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Genomics and introgression： Discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing

Current Zoology 2015年第1期61卷 146-154页

作者： Brian K. HAND Tyler D. HETHER Ryan P. KOVACH Clint C. MUHLFELD Stephen J. AMISH Matthew C. BOYER Sean M. O'ROURKE Michael R. MILLER Winsor H. LOWE Paul A. HOHENLOHE Gordon LUIKART Flathead Lake Biological Station Fish and Wildlife Genomics Group University of Montana Poison MT 59860 USA Institute for Bioinformatics and Evolutionary Studies Department of Biological Sciences University of Idaho Moscow ID 83844 USA U. S. Geological Survey Northem Rocky Mountain Science Center Glacier National Park West Glacier Montana 59936 USA fish and Wildlife Genomics Group Division of Biological Sciences The University of Montana Missoula Montana 59812USA montana fish Wildlife and Parks Kalispell Montana 59901 USA Department of Animal Science University of California Davis One Shields Avenue Davis CA 95616 USA University of montana Division of Biological Sciences Missoula Montana 59812 USA

Invasive hybridization and introgression pose a serious threat to the persistence of many native species. Understand- ing the effects of hybridization on native populations （e.g., fitness consequences） requires numerous species-diagnostic loci dis- tributed genome-wide. Here we used RAD sequencing to discover thousands of single-nucleotide polymorphisms （SNPs） that are diagnostic between rainbow trout （RBT, Oncorhynchus mykiss）, the world＇s most widely introduced fish, and native westslope cutthroat trout （WCT, （9. clarkii lewisi） in the northern Rocky Mountains, USA. We advanced previous work that identified 4,914 species-diagnostic loci by using longer sequence reads （100 bp vs. 60 bp） and a larger set of individuals （n = 84）. We sequenced RAD libraries for individuals from diverse sampling sources, including native populations of WCT and hatchery broodstocks of WCT and RBT. We also took advantage of a newly released reference genome assembly for RBT to align our RAD loci. In total, we discovered 16,788 putatively diagnostic SNPs, 10,267 of which we mapped to anchored chromosome locations on the RBT genome. A small portion of previously discovered putative diagnostic loci （325 of 4,914） were no longer diagnostic （i.e., fixed between species） based on our wider survey of non-hybridized RBT and WCT individuals. Our study suggests that RAD loci mapped to a draft genome assembly could provide the marker density required to identify genes and chromosomal regions in- fluencing selection in admixed populations of conservation concern and evolutionary interest [Current Zoology 61 （1）： 146-154, 2015].

关键词： Conservation genetics Hybridization Invasive species Next generation sequencing Salmonid fish SNP discovery

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Developmental rate： A unifying mechanism for sympatric divergence in postglacial fishes？

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Current Zoology 2012年第1期58卷 21-34页

作者： Mcphee, Megan V. Noakes, David L. G. Allendorf, Fred W. fisheries Division University of Alaska Fairbanks Juneau Alaska 99801 USA Department of fisheries and Wildlife and Oregon Hatchery Research Center Oregon State University Corvallis Oregon 97331-3803 USA Division of Biological Sciences University of Montana Missoula MT 59812 USA

Morphologically divergent ecotypes arise in fish populations on postglacial time scales, and resource polymorphisms are often invoked to explain their origin. However, genetic recombination can constrain the ability of divergent selection to pro- duce reproductive isolation in sympatry. Recombination breaks up favorable combinations of traits （＂adaptive suites＂） if indivi- dual traits are affected by different loci. Recombination also breaks up any association between traits under divergent selection and traits contributing to reproductive isolation. Thus, ecological speciation in the absence of preexisting barriers to gene flow is more likely when pleiotropy minimizes the number of loci involved. Here, we revisit research conducted by Carl Hubbs in the early 1900s on the effects of developmental rate on morphological traits in fishes. Hubbs＇ work provides a mechanism to explain how sympatric divergence by trophic polymorphism can occur despite the challenges of recombination. We consider the implica- tions of Hubbs＇ observations for ecological speciation with gene flow in fishes, as well as rapid evolution in captive fish popula- tions [Current Zoology 58 （1）： 21-34, 2012].

关键词： Pleiotropy Resource polymorphism Selection-recombination antagonism

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Reimagining large river management using the Resist-Accept-Direct(RAD)framework in the Upper Mississippi River

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Ecological Processes 2023年第1期12卷 645-664页

作者： Nicole K.Ward Abigail J.Lynch Erik A.Beever Joshua Booker Kristen L.Bouska Holly Embke Jeffrey N.Houser John F.Kocik Joshua Kocik David J.Lawrence Mary Grace Lemon Doug Limpinsel Madeline R.Magee Bryan M.Maitland Owen McKenna Andrew Meier John M.Morton Jeffrey D.Muehlbauer Robert Newman Devon C.Oliver Heidi M.Rantala Greg G.Sass Aaron Shultz Laura M.Thompson Jennifer L.Wilkening Minnesota Department of Natural Resources Lake CityMN 55041USA U.S.Geological Survey National Climate Adaptation Science CenterRestonVA 22041USA U.S.Geological Survey Northern Rocky Mountain Science CenterBozemanMT 59715USA Department of Ecology Montana State UniversityBozemanMT 59715USA U.S.fish and Wildlife Service National Wildlife Refuge SystemOak HarborOH 43449USA U.S.Geological Survey Upper Midwest Environmental Sciences CenterLa CrosseWI 54603USA U.S.Geological Survey Midwest Climate Adaptation Science CenterSt.PaulMN 55108USA NOAA NEFSC OronoME 04473USA University of Nebraska-Lincoln LincolnNE 68503USA National Park Service Climate Change Response ProgramFort CollinsCO 80525USA U.S.fish and Wild-life Service National Wildlife Refuge SystemBloomingtonMN 55437USA Habitat Conservation Division NOAAAlaska RegionAnchorageAK 99513USA Wisconsin Department of Natural Resources MadisonWI 53703USA Aquatic Sciences Center Center for LimnologyUW-MadisonMadisonWI 53706USA U.S.Geological Survey Northern Prairie Wildlife Research Center and Midwest Climate Adaptation Science CenterJamestownND 58401USA U.S.Army Corps of Engineers La CrescentMN 55947USA Alaska Wildlife Alliance AnchorageAK 99520USA U.S.Geological Survey Alaska Cooperative Fish and Wildlife Research UnitUniversity of Alaska FairbanksFairbanksAK 99775USA University of North Dakota Grand ForksND 58202USA Minnesota Department of Natural Resources DuluthMN 55804USA Wisconsin Department of Natural Resources Boulder JunctionWI 54512USA Great Lakes Indian fish and Wildlife Commission(GLIFWC) OdanahWI 54861USA U.S.Geological Survey National Climate Adaptation Science Centerand School of Natural ResourcesUniversity of TennesseeKnoxvilleTN 37996USA U.S.fish and Wildlife Service National Wildlife Refuge SystemFort CollinsCO 80526USA

Background Large-river decision-makers are charged with maintaining diverse ecosystem services through unprec-edented social-ecological transformations as climate change and other global stressors *** interconnected,dendritic habitats of rivers,which often demarcate jurisdictional boundaries,generate complex management ***,we explore how the Resist–Accept–Direct(RAD)framework may enhance large-river management by promoting coordinated and deliberate responses to social-ecological trajectories of *** RAD frame-work identifies the full decision space of potential management approaches,wherein managers may resist change to maintain historical conditions,accept change toward different conditions,or direct change to a specified future with novel *** the Upper Mississippi River System,managers are facing social-ecological transformations from more frequent and extreme high-water *** illustrate how RAD-informed basin-,reach-,and site-scale decisions could:(1)provide cross-spatial scale framing;(2)open the entire decision space of potential management approaches;and(3)enhance coordinated inter-jurisdictional management in response to the trajectory of the Upper Mississippi River *** The RAD framework helps identify plausible long-term trajectories in different reaches(or subbasins)of the river and how the associated social-ecological transformations could be managed by altering site-scale *** reach-scale objectives may reprioritize how,where,and when site conditions could be altered to contribute to the basin goal,given the basin’s plausible trajectories of change(e.g.,by coordinating action across sites to alter habitat connectivity,diversity,and redundancy in the river mosaic).Conclusions When faced with long-term systemic transformations(e.g.,>50 years),the RAD framework helps explicitly consider whether or when the basin vision or goals may no longer be achievable,and direct options may open y

关键词： Ecosystem Management Transformation Social-ecological system Anthropocene Climate change Basin planning Cross-scale interactions

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