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Hessels EW, Lofroth EC, Weir RD, Gorrell JC. Characterizing the elusive Vancouver Island wolverine, Gulo gulo vancouverensis, using historical DNA. J Mammal 2021. [DOI: 10.1093/jmammal/gyaa175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The wolverine (Gulo gulo) is a Holarctic species found in North America primarily across the boreal forest, the subarctic, and along the Pacific coast, including Vancouver Island (VI), British Columbia. While wolverines on VI are rare and possibly extirpated, they have been previously described as a unique subspecies, G. g. vancouverensis, distinct from G. g. luscus from the mainland of North America. However, the validity of the VI subspecies is contentious, with conflicting results from studies of skull morphology. Here, we used molecular analyses to characterize the genetic diversity of the VI population and resolve this taxonomic debate to assist with conservation priorities. Historical DNA of VI wolverines was obtained from museum specimens, amplified at 16 nuclear microsatellite loci, and sequenced at the mitochondrial D-loop control region to compare with wolverines from mainland British Columbia. The VI population had lower allelic richness and was fixed for a single common mtDNA haplotype. Bayesian and non-Bayesian assignments using microsatellites generally revealed admixture across populations, implying allele frequencies between the VI and mainland populations were not significantly different. Hence, both types of genetic markers showed little evolutionary divergence between VI and the mainland population. Combined, these results do not provide evidence of significant genetic distinction for VI wolverines, nor support the subspecific classification. Immediate conservation efforts should focus on estimating population size, while future conservation planning can assume VI wolverines likely are not a unique genetic population and there remains the potential for natural recolonization of wolverines to VI.
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Affiliation(s)
- Evan W Hessels
- Biology Department, Vancouver Island University, Nanaimo, BC, Canada
| | | | - Richard D Weir
- Ministry of Environment, Government of British Columbia, Victoria, BC, Canada
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2
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Wettewa E, Wallace LE. Molecular phylogeny and ancestral biogeographic reconstruction of Platanthera subgenus Limnorchis (Orchidaceae) using target capture methods. Mol Phylogenet Evol 2021; 157:107070. [PMID: 33421614 DOI: 10.1016/j.ympev.2021.107070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/05/2020] [Accepted: 01/04/2021] [Indexed: 12/01/2022]
Abstract
Platanthera is one of the largest genera of temperate orchids in the Holarctic and exemplifies a lineage that has adaptively radiated into diverse habitats within North America, Asia, Europe, North Africa, Borneo, and Sarawak. Major centers of diversity in this genus are North America and eastern Asia. Despite its diversity, a thorough phylogenetic hypothesis for the genus is lacking because no studies have yet sampled taxa exhaustively or developed a robust molecular toolkit. While there is strong evidence that suggests monophyly of subgenus Limnorchis, most taxa in this group have not been included in a phylogenetic analysis. In this study, we developed a new toolkit for Platanthera consisting of genomic information from 617 low-copy nuclear loci. Using a targeted enrichment approach, we collected high-throughput sequence data in 23 accessions of nine of the 12 diploid species of subgenus Limnorchis and outgroup species across Platanthera. A maximum likelihood analysis resolved a strongly supported monophyletic clade for subgenus Limnorchis. Ancestral biogeographic reconstruction indicated that subgenus Limnorchis originated in western North America ca. 3-4.5 Mya from an ancestor that was widespread in western North America and eastern Asia and subsequently diversified in western North America, followed by dispersal of some species to eastern North America. Our results indicate complex biogeographic connections between Asia and North America, and therefore it suggests that Platanthera is a suitable system to test biogeographic hypotheses over time and space in the Holarctic. Our results are also expected to facilitate further study of diversification and biogeographic spread across Platanthera and lay the groundwork for understanding independent origins, biogeography, and morphological diversification of polyploid species within subgenus Limnorchis.
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Affiliation(s)
- Eranga Wettewa
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Lisa E Wallace
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529, USA.
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3
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Capron A, Feau N, Heinzelmann R, Barnes I, Benowicz A, Bradshaw RE, Dale A, Lewis KJ, Owen TJ, Reich R, Ramsfield TD, Woods AJ, Hamelin RC. Signatures of Post-Glacial Genetic Isolation and Human-Driven Migration in the Dothistroma Needle Blight Pathogen in Western Canada. PHYTOPATHOLOGY 2021; 111:116-127. [PMID: 33112215 DOI: 10.1094/phyto-08-20-0350-fi] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Many current tree improvement programs are incorporating assisted gene flow strategies to match reforestation efforts with future climates. This is the case for the lodgepole pine (Pinus contorta var. latifolia), the most extensively planted tree in western Canada. Knowledge of the structure and origin of pathogen populations associated with this tree would help improve the breeding effort. Recent outbreaks of the Dothistroma needle blight (DNB) pathogen Dothistroma septosporum on lodgepole pine in British Columbia and its discovery in Alberta plantations raised questions about the diversity and population structure of this pathogen in western Canada. Using genotyping-by-sequencing on 119 D. septosporum isolates from 16 natural pine populations and plantations from this area, we identified four genetic lineages, all distinct from the other DNB lineages from outside of North America. Modeling of the population history indicated that these lineages diverged between 31.4 and 7.2 thousand years ago, coinciding with the last glacial maximum and the postglacial recolonization of lodgepole pine in western North America. The lineage found in the Kispiox Valley from British Columbia, where an unprecedented DNB epidemic occurred in the 1990s, was close to demographic equilibrium and displayed a high level of haplotypic diversity. Two lineages found in Alberta and Prince George (British Columbia) showed departure from random mating and contemporary gene flow, likely resulting from pine breeding activities and material exchanges in these areas. The increased movement of planting material could have some major consequences by facilitating secondary contact between genetically isolated DNB lineages, possibly resulting in new epidemics.
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Affiliation(s)
- Arnaud Capron
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Renate Heinzelmann
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Andy Benowicz
- Alberta Agriculture and Forestry, 9920-108 Street, Edmonton, AB, T5K 2M4, Canada
| | - Rosie E Bradshaw
- School of Fundamental Sciences, Massey University, Palmerston North, 4410, New Zealand
| | - Angela Dale
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- SC-New Construction Materials, FPInnovations, Vancouver, BC, V6T 1Z4, Canada
| | - Kathy J Lewis
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, BC, V2N 4Z9, Canada
| | - Timothy J Owen
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, BC, V2N 4Z9, Canada
| | - Richard Reich
- Natural Resources and Forest Technology, College of New Caledonia, Prince George, BC, V2N 1P8, Canada
| | - Tod D Ramsfield
- Natural Resources Canada, Canadian Forest Service, 5320 - 122 St., Edmonton, AB, T6H 3S5, Canada
| | - Alex J Woods
- BC Ministry of Forests Lands and Natural Resource Operations and Rural Development, Skeena Region, Smithers, BC, V0J 2N0, Canada
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Faculté de foresterie et géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V0A6, Canada
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Bisbing SM, Urza AK, Buma BJ, Cooper DJ, Matocq M, Angert AL. Can long‐lived species keep pace with climate change? Evidence of local persistence potential in a widespread conifer. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13191] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Sarah M. Bisbing
- Department of Natural Resources & Environmental Science Program in Ecology, Evolution, & Conservation Biology University of Nevada ‐ Reno Reno NV USA
| | - Alexandra K. Urza
- Department of Natural Resources & Environmental Science Program in Ecology, Evolution, & Conservation Biology University of Nevada ‐ Reno Reno NV USA
- Rocky Mountain Research Station USDA Forest Service Reno NV USA
| | - Brian J. Buma
- Department of Integrative Biology University of Colorado Denver CO USA
| | - David J. Cooper
- Department of Forest and Rangeland Stewardship & Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - Marjorie Matocq
- Department of Natural Resources & Environmental Science Program in Ecology, Evolution, & Conservation Biology University of Nevada ‐ Reno Reno NV USA
| | - Amy L. Angert
- Departments of Botany and Zoology University of British Columbia Vancouver BC Canada
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5
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Bagley JC, Heming NM, Gutiérrez EE, Devisetty UK, Mock KE, Eckert AJ, Strauss SH. Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen ( Populus tremuloides). Ecol Evol 2020; 10:4609-4629. [PMID: 32551047 PMCID: PMC7297775 DOI: 10.1002/ece3.6214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 01/01/2023] Open
Abstract
Populus tremuloides is the widest-ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome-wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of P. tremuloides, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal-Cascades (cluster 1), east-slope Cascades-Sierra Nevadas-Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the P. tremuloides range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the "stable-edge hypothesis" that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited "trailing-edge" dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the "inland dispersal hypothesis" predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific-coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable-edge, refugial locations, and postglacial expansion within P. tremuloides. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific-coastal genetic lineage of quaking aspen.
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Affiliation(s)
- Justin C. Bagley
- Plant Evolutionary Genomics LaboratoryDepartment of BiologyVirginia Commonwealth UniversityRichmondVAUSA
- Departamento de ZoologiaInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
| | - Neander M. Heming
- Departamento de ZoologiaInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
| | - Eliécer E. Gutiérrez
- Departamento de ZoologiaInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
- Programa de Pos‐Graduação em Biodiversidade AnimalCentro de Ciências Naturais e ExatasUniversidade Federal de Santa MariaSanta MariaBrazil
| | | | - Karen E. Mock
- Department of Wildland Resources and Ecology CenterUtah State UniversityLoganUTUSA
| | - Andrew J. Eckert
- Plant Evolutionary Genomics LaboratoryDepartment of BiologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Steven H. Strauss
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
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6
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Deakin S, Gorrell JC, Kneteman J, Hik DS, Jobin RM, Coltman DW. Spatial genetic structure of Rocky Mountain bighorn sheep (Ovis canadensis canadensis) at the northern limit of their native range. CAN J ZOOL 2020. [DOI: 10.1139/cjz-2019-0183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Canadian Rocky Mountains are one of the few places on Earth where the spatial genetic structure of wide-ranging species has been relatively unaffected by anthropogenic disturbance. We characterized the spatial genetic structure of Rocky Mountain bighorn sheep (Ovis canadensis canadensis Shaw, 1804) in the northern portion of their range. Using microsatellites from 1495 individuals and mitochondrial DNA sequences from 188 individuals, we examined both broad- and fine-scale spatial genetic structure, assessed sex-biased gene flow within the northern portion of the species range, and identified geographic patterns of genetic diversity. We found that broad-scale spatial genetic structure was consistent with barriers to movement created by major river valleys. The fine-scale spatial genetic structure was characterized by a strong isolation-by-distance pattern, and analysis of neighborhood size using spatial autocorrelation indicated gene flow frequently occurred over distances of up to 100 km. However, analysis of sex-specific spatial autocorrelation and analysis of mitochondrial haplotype distributions failed to detect any evidence of sex-biased gene flow. Finally, our analyses reveal decreasing genetic diversity with increasing latitude, consistent with patterns of post-glacial recolonization of the Rocky Mountains.
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Affiliation(s)
- Samuel Deakin
- Department of Biological Sciences, University of Alberta, CW 405, Biological Sciences Building, Edmonton, AB T6G 2E9, Canada
| | - Jamieson C. Gorrell
- Department of Biological Sciences, Vancouver Island University, 900 Fifth Street, Nanaimo, BC V9R 5S5, Canada
| | - Jeffery Kneteman
- Alberta Environment and Parks, 131 Civic Centre Road, Hinton, AB T7V 2E6, Canada
| | - David S. Hik
- Department of Biological Sciences, University of Alberta, CW 405, Biological Sciences Building, Edmonton, AB T6G 2E9, Canada; Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Richard M. Jobin
- Alberta Fish and Wildlife Enforcement Branch, 6909 – 116 Street, Edmonton, AB T6H 4P2, Canada
| | - David W. Coltman
- Department of Biological Sciences, University of Alberta, CW 405, Biological Sciences Building, Edmonton, AB T6G 2E9, Canada
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7
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Slager DL, Epperly KL, Ha RR, Rohwer S, Wood C, Van Hemert C, Klicka J. Cryptic and extensive hybridization between ancient lineages of American crows. Mol Ecol 2020; 29:956-969. [PMID: 32034818 DOI: 10.1111/mec.15377] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/30/2019] [Accepted: 02/05/2020] [Indexed: 01/02/2023]
Abstract
Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa that lack reliable traditional characters for identification. In this first population genomic study of Northwestern and American crows, we use genomic SNPs (nuDNA) and mtDNA to investigate the degree of genetic differentiation between these crows and the extent to which they may hybridize. Our results indicate that American and Northwestern crows have distinct evolutionary histories, supported by two nuDNA ancestry clusters and two 1.1%-divergent mtDNA clades dating to the late Pleistocene, when glacial advances may have isolated crow populations in separate refugia. We document extensive hybridization, with geographic overlap of mtDNA clades and admixture of nuDNA across >900 km of western Washington and western British Columbia. This broad hybrid zone consists of late-generation hybrids and backcrosses, but not recent (e.g., F1) hybrids. Nuclear DNA and mtDNA clines had concordant widths and were both centred in southwestern British Columbia, farther north than previously postulated. Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, perhaps due to recurring neutral expansion(s) from Pleistocene glacial refugia followed by lineage fusion(s). However, we do not rule out a contributing role for more recent potential drivers of hybridization, such as expansion into human-modified habitats.
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Affiliation(s)
- David L Slager
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Kevin L Epperly
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Renee R Ha
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Sievert Rohwer
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Chris Wood
- Burke Museum of Natural History and Culture, Seattle, WA, USA
| | | | - John Klicka
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
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8
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Dempsey ZW, Goater CP, Burg TM. Living on the edge: comparative phylogeography and phylogenetics of Oreohelix land snails at their range edge in Western Canada. BMC Evol Biol 2020; 20:3. [PMID: 31906912 PMCID: PMC6945528 DOI: 10.1186/s12862-019-1566-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/17/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The biodiversity and distributions of terrestrial snails at local and regional scales are influenced by their low vagility and microhabitat specificity. The accessibility of large-bodied species and their characteristically high levels of genetic polymorphism make them excellent ecological and evolutionary models for studies on the phylogeography, phylogenetics, and conservation of organisms in fragmented populations. This study aims to elucidate the biodiversity, systematics, and distributions of genetic lineages within the genus Oreohelix at the northern and western periphery of their range. RESULTS We found four mitochondrial clades, three of which are putative subspecies of Oreohelix subrudis. One clade was geographically widespread, occurring within numerous sites in Cypress Hills and in the Rocky Mountains, a second was geographically restricted to the Rocky Mountains in Alberta, and a third was restricted to the Cypress Hills region. A fourth clade was the small-bodied species, O. cooperi. ITS2 sequence and screening data revealed three genetic clusters, of which one was O. cooperi. Cluster 1 contained most individuals in COI clade X and some from clade B and cluster 2 was predominantly made up of individuals from COI clades B and B' and a few from clade X. ITS2 alleles were shared in a narrow contact zone between two COI clades, suggestive of hybridization between the two. CONCLUSIONS A sky island known as Cypress Hills, in southeastern Alberta, Canada, is a biodiversity hotspot for terrestrial land snails in the genus Oreohelix. The observed phylogeographic patterns likely reflect reproductive isolation during the Last Glacial Maximum, followed by secondary contact due to passive, long-range dispersal resulting from low vagility, local adaptation, and complex glacial history.
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Affiliation(s)
- Z. W. Dempsey
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4 Canada
| | - C. P. Goater
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4 Canada
| | - T. M. Burg
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4 Canada
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9
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Lu M, Hodgins KA, Degner JC, Yeaman S. Purifying selection does not drive signatures of convergent local adaptation of lodgepole pine and interior spruce. BMC Evol Biol 2019; 19:110. [PMID: 31138118 PMCID: PMC6537219 DOI: 10.1186/s12862-019-1438-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lodgepole pine (Pinus contorta) and interior spruce (Picea glauca, Picea engelmannii, and their hybrids) are distantly related conifer species. Previous studies identified 47 genes containing variants associated with environmental variables in both species, providing evidence of convergent local adaptation. However, if the intensity of purifying selection varies with the environment, clines in nucleotide diversity could evolve through linked (background) selection that would yield allele frequency-environment signatures resembling local adaptation. If similar geographic patterns in the strength of purifying selection occur in these species, this could result in the convergent signatures of local adaptation, especially if the landscape of recombination is conserved. In the present study, we investigated whether spatially/environmentally varying purifying selection could give rise to the convergent signatures of local adaptation that had previously reported. RESULTS We analyzed 86 lodgepole pine and 50 interior spruce natural populations spanning heterogeneous environments in western Canada where previous analyses had found signatures of convergent local adaptation. We estimated nucleotide diversity and Tajima's D for each gene within each population and calculated the strength of correlations between nucleotide diversity and environmental variables. Overall, these estimates in the genes with previously identified convergent local adaptation signatures had no similar pattern between pine and spruce. Clines in nucleotide diversity along environmental variables were found for interior spruce, but not for lodgepole pine. In spruce, genes with convergent adaption signatures showed a higher strength of correlations than genes without convergent adaption signatures, but there was no such disparity in pine, which suggests the pattern in spruce may have arisen due to a combination of selection and hybridization. CONCLUSIONS The results rule out purifying/background selection as a driver of convergent local adaption signatures in lodgepole pine and interior spruce.
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Affiliation(s)
- Mengmeng Lu
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, T2N 4S8, Canada.
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University - Clayton Campus, Building 17, Wellington Road, Melbourne, 3800, Australia
| | - Jon C Degner
- Department of Forest and Conservation Sciences, Forest Sciences Centre 3041, University of British Columbia, 2424 Main Mall, Vancouver, V6T 1Z4, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, T2N 4S8, Canada
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10
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Isaac-Renton M, Montwé D, Hamann A, Spiecker H, Cherubini P, Treydte K. Northern forest tree populations are physiologically maladapted to drought. Nat Commun 2018; 9:5254. [PMID: 30531998 PMCID: PMC6288165 DOI: 10.1038/s41467-018-07701-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 11/14/2018] [Indexed: 11/08/2022] Open
Abstract
Northern forests at the leading edge of their distributions may not show increased primary productivity under climate warming, being limited by climatic extremes such as drought. Looking beyond tree growth to underlying physiological mechanisms is fundamental for accurate predictions of forest responses to climate warming and drought stress. Within a 32-year genetic field trial, we analyze relative contributions of xylem plasticity and inferred stomatal response to drought tolerance in regional populations of a widespread conifer. Genetic adaptation leads to varying responses under drought. Trailing-edge tree populations produce fewer tracheids with thicker cell walls, characteristic of drought-tolerance. Stomatal response explains the moderate drought tolerance of tree populations in central areas of the species range. Growth loss of the northern population is linked to low stomatal responsiveness combined with the production of tracheids with thinner cell walls. Forests of the western boreal may therefore lack physiological adaptations necessary to tolerate drier conditions.
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Affiliation(s)
- Miriam Isaac-Renton
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2H1, Canada.
| | - David Montwé
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2H1, Canada
| | - Andreas Hamann
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2H1, Canada
| | - Heinrich Spiecker
- Chair of Forest Growth and Dendroecology, Albert-Ludwigs-Universität-Freiburg, Tennenbacherstrasse 4, 79106, Freiburg, Germany
| | - Paolo Cherubini
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Kerstin Treydte
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
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11
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Dowle EJ, Bracewell RR, Pfrender ME, Mock KE, Bentz BJ, Ragland GJ. Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae). Mol Ecol 2017; 26:6071-6084. [PMID: 29116665 DOI: 10.1111/mec.14342] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 05/12/2017] [Accepted: 08/05/2017] [Indexed: 12/23/2022]
Abstract
Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and geneflow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert. Despite close geographic proximity between populations on the boundaries of each Y haplogroup, there was extremely low Y haplogroup mixing among populations, and gene flow on the autosomes was reduced across Y haplogroup boundaries. These results are consistent with a previous study suggesting that independent degradation of a recently evolved neo-Y chromosome in previously isolated populations causes male sterility or inviability among Y haplotype lineages. Phylogeographic results supported historic contraction of MPB into three separate Pleistocene glacial refugia followed by postglacial range expansion and secondary contact. Distinct sets of SNPs were statistically associated with environmental data among the most genetically distinct sets of geographic populations. This finding suggests that the process of adaptation to local climatic conditions is influenced by population genetic structure, with evidence for largely independent evolution in the most genetically isolated Y haplogroup.
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Affiliation(s)
- Eddy J Dowle
- Department of Entomology, Kansas State University, Manhattan, KS, USA.,Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Ryan R Bracewell
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Karen E Mock
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Barbara J Bentz
- Department of Wildland Resources, Utah State University, Logan, UT, USA.,USDA Forest Service, Rocky Mountain Research Station, Logan, UT, USA
| | - Gregory J Ragland
- Department of Entomology, Kansas State University, Manhattan, KS, USA.,Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
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12
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Dohms KM, Graham BA, Burg TM. Multilocus genetic analyses and spatial modeling reveal complex population structure and history in a widespread resident North American passerine ( Perisoreus canadensis). Ecol Evol 2017; 7:9869-9889. [PMID: 29238522 PMCID: PMC5723591 DOI: 10.1002/ece3.3478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/08/2017] [Accepted: 08/19/2017] [Indexed: 11/29/2022] Open
Abstract
An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, ΦST, SAMOVA, FST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay's contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.
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Affiliation(s)
- Kimberly M Dohms
- Department of Biological Sciences University of Lethbridge Lethbridge AB Canada.,Present address: Canadian Wildlife Service, Environment and Climate Change Canada Delta BC Canada
| | - Brendan A Graham
- Department of Biological Sciences University of Windsor Windsor ON Canada
| | - Theresa M Burg
- Department of Biological Sciences University of Lethbridge Lethbridge AB Canada
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13
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Jeger M, Caffier D, Candresse T, Chatzivassiliou E, Dehnen-Schmutz K, Gilioli G, Grégoire JC, Jaques Miret JA, MacLeod A, Navajas Navarro M, Niere B, Parnell S, Potting R, Rafoss T, Urek G, Van Bruggen A, Van Der Werf W, West J, Winter S, Boberg J, Porta Puglia A, Vettraino AM, Pautasso M, Rossi V. Pest risk assessment of Atropellis spp. for the EU territory. EFSA J 2017; 15:e04877. [PMID: 32625544 PMCID: PMC7010044 DOI: 10.2903/j.efsa.2017.4877] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Following a request from the European Commission, the EFSA Plant Health (PLH) Panel performed a risk assessment for Atropellis spp. in the EU focusing on the risk of entry, the host range and the potential impacts. Atropellis is a fungal pathogen of several Pinus spp. in North America. The pathogen has not been reported from Europe and is a quarantine pest regulated in Annex IIAI of Council Directive 2000/29/EC on plants (other than fruit and seeds), isolated bark and wood of Pinus. The main pathways of entry considered were Pinus plants, wood and isolated bark. Given the ban of importing Pinus plants from outside Europe into the EU and the lack of information on EU imports of isolated Pinus bark, only the wood pathway was assessed quantitatively. The conclusion of the assessment of entry for scenario A0 (current regulatory situation) is that the risk of entry of Atropellis spp. is close to zero. This conclusion is expected to apply also in the case of removing the specific Atropellis regulations, because of the remaining generic Pinus requirements, as well as in a scenario with additional risk reduction options. The uncertainty associated with this assessment is relatively limited, given that all the quartiles of the estimated distribution of the number of potential founder populations are close to zero. For the North American Pinus spp. known to be susceptible and widely planted in the EU (mainly P. contorta and P. strobus), the damage observed in North America (loss of wood quality, stem deformations, mortality in young stands, environmental consequences) is expected in the EU to a similar (or higher) degree, should the pathogen be introduced. Similar impacts are expected on the European Pinus spp. known to be host of Atropellis spp. These include widespread and locally abundant species such as P. nigra, P. sylvestris and P. pinaster. There are, however, large uncertainties associated with this impact assessment due to the unknown susceptibility of several other Pinus spp. present in Europe. There is a need for research on the susceptibility to Atropellis spp. of those European Pinus spp.
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14
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Ding C, Schreiber SG, Roberts DR, Hamann A, Brouard JS. Post-glacial biogeography of trembling aspen inferred from habitat models and genetic variance in quantitative traits. Sci Rep 2017; 7:4672. [PMID: 28680120 PMCID: PMC5498503 DOI: 10.1038/s41598-017-04871-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/17/2017] [Indexed: 11/22/2022] Open
Abstract
Using species distribution models and information on genetic structure and within-population variance observed in a series of common garden trials, we reconstructed a historical biogeography of trembling aspen in North America. We used an ensemble classifier modelling approach (RandomForest) to reconstruct palaeoclimatic habitat for the periods 21,000, 14,000, 11,000 and 6,000 years before present. Genetic structure and diversity in quantitative traits was evaluated in common garden trials with 43 aspen collections ranging from Minnesota to northern British Columbia. Our main goals were to examine potential recolonisation routes for aspen from southwestern, eastern and Beringian glacial refugia. We further examined if any refugium had stable habitat conditions where aspen clones may have survived multiple glaciations. Our palaeoclimatic habitat reconstructions indicate that aspen may have recolonised boreal Canada and Alaska from refugia in the eastern United States, with separate southwestern refugia for the Rocky Mountain regions. This is further supported by a southeast to northwest gradient of decreasing genetic variance in quantitative traits, a likely result of repeated founder effects. Stable habitat where aspen clones may have survived multiple glaciations was predicted in Mexico and the eastern United States, but not in the west where some of the largest aspen clones have been documented.
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Affiliation(s)
- Chen Ding
- University of Alberta, Department of Renewable Resources, 751 General Services Building Edmonton, AB, Alberta, T6G 2H1, Canada
| | - Stefan G Schreiber
- University of Alberta, Department of Renewable Resources, 751 General Services Building Edmonton, AB, Alberta, T6G 2H1, Canada
| | - David R Roberts
- University of Alberta, Department of Renewable Resources, 751 General Services Building Edmonton, AB, Alberta, T6G 2H1, Canada
| | - Andreas Hamann
- University of Alberta, Department of Renewable Resources, 751 General Services Building Edmonton, AB, Alberta, T6G 2H1, Canada.
| | - Jean S Brouard
- Isabella Point Forestry Ltd., 331 Roland Road, Salt Spring Island, BC, Alberta, V8K 1V1, Canada
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15
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Bentz BJ, Hood SM, Hansen EM, Vandygriff JC, Mock KE. Defense traits in the long-lived Great Basin bristlecone pine and resistance to the native herbivore mountain pine beetle. THE NEW PHYTOLOGIST 2017; 213:611-624. [PMID: 27612209 PMCID: PMC5213150 DOI: 10.1111/nph.14191] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 08/05/2016] [Indexed: 05/11/2023]
Abstract
Mountain pine beetle (MPB, Dendroctonus ponderosae) is a significant mortality agent of Pinus, and climate-driven range expansion is occurring. Pinus defenses in recently invaded areas, including high elevations, are predicted to be lower than in areas with longer term MPB presence. MPB was recently observed in high-elevation forests of the Great Basin (GB) region, North America. Defense and susceptibility in two long-lived species, GB bristlecone pine (Pinus longaeva) and foxtail pine (P. balfouriana), are unclear, although they are sympatric with a common MPB host, limber pine (P. flexilis). We surveyed stands with sympatric GB bristlecone-limber pine and foxtail-limber pine to determine relative MPB attack susceptibility and constitutive defenses. MPB-caused mortality was extensive in limber, low in foxtail and absent in GB bristlecone pine. Defense traits, including constitutive monoterpenes, resin ducts and wood density, were higher in GB bristlecone and foxtail than in limber pine. GB bristlecone and foxtail pines have relatively high levels of constitutive defenses which make them less vulnerable to climate-driven MPB range expansion relative to other high-elevation pines. Long-term selective herbivore pressure and exaptation of traits for tree longevity are potential explanations, highlighting the complexity of predicting plant-insect interactions under climate change.
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Affiliation(s)
- Barbara J. Bentz
- USDA Forest Service Rocky Mountain Research StationLoganUT84321USA
| | - Sharon M. Hood
- USDA Forest Service Rocky Mountain Research StationMissoulaMT59808USA
| | | | | | - Karen E. Mock
- Department of Wildland Resources and Ecology CenterUtah State UniversityLoganUT84321USA
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16
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Sawyer YE, Cook JA. Phylogeographic structure in long-tailed voles (Rodentia: Arvicolinae) belies the complex Pleistocene history of isolation, divergence, and recolonization of Northwest North America's fauna. Ecol Evol 2016; 6:6633-6647. [PMID: 27777736 PMCID: PMC5058534 DOI: 10.1002/ece3.2393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/01/2016] [Indexed: 11/24/2022] Open
Abstract
Quaternary climate fluctuations restructured biodiversity across North American high latitudes through repeated episodes of range contraction, population isolation and divergence, and subsequent expansion. Identifying how species responded to changing environmental conditions not only allows us to explore the mode and tempo of evolution in northern taxa, but also provides a basis for forecasting future biotic response across the highly variable topography of western North America. Using a multilocus approach under a Bayesian coalescent framework, we investigated the phylogeography of a wide‐ranging mammal, the long‐tailed vole, Microtus longicaudus. We focused on populations along the North Pacific Coast to refine our understanding of diversification by exploring the potentially compounding roles of multiple glacial refugia and more recent fragmentation of an extensive coastal archipelago. Through a combination of genetic data and species distribution models (SDMs), we found that historical climate variability influenced contemporary genetic structure, with multiple isolated locations of persistence (refugia) producing multiple divergent lineages (Beringian or northern, southeast Alaska or coastal, and southern or continental) during glacial advances. These vole lineages all occur along the North Pacific Coast where the confluence of numerous independent lineages in other species has produced overlapping zones of secondary contact, collectively a suture zone. Finally, we detected high levels of neoendemism due to complex island geography that developed in the last 10,000 years with the rising sea levels of the Holocene.
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Affiliation(s)
- Yadéeh E Sawyer
- Department of Biology and Museum of Southwestern Biology University of New Mexico MSC03 2020 Albuquerque New Mexico 87131-0001
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology University of New Mexico MSC03 2020 Albuquerque New Mexico 87131-0001
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17
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Dowie NJ, Grubisha LC, Trowbridge SM, Klooster MR, Miller SL. Variability of ecological and autotrophic host specificity in a mycoheterotrophic system: Pterospora andromedea and associated fungal and conifer hosts. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2015.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Roberts DR, Hamann A. Glacial refugia and modern genetic diversity of 22 western North American tree species. Proc Biol Sci 2015; 282:20142903. [PMID: 25761711 DOI: 10.1098/rspb.2014.2903] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
North American tree species, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American trees since the last glacial maximum using species distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 tree species. We find that species with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas species with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r(2) = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles.
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Affiliation(s)
- David R Roberts
- Department of Renewable Resources, University of Alberta, 751 General Services Building, Edmonton, Alberta, Canada T6G 2H1
| | - Andreas Hamann
- Department of Renewable Resources, University of Alberta, 751 General Services Building, Edmonton, Alberta, Canada T6G 2H1
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19
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Nadeau S, Godbout J, Lamothe M, Gros-Louis MC, Isabel N, Ritland K. Contrasting patterns of genetic diversity across the ranges of Pinus monticola and P. strobus: a comparison between eastern and western North American postglacial colonization histories. AMERICAN JOURNAL OF BOTANY 2015; 102:1342-1355. [PMID: 26290557 DOI: 10.3732/ajb.1500160] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/09/2015] [Indexed: 06/04/2023]
Abstract
UNLABELLED • Premises of the study: Understanding the influence of recent glacial and postglacial periods on species' distributions is key for predicting the effects of future environmental changes. We investigated the influence of two physiographic landscapes on population structure and postglacial colonization of two white pine species of contrasting habitats: P. monticola, which occurs in the highly mountainous region of western North America, and P. strobus, which occurs in a much less mountainous area in eastern North America.• METHODS To characterize the patterns of genetic diversity and population structure across the ranges of both species, 158 and 153 single nucleotide polymorphism (SNP) markers derived from expressed genes were genotyped on range-wide samples of 61 P. monticola and 133 P. strobus populations, respectively.• KEY RESULTS In P. monticola, a steep latitudinal decrease in genetic diversity likely resulted from postglacial colonization involving rare long-distance dispersal (LDD) events. In contrast, no geographic patterns of diversity were detected in P. strobus, suggesting recolonization via a gradually advancing front or frequent LDD events. For each species, structure analyses identified two distinct southern and northern genetic groups that likely originated from two different glacial lineages. At a finer scale, and for the two species, smaller subgroups were detected that could be remnants of cryptic refugia.• CONCLUSION During postglacial colonization, the western and eastern North American landscapes had different impacts on genetic signatures in P. monticola compared with P. strobus. We discuss the importance of our findings for conservation programs and predictions of species' response to climate change.
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Affiliation(s)
- Simon Nadeau
- The University of British Columbia, Department of Forest and Conservation Sciences, Forest Science Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380 Stn., Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Julie Godbout
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380 Stn., Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380 Stn., Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Marie-Claude Gros-Louis
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380 Stn., Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380 Stn., Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Kermit Ritland
- The University of British Columbia, Department of Forest and Conservation Sciences, Forest Science Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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20
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Campbell MA, Takebayashi N, López JA. Beringian sub-refugia revealed in blackfish (Dallia): implications for understanding the effects of Pleistocene glaciations on Beringian taxa and other Arctic aquatic fauna. BMC Evol Biol 2015; 15:144. [PMID: 26187279 PMCID: PMC4506597 DOI: 10.1186/s12862-015-0413-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 06/08/2015] [Indexed: 12/03/2022] Open
Abstract
Background Pleistocene climatic instability had profound and diverse effects on the distribution and abundance of Arctic organisms revealed by variation in phylogeographic patterns documented in extant Arctic populations. To better understand the effects of geography and paleoclimate on Beringian freshwater fishes, we examined genetic variability in the genus Dallia (blackfish: Esociformes: Esocidae). The genus Dallia groups between one and three nominal species of small, cold- and hypoxia-tolerant freshwater fishes restricted entirely in distribution to Beringia from the Yukon River basin near Fairbanks, Alaska westward including the Kuskokwim River basin and low-lying areas of Western Alaska to the Amguema River on the north side of the Chukotka Peninsula and Mechigmen Bay on the south side of the Chukotka Peninsula. The genus has a non-continuous distribution divided by the Bering Strait and the Brooks Range. We examined the distribution of genetic variation across this range to determine the number and location of potential sub-refugia within the greater Beringian refugium as well as the roles of the Bering land bridge, Brooks Range, and large rivers within Beringia in shaping the current distribution of populations of Dallia. Our analyses were based on DNA sequence data from two nuclear gene introns (S7 and RAG1) and two mitochondrial genome fragments from nineteen sampling locations. These data were examined under genetic clustering and coalescent frameworks to identify sub-refugia within the greater Beringia refugium and to infer the demographic history of different populations of Dallia. Results We identified up to five distinct genetic clusters of Dallia. Four of these genetic clusters are present in Alaska: (1) Arctic Coastal Plain genetic cluster found north of the Brooks Range, (2) interior Alaska genetic cluster placed in upstream locations in the Kuskokwim and Yukon river basins, (3) a genetic cluster found on the Seward Peninsula, and (4) a coastal Alaska genetic cluster encompassing downstream Kuskokwim River and Yukon River basin sample locations and samples from Southwest Alaska not in either of these drainages. The Chukotka samples are assigned to their own genetic cluster (5) similar to the coastal Alaska genetic cluster. The clustering and ordination analyses implemented in Discriminant Analysis of Principal Components (DAPC) and STRUCTURE showed mostly concordant groupings and a high degree of differentiation among groups. The groups of sampling locations identified as genetic clusters correspond to geographic areas divided by likely biogeographic barriers including the Brooks Range and the Bering Strait. Estimates of sequence diversity (θ) are highest in the Yukon River and Kuskokwim River drainages near the Bering Sea. We also infer asymmetric migration rates between genetic clusters. The isolation of Dallia on the Arctic Coastal Plain of Alaska is associated with very low estimated migration rates between the coastal Alaska genetic cluster and the Arctic Coastal Plain genetic cluster. Conclusions Our results support a scenario with multiple aquatic sub-refugia in Beringia during the Pleistocene and the preservation of that structure in extant populations of Dallia. An inferred historical presence of Dallia across the Bering land bridge explains the similarities in the genetic composition of Dallia in West Beringia and western coastal Alaska. In contrast, historic and contemporary isolation across the Brooks Range shaped the distinctiveness of present day Arctic Coastal Plain Dallia. Overall this study uncovered a high degree of genetic structuring among populations of Dallia supporting the idea of multiple Beringian sub-refugia during the Pleistocene and which appears to be maintained to the present due to the strictly freshwater nature and low dispersal ability of this genus. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0413-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew A Campbell
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA. .,Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand.
| | - Naoki Takebayashi
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA. .,Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA.
| | - J Andrés López
- School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA. .,University of Alaska Museum, Fairbanks, AK, 99775, USA.
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Cinget B, de Lafontaine G, Gérardi S, Bousquet J. Integrating phylogeography and paleoecology to investigate the origin and dynamics of hybrid zones: insights from two widespread North American firs. Mol Ecol 2015; 24:2856-70. [DOI: 10.1111/mec.13194] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Benjamin Cinget
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute for Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC Canada G1V0A6
| | - Guillaume de Lafontaine
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute for Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC Canada G1V0A6
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute for Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC Canada G1V0A6
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute for Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC Canada G1V0A6
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22
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Cinget B, Gérardi S, Beaulieu J, Bousquet J. Less pollen-mediated gene flow for more signatures of glacial lineages: congruent evidence from balsam fir cpDNA and mtDNA for multiple refugia in eastern and central North America. PLoS One 2015; 10:e0122815. [PMID: 25849816 PMCID: PMC4388536 DOI: 10.1371/journal.pone.0122815] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 02/23/2015] [Indexed: 11/18/2022] Open
Abstract
The phylogeographic structure and postglacial history of balsam fir (Abies balsamea), a transcontinental North American boreal conifer, was inferred using mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) markers. Genetic structure among 107 populations (mtDNA data) and 75 populations (cpDNA data) was analyzed using Bayesian and genetic distance approaches. Population differentiation was high for mtDNA (dispersed by seeds only), but also for cpDNA (dispersed by seeds and pollen), indicating that pollen gene flow is more restricted in balsam fir than in other boreal conifers. Low cpDNA gene flow in balsam fir may relate to low pollen production due to the inherent biology of the species and populations being decimated by recurrent spruce budworm epidemics, and/or to low dispersal of pollen grains due to their peculiar structural properties. Accordingly, a phylogeographic structure was detected using both mtDNA and cpDNA markers and population structure analyses supported the existence of at least five genetically distinct glacial lineages in central and eastern North America. Four of these would originate from glacial refugia located south of the Laurentide ice sheet, while the last one would have persisted in the northern Labrador region. As expected due to reduced pollen-mediated gene flow, congruence between the geographic distribution of mtDNA and cpDNA lineages was higher than in other North American conifers. However, concordance was not complete, reflecting that restricted but nonetheless detectable cpDNA gene flow among glacial lineages occurred during the Holocene. As a result, new cpDNA and mtDNA genome combinations indicative of cytoplasmic genome capture were observed.
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Affiliation(s)
- Benjamin Cinget
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Wood and Forest Sciences, Laval University, Québec, Québec, Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Wood and Forest Sciences, Laval University, Québec, Québec, Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Wood and Forest Sciences, Laval University, Québec, Québec, Canada
- Natural Resources Canada, Canadian Wood Fibre Centre, Canadian Wood Fibre Centre, Natural Resources Canada, Québec, Québec, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Wood and Forest Sciences, Laval University, Québec, Québec, Canada
- * E-mail:
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van Loo M, Hintsteiner W, Pötzelsberger E, Schüler S, Hasenauer H. Intervarietal and intravarietal genetic structure in Douglas-fir: nuclear SSRs bring novel insights into past population demographic processes, phylogeography, and intervarietal hybridization. Ecol Evol 2015; 5:1802-17. [PMID: 26140197 PMCID: PMC4485962 DOI: 10.1002/ece3.1435] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 10/23/2014] [Accepted: 01/21/2015] [Indexed: 01/22/2023] Open
Abstract
Douglas-fir (Pseudotsuga menziesii) is one of numerous wide-range forest tree species represented by subspecies/varieties, which hybridize in contact zones. This study examined the genetic structure of this North American conifer and its two hybridizing varieties, coastal and Rocky Mountain, at intervarietal and intravarietal level. The genetic structure was subsequently associated with the Pleistocene refugial history, postglacial migration and intervarietal hybridization/introgression. Thirty-eight populations from the USA and Canada were genotyped for 13 nuclear SSRs and analyzed with simulations and traditional population genetic structuring methods. Eight genetic clusters were identified. The coastal clusters embodied five refugial populations originating from five distinct refugia. Four coastal refugial populations, three from California and one from western Canada, diverged during the Pleistocene (56.9–40.1 ka). The three Rocky Mountain clusters reflected distinct refugial populations of three glacial refugia. For Canada, ice covered during the Last Glacial Maximum, we present the following three findings. (1) One refugial population of each variety was revealed in the north of the distribution range. Additional research including paleodata is required to support and determine whether both northern populations originated from cryptic refugia situated south or north of the ice-covered area. (2) An interplay between intravarietal gene flow of different refugial populations and intervarietal gene flow by hybridization and introgression was identified. (3) The Canadian hybrid zone displayed predominantly introgressants of the Rocky Mountain into the coastal variety. This study provides new insights into the complex Quaternary dynamics of this conifer essential for understanding its evolution (outside and inside the native range), adaptation to future climates and for forest management.
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Affiliation(s)
- Marcela van Loo
- Institute of Silviculture, University of Natural Resources and Life Sciences Peter Jordan Straße 82, 1190, Wien, Austria
| | - Wolfgang Hintsteiner
- Institute of Silviculture, University of Natural Resources and Life Sciences Peter Jordan Straße 82, 1190, Wien, Austria ; alpS-GmbH Grabenweg 68, 6020, Innsbruck, Austria
| | - Elisabeth Pötzelsberger
- Institute of Silviculture, University of Natural Resources and Life Sciences Peter Jordan Straße 82, 1190, Wien, Austria
| | - Silvio Schüler
- Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscapes Hauptstr. 7, 1140, Vienna, Austria
| | - Hubert Hasenauer
- Institute of Silviculture, University of Natural Resources and Life Sciences Peter Jordan Straße 82, 1190, Wien, Austria
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Sork VL, Werth S. Phylogeography of Ramalina menziesii, a widely distributed lichen-forming fungus in western North America. Mol Ecol 2014; 23:2326-39. [PMID: 24673777 DOI: 10.1111/mec.12735] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 03/13/2014] [Indexed: 11/28/2022]
Abstract
The complex topography and climate history of western North America offer a setting where lineage formation, accumulation and migration have led to elevated inter- and intraspecific biodiversity in many taxa. Here, we study Ramalina menziesii, an epiphytic lichenized fungus with a range encompassing major ecosystems from Baja California to Alaska to explore the predictions of two hypotheses: (i) that the widespread distribution of R. menziesii is due to a single migration episode from a single lineage and (ii) that the widespread distribution is due to the formation and persistence of multiple lineages structured throughout the species' range. To obtain evidence for these predictions, we first construct a phylogenetic tree and identify multiple lineages structured throughout the species' range--some ancient ones that are localized and other more recent lineages that are widely distributed. Second, we use an isolation with migration model to show that sets of ecoregion populations diverged from each other at different times, demonstrating the importance of historical and current barriers to gene flow. Third, we estimated migration rates among ecoregions and find that Baja California populations are relatively isolated, that inland California ecoregion populations do not send out emigrants and that migration out of California coastal and Pacific Northwest populations into inland California ecoregions is high. Such intraspecific geographical patterns of population persistence and dispersal both contribute to the wide range of this genetically diverse lichen fungus and provide insight into the evolutionary processes that enhance species diversity of the California Floristic Province.
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Affiliation(s)
- Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095-7239, USA; Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095-1496, USA
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Chavez AS, Maher SP, Arbogast BS, Kenagy GJ. DIVERSIFICATION AND GENE FLOW IN NASCENT LINEAGES OF ISLAND AND MAINLAND NORTH AMERICAN TREE SQUIRRELS (TAMIASCIURUS). Evolution 2014; 68:1094-109. [DOI: 10.1111/evo.12336] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 11/29/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Andreas S. Chavez
- Burke Museum and Department of Biology; University of Washington; Seattle Washington 98195
| | - Sean P. Maher
- Museum of Vertebrate Zoology; University of California; Berkeley California 94720
| | - Brian S. Arbogast
- Department of Biology and Marine Biology; University of North Carolina Wilmington; Wilmington North Carolina 28403
| | - G. J. Kenagy
- Burke Museum and Department of Biology; University of Washington; Seattle Washington 98195
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Cullingham CI, Cooke JE, Coltman DW. Effects of introgression on the genetic population structure of two ecologically and economically important conifer species: lodgepole pine (Pinus contorta var. latifolia) and jack pine (Pinus banksiana). Genome 2013; 56:577-85. [DOI: 10.1139/gen-2013-0071] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Forest trees exhibit a remarkable range of adaptations to their environment, but as a result of frequent and long-distance gene flow, populations are often only weakly differentiated. Lodgepole and jack pine hybridize in western Canada, which adds the opportunity for introgression through hybridization to contribute to population structure and (or) adaptive variation. Access to large sample size, high density SNP datasets for these species would improve our ability to resolve population structure, parameterize introgression, and separate the influence of demography from adaptation. To accomplish this, 454 transcriptome reads for lodgepole and jack pine were assembled using Newbler and MIRA, the assemblies mined for SNPs, and 1536 SNPs were selected for typing on lodgepole pine, jack pine, and their hybrids (N = 536). We identified population structure using both Bayesian clustering and discriminate analysis of principle components. Introgressed SNP loci were identified and their influence on observed population structure was assessed. We found that introgressed loci resulted in increased differentiation both within lodgepole and jack pine populations. These findings are timely given the recent mountain pine beetle population expansion in the hybrid zone, and will facilitate future studies of adaptive traits in these ecologically important species.
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Affiliation(s)
- Catherine I. Cullingham
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Janice E.K. Cooke
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - David W. Coltman
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada
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Potter KM, Hipkins VD, Mahalovich MF, Means RE. Mitochondrial DNA haplotype distribution patterns in Pinus ponderosa (Pinaceae): range-wide evolutionary history and implications for conservation. AMERICAN JOURNAL OF BOTANY 2013; 100:1562-1579. [PMID: 23876453 DOI: 10.3732/ajb.1300039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Ponderosa pine (Pinus ponderosa Douglas ex P. Lawson & C. Lawson) exhibits complicated patterns of morphological and genetic variation across its range in western North America. This study aims to clarify P. ponderosa evolutionary history and phylogeography using a highly polymorphic mitochondrial DNA marker, with results offering insights into how geographical and climatological processes drove the modern evolutionary structure of tree species in the region. METHODS We amplified the mtDNA nad1 second intron minisatellite region for 3,100 trees representing 104 populations, and sequenced all length variants. We estimated population-level haplotypic diversity and determined diversity partitioning among varieties, races and populations. After aligning sequences of minisatellite repeat motifs, we evaluated evolutionary relationships among haplotypes. KEY RESULTS The geographical structuring of the 10 haplotypes corresponded with division between Pacific and Rocky Mountain varieties. Pacific haplotypes clustered with high bootstrap support, and appear to have descended from Rocky Mountain haplotypes. A greater proportion of diversity was partitioned between Rocky Mountain races than between Pacific races. Areas of highest haplotypic diversity were the southern Sierra Nevada mountain range in California, northwestern California, and southern Nevada. CONCLUSIONS Pinus ponderosa haplotype distribution patterns suggest a complex phylogeographic history not revealed by other genetic and morphological data, or by the sparse paleoecological record. The results appear consistent with long-term divergence between the Pacific and Rocky Mountain varieties, along with more recent divergences not well-associated with race. Pleistocene refugia may have existed in areas of high haplotypic diversity, as well as the Great Basin, Southwestern United States/northern Mexico, and the High Plains.
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Affiliation(s)
- Kevin M Potter
- Department of Forestry and Environmental Resources, North Carolina State University, Research Triangle Park, North Carolina 27709, USA.
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Evolution of an Ancient Microsatellite Hotspot in the Conifer Mitochondrial Genome and Comparison with Other Plants. J Mol Evol 2013; 76:146-57. [DOI: 10.1007/s00239-013-9547-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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29
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Vidyakin AI, Semerikov VL, Polezhaeva MA, Dymshakova OS. Spread of mitochondrial DNA haplotypes in population of scots pine (Pinus sylvestris L.) in northern European Russia. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412120150] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Lee-Yaw JA, Irwin DE. Large geographic range size reflects a patchwork of divergent lineages in the long-toed salamander (Ambystoma macrodactylum). J Evol Biol 2012; 25:2276-87. [DOI: 10.1111/j.1420-9101.2012.02604.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/28/2022]
Affiliation(s)
- J. A. Lee-Yaw
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
| | - D. E. Irwin
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
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Godbout J, Yeh FC, Bousquet J. Large-scale asymmetric introgression of cytoplasmic DNA reveals Holocene range displacement in a North American boreal pine complex. Ecol Evol 2012; 2:1853-66. [PMID: 22957188 PMCID: PMC3433990 DOI: 10.1002/ece3.294] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 05/08/2012] [Accepted: 05/09/2012] [Indexed: 11/11/2022] Open
Abstract
Jack pine (Pinus banksiana) and lodgepole pine (Pinus contorta var. latifolia) are two North American boreal hard pines that hybridize in their zone of contact in western Canada. The main objective of this study was to characterize their patterns of introgression resulting from past and recent gene flow, using cytoplasmic markers having maternal or paternal inheritance. Mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) diversity was assessed in allopatric populations of each species and in stands from the current zone of contact containing morphological hybrids. Cluster analyses were used to identify genetic discontinuities among groups of populations. A canonical analysis was also conducted to detect putative associations among cytoplasmic DNA variation, tree morphology, and site ecological features. MtDNA introgression was extensive and asymmetric: it was detected in P. banksiana populations from the hybrid zone and from allopatric areas, but not in P. contorta populations. Very weak cpDNA introgression was observed, and only in P. banksiana populations. The mtDNA introgression pattern indicated that central Canada was first colonized by migrants from a P. contorta glacial population located west of the Rocky Mountains, before being replaced by P. banksiana migrating westward during the Holocene. In contrast, extensive pollen gene flow would have erased the cpDNA traces of this ancient presence of P. contorta. Additional evidence for this process was provided by the results of canonical analysis, which indicated that the current cpDNA background of trees reflected recent pollen gene flow from the surrounding dominant species rather than historical events that took place during the postglacial colonization.
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Affiliation(s)
- Julie Godbout
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval1030 avenue de la Médecine, Québec, Québec, Canada, G1V 0A6
| | - Francis C Yeh
- Department of Renewable Resources, Faculty of Agricultural, Life and Environmental Sciences, University of AlbertaEdmonton, Alberta, Canada, T6G 2P5
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval1030 avenue de la Médecine, Québec, Québec, Canada, G1V 0A6
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Cullingham CI, James PMA, Cooke JEK, Coltman DW. Characterizing the physical and genetic structure of the lodgepole pine × jack pine hybrid zone: mosaic structure and differential introgression. Evol Appl 2012; 5:879-91. [PMID: 23346232 PMCID: PMC3552405 DOI: 10.1111/j.1752-4571.2012.00266.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 04/08/2012] [Indexed: 01/07/2023] Open
Abstract
Understanding the physical and genetic structure of hybrid zones can illuminate factors affecting their formation and stability. In north-central Alberta, lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia) and jack pine (Pinus banksiana Lamb) form a complex and poorly defined hybrid zone. Better knowledge of this zone is relevant, given the recent host expansion of mountain pine beetle into jack pine. We characterized the zone by genotyping 1998 lodgepole, jack pine, and hybrids from British Columbia, Alberta, Saskatchewan, Ontario, and Minnesota at 11 microsatellites. Using Bayesian algorithms, we calculated genetic ancestry and used this to model the relationship between species occurrence and environment. In addition, we analyzed the ancestry of hybrids to calculate the genetic contribution of lodgepole and jack pine. Finally, we measured the amount of gene flow between the pure species. We found the distribution of the pine classes is explained by environmental variables, and these distributions differ from classic distribution maps. Hybrid ancestry was biased toward lodgepole pine; however, gene flow between the two species was equal. The results of this study suggest that the hybrid zone is complex and influenced by environmental constraints. As a result of this analysis, range limits should be redefined.
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Gayathri Samarasekera GDN, Bartell NV, Lindgren BS, Cooke JEK, Davis CS, James PMA, Coltman DW, Mock KE, Murray BW. Spatial genetic structure of the mountain pine beetle (Dendroctonus ponderosae) outbreak in western Canada: historical patterns and contemporary dispersal. Mol Ecol 2012; 21:2931-48. [PMID: 22554298 DOI: 10.1111/j.1365-294x.2012.05587.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Environmental change has a wide range of ecological consequences, including species extinction and range expansion. Many studies have shown that insect species respond rapidly to climatic change. A mountain pine beetle epidemic of record size in North America has led to unprecedented mortality of lodgepole pine, and a significant range expansion to the northeast of its historic range. Our goal was to determine the spatial genetic variation found among outbreak population from which genetic structure, and dispersal patterns may be inferred. Beetles from 49 sampling locations throughout the outbreak area in western Canada were analysed at 13 microsatellite loci. We found significant north-south population structure as evidenced by: (i) Bayesian-based analyses, (ii) north-south genetic relationships and diversity gradients; and (iii) a lack of isolation-by-distance in the northernmost cluster. The north-south structure is proposed to have arisen from the processes of postglacial colonization as well as recent climate-driven changes in population dynamics. Our data support the hypothesis of multiple sources of origin for the outbreak and point to the need for population specific information to improve our understanding and management of outbreaks. The recent range expansion across the Rocky Mountains into the jack/lodgepole hybrid and pure jack pine zones of northern Alberta is consistent with a northern British Columbia origin. We detected no loss of genetic variability in these populations, indicating that the evolutionary potential of mountain pine beetle to adapt has not been reduced by founder events. This study illustrates a rapid range-wide response to the removal of climatic constraints, and the potential for range expansion of a regional population.
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Affiliation(s)
- G D N Gayathri Samarasekera
- Natural Resources and Environmental Studies Institute, University of Northern British Columbia, 3333 University Way, Prince George, British Columbia, Canada V2N 4Z9
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Dowie NJ, Hemenway JJ, Miller SL. Identity, genetic lineages and putative hybrids of an obligate mycobiont associated with the mycoheterotrophic plant Pterospora andromedea in the south-central Rocky Mountains. FUNGAL ECOL 2012. [DOI: 10.1016/j.funeco.2011.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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PARCHMAN THOMASL, GOMPERT ZACHARIAH, MUDGE JOANN, SCHILKEY FAYED, BENKMAN CRAIGW, BUERKLE CALEX. Genome-wide association genetics of an adaptive trait in lodgepole pine. Mol Ecol 2012; 21:2991-3005. [DOI: 10.1111/j.1365-294x.2012.05513.x] [Citation(s) in RCA: 329] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Tsui CKM, Roe AD, El-Kassaby YA, Rice AV, Alamouti SM, Sperling FAH, Cooke JEK, Bohlmann J, Hamelin RC. Population structure and migration pattern of a conifer pathogen, Grosmannia clavigera, as influenced by its symbiont, the mountain pine beetle. Mol Ecol 2011; 21:71-86. [PMID: 22118059 DOI: 10.1111/j.1365-294x.2011.05366.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated the population structure of Grosmannia clavigera (Gc), a fungal symbiont of the mountain pine beetle (MPB) that plays a crucial role in the establishment and reproductive success of this pathogen. This insect-fungal complex has destroyed over 16 million ha of lodgepole pine forests in Canada, the largest MPB epidemic in recorded history. During this current epidemic, MPB has expanded its range beyond historically recorded boundaries, both northward and eastward, and has now reached the jack pine of Alberta, potentially threatening the Canadian boreal forest. To better understand the dynamics between the beetle and its fungal symbiont, we sampled 19 populations in western North America and genotyped individuals from these populations with eight microsatellite markers. The fungus displayed high haplotype diversity, with over 250 unique haplotypes observed in 335 single spore isolates. Linkage equilibria in 13 of the 19 populations suggested that the fungus reproduces sexually. Bayesian clustering and distance analyses identified four genetic clusters that corresponded to four major geographical regions, which suggested that the epidemic arose from multiple geographical sources. A genetic cluster north of the Rocky Mountains, where the MPB has recently become established, experienced a population bottleneck, probably as a result of the recent range expansion. The two genetic clusters located north and west of the Rocky Mountains contained many fungal isolates admixed from all populations, possibly due to the massive movement of MPB during the epidemic. The general agreement in north-south differentiation of MPB and G. clavigera populations points to the fungal pathogen's dependence on the movement of its insect vector. In addition, the patterns of diversity and the individual assignment tests of the fungal associate suggest that migration across the Rocky Mountains occurred via a northeastern corridor, in accordance with meteorological patterns and observation of MPB movement data. Our results highlight the potential of this pathogen for both expansion and sexual reproduction, and also identify some possible barriers to gene flow. Understanding the ecological and evolutionary dynamics of this fungus-beetle association is important for the modelling and prediction of MPB epidemics.
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Affiliation(s)
- Clement K M Tsui
- Department of Forest Sciences, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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Parchman TL, Benkman CW, Jenkins B, Buerkle CA. Low levels of population genetic structure in Pinus contorta (Pinaceae) across a geographic mosaic of co-evolution. AMERICAN JOURNAL OF BOTANY 2011; 98:669-679. [PMID: 21613166 DOI: 10.3732/ajb.1000378] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Population genetic analyses provide information on the population context in which evolutionary processes operate and are important for understanding the evolution of geographically variable traits. Earlier studies showed that cone structure of lodgepole pine in the Rocky Mountains diverged among populations because of geographic variation in coevolutionary interactions involving mammalian and avian seed predators. Analyses of population genetic variation are needed to determine whether this divergence has arisen despite extensive gene flow and whether populations to the east and west of the Rocky Mountains have evolved convergent phenotypes independently. METHODS We investigated genetic structuring across 22 stands of lodgepole pine in the central Rocky Mountains and in isolated peripheral populations that experience different seed predators and exhibit parallel divergence in cone traits using a set of nine simple sequence repeats and 235 AFLP loci. KEY RESULTS Our analyses reveal high levels of genetic diversity within and low genetic differentiation among populations. Nonetheless, geographic and genetic distances were correlated, and isolated populations to the east and west of the Rocky Mountains had higher levels of differentiation than did populations in the central part of the range. CONCLUSIONS These data indicate not only that adaptive divergence of cone traits across a geographic mosaic of coevolution has occurred despite minimal genetic differentiation, but also that isolated populations to the east and west of the Rocky Mountains have evolved distinctive cones independently and in parallel. The population structure quantified here will inform future research aimed at detecting genetic variants associated with divergent adaptive traits.
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Affiliation(s)
- Thomas L Parchman
- Department of Botany, Dept. 3165, 1000 E. University Ave., University of Wyoming, Laramie, Wyoming 82071, USA.
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Species delimitation and biogeography of two fir species (Abies) in central China: cytoplasmic DNA variation. Heredity (Edinb) 2011; 107:362-70. [PMID: 21448232 DOI: 10.1038/hdy.2011.22] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
It remains unclear how speciation history might contribute to species-specific variation and affect species delimitation. We examined concordance between cytoplasmic genetic variation and morphological taxonomy in two fir species, Abies chensiensis and A. fargesii, with overlapping distributions in central China. Range-wide genetic variation was investigated using mitochondrial (mt) and plastid (pt) DNA sequences, which contrast in their rates of gene flow. Four mtDNA haplotypes were recovered and showed no obvious species' bias in terms of relative frequency. In contrast, a high level of ptDNA variation was recorded in both species with 3 common ptDNA haplotypes shared between them and 21 rare ptDNA haplotypes specific to one or other species. We argue that the lack of concordance between morphological and molecular variation between the two fir species most likely reflects extensive ancestral polymorphism sharing for both forms of cytoplasmic DNA variation. It is feasible that a relatively fast mutation rate for ptDNA contributed to the production of many species-specific ptDNA haplotypes, which remained rare due to insufficient time passing for their spread and fixation in either species, despite high levels of intraspecific ptDNA gene flow. Our phylogeographic analyses further suggest that polymorphisms in both organelle genomes most likely originated during and following glacial intervals preceding the last glacial maximum, when species distributions became fragmented into several refugia and then expanded in range across central China.
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Genetic architecture and phenotypic plasticity of thermally-regulated traits in an eruptive species, Dendroctonus ponderosae. Evol Ecol 2011. [DOI: 10.1007/s10682-011-9474-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Jardón-Barbolla L, Delgado-Valerio P, Geada-López G, Vázquez-Lobo A, Piñero D. Phylogeography of Pinus subsection Australes in the Caribbean Basin. ANNALS OF BOTANY 2011; 107:229-41. [PMID: 21118838 PMCID: PMC3025731 DOI: 10.1093/aob/mcq232] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 07/26/2010] [Accepted: 10/27/2010] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS Four species of Pinus subsection Australes occur in the Caribbean Basin: P. caribaea, P. cubensis, P. maestrensis and P. occidentalis. This study analyses the phylogeography of these species to assess possible colonization events from Central America to the islands and subsequent population expansions during glacial periods driven by both drier climate and larger emerged land areas. METHODS Allele size data were obtained for plastid microsatellites for 314 individuals from 24 populations, covering the distribution range of subsection Australes in the Caribbean Basin. KEY RESULTS In total, 113 plastid haplotypes were identified. The highest genetic diversity was found in populations of P. caribaea. Overall, Caribbean Basin populations fit the isolation by distance model. Significant phylogeographical structure was found (R(ST) = 0·671 > permuted R(ST) = 0·101; P < 0·0001). The haplotype network and a Bayesian analysis of population structure (BAPS) indicated different Central American origins for P. caribaea var. bahamensis and P. caribaea var. caribaea plastids, with Central America populations in northern and south-eastern groups. Sudden expansion times for BAPS clusters were close to three glacial maxima. CONCLUSIONS Central America contains ancestral plastid haplotypes. Population expansion has played a major role in the distribution of genetic diversity in P. caribaea var. hondurensis. Two colonization events gave rise to the P. caribaea var. bahamensis and P. caribaea var. caribaea lineages. Plastid variation in the eastern species (P. cubensis, P. maestrensis and P. occidentalis) evolved independently from that in P. caribaea var. caribaea. Incomplete lineage sorting between P. cubensis and P. maestrensis is apparent. Inferred expansion times for P. caribaea var. bahamensis and for the eastern lineages correspond to glacial maxima, whereas those for P. caribaea var. hondurensis correspond to the beginning of the temperature decrease that led to Marine Isotope Stage 8.
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Affiliation(s)
- Lev Jardón-Barbolla
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-275, Mexico D.F. 04510, Mexico.
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Bracewell RR, Pfrender ME, Mock KE, Bentz BJ. Cryptic postzygotic isolation in an eruptive species of bark beetle (Dendroctonus ponderosae). Evolution 2010; 65:961-75. [PMID: 21108639 DOI: 10.1111/j.1558-5646.2010.01201.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Studies of postzygotic isolation often involve well-differentiated taxa that show a consistent level of incompatibility, thereby limiting our understanding of the initial stages and development of reproductive barriers. Dendroctonus ponderosae provides an informative system because recent evidence suggests that distant populations produce hybrids with reproductive incompatibilities. Dendroctonus ponderosae shows an isolation-by-distance gene flow pattern allowing us to characterize the evolution of postzygotic isolation (e.g., hybrid inviability, hybrid sterility) by crossing populations along a continuum of geographic/genetic divergence. We found little evidence of hybrid inviability among these crosses. However, crosses between geographically distant populations produced sterile males (consistent with Haldane's rule). This effect was not consistent with the fixation of mutations in an isolation-by-distance pattern, but instead is spatially localized. These reproductive barriers are uncorrelated with a reduction in gene flow suggesting their recent development. Crosses between geographically proximal populations bounding the transition from compatibility to hybrid male sterility showed evidence of unidirectional reduction in hybrid male fecundity. Our study describes significant postzygotic isolation occurring across a narrow and molecularly cryptic geographic zone between the states of Oregon and Idaho. This study provides a view of the early stages of postzygotic isolation in a geographically widespread species.
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Affiliation(s)
- Ryan R Bracewell
- Wildland Resources Department, Utah State University, 5230 Old Main Hill, Logan, Utah 84322, USA.
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GÉRARDI SÉBASTIEN, JARAMILLO-CORREA JUANP, BEAULIEU JEAN, BOUSQUET JEAN. From glacial refugia to modern populations: new assemblages of organelle genomes generated by differential cytoplasmic gene flow in transcontinental black spruce. Mol Ecol 2010; 19:5265-80. [DOI: 10.1111/j.1365-294x.2010.04881.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Godbout J, Beaulieu J, Bousquet J. Phylogeographic structure of jack pine (Pinus banksiana; Pinaceae) supports the existence of a coastal glacial refugium in northeastern North America. AMERICAN JOURNAL OF BOTANY 2010; 97:1903-1912. [PMID: 21616829 DOI: 10.3732/ajb.1000148] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
PREMISE OF THE STUDY The genetic structure of jack pine (Pinus banksiana Lamb.), a North American boreal conifer with large longitudinal distribution, was investigated to test for the possible existence of a genetically distinct lineage in the Maritimes region in northeastern North America, which could be indicative of a mid-latitude coastal refuge during the last glaciation. • METHODS One maternally inherited mitochondrial DNA (mtDNA) minisatellite marker and four paternally inherited chloroplast DNA (cpDNA) microsatellite markers were used to assess the range-wide geographical structure of jack pine populations with particular focus on northeastern North America. • KEY RESULTS The populations from the Maritimes region presented a unique mtDNA background characterized by very low diversity and the preponderance of a distinctive mitotype. The distribution of cpDNA diversity was not spatially structured, though three chlorotypes were restricted to the east. • CONCLUSIONS MtDNA data suggest that populations from the Maritimes region derive from a genetically depauperated north-coastal refugium. Contrastingly, the much higher geographical uniformity observed for cpDNA variation indicates that gene flow by pollen had been much more effective than seed gene flow at homogenizing population structure.
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Affiliation(s)
- Julie Godbout
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, 1030 Avenue de la Médecine, Université Laval, Quebec, Quebec G1V 0A6 Canada
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BEATTY GEMMAE, PROVAN JIM. Refugial persistence and postglacial recolonization of North America by the cold-tolerant herbaceous plant Orthilia secunda. Mol Ecol 2010; 19:5009-21. [DOI: 10.1111/j.1365-294x.2010.04859.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Shafer ABA, Côté SD, Coltman DW. HOT SPOTS OF GENETIC DIVERSITY DESCENDED FROM MULTIPLE PLEISTOCENE REFUGIA IN AN ALPINE UNGULATE. Evolution 2010; 65:125-38. [DOI: 10.1111/j.1558-5646.2010.01109.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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SHAFER AARONBA, CULLINGHAM CATHERINEI, CÔTÉ STEEVED, COLTMAN DAVIDW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010; 19:4589-621. [PMID: 20849561 DOI: 10.1111/j.1365-294x.2010.04828.x] [Citation(s) in RCA: 261] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- AARON B. A. SHAFER
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - CATHERINE I. CULLINGHAM
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - STEEVE D. CÔTÉ
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec, Québec G1V 0A6, Canada
| | - DAVID W. COLTMAN
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Bentz BJ, Régnière J, Fettig CJ, Hansen EM, Hayes JL, Hicke JA, Kelsey RG, Negrón JF, Seybold SJ. Climate Change and Bark Beetles of the Western United States and Canada: Direct and Indirect Effects. Bioscience 2010. [DOI: 10.1525/bio.2010.60.8.6] [Citation(s) in RCA: 848] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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GUGGER PAULF, SUGITA SHINYA, CAVENDER-BARES JEANNINE. Phylogeography of Douglas-fir based on mitochondrial and chloroplast DNA sequences: testing hypotheses from the fossil record. Mol Ecol 2010; 19:1877-97. [DOI: 10.1111/j.1365-294x.2010.04622.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zhou YF, Abbott RJ, Jiang ZY, Du FK, Milne RI, Liu JQ. Gene flow and species delimitation: a case study of two pine species with overlapping distributions in southeast China. Evolution 2010; 64:2342-52. [PMID: 20298431 DOI: 10.1111/j.1558-5646.2010.00988.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Species delimitation detected by molecular markers is complicated by introgression and incomplete lineage sorting between species. Recent modeling suggests that fixed genetic differences between species are highly related to rates of intraspecific gene flow. However, it remains unclear whether such differences are due to high levels of intraspecific gene flow overriding the spread of introgressed alleles or favoring rapid lineage sorting between species. In pines, chloroplast (cp) and mitochondrial (mt) DNAs are normally paternally and maternally inherited, respectively, and thus their relative rates of intraspecific gene flow are expected to be high and low, respectively. In this study, we used two pine species with overlapping geographical distributions in southeast China, P. massoniana and P. hwangshanensis, as a model system to examine the association between organelle gene flow and variation within and between species. We found that cpDNA variation across these two pine species is more species specific than mtDNA variation and almost delimits taxonomic boundaries. The shared mt/cp DNA genetic variation between species shows no bias in regard to parapatric versus allopatric species' distributions. Our results therefore support the hypothesis that high intraspecific gene flow has accelerated cpDNA lineage sorting between these two pine species.
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Affiliation(s)
- Yong Feng Zhou
- Division of Molecular Ecology, Key Laboratory of Arid and Grassland Ecology, College of Life Science, Lanzhou University, Lanzhou 730000, Gansu, P R China
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