Publications:

Praveen, P, Gopal, R and Ramakrishnan, U. The population structure of invasive Lantana Camara is shaped by its mating system, (in review eLife).

Rana, D, Boyer, F, Barba, MD, Taberlet, P and Ramakrishnan, U. From single species to communities: microsatellite amplicon sequencing to monitor felids using Feliplex. (in review, Molecular Ecology Resources)

Aditi, BV and Ramakrishnan, U. Beyond neutral loci: Examining immune gene variation in tigers (Panthera tigris), (in review, Molecular Ecology)

Solari KA, Morgan SA, Poyarkov AD, Weckworth B, Samelius G, Sharma K, Ostrowski S, Ramakrishnan U, Kubanychbekov Z, Kachel S, Johansson O et al., (2023) Extreme in Every Way: Exceedingly Low Genetic Diversity in Snow Leopards Due to Persistently Small Population Size. bioRxiv, pp2023-12. (in review, Molecular Biology and Evolution)

Ansil, BR, Sanyal, A, Sreenivas, D, Garg, KM, Ramakrishnan, U and Chattopadhyay, B. Identification of distinct rodent-associated adenovirus lineages from a mixed-use landscape in the Western Ghats biodiversity hotspot (in revision, EcoHealth)

Chhattani, H, Harihar, A, Dean, R, Yadav, A, Patel, K, Rana, D, Pandit, A, Shukla, SK, Rahim, V and Ramakrishnan, U. Trace DNA from kill sites identifies predating tigers (in revision, Biological Conservation)

Ansil, BR, Vishwanathan, A, Ramachandran, V, Yeshwanth, HM, Sanyal, A and Ramakrishnan, U. Host-pathogen-vector continuum in a changing landscape: potential transmission pathways for Bartonella in a small mammal community (in revision, Ecology and Evolution)

Grossen, C and Ramakrishnan, U. Genetic Load. Primer (accepted, Current Biology)

Khan A, Sil M, Thekaekara, T, Sinha, I, Khurana, R, Sukumar, R and Ramakrishnan, U (2024) Divergence and serial colonization shape genetic variation and define conservation units in Asian elephants. Current Biology, 34 (20), 4692-4703. e5

Armstrong EE, Mooney JA, Solari KA, Kim BY, Barsh GS, Grant VB, Greenbaum G, Kaelin CB, Panchenko K, Pickrell JK, Rosenberg N et al. (including Ramakrishnan, U) (2024) Unraveling the Genomic Diversity and Evolutionary History of Captive Tigers in the United States. Proc. Nat. Acad. Sci., 121 (39), e2402924121

Rana, D, Sartor, CC, Chiaverini, L, Cushman, SA, Kaszta, Z, Ramakrishnan, U and Macdonald, DW (2024) Bottom of Form Differentially biased sampling strategies reveal the non-stationarity of species distribution models for Indian small felids. Ecological Modelling, 493, 110749.

Tyagi, A, Yadav, N, Pandit, A and Ramakrishnan, U (2024) On the road to losing connectivity: Fecal samples provide genome-wide insights into anthropogenic impacts on two large herbivore species in central India. Molecular Ecology, https://doi.org/10.1111/mec.17461

Ghosh-Harihar M, Yadav N, Gurung N, CS D, CK V, Prakash V, Green RE, Ramakrishnan U (2024) Spatial patterns in the diet of Gyps vultures in India and their implications for conservation. Biological Conservation, 292 (110551)

Ansil, BR, George, CE, Chandrasingh, S, Vishwanathan, A, Thattai, M, Padinjat, R, Devadiga, S, Harikumar, AG, Harsha, PK, Nair, I, Ramakrishnan, U, Mayor, S (2023) Validating saliva as a biological sample for cost-effective, rapid and routine screening for SARS-CoV-2. Indian Journal of Medical Microbiology, 45 (100384)

Srivathsa, A, Ramachandran, V, Saravanan, P, Sureshbabu, A, Ganguly, D and Ramakrishnan, U (2023) Topcats and underdogs: intraguild interactions among three apex carnivores across Asia's forestscapes. Biological Reviews, https://doi.org/10.1111/brv.12998

Tyagi, A, Godbole, M, Vanak, A and Ramakrishnan, U (2023) Citizen science facilitates first ever genetic detection of wolf-dog hybridization in Indian savannahs. Ecology and Evolution, https://doi.org/10.1002/ece3.10100

Srivathsa, A, Vasudev, D, Nair, T, Chakrabarti, S, Chanchani, P, DeFries, R, Deomurari, A, Dutta, S, Ghose, D, Goswami, V R, Nayak, R, Neelakantan, A, Thatte, P, Vaidyanathan, S, Verma, M, Krishnaswamy, J, Sankaran, M, Ramakrishnan, U (2023) Prioritizing landscapes to reconcile biodiversity conservation, ecosystem services, and human well-being in India, Nature Sustainability. 1-10.

Shukla, H, Suryamohan, K, Khan, A, Katta, AVS. Krishna Mohan, P, Rajadurai, M, Oommen, M, Ramesh, D, Mandumpala, Muraleedharan, M, Kuriakose, B, Michael, S, Krishnankutty, S, Zachariah, A, Seshagiri, S, Ramakrishnan, U (2023) Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex-predation. Gigascience, 12; giac112

Aylward, M, Sagar, V, Natesh, M and Ramakrishnan, U (2022). How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India. Philosophical Transaction, B https://doi.org/10.1098/rstb.2020.0418

Tyagi, A, Khan, A, Thatte, P, Ramakrishnan, U (2022). Genome-wide SNP markers from fecal samples reveal anthropogenic impacts on connectivity: case of a small carnivore in the central Indian landscape. Animal Conservation. https://doi.org/10.1111/acv.12770

Schoen, J, Neelakantan, A, Cushman, SA, Dutta, T, Habib, B, Jhala, VY, Mondal, Ramakrishnan, U, Reddy, AP, Saini, S, Sharma, S, Thatte, P, Yumnam, B, DeFries, R (accepted, Conservation Biology). Synthesizing connectivity analyses for co-management of a globally important human-dominated tiger (Panthera tigris) conservation landscape.

Khan A, Krishna SM, Ramakrishnan U, Das R (2021) Recapitulating whole genome based population genetic structure for Indian wild tigers through an ancestry informative marker panel. Heredity. Dec 2:1-9.

Khan, A, Patel, K, Shukla, H, Vishwanathan, A, van der Valk, T, Borthakur, U, Nigam, P, Zachariah, A, Jhala, YV, Kardos, M and Ramakrishnan, U (2021). Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. Proc. Nat. Acad. Sci.  Dec 7; 118(49).

Sagar, V, Kaelin, CB, Natesh, M, Reddy, AP, Mohapatra, R, Chhattani, H, Thatte, P, Vaidyanathan, S, Biswas, S, Bhat, S, Paul, S, Jhala, YV, Varma, MN, Pandav, B, Mondol, S, Barsh, GS, Swain, D and Ramakrishnan, U (2021). High frequency of an otherwise rare phenotype in a small and isolated tiger population Proc. Nat. Acad. Sci. Sep 28;118(39).

Ramakrishnan U (2021). At the crossroads: molecular ecology and wildlife conservation. Journal of the Indian Institute of Science. 101(2):115-6. Ansil BR, Mendelhall, I and Ramakrishnan, U (2021). Small mammals in the biodiverse Western Ghats harbor high prevalence and diversity of zoonotic Bartonella. PLoS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0009178

Srivathsa, A, Rodrigues, RG, Kok, BT, Taylor, RW, Zachariah, A, Oli, MK and Ramakrishnan, U (2021). The truth about scats and dogs: Next-generation sequencing and spatial capture–recapture models offer opportunities for conservation monitoring of an endangered social canid Biological Conservation, 256, 109028

Armstrong, E…. and Ramakrishnan, U (2021), Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection Molecular Biology and Evolution, https://doi.org/10.1093/molbev/msab032

Bawa, KS, Nawn, N, Chellam, R, Krishnaswamy, J, Mathur, V, Olsson, SB, ... and Quader, S (including Uma Ramakrishnan) (2020) Opinion: Envisioning a biodiversity science for sustaining human well-being. Proceedings of the National Academy of Sciences, 117(42), 25951-25955.

Dinesh AS, Mathur V, Ansil BR, Chandru V, Chellam R, Vanak AT, Ramakrishnan U, Rajagopal P (2020) Health Heatmap of India: An Open Data Platform. Journal of the Indian Institute of Science. 18:1-6.

Ghosh-Harihar, M, Gurung, N, Shukla, H, Sinha, I, Pandit, A, Prakash, V, Green, RE and Ramakrishnan, U (2020) Metabarcoding for parallel identification of species, sex and diet of obligate scavengers: an application to globally-threatened Gyps vultures. Conservation Genetics Resources. https://doi.org/10.1007/s12686-020-01171-7

Hoban, S and others (including Uma Ramakrishnan) (2020) Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved. Biological Conservation 248: 108654.

Thatte P, Chandramouli A, Tyagi A, Patel K, Baro P, Chhattani H, Ramakrishnan U (2020) Human footprint differentially impacts genetic connectivity of four wide‐ranging mammals in a fragmented landscape. Diversity and Distributions. 26(3):299-314.

Khan, A, Patel, K, Bhattacharjee, S, Sharma, S, Chugani, A, Sivaraman, K, Hosawad, V, Sahu, Y, Reddy, GV and Ramakrishnan, U (2020) Are shed hair genomes the most effective non-invasive resource for estimating relationships in the wild? Ecology and Evolution 10(11): 4583-4594.

Bajaru SB, Lajmi A, Manakadan R, Kulavmode AR, Ramakrishnan U (2020) Assessing the status of critically endangered Kondana soft-furred rat (Millardia kondana) using integrative taxonomy: combining evidence from morphological, molecular and environmental niche modeling. Mammalia. 9;1(ahead-of-print).

Dahal, N, Kumar, S, Noon, B and Ramakrishnan, U (2020) Climatic niche and phylogeny jointly shape the distribution of pikas in the Himalaya, Ecology and Evolution.10 (3), 1539-1551

Dovih, P, Laing, ED, Chen, Y, Low, DHW, Ansil, BR, Yang, X, Shi, Z, Broder, CC, Smith, GJD, Linster, M, Ramakrishnan, U and Mendenhall, IH (2019) Filovirus-reactive antibodies in humans and bats in Northeast India imply zoonotic spillover. PLoS Neglected Tropical Diseases 13(10): e0007733.

Alcala, N, Goldberg, A, Ramakrishnan, U and Rosenberg, NA (2019). Coalescent theory of migration network motifs. Molecular Biology and Evolution 36(10):2358-74.

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. *authors listed alphabetically

Gupta P, Vishnudas CK, Ramakrishnan U, Robin VV and 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 286:20190439.

Mukherjee S, Singh P, Silva AP, Ri C, Kakati K et al… and Ramakrishnan, U (2019) Activity patterns of the small and medium felid (Mammalia: Carnivora: Felidae) guild in northeastern India. Journal of Threatened Taxa 11(4):13432-47.

Agarwal I, Khandekar A, Giri VB, Ramakrishnan U and 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.

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 *Equal contribution

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

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

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

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, 52(13):818-847.

Thatte, 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.

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.

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 Science 5(2): 172024.

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

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

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

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

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

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): 635-1641.

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 44(9): 2021-2032.

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

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.

Ramachandran, V., Robin, V.V., Tamma, K. and Ramakrishnan, U (2016) Climatic and geographic barriers drive distributional patterns of bird phenotypes within peninsular India. Journal of Avian Biology 48(5):620-630.

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

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): https://doi.org/10.21425/F5FBG26262

Robin, VV, Vishnudas, CK, Gupta, P and Ramakrishnan, U (2015) Deep and wide valleys drive nested phylogeographic patterns across a montane bird community. Proceeding of the Royal Society B 282 (1810)

Robin, VV, Gupta, P, Thatte, P and Ramakrishnan, U (2015) Islands within islands: two montane paleo-endemic birds impacted by recent anthropogenic fragmentation. Molecular Ecology 24 (14):3572-3584.

Varudkar, A and Ramakrishnan, U (2015) Commensalism facilitates gene flow in mountains: A comparison between two Rattus species. Heredity 115:253-261.

Garg, KM, Chattopadhyay, C, Vinoth Kumar, AK, Swami Doss, DP, Sivasundar, A, Kandula, S and Ramakrishnan, U (2015) Males and females gain differentially from sociality in a promiscuous fruit bat Cynopterus sphinx PLoS One 10(3):e0122180

Tamma, K and Ramakrishnan, U (2015) Mammal diversity gradients in mainland Asia. BMC Evolutionary Biology 15 (1):11

Mondol, S, Sridhar, V, Yadav, P, Gubbi, S and Ramakrishnan, U (2015) Tracing the geographic origin of traded leopard body parts in the Indian subcontinent. Conservation Biology 29 (2):556-564.

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

Chattopadhyay, C, Garg, KM and Ramakrishnan, U (2014) Effect of diversity and missing data on genetic assignment with RAD-Seq markers. BMC Research Notes 7:241.

Mondol, S, Kumar, NS, Gopalaswamy, AM, Sunagar, K, Karanth, KU and Ramakrishnan U (2014) Identifying species, sex and individual tigers and leopards in the Malenad-Mysore Tiger Landscape, Western Ghats, India. Conservation Genetics Resources DOI:10.1007/s12686-014-0371-9.

Chakraborty D, Sinha A and 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. doi:10.1371/journal.pone.0097061

Chakraborty D, Ramakrishnan U and 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

Robin, VV, Vishnudas, CK and 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.

Savory, F and Ramakrishnan, U (2014) Asymmetric patterns of reassortment and concerted evolution in Cardamom Bushy Dwarf Virus. Infection, Genetics and Evolution 24:15-24.

Savory, F, Varma, V and Ramakrishnan, U (2014) Identifying geographic hotspots of reassortment in a multipartite plant virus. Evolutionary Applications 7(5):569-579.

Bay, RA, Ramakrishnan, U and Hadly, EA (2014) A call for tiger management using “Reserves” of genetic diversity. Journal of Heredity 105(3): 295-302.

Srinivasan, U, Tamma, K and 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.

Joshi, A, Vaidyanathan, S, Mondol, S, Edgaonkar, A and Ramakrishnan, U (2013) Connectivity of Tiger (Panthera tigris) Populations in the human-influenced forest mosaic of central India. PloS One 8(11): e77980

Mondol, S, Bruford, MW and Ramakrishnan, U (2013) Demographic loss, genetic structure and the conservation implications for Indian tigers. Proceedings of the Royal Society B 280 (1762)

Mukherjee, M, Adhya, T, Thatte, P and 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

Garg, KM, Chattopadhyay, B, Doss, DPS, Vinoth Kumar, AK, Kandula, S and 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

Chattopadhyay, B, Garg, KM, Vinoth Kumar, AK , Doss, DPS, Ramakrishnan, U and Kandula, S (2012) Sibling species in South Indian populations of the rufous horse-shoe bat, Rhinolophus rouxii. Conservation Genetics 13(6):1435-1445

Mondol, S, Thatte, P, Yadav, P and 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.4, 63-66.

Malhi, RS, Satkoski-Trask, J, Shattuck, M, Johnson, J, Chakraborty, D, Kanthaswamy, S, Ramakrishnan, U and Smith, DG (2011). Genotyping single nucleotide polymorphisms (SNPs) across species in Old World Monkeys. American Journal of Primatology 73:1–10.

Robin VV, Sinha A and 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.

Mukherjee, S, Krishnan, A, Tamma, K, Home, C, Navya R, Joseph, S and 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.

Mukherjee, S, Ashalakshmi, CN, Home, C and 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

Chakraborty, S, Chakraborty, D, Mukherjee, O, Jain, S, Ramakrishnan, U and Sinha, A (2010) Genetic polymorphism in the serotonin transporter promoter region and ecological success in macaques. Behavior Genetics 40(5):672-9

Mondol, S, Navya, R, Athreya, V, Velu Mani, S, Sunagar, K and Ramakrishnan, U. A panel of microsatellites to identify leopards (Panthera pardus) individually from non-invasive samples BMC Genetics 10:79 doi:10.1186/1471‐2156‐10‐79

O’Keefe, K, Ramakrishnan, U, van Tuinen, M and Hadly, EA (2009) Source-sink dynamics in a common montane mammal. Molecular Ecology 18(23):4775‐4789

Ramakrishnan, U and Hadly, EA (2009) Invited perspective: Do complex population histories drive higher estimates of substitution rate in phylogenetic reconstructions? Molecular Ecology 18(21):4341-4343

Mondol, S, Karanth, KU, Kumar, S, Gopalswamy, A, Andheria, A and Ramakrishnan, U (2009) Evaluation of non-invasive genetic sampling methods for estimating tiger population size. Biological Conservation 142:2350-2360

Mondol, S, Karanth, KU and Ramakrishnan, U (2009) Why the Indian subcontinent holds the key to global tiger recovery. PLoS Genetics 5(8): e1000603

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

van Tuinen, M, O’Keefe, K, Ramakrishnan, U and 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

James, J, Ramakrishnan, U and 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

Tishkoff, SA, Gonder, MK, Henn, BM, Mortense, H, Fernandopulle, F, Gignoux, C, Godfrey, L, Nyambo, TB, Underhill, PA, Ramakrishnan, U, Reed, FA and 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

Mukherjee, N, Mondol, S, Andheria, A and Ramakrishnan, U (2007) Rapid multiplex PCR based species identification of wild tigers using non-invasive samples. Conservation Genetics 8(6): 465-1470

Chakraborty, D, Ramakrishnan, U, Panor, J, Mishra, C and 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

Belle, E, Ramakrishnan, U Mountain, JL and Barbujani, G (2006) Serial coalescent simulations suggest a weak genealogical relationship between Etruscans and modern Tuscans. Proceedings of the National Academy of Sciences (USA) 103(21):8012-8017 Ramakrishnan, U, Hadly, EA and Mountain, JL (2005) Detecting past population bottlenecks using temporal genetic data. Molecular Ecology 14(10):2915-2922

Anderson CNK, Ramakrishnan, U, Chan YL and Hadly EA (2005) Serial SIMCOAL: A population genetic model for data from multiple populations and points in time. Bioinformatics 21(8):1733-1734

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

Ramakrishnan, U, Storz, JF, Taylor, BL and Lande, R (2004) Rejection algorithm based estimation of the effective number of breeding males using genetic data. Molecular Ecology 13:3283-3292

Ramakrishnan, U and Mountain, JL (2004) Precision and accuracy of divergence time estimates from SNPSTR and STR variation. Molecular Biology and Evolution 21(10): 1960-1971

Hadly, EA, Ramakrishnan, U, Chan, YL, van Tuinen, M, Conroy, C, Spaeth, PE and O’Keefe, K (2004) Genetic response to climatic change: insights from ancient DNA and phylochronology. Public Library of Science, Biology 2(10): e290

van Tuinen, M, Ramakrishnan, U and 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

Storz, JF, Ramakrishnan, U and Alberts, SC (2002) Genetic effective size of a wild primate population: influence of current and historical demography. Evolution 56(4): 817-829

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

Storz, JF, Ramakrishnan, U and Alberts, SC (2001) Determinants of effective population size for loci with different modes of inheritance. Journal of Heredity, 92: 497-502

Nievergelt, CM, Digby, LJ, Ramakrishnan, U and 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

Eggert, LE, Ramakrishnan, U, Mundy, N and 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

Ramakrishnan, U*, Santosh, JA, Ramakrishnan, U and 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