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Meeting Time: 5:00 PM - 6:00 PM Wednesdays
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Meeting room: ESB 121
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Zoom Link
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MeetingDateActivityLeaderUnitPrimary TopicSecondary TopicsManuscriptManuscript LinkNotes
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1Aug 31ReadJillIntro to Conservation Genomics & the courseWhat is conservation genomics?What is conservation genomics? Course Goals & Objectives.Taylor, Helen R., 'Conservation Genetics in Practice', Conservation and the Genomics of Populations, 3rd edn (Oxford, 2022; online edn, Oxford Academic, 21 Apr. 2022), accessed 24 Aug. 2022.https://doi.org/10.1093/oso/9780198856566.003.0024 (PDF)
Conservation Genetics Introduction (short book chapter)
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2Sept 7Lecture/IntroCynthiaTechnology & MethodsGenome to populations (sequencing technologies) (Cynthia)What is conservation genomics (continued) Paez, S., Kraus, R. H., Shapiro, B., Gilbert, M. T. P., Jarvis, E. D., Vertebrate Genomes Project Conservation Group, ... & Venkatesh, B. (2022). Reference genomes for conservation. Science, 377(6604), 364-366.https://www.science.org/doi/10.1126/science.abm8127
Current commentary on what reference genomes can do for conservation
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3Sept 14ReadJillTechnology & MethodsMethods in conservation genomicsSkill development: big data and experimental designSchweizer, R. M., Saarman, N., Ramstad, K. M., Forester, B. R., Kelley, J. L., Hand, B. K., ... & Luikart, G. (2021). Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field. Journal of Heredity, 112(4), 313-327.https://academic.oup.com/jhered/article/112/4/313/6226929
Technologies and design - more about assessing populations than single reference genomes
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4Sept 21ReadJillTechnology & MethodsMethods in conservation genomicsGenome Assembly and AnnotationPodsiadlowski, L., Tunström, K., Espeland, M., & Wheat, C. W. (2021). The genome assembly and annotation of the Apollo butterfly Parnassius apollo, a flagship species for conservation biology. Genome Biology and Evolution, 13(8), evab122.
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Twort, V. G., Blande, D., & Duplouy, A. (2022). One’s trash is someone else’s treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts. BMC microbiology, 22(1), 1-16.		https://academic.oup.com/gbe/article/13/8/evab122/6296838 AND https://link.springer.com/article/10.1186/s12866-022-02602-1
Example of a 'genome note' - basis for the discussion next week and also an introduction to some standard approaches - can focus on methods - fast paper
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5Sept 28No Meeting----
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6Oct 5Lecture/IntroKarlPopulation DynamicsPopulation dynamics influencing conservation (Karl)How do population dynamics influence conservation?Hampe, A., & Petit, R. J. (2005). Conserving biodiversity under climate change: the rear edge matters. Ecology letters, 8(5), 461-467. https://doi.org/10.1111/j.1461-0248.2005.00739.x
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7Oct 12ReadNick VGPopulation DynamicsLandscape genetics & biogeographyGenetic diversity, effective population size, coalescent modelsCapblancq, T., et al. (2020). Whole‐exome sequencing reveals a long‐term decline in effective population size of red spruce (Picea rubens). Evolutionary applications, 13(9), 2190-2205.https://doi.org/10.1111/eva.12985
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8Oct 19ReadVidyaPopulation DynamicsFitness traits & genetic diversityHeterozygosity, seed germination biologyCapblancq, T., Munson, H., Butnor, J.R. et al. Genomic drivers of early-life fitness in Picea rubens. Conserv Genet 22, 963–976 (2021). https://doi.org/10.1007/s10592-021-01378-7
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9Oct 26ReadAKRITI Population DynamicsPest resistanceQuantitative GeneticsCarey Louise, et al. (2022). Genomic evidence of natural selection for ash dieback resistance. bioRxiv 2022.08.01.502033https://www.biorxiv.org/content/10.1101/2022.08.01.502033v3
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10Nov 2Lecture/IntroMichelleGenome Enabled ConservationApplying genome methods for conservation (Michelle)Introducing the Greater Prairie-Chicken & Genetic RescueWestemeier, R. L. et al. Tracking the Long-Term Decline and Recovery of an Isolated Population. Science 282, 1695–1698 (1998).https://doi.org/10.1126/science.282.5394.1695
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11Nov 9ReadJulia and EmilyGenome Enabled ConservationPost-genetic rescue impact assessment using microsatellite & mitochondrial markersBouzat, J. L. et al. Beyond the beneficial effects of translocations as an effective tool for the genetic restoration of isolated populations. Conserv Genet 10, 191–201 (2009).https://link.springer.com/article/10.1007/s10592-008-9547-8
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12Nov 16ReadCindyGenome Enabled ConservationPost-genetic rescue impact assessment using ddRADseqPopulation structure, heterozygosityCapel, S. L. R. et al. Evaluating the genome-wide impacts of species translocations: the greater prairie-chicken as a case study. Conserv Genet 23, 179–191 (2022).https://doi.org/10.1007/s10592-021-01412-8
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13Nov 30ReadCristopher and HannahGenome Enabled ConservationAssessing inbreeding depression by WGSSimulation modelingRobinson, J. A. et al. The critically endangered vaquita is not doomed to extinction by inbreeding depression. Science 376, 635–639 (2022).https://www.science.org/doi/10.1126/science.abm1742
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14Dec 7Group ActivityAllGenome Enabled ConservationDescribe an example of applying genomics in conservationDescribe an application of a genomic method in a conservation context.
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