Last Updated: 03/06/15
1. 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)

2. 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)

3. 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.

4. 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

5. 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

6. 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

7. Savory, F & Ramakrishnan (2015) Cryptic diversity and habitat partitioning in an economically important aphid species complex Infection, Genetics and Evolution, 30:230-237.

8. 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.

9. 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.

10. 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

11. 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.*

*highlighted in Nature Research highlights, November, 2014,

12. 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.

13. Savory, F & Ramakrishnan, U (2014) Asymmetric patterns of Reassortment and Concerted Evolution in Cardamom Bushy Dwarf Virus. Infection, Genetics and Evolution 24:15-24.

14. Savory, F, Varma, V & Ramakrishnan, U (2014) Identifying Geographic Hotspots of Reassortment in a Multipartite Plant Virus Evolutionary Applications 7(5):569-579.*

*Research highlighted in Nature India

15. 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*

*Research highlighted on Woods Institute website

16. 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

17. 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

18. 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.

19. 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

20. 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.

21. 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

22. 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.

23. 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

24. 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.

25. 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.

26. 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.

27. 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

28. 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.

29. 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

30. Ramakrishnan, U & Hadly, EAH (2009) Do complex population histories drive higher estimates of substitution rate in phylogenetic reconstructions? Molecular Ecology, 18(21):4341-4343

31. 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.

32. 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

33. Ramakrishnan, U & Hadly, EA (2009) Using phylochronology to reveal cryptic population histories. Molecular Ecology, 18(7):1310-1330.

34. 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. 

35. 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.

36. 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. 

37. 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.

38. 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 

39. 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.

40. Ramakrishnan, U, Hadly, EA & Mountain, JL (2005) Detecting past population bottlenecks using temporal genetic data . Molecular Ecology, 14(10):2915-2922.

41. 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

42. Mountain, JL & Ramakrishnan, U (2005) Individual genetic difference and human population history . Human Genomics, 2(1):4-19.

43. 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.

44. 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.

45. 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.

46. 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.

47. 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.

48. 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.

49. Ramakrishnan, U & Taylor, BL (2001) Can gray whale management units be assessed using mitochondrial DNA? International Journal of Cetacean Research and Management, 3(1):1-12.

50. Storz, JF, Ramakrishnan, U & Alberts, SC (2001) Determinants of Effective Population Size for Loci with Different Modes of Inheritance . Journal of Heredity, 92: 497-502.

51. Nievergelt, CM, Digby, LJ, Ramakrishnan, U & Woodruff, DS (2000) Genetic analysis of group composition and breeding system in a wild common marmoset (Callithrix jacchus) population. International Journal of Primatology, 21(1):1-20.

52. Eggert, LE, Ramakrishnan, U, Mundy, N & Woodruff, DW (2000) Polymorphic microsatellite DNA markers in the African elephant (Loxodinta africana) and their use in Asian elephant (Elephas maximus). Molecular Ecology, 9(12): 2223-2225.

53. Ramakrishnan, U*, Santosh, JA, Ramakrishnan, U & Sukumar, R (1998) The population and conservation status of Asian elephants in the Periyar Tiger Reserve, southern India. Current Science (Bangalore), 74(2):110-113. * Unrelated researcher.