38. *highlighted in Nature Research highlights, November, 2014, http://www.nature.com/nature/journal/v515/n7527/full/515315a.html
  39.  Robin, VV, Vishnudas, CK & Ramakrishnan, U (2014) Reassessment of the distribution and the threat status of the Western Ghats endemic bird, Nilgiri Pipit Anthus nilghiriensis. Current Science 107(4):622-629.
  40. Savory, F & Ramakrishnan, U (2014) Asymmetric patterns of Reassortment and Concerted Evolution in Cardamom Bushy Dwarf Virus. Infection, Genetics and Evolution 24:15-24.
  41. Savory, F, Varma, V & Ramakrishnan, U (2014) Identifying Geographic Hotspots of Reassortment in a Multipartite Plant Virus Evolutionary Applications 7(5):569-579.*
  42. *Research highlighted in Nature India
  43.  Bay, Rachael A, Uma Ramakrishnan, and Elizabeth A Hadly (2014) A Call for Tiger Management Using “Reserves” of Genetic Diversity. Journal of Heredity 105(3): 295-302*
  44. *Research highlighted on Woods Institute website
  45.  Srinivasan U, Tamma K & Ramakrishnan U (2014). Past climate and species ecology drive nested species richness patterns along an east-west axis in the Himalaya. Global Ecology and Biogeography, 23 (1): 52-60. doi: 10.1111/geb.12082
  46. Joshi A, Vaidyanathan S, Mondol S, Edgaonkar A, Ramakrishnan U (2013). Connectivity of Tiger (Panthera tigris) Populations in the Human-Influenced Forest Mosaic of Central India. PLoS ONE 8(11): e77980. doi:10.1371/journal.pone.0077980
  47.  Mukherjee, M, Adhya, T, Thatte, P & Ramakrishnan, U (2012). Survey of the Fishing cat, Prionailurus viverrinus Bennet, 1833 (Carnivora: Felidae) and some aspects of its conservation in India. Journal of Threatened Taxa 4(14): 3355-3361.
  48. Garg, KM, Chattopadhyay, B, Doss, DPS, Vinoth Kumar, AK, Kandula, S & Ramakrishnan, U (2012). Promiscuous mating in the harem-roosting fruit bat, Cynopterus sphinx. Molecular Ecology, 21: 4093–4105. doi: 10.1111/j.1365-294X.2012.05665.x
  49. Chattopadhyay, B, Garg, KM, Vinoth Kumar, AK , Doss, DPS, Ramakrishnan, U & Kandula, S (2012) Sibling species in South Indian populations of the rufous horse-shoe bat, Rhinolophus rouxii. Conservation genetics, 13(6):1435-1445.
  50. Mondol, S, Thatte, P, Yadav, P & Ramakrishnan, U (2011) A set of miniSTRs for population genetic analyses of tigers (Panthera tigris) with cross-species amplification for seven other Felidae. Conservation Genetics Resources. DOI: 10.1007/s12686-011-9475-7
  51. Malhi, RS, Satkoski-Trask, J, Shattuck, M, Johnson, J, Chakraborty, D, Kanthaswamy, S, Ramakrishnan, U & Smith, DG (2011). Genotyping single nucleotide polymorphisms (SNPs) across species in Old World Monkeys. American Journal of Primatology. 73(10):1031–1040.
  52. Chattopadhyay B, Garg KM, Doss PS, Ramakrishnan U, Kandula S (2011). Molecular genetic perspective of group-living in a polygynous fruit bat, Cynopterus sphinx. Mammalian Biology - Zeitschrift für Säugetierkunde, Volume 76, Issue 3, Pages 290-294. doi:10.1016/j.mambio.2010.08.003
  53.  Robin VV, Sinha A & Ramakrishnan, U (2010) Ancient Geographical Gaps and Paleo-climate Shape the Phylogeography of an Endemic Bird in the Sky Islands of Southern India. PLoS ONE 5(10): e13321. doi:10.1371/journal.pone.0013321.
  54.  Mukherjee, S, Krishnan, A, Tamma, K, Home, C, Navya R, Joseph, S & Ramakrishnan, U (2010) Ecology driving genetic variation: A comparative phylogeography of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). PLoS ONE 5(10): e13724. doi:10.1371/journal.pone.0013724.
  55.  Mukherjee, S, Ashalakshmi, CN, Home, C & Ramakrishnan, U (2010) An evaluation of the PCR-RFLP technique to aid molecular-based monitoring of felids and canids in India. BMC Research Notes 3:159.
  56.  Chakraborty, S, Chakraborty, D, Mukherjee, O, Jain, S, Ramakrishnan, U & Sinha, A (2010) Genetic Polymorphism in the Serotonin Transporter Promoter Region and Ecological Success in Macaques. Behavior Genetics: DOI: 10.1007/s10519-010-9360-2
  57. O’Keefe, K, Ramakrishnan, U, van Tuinen, M & Hadly, EA (2009) Source-sink dynamics in a common montane mammal. Molecular Ecology,18(23):4775-4789.
  58. Mondol, S, Athreya, V, Velu Mani, S, Sunagar, K & Ramakrishnan, U (2009) A panel of microsatellites to individually identify leopards and its application to leopard monitoring in human dominated landscapes. BMC Genetics, 10:79 doi:10.1186/1471-2156-10-79
  59.  Ramakrishnan, U & Hadly, EAH (2009) Do complex population histories drive higher estimates of substitution rate in phylogenetic reconstructions? Molecular Ecology, 18(21):4341-4343
  60.  Mondol, S, Karanth, KU, Kumar, S, Gopalswamy, A, Andheria, A & Ramakrishnan, U (2009) Evaluation of non-invasive genetic sampling methods for estimating tiger population size. Biological Conservation, 142(10): 2350-2360.
  61. Mondol, S, Karanth, KU, Ramakrishnan, U (2009) Why the Indian subcontinent holds the key to tiger recovery. PLoS Genetics, 5(8): e1000585. doi:10.1371/journal.pgen.1000585
  62.  Ramakrishnan, U & Hadly, EA (2009) Using phylochronology to reveal cryptic population histories. Molecular Ecology, 18(7):1310-1330.
  63.  van Tuinen, M, O’Keefe, K, Ramakrishnan, U & Hadly, E (2008) Fire and Ice: Genetic Structure of the Uinta Ground Squirrel (Spermophilus armatus) across the Yellowstone Hotspot . Molecular Ecology, 17(7):1776-1788. 
  64.  James, J, Ramakrishnan, U & Datta, A (2008) Molecular evidence for the occurrence of the leaf deer Muntiacus putaoensis in Arunachal Pradesh, north-east India. Conservation genetics, 9(4):927-931.
  65.  Tishkoff, SA, Gonder, MK, Henn, BM, Mortense, H, Fernandopulle, F, Gignoux, C, Godfrey, L, Nyambo, TB, Underhill, PA, Ramakrishnan, U, Reed, FA & Mountain, JL (2007) History of click-speaking populations of Africa inferred from mtDNA and Y chromosome variation . Molecular Biology and Evolution, 24(10):2180-2195. 
  66. Mukherjee, N, Mondol, S, Andheria, A & Ramakrishnan, U (2007) Rapid multiplex PCR based species identification of wild tigers using non-invasive samples. Conservation genetics, 8(6): 1465-1470.
  67.  Chakraborty, D, Ramakrishnan, U, Panor, J, Mishra, C & Sinha, A (2007) Phylogenetic relationships and morphometric affinities of the Arunachal macaque Macaca munzala, a newly described primate from Arunachal Pradesh, Northeastern India. Molecular Phylogenetics and Evolution, 44:838-849 
  68. Belle, E, Ramakrishnan, U Mountain, JL & Barbujani, G (2006) Serial coalescent simulations suggest a weak genealogical relationship between Etruscans and modern Tuscans . Proc. Nat. Acad. Sci (USA), 103(21):8012-8017.
  69.  Ramakrishnan, U, Hadly, EA & Mountain, JL (2005) Detecting past population bottlenecks using temporal genetic data . Molecular Ecology, 14(10):2915-2922.
  70.  Anderson CNK, Ramakrishnan, U, Chan YL & Hadly EA (2005) Serial SIMCOAL: A population genetic model for data from multiple populations and points in time . Bioinformatics, 21(8):1733-1734
  71.  Mountain, JL & Ramakrishnan, U (2005) Individual genetic difference and human population history . Human Genomics, 2(1):4-19.
  72. Ramakrishnan, U, Storz, JF, Taylor, BL & Lande, R (2004) Rejection algorithm based estimation of the effective number of breeding males using genetic data . Molecular Ecology, 13:3283-3292.
  73.  Ramakrishnan, U & Mountain, JL (2004) Precision and accuracy of divergence time estimates from SNPSTR and STR variation . Molecular Biology and Evolution, 21(10): 1960-1971.
  74.  Hadly, EA, Ramakrishnan, U, Chan, YL, van Tuinen, M, Conroy, C, Spaeth, PE & O’Keefe, K (2004) Genetic response to climatic change: insights from ancient DNA and phylochronology . Public Library of Science, Biology, 2(10): e290.
  75.  van Tuinen, M, Ramakrishnan, U & Hadly, EA (2004) Studying the effect of environmental change on biotic evolution: past genetic contributions, current work and future directions . Philosophical Transactions of the Royal Society (London), Series A), 362(1825):2795-2820.
  76. Taylor, BL, Wade, PW, Ramakrishnan, U, Gilpin, ME & Akcacaya, R (2002) Incorporating uncertainty in PVAs for the purpose of classifying species by risk. In POPULATION VIABILITY ANALYSIS (chapter 6). Beissinger, S. and D. McCullough (eds.). Chicago University Press, Chicago, U.S.A.
  77.  Storz, JF, Ramakrishnan, U & Alberts, SC (2002) Genetic effective size of a wild primate population: influence of current and historical demography . Evolution, 56(4): 817-829.