Jan JaneckaAssociate Professor
Bayer School of Natural and Environmental Sciences
Department of Biological Sciences
236 Mellon Hall
Education:B.S., Biology, Cornell University, 1999
M.S., Wildlife and Fisheries Biology, University of Vermont, 2002
Ph.D., Wildlife Sciences, Texas A&M University, 2006
Postdoctoral Associate, Texas A&M University, 2006-2010
Research Assistant Professor, Texas A&M University, 2010-2013
Dr. Janecka is an Associate Professor in the Department of Biological Sciences at Duquesne. He also serves as an Associate of the Snow Leopard Conservancy, and a member of the IUCN/SSC Cat Specialist Group, and the Snow Leopard Network.
He received his B.S. degree in Biology from Cornell University. He examined social structure and dispersal of bobcats for his Master's thesis in Wildlife and Fisheries Biology at University of Vermont. His Ph.D. dissertation from Texas A&M University examined the effects of habitat fragmentation on the genetic diversity of ocelots. For his post-doctoral research, Dr. Janecka studied mammalian phylogenetics, patterns in the diversification of mammals, speciation of colugos, and snow leopard conservation genetics at Texas A&M University. He has conducted field expeditions, trained biologists, and taught genetics in numerous Asian Countries including Mongolia, China, Nepal, India, and Bhutan.
Currently, Dr. Janecka is focusing on conservation genetics of snow leopards, molecular adaptation of bobcats to diverse environmental conditions, genomics of the Dromedarian camel in Oman, and evolution of mammals in the Paleocene. His laboratory has also recently established DNA testing services in wildlife forensics for the PA Game Commission. If you are interested in submitting cases please contact Dr. Janecka.
Janecka Genomics Laboratory
Genomics, Population Genetics, Phylogenetics, Conservation Biology, and Wildlife Forensics
My lab addresses three fundamental questions in biology:
(1) How is the distribution and structure of wild populations determined?
(2) What are the molecular mechanisms that lead to adaptation?
(3) How do genomic factors contribute to important phenotypes?
Answering these questions expands our understanding of evolution and ecology, improves conservation and management, and has the potential to advance the treatment of various diseases and genetic disorders. Our projects incorporate diverse fields of biology including population genetics, phylogenetics, genomics, ecology, conservation biology, physiology, and bioinformatics. In order to make concrete contributions to wildlife management, the Janecka Genomics Lab recently expanded into wildlife forensics by establishing a DNA testing service for poaching cases in Pennsylvania. Currently, we analyze samples for the PA Game Commission and we are working on expanding our service to other states.Research Projects
One of our main areas of focus is on the snow leopard, which occurs in high-altitude mountains of Asia. We use noninvasive genetics to study this elusive felid in countries including Mongolia, Pakistan, and China. We work with many partners including Mongolian Academy of Sciences, Chinese Academy of Forestry, Irbis Mongolia, Snow Leopard Conservancy, and Panthera.
Various approaches are used to understand distribution, phylogeography, population structure, prey use, and the adaptations that have enabled snow leopards to thrive in high-altitude ecosystems. This cat shares recent ancestry with the tiger, which occurs at low elevations. By studying the genomics of both wild and captive populations of these two species, we are beginning to understand the changes that occurred during their speciation. In addition, the information we obtain has important ramifications for conservation and management.
Our lab is also examining genomics of bobcats in order to elucidate how species adapt to different environmental variables. The research on bobcats not only includes sequencing genomes, but also camera trapping in Powdermill Nature Reserve and Penguin Court to examine distribution in southwestern Pennsylvania. We have begun to diversify our lab regarding the species we are studying. For example, we are now doing research on the genomics of Dromedarian camels in Oman. In this region, the camel is one of the most valuable domestic animals, both culturally and economically; we are therefore examining its genomic diversity and breed structure.
Another aspect of our research is looking at the evolution of mammals. We are collaborating with the Carnegie Museum of Natural History and several other institutions to examine patterns of mammalian diversification in the early Paleocene, just after the extinction of the dinosaurs.
Finally, we consider it very important to also apply biological research to positively impact wildlife. The methods we use for noninvasive genetics, such microsatellite profiling to identify individual snow leopards from scat, are the same ones used in forensics to match samples collected at a crime scene. We therefore recently established a DNA testing service of deer for poaching cases submitted by Wildlife Conservation Officers. It is our goal to support the PA Game Commission in enforcing wildlife laws. We are working on expanding the number of species we can test and also the regions from which we can analyze cases.
Hacker CH, Jevit MJ, Hussain S, Muhammad G, Munkhtsog Bar., Munkhtsog Bay., Zhang Y, Li D, Liu Y, Farrington J, Balbakova F, Almanov A, Kurmanaliev O, Buyanaa C, Bayandonoi G, Ochirjav M, Liang X, Bian X, Weckworth B. Jackson R, Janecka JE. (2021) Regional comparison of snow leopard (Panthera uncia) diet via NGS sequencing of 12S and COI markers. Biodiversity and Conservation 30:797-817.
Cancellare IA, Kierepka EM, Janecka J, Weckworth B, Kasmaier RT, Ward R (2021) Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats. PeerJ 9:e11498:1-22. DOI 10.7717/peerj.11498.
Hacker CE, Janecka JE, Jackson RM, Li D, Zhang Y (2020) Pastoralism Partnerships: Recognizing the value of local involvement in China's Snow Leopard Conservation Efforts. Sustainability 12:6491:1-17.
Janecka JE, Hacker C, Broderick J, Pulugulla S, Auron P, Ringling M, Nelson B, Munkhtsog B, Hussain S, Davis B, Jackson R. (2020) Noninvasive genetics and genomics shed light on the status, phylogeography, and evolution of the elusive snow leopard. Pp. 83-121. In: Conservation Genetics in Mammals-Integrative Research Using Novel Approaches. J. Ortega and J. E. Maldonado, Editors. Springer, Switzerland.
Wells M, Kanmanii NJ, Zadjali AMA, Janecka JE, Basu P, Oremland RS, Stolz JS (2020) Methane, arsenic, selenium and the origins of the DMSO reductase family. Scientific Reports 10:10946.
Hacker CE, Yunchuan D, Yifan C, Zhang Y, Zhang YG, Miller LJ, Janecka JE. (2020) Determinants of herder attitudes towards the threatened snow leopard (Panthera uncia) in Yushu Prefecture, China. Oryx. Published online 2 Jun 2020. doi:10.1017/S0030605319001315
Zhang YG, Hacker C, Zhang Y, Xue Y, Wu L, Dai Y, Luo P, Xierannima, Janecka JE, Li D. (2019) An analysis of genetic structure of snow leopard populations in Sanjiangyuan and Qilianshan National Parks. Acta Theriologica Sinica 39:442-449.
Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Ottmar Distl O, Fries R, Jagannathan V, Janecka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, Rubin C-J, Schaefer R, Schlötterer C, Thaller G, Tetens J, Velie B, Brem G, Wallner B (2019). The horse Y chromosome as an informative marker for tracing sire lines. Scientific Reports 9:6095:1-12.
Janecka JE, Davis B, Ghosh S, Paria N, Das PJ, Orlando L, Schubert M, Nielsen M, Stout TAE, Brashear W, Li G, Johnson C, Metz R, AMA Zadjali, Love CL, Varner DD, Bellott DW, Murphy W, Chowdhary BP, Raudsepp T (2018) Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nature Communications. 9:2945: 1-15.
Janecka JE, Janecka MJ (2018) Cynocephalidae. Family and Species Accounts. 14 pgs. In: The Handbook of the Mammals of the World, Insectivores, Sloths and Colugos, Volume 8 (D. Wilson editor). Lynx Edicion, Barcelona, Spain.
Janecka JE, Janecka MJ, Helgen K, Murphy WJ. (2018) The validity of three snow leopard subspecies: response to Senn et al. Heredity 120:586-590.
Warzecha CM, Coverdale JA, Janecka JE, Leatherwood JL, Pinchak WE, Wickersham TA, McCann JC (2017) Influence of short-term dietary starch inclusion on the equine cecal microbiome. Journal of Animal Science 95:5077-5090.
Gatesy J, Meredith R, Janecka JE, Simmons M, Murphy WJ, Springer M (2017) Resolution of a concatenation/coalescence kerfuffle: Partitioned coalescence support and a robust family-level tree of Mammalia. Cladistics 33:295-332.
Janecka JE, Zhang Y, Li D, Munkhtsog B, Bayaraa M, Galsandorj N, Wangchuk TR, Karmacharya D, Li J, Zhi L, Uulu KZ, Gaur A, Kumar S, Hussain S, Muhammad G, Jevit M, Hacker C, Burger P, Wultsch C, Janecka MJ, Helgen K, Murphy WJ, Jackson R (2017) Range-wide snow leopard phylogeography supports three subspecies. Journal of Heredity 108:597-607. Journal Cover.
Merson C, Statham MJ, Janecka JE, Lopez RE, Sacks BN (2017) Distribution of native and nonnative ancestry in red foxes along an elevational gradient in Central Colorado. Journal of Mammalogy 98:365-377.
Springer MS, Emerling CA, Meredith RW, Janecka JE, Eizirik E, Murphy WJ (2017) Waking the undead: implications of a soft explosive model for the timing of placental mammal diversification. Molecular Phylogenetics and Evolution 106:86-102.
Karmacharya D, Manandhar S, Shakya J, Thapa K, Bista M, Sah GP, Sharma A, Sherchan A, Dhakal M, Janecka JE, Kelly M, Waits L (2016) Incidental discovery of non-focal carnivore species during genetic study of Bengal tiger (Panthera tigris tigris) and snow leopard (Panthera uncia) in Nepal. Asian Journal of Conservation Biology 5:81-88.
Rafati M, Andersson LS, Mikko S, Feng C, Raudsepp T, Pettersson J, Janecka JE, Wattle O, Ameur A, Thyreen G, Eberth J, Huddleston J, Malig M, Bailey E, Eichler E, Penedo C, Dalin G, Chowdary B, Andersson L, Lindgren G, Rubin C-J (2016) Large deletions at the SHOX locus in the Pseudoautosomal Region are associated with Skeletal Atavism in Shetland Ponies. G3 Genes Genomes Genetics 6:2213-2223.
Janecka JE, Tewes ME, Davis IA, Haines A, Caso A, Blankenship T, Honeycutt RL (2016) Genetic differences in the response to landscape fragmentation by a habitat generalist, the bobcat, and a habitat specialist, the ocelot. Conservation Genetics 17:1093-1108.
Janecka JE, Nielsen SSE, Andersen SD, Hoffman FG, Weber RE, Anderson T, Storz JF, Fago A (2015) Genetically based low oxygen affinities of felid hemoglobins: lack of biochemical adaptation to high-altitude hypoxia in the snow leopard. Journal of Experimental Biology 218:2402-2409.
Rodgers TW, Giacalone J, Heske EJ, Janecka JE, Jansen PA, Phillips, CA, Schooley RL (2015) Socio-spatial organization and kin structure in ocelots from integration of camera trapping and noninvasive genetics. Journal of Mammalogy 96:120-128.
Avila F, Baily MP, Merriwether DA, Trifonov VA, Rubes J, Kutzler M, Chowdhary R, Janecka JE, Raudsepp T (2015) A cytogenetic and comparative map of camelid chromosome 36 and the minute in alpacas. Chromosome Research 23:237-251.
Rodgers T, Giacalone J, Heske E, Janecka JE, Phillips C, Schooley R (2014) Support for fecal noninvasive genetics as a valid technique for estimating population density of elusive animals. Tropical Conservation Science 7:690-705. Journal Cover.
Statham MJ, Murdoch J, Janecka JE, Aubry KB, Edwards CJ, Soulsbury CD, Berry O, Wang Z, Harrison D, Pearch M, Tomsett L, Chupasko J, Sacks B (2014) Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories. Molecular Ecology 23:4813-4830.
Janecka JE, Tewes ME, Laack L, Caso A, Grassman LI, Honeycutt RL (2014) Loss of genetic diversity among ocelots in the United States during the 20th century linked to human induced population reductions. Plos One 9:2:e98384:1-10.
Janecka JE, Jackson R, Munkhtsog B, Murphy WJ (2014) Characterization of 9 microsatellites and primers in snow leopards and a species-specific PCR assay for identifying noninvasive samples. Conservation Genetic Resources 6:369-373.
Janecka JE, Alves P, Karmacharya D, Samsel N, Tallmon D, Schwartz M, Cheng E (2013) Wildlife genetics in rugged landscapes: methods, applications, and examples. Pp. 35-61. In: Wildlife Research Techniques in Rugged Mountainous Asian Landscapes. Scott L. Mills & Tshering Tempa, Editors. Ugyen Wangchuck Institute for Conservation and Environment, Bhutan.
Rodgers T, Janecka JE (2013) Applications and techniques for non-invasive faecal genetics research in felid conservation. European Journal of Wildlife Research 59:1-16.
Holbrook JD, De Young RW, Janecka JE, Tewes ME, Honeycutt RL, Young JH (2012) Genetic diversity, population structure, and movements of mountain lions (Puma concolor) in Texas. Journal of Mammalogy 93:989-1000.
Janecka JE. (2012) Tracks of my soul. Pp. 25-31. In: Snow Leopard Stories from the Roof of the World. Don Hunter, Editor. University Colorado Press, Boulder, CO.
Janecka JE, Chowdhary B, Murphy WJ (2012) Exploring the correlations between sequence evolution rate and phenotypic divergence across the mammalian tree provides insights into adaptive evolution. Journal of Bioscience 37:1-13.
Murphy WJ, Janecka JE, Stadler T, Eizirik E, Ryder OA, Gatesy J, Meredith RW, Springer MS (2012) Response to comment on "Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification". Science 337:34-35.
Rosen T, Hussain S, Mohammad G, Jackson R, Janecka JE, Michel S (2012) Reconciling sustainable development of mountain communities with large carnivore conservation. Mountain Research and Development 32:286-293. Translated to Russian.
Springer MS, Meredith R, Gatesy J, Emerling C, Park J, Rabosky D, Stadler TC, Ryder O, Janecka JE, Fisher C, Murphy W (2012) Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS ONE 7:11:e49521:1-23.
Steelman S, Chowdhary B, Suchodolski J, Dowd S, Janecka JE (2012) Pyrosequencing of 16s rRNA Genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis. BMC Veterinary Research 8:231:1-11.
Anwar MB, Jackson R, Nadeem MS, Janecka JE, S Hussain, Beg MA, Ghulam M, and Qayyum M (2011) Food habits of snow leopard Panthera uncia (Schreber, 1775) in Baltistan, Northern Pakistan. European Journal of Wildlife Research 57:1077-1083.
Gilad O, Janecka, JE, Armstrong F, Tewes ME, Honeycutt TL (2011) Mountain lions in Guadalupe Mountains National Park: Estimates of occurrence and distribution through DNA analysis. The Southwestern Naturalist 56:297-304.
Janecka JE, Munkhtsog B, Jackson RM, Mallon DP, Naranbaatar G, Murphy WJ (2011) Comparison of noninvasive genetic and camera-trapping techniques for surveying snow leopards. Journal of Mammalogy 92:771-783.
Janecka JE, Tewes ME, Laack LL, Caso A, Grassman LI Jr, Haines AM, Shindle D, Davis B, Murphy WJ, Honeycutt RL (2011) Reduced genetic diversity and isolation of remnant ocelot populations occupying a severely fragmented landscape in southern Texas. Animal Conservation 14:608-619.
Karmacharya DB, Thapa K, Shrestha R, Dhakal M, Janecka JE (2011) Noninvasive genetic population survey of snow leopards (Panthera uncia) in Kangchenjunga Conservation Area, Shey Phoksundo National Park and surrounding buffer zones of Nepal. BMC Research Notes 4:1-8. Li G, Janecka JE, Murphy WJ (2011) Accelerated evolution of CES7, a gene encoding a novel major urinary protein in the Cat Family. Molecular Biology and Evolution 28:911-920.
*Meredith, RW, *Janecka JE (Co-first authors contributed equally), Gatesy J, Ryder OA, Fisher CA, Teeling EC, Alisha Goodbla A, Eizirik E, Simão TLL, Stadler T, Rabosky DL, Honeycutt RL, Flynn JF, Ingram CI, Steiner C, Williams TL, Robinson TJR, Burk-Herrick A, Westerman M, Ayoub NA, *Springer MS, *Murphy WJ (2011) Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on extant mammal diversification. Science 334:521-524. *First and last authorship determined by coin flip.
Springer MS, Meredith RW, Janecka JE, Murphy WJ (2011) The historical biogeography of Mammalia. Philosophical Transactions of the Royal Society B: Biological Sciences 366:2478-2502.
Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert MTP, Dalén L, Arsuaga JL, Ericson PGP, Huson DH, Helgen KM, Murphy WJ, Götherström A, Schuster SC (2009) The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Research 19:213-220. Journal Cover.
Janecka JE, Jackson R, Zhang Y, Li D, Munkhtsog B, Buckley-Beason V, Murphy WJ (2008) Population monitoring of snow leopards using noninvasive collection of scat samples: A pilot study. Animal Conservation 11:401-411. Journal Cover.
Janecka JE, Lim NT-L, Baba M, Izawa M, Boeadi, Murphy WJ (2008) Evidence for multiple species of Sunda colugo. Current Biology 18:R1001-R1002.
Janecka JE, Tewes ME, Laack LL, Grassman LI Jr, Haines AM, Honeycutt RL (2008) Small effective population sizes of two remnant ocelot populations (Leopardus pardalis albescens) in the United States. Conservation Genetics 9:869-878.
Janecka JE, Blankenship TL, Hirth DH, Kilpatrick CW, Tewes ME, Grassman LI Jr (2007) Evidence for male-biased dispersal in bobcats Lynx rufus using relatedness analysis. Wildlife Biology 13:38-47.
Janecka JE, Grassman LI Jr, Honeycutt RL, Tewes ME (2007) Whole genome amplification for sequencing and applications in conservation genetics. The Journal of Wildlife Management 71:1357-1360.
Janecka JE, Miller W, Pringle TH, Wiens F, Zitzmann A, Helgen KM, Springer MS, Murphy WJ (2007) Molecular and genomic data identify the closest living relative of primates. Science 318:792-795.
Janecka JE, Walker CW, Tewes ME, Caso A, Laack LL, Honeycutt RL (2007) Phylogenetic relationships of ocelot (Leopardus pardalis albescens) populations from the Tamaulipan Biotic Province and implications for recovery. Southwestern Naturalist 52:89-96. Journal Cover.
Grassman LI, Haines AM, Janecka JE, Tewes ME (2006) Activity periods of photo-captured mammals in northcentral Thailand. Mammalia 70:306-309.
Grassman LI, Janecka JE, Austin SC, Tewes ME, Silvy NJ (2006) Chemical immobilization of free-ranging dhole (Cuon alpinus), binturong (Arctis binturong), and yellow-throated marten (Martes flavigula) in Thailand. European Journal of Wildlife Research 52:297-300.
Grassman LI, Janecka JE, Tewes ME (2006) Ecological separation of Martes flavigula with 5 sympatric mesocarnivores in northcentral Thailand. Pp. 63-73. In: Martes in Carnivore Communities: Proceedings of the 4th International Martes Symposium. Santos-Reis M, Proulx G, Birks JDS, O'Doherty EC, Editors. Alpha Wildlife Publications, Sherwood Park, Alberta, Canada.
Haines AM, Grassman LI, Janecka JE, Tewes ME (2006) First ocelot (Leopardus pardalis) monitored with GPS telemetry. European Journal of Wildlife Research 52:216-218.
Haines AM, Janecka JE, Tewes ME, Grassman LI, Morton P (2006) The importance of private lands for ocelot Leopardus pardalis conservation in the United States. Oryx 40:1-5.
Janecka JE, Blankenship TL, Hirth DH, Tewes ME, CW Kilpatrick, LI Grassman Jr (2006) Kinship and social structure of bobcats (Lynx rufus) inferred from microsatellite and radio-telemetry data. Journal of Zoology (London) 269:494-501.
Janecka JE, Grassman LI Jr, Derr JN, Honeycutt RL, Eiadthong W, Tewes ME (2006) Rapid whole genome amplification of DNA from felids: Applications for conservation genetics. Wildlife Society Bulletin 34:1134-1141.
Janecka JE, Jenkins MB, Brackett NS, Lion LW, Ghiorse WC (2002) Characterization of a Sinorhizobium isolate and its extracellular polymer implicated in pollutant transport in soil. Applied and Environmental Microbiology 68:423-425.
Pimentel D, McNair S, Janecka JE, Wightman J, Simmonda C, O'Connel C, Wong E, Russel L, Zern J, Aquino T, Tsomondo T (2001) Economic and environmental threats of alien plant, animal, and microbe invasions. Agriculture, Ecosystems and Environment 84:1-20.
Courses Currently Taught by Dr. Janecka:
BIOL 419/619: Bioinformatics: Analysis of Molecular and Genomic Data, 3 credits (Fall, 2015-Present)
Bioinformatics is the statistical analysis of biological data. This course covers the theory, approaches, and applications to interpreting DNA, RNA, protein and genomic data. Topics covered include sequence analysis, alignment, phylogenetics, analysis of RNA and proteins, functional genomics, application of next-generation sequencing technology, de novo assembly, read mapping, variant detection, gene annotation, differential expression using RNAseq, genome wide association studies, and statistical analysis and interpretation genomic data. Course provides an immersion in the R environment and teaches numerous computational programs.
BIOL 250: Genetics, 3 credits (Spring, 2014-present)
This course covers major topics in genetics and the theory, methods, approaches, and breakthroughs in this exciting field. A problem solving approach is used to teach fundamental principles. Attention is given to relevant examples that illustrates the applications of genetics to our society, health, conservation, and other important aspects of the world. Topics include classical Mendelian genetics, chromosomal inheritance, disease, population genetics, evolution, and gene expression.
BIOL 494/594/ENVI 594 Environmental Sampling and Analysis, 3 credits (summer, odd years) co-taught with Dr. Beth Dakin
This is a hands-on 6-week summer course focused on techniques for environmental analysis. Dr. Janecka covers exploring variables that contribute to population declines, biodiversity assessments, wildlife surveys (track stations, small mammal trapping, and camera traps), occupancy modeling, population genetics, and microsatellite analysis.
Courses Previously Taught by Dr. Janecka:
BIOL 646: Advanced Topics: Illumina Sequencing and NGS Analysis, 3 credits (Spring 2019)
This was a hands-on course that taught Nextera DNA Flex library preparation, sequencing on Illumina MiSeq, post-processing of reads, de novo assembly, BLAST, sequence alignment, and phylogenetics. Groups of 3 students were provided an unknown BAC at the beginning of the course which they then sequenced and determined its identity and content.
BIOL 646: Advanced Topics: Bioinformatics - Analysis of Genomic Data, 1 credit (Fall 2014)
This course provided an abridged introduction to analyzing and interpreting next generation sequencing data and using bioinformatics software in Linux. Topics covered included processing sequencing reads, de novo assembly, read mapping, variant detection, gene annotation, differential expression using RNAseq, genome wide association studies, and statistical analysis and interpretation genomic data.
BIOL 394: Undergraduate Biology Seminar, 1 credit (Fall 2014, 2015)
This course applied active learning to give students a solid foundation in developing, writing, and presenting scientific research. Students read and discussed scientific literature, critically assessed methods and results, evaluated hypotheses based on results, and presented their ideas in both written and oral form. During the course they wrote a proposal or manuscript, and developed a PowerPoint presentation. The goal was to produce a proposal/manuscript that could be either be submitted to a funding agency or be the basis for a final report or journal submission. They were encouraged to give their PowerPoint presentations at a scientific conference the following semester.
BIOL 490/690: Seminar, 1 credit (Fall 2015)
Department of Biological Sciences seminar series.