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Uckele KA, Adams RP, Schwarzbach AE, Parchman TL. Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny. Mol Phylogenet Evol 2020; 156:107022. [PMID: 33242585 DOI: 10.1016/j.ympev.2020.107022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 10/06/2020] [Accepted: 11/17/2020] [Indexed: 12/22/2022]
Abstract
Juniper (Juniperus) is an ecologically important conifer genus of the Northern Hemisphere, the members of which are often foundational tree species of arid regions. The serrate leaf margin clade is native to topologically variable regions in North America, where hybridization has likely played a prominent role in their diversification. Here we use a reduced-representation sequencing approach (ddRADseq) to generate a phylogenomic data set for 68 accessions representing all 22 species in the serrate leaf margin clade, as well as a number of close and distant relatives, to improve understanding of diversification in this group. Phylogenetic analyses using three methods (SVDquartets, maximum likelihood, and Bayesian) yielded highly congruent and well-resolved topologies. These phylogenies provided improved resolution relative to past analyses based on Sanger sequencing of nuclear and chloroplast DNA, and were largely consistent with taxonomic expectations based on geography and morphology. Calibration of a Bayesian phylogeny with fossil evidence produced divergence time estimates for the clade consistent with a late Oligocene origin in North America, followed by a period of elevated diversification between 12 and 5 Mya. Comparison of the ddRADseq phylogenies with a phylogeny based on Sanger-sequenced chloroplast DNA revealed five instances of pronounced discordance, illustrating the potential for chloroplast introgression, chloroplast transfer, or incomplete lineage sorting to influence organellar phylogeny. Our results improve understanding of the pattern and tempo of diversification in Juniperus, and highlight the utility of reduced-representation sequencing for resolving phylogenetic relationships in non-model organisms with reticulation and recent divergence.
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Affiliation(s)
- Kathryn A Uckele
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
| | - Robert P Adams
- Baylor University, Utah Lab, 201 N 5500 W, Hurricane, UT 84790, USA.
| | - Andrea E Schwarzbach
- Department of Health and Biomedical Sciences, University of Texas - Rio Grande Valley, 1 W University Drive, Brownsville, TX 78520, USA.
| | - Thomas L Parchman
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
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Xiang KL, Erst AS, Xiang XG, Jabbour F, Wang W. Biogeography of Coptis Salisb. (Ranunculales, Ranunculaceae, Coptidoideae), an Eastern Asian and North American genus. BMC Evol Biol 2018; 18:74. [PMID: 29793422 PMCID: PMC5968522 DOI: 10.1186/s12862-018-1195-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 05/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Numerous studies have favored dispersal (colonization) over vicariance (past fragmentation) events to explain eastern Asian-North American distribution patterns. In plants, however the disjunction between eastern Asia and western North America has been rarely examined using the integration of phylogenetic, molecular dating, and biogeographical methods. Meanwhile, the biogeographic patterns within eastern Asia remain poorly understood. The goldthread genus Coptis Salisb. includes 15 species disjunctly distributed in North America, Japan, mainland China, and Taiwan. We present a dated phylogeny for Coptis under the optimal clock model and infer its historical biogeography by comparing different biogeographic models. RESULTS The split of Coptis and Xanthorhiza Marshall occurred in the middle Miocene (ca. 15.47 Ma). Coptis started their diversification in the early late Miocene (ca. 9.55 Ma). A late Miocene vicariance event resulted in the eastern Asian and western North American disjunction in the genus. Within eastern Asia, dispersals from mainland Asia to Japan and from Japan to Taiwan occurred at ca. 4.85 Ma and at ca. 1.34 Ma, respectively. CONCLUSIONS Our analyses provide evidence that both vicariance and dispersal events have played important roles in shaping the current distribution and endemism of Coptis, likely resulting from eustatic sea-level changes, mountain formation processes and an increasing drier and cooler climate from the middle Miocene onwards.
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Affiliation(s)
- Kun-Li Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Andrey S Erst
- Central Siberian Botanical Garden of the Siberian Branch of Russian Academy of Sciences, Zolotodolinskaya str. 101, Novosibirsk, 630090, Russia.,Laboratory of Systematics and Phylogeny of Plants, Tomsk State University, Tomsk, 634050, Russia
| | - Xiao-Guo Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Florian Jabbour
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP39, 75005, Paris, France
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Eckley CS, Tate MT, Lin CJ, Gustin M, Dent S, Eagles-Smith C, Lutz MA, Wickland KP, Wang B, Gray JE, Edwards GC, Krabbenhoft DP, Smith DB. Surface-air mercury fluxes across Western North America: A synthesis of spatial trends and controlling variables. Sci Total Environ 2016; 568:651-665. [PMID: 26936663 DOI: 10.1016/j.scitotenv.2016.02.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/04/2016] [Accepted: 02/17/2016] [Indexed: 06/05/2023]
Abstract
Mercury (Hg) emission and deposition can occur to and from soils, and are an important component of the global atmospheric Hg budget. This paper focuses on synthesizing existing surface-air Hg flux data collected throughout the Western North American region and is part of a series of geographically focused Hg synthesis projects. A database of existing Hg flux data collected using the dynamic flux chamber (DFC) approach from almost a thousand locations was created for the Western North America region. Statistical analysis was performed on the data to identify the important variables controlling Hg fluxes and to allow spatiotemporal scaling. The results indicated that most of the variability in soil-air Hg fluxes could be explained by variations in soil-Hg concentrations, solar radiation, and soil moisture. This analysis also identified that variations in DFC methodological approaches were detectable among the field studies, with the chamber material and sampling flushing flow rate influencing the magnitude of calculated emissions. The spatiotemporal scaling of soil-air Hg fluxes identified that the largest emissions occurred from irrigated agricultural landscapes in California. Vegetation was shown to have a large impact on surface-air Hg fluxes due to both a reduction in solar radiation reaching the soil as well as from direct uptake of Hg in foliage. Despite high soil Hg emissions from some forested and other heavily vegetated regions, the net ecosystem flux (soil flux+vegetation uptake) was low. Conversely, sparsely vegetated regions showed larger net ecosystem emissions, which were similar in magnitude to atmospheric Hg deposition (except for the Mediterranean California region where soil emissions were higher). The net ecosystem flux results highlight the important role of landscape characteristics in effecting the balance between Hg sequestration and (re-)emission to the atmosphere.
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Affiliation(s)
- Chris S Eckley
- US Environmental Protection Agency, Region-10, Seattle, WA 98101, USA.
| | - Mike T Tate
- US Geological Survey, Middleton, WI 53562, USA
| | - Che-Jen Lin
- Center for Advances on Water and Air quality, Lamar University, Beaumont, TX 77710, USA
| | - Mae Gustin
- Department of Natural Resources & Environmental Science, University of Nevada, Reno, NV 89557, USA
| | | | | | | | | | | | | | - Grant C Edwards
- Department of Environment and Geography, Macquarie University, North Ryde, NSW 2109, Australia
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Drevnick PE, Cooke CA, Barraza D, Blais JM, Coale KH, Cumming BF, Curtis CJ, Das B, Donahue WF, Eagles-Smith CA, Engstrom DR, Fitzgerald WF, Furl CV, Gray JE, Hall RI, Jackson TA, Laird KR, Lockhart WL, Macdonald RW, Mast MA, Mathieu C, Muir DCG, Outridge PM, Reinemann SA, Rothenberg SE, Ruiz-Fernández AC, Louis VLS, Sanders RD, Sanei H, Skierszkan EK, Van Metre PC, Veverica TJ, Wiklund JA, Wolfe BB. Spatiotemporal patterns of mercury accumulation in lake sediments of western North America. Sci Total Environ 2016; 568:1157-1170. [PMID: 27102272 DOI: 10.1016/j.scitotenv.2016.03.167] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 05/04/2023]
Abstract
For the Western North America Mercury Synthesis, we compiled mercury records from 165 dated sediment cores from 138 natural lakes across western North America. Lake sediments are accepted as faithful recorders of historical mercury accumulation rates, and regional and sub-regional temporal and spatial trends were analyzed with descriptive and inferential statistics. Mercury accumulation rates in sediments have increased, on average, four times (4×) from 1850 to 2000 and continue to increase by approximately 0.2μg/m(2) per year. Lakes with the greatest increases were influenced by the Flin Flon smelter, followed by lakes directly affected by mining and wastewater discharges. Of lakes not directly affected by point sources, there is a clear separation in mercury accumulation rates between lakes with no/little watershed development and lakes with extensive watershed development for agricultural and/or residential purposes. Lakes in the latter group exhibited a sharp increase in mercury accumulation rates with human settlement, stabilizing after 1950 at five times (5×) 1850 rates. Mercury accumulation rates in lakes with no/little watershed development were controlled primarily by relative watershed size prior to 1850, and since have exhibited modest increases (in absolute terms and compared to that described above) associated with (regional and global) industrialization. A sub-regional analysis highlighted that in the ecoregion Northwestern Forest Mountains, <1% of mercury deposited to watersheds is delivered to lakes. Research is warranted to understand whether mountainous watersheds act as permanent sinks for mercury or if export of "legacy" mercury (deposited in years past) will delay recovery when/if emissions reductions are achieved.
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Affiliation(s)
- Paul E Drevnick
- University of Michigan Biological Station, 9133 Biological Rd., Pellston, MI 49769, USA; University of Michigan School of Natural Resources and Environment, 440 Church St., Ann Arbor, MI 48109, USA.
| | - Colin A Cooke
- Alberta Environmental Monitoring, Evaluation and Reporting Agency, 10th Floor, 9888 Jasper Avenue NW, Edmonton, AB T5J 5C6, Canada; Department of Earth and Atmospheric Sciences, 1-26 Earth Sciences Building, University of Alberta, Edmonton, AB T6G 2E3, Canada
| | - Daniella Barraza
- University of Michigan School of Natural Resources and Environment, 440 Church St., Ann Arbor, MI 48109, USA
| | - Jules M Blais
- Program in Chemical and Environmental Toxicology, Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Kenneth H Coale
- Moss Landing Marine Laboratories, 8272 Moss Landing Road, Moss Landing, CA 95039, USA
| | - Brian F Cumming
- Paleoecological Environmental Assessment and Research Laboratory, Department of Biology, Queen's University, Biosciences Complex, Kingston, ON K7L 3N6, Canada
| | - Chris J Curtis
- Environmental Change Research Centre, University College London, Gower Street, London WC1E 6BT, UK
| | - Biplob Das
- Saskatchewan Water Security Agency, 420-2365 Albert St., Regina, SK S4P 4K1, Canada
| | - William F Donahue
- Alberta Environmental Monitoring, Evaluation and Reporting Agency, 10th Floor, 9888 Jasper Avenue NW, Edmonton, AB T5J 5C6, Canada
| | - Collin A Eagles-Smith
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, 3200 SW Jefferson Way, Corvallis, OR 97331, USA
| | - Daniel R Engstrom
- St. Croix Watershed Research Station, Science Museum of Minnesota, Marine on St. Croix, MN 55047, USA
| | | | - Chad V Furl
- Washington State Department of Ecology, Environmental Assessment Program, P.O. Box 47600, Olympia, WA 98504, USA
| | - John E Gray
- U.S. Geological Survey, MS 973, Denver Federal Center, Denver, CO 80225, USA
| | - Roland I Hall
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Togwell A Jackson
- Aquatic Contaminants Research Division, Water Science & Technology Directorate, Environment & Climate Change Canada, Canada Centre for Inland Waters, 867 Lakeshore Road, Burlington, ON L7R 4A6, Canada
| | - Kathleen R Laird
- Paleoecological Environmental Assessment and Research Laboratory, Department of Biology, Queen's University, Biosciences Complex, Kingston, ON K7L 3N6, Canada
| | - W Lyle Lockhart
- Department of Fisheries and Oceans, 501 University Crescent, Winnipeg, MB R3T 2N6, Canada
| | - Robie W Macdonald
- Department of Fisheries and Oceans, Institute of Ocean Sciences, P.O. Box 6000, Sidney, BC V8L 4B2, Canada
| | - M Alisa Mast
- U.S. Geological Survey, Colorado Water Science Center, MS 415, Denver Federal Center, Denver, CO 80225, USA
| | - Callie Mathieu
- Washington State Department of Ecology, Environmental Assessment Program, P.O. Box 47600, Olympia, WA 98504, USA
| | - Derek C G Muir
- Aquatic Contaminants Research Division, Water Science & Technology Directorate, Environment & Climate Change Canada, Canada Centre for Inland Waters, 867 Lakeshore Road, Burlington, ON L7R 4A6, Canada
| | - Peter M Outridge
- Geological Survey of Canada, 601 Booth Street, Ottawa, ON K1A 0E8, Canada
| | - Scott A Reinemann
- Department of Geography, The Ohio State University, 1036 Derby Hall, 154 North Oval Mall, Columbus, OH 43210, USA
| | - Sarah E Rothenberg
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly Street, Columbia, SC 29208, USA
| | - Ana Carolina Ruiz-Fernández
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Calz. Joel Montes Camarena s/n, CP 82040 Mazatlán, Sinaloa, Mexico
| | - Vincent L St Louis
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Rhea D Sanders
- Moss Landing Marine Laboratories, 8272 Moss Landing Road, Moss Landing, CA 95039, USA
| | - Hamed Sanei
- Geological Survey of Canada, 3303-33rd Street N.W., Calgary, AB T2L 2A7, Canada
| | - Elliott K Skierszkan
- Program in Chemical and Environmental Toxicology, Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | | | - Timothy J Veverica
- University of Michigan Biological Station, 9133 Biological Rd., Pellston, MI 49769, USA
| | - Johan A Wiklund
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Brent B Wolfe
- Department of Geography and Environmental Studies, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON N2L 3C5, Canada
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