1
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Lo T, Coombe L, Gagalova KK, Marr A, Warren RL, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I, Thomson A. Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response. G3 (BETHESDA, MD.) 2023; 14:jkad247. [PMID: 37875130 PMCID: PMC10755193 DOI: 10.1093/g3journal/jkad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/17/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]
Abstract
Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.
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Affiliation(s)
- Theodora Lo
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Lauren Coombe
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Kristina K Gagalova
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Alex Marr
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - René L Warren
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Heather Kirk
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Pawan Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Richard A Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Carol Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Steven J M Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Joerg Bohlmann
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Inanç Birol
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Ashley Thomson
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
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2
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Kou Y, Fan D, Cheng S, Yang Y, Wang M, Wang Y, Zhang Z. Peripatric speciation within Torreya fargesii (Taxaceae) in the Hengduan Mountains inferred from multi-loci phylogeography. BMC Ecol Evol 2023; 23:74. [PMID: 38087226 PMCID: PMC10714551 DOI: 10.1186/s12862-023-02183-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The Hengduan Mountains (HDM) are one of the major global biodiversity hotspots in the world. Several evolutionary scenarios, especially in-situ diversification, have been proposed to account for the high species richness of temperate plants. However, peripatric speciation, an important mode of allopatric speciation, has seldom been reported in this region. RESULTS Here, two chloroplast DNA regions and 14 nuclear loci were sequenced for 112 individuals from 10 populations of Torreya fargesii var. fargesii and 63 individuals from 6 populations of T. fargesii var. yunnanensis. Population genetic analyses revealed that the two varieties are well differentiated genetically (FST, 0.5765) and have uneven genetic diversity (π, 0.00221 vs. 0.00073 on an average of nuclear loci). The gene genealogical relationship showed that T. fargesii var. yunnanensis is inferred as derived from T. fargesii var. fargesii, which was further supported by the coalescent simulations (DIYABC, fastsimcoal2 and IMa2). By the coalescent simulations, the divergence time (~ 2.50-3.65 Ma) and the weak gene flow between the two varieties were detected. The gene flow was asymmetrical and only occurred in later stages of divergence, which is caused by second contact due to the population expansion (~ 0.61 Ma) in T. fargesii var. fargesii. In addition, niche modeling indicated that the two varieties are differentiated geographically and ecologically and have unbalanced distribution range. CONCLUSIONS Overall, T. fargesii var. fargesii is always parapatric with respect to T. fargesii var. yunnanensis, and the latter derived from the former in peripatry of the HDM following a colonization from central China during the late Pliocene. Our findings demonstrate that peripatric speciation following dispersal events may be an important evolutionary scenario for the formation of biodiversity hotspot of the HDM.
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Affiliation(s)
- Yixuan Kou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Yi Yang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Meixia Wang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Yujin Wang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China.
| | - Zhiyong Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China.
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China.
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China.
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3
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Gagalova KK, Warren RL, Coombe L, Wong J, Nip KM, Yuen MMS, Whitehill JGA, Celedon JM, Ritland C, Taylor GA, Cheng D, Plettner P, Hammond SA, Mohamadi H, Zhao Y, Moore RA, Mungall AJ, Boyle B, Laroche J, Cottrell J, Mackay JJ, Lamothe M, Gérardi S, Isabel N, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1469-1485. [PMID: 35789009 DOI: 10.1111/tpj.15889] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.
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Affiliation(s)
- Kristina K Gagalova
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Lauren Coombe
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Johnathan Wong
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Justin G A Whitehill
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jose M Celedon
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Carol Ritland
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Greg A Taylor
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Dean Cheng
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Patrick Plettner
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Hamid Mohamadi
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Joan Cottrell
- Forest Research, U.K. Forestry Commission, Northern Research Station, Roslin, EH25 9SY, Midlothian, UK
| | - John J Mackay
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Sébastien Gérardi
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Pavy
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jean Bousquet
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
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4
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Laverdière J, Lenz P, Nadeau S, Depardieu C, Isabel N, Perron M, Beaulieu J, Bousquet J. Breeding for adaptation to climate change: genomic selection for drought response in a white spruce multi-site polycross test. Evol Appl 2022; 15:383-402. [PMID: 35386396 PMCID: PMC8965362 DOI: 10.1111/eva.13348] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/30/2022] Open
Abstract
With climate change, increasingly intense and frequent drought episodes will be affecting water availability for boreal tree species, prompting tree breeders and forest managers to consider adaptation to drought stress as a priority in their reforestation efforts. We used a 19-year-old polycross progeny test of the model conifer white spruce (Picea glauca) replicated on two sites affected by distinct drought episodes at different ages to estimate the genetic control and the potential for improvement of drought response in addition to conventional cumulative growth and wood quality traits. Drought response components were measured from dendrochronological signatures matching drought episodes in wood ring increment cores. We found that trees with more vigorous growth during their lifespan resisted better during the current year of a drought episode when the drought had more severe effects. Phenotypic data were also analyzed using genomic prediction (GBLUP) relying on the genomic relationship matrix of multi-locus gene SNP marker information, and conventional analysis (ABLUP) based on validated pedigree information. The accuracy of predicted breeding values for drought response components was marginally lower than that for conventional traits and comparable between GBLUP and ABLUP. Genetic correlations were generally low and nonsignificant between drought response components and conventional traits, except for resistance which was positively correlated to tree height. Heritability estimates for the components of drought response were slightly lower than for conventional traits, but similar single-trait genetic gains could be obtained. Multi-trait genomic selection simulations indicated that it was possible to improve simultaneously for all traits on both sites while sacrificing little on gain in tree height. In a context of rapid climate change, our results suggest that with careful phenotypic assessment, drought response may be considered in multi-trait improvement of white spruce, with accelerated screening of large numbers of candidates and selection at young age with genomic selection.
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Affiliation(s)
- Jean‐Philippe Laverdière
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative Biology and Centre for Forest ResearchUniversité LavalQuébecQCCanada
| | - Patrick Lenz
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative Biology and Centre for Forest ResearchUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceCanadian Wood Fibre CentreQuébecQCCanada
| | - Simon Nadeau
- Natural Resources CanadaCanadian Forest ServiceCanadian Wood Fibre CentreQuébecQCCanada
| | - Claire Depardieu
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative Biology and Centre for Forest ResearchUniversité LavalQuébecQCCanada
| | - Nathalie Isabel
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative Biology and Centre for Forest ResearchUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CentreQuébecQCCanada
| | - Martin Perron
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative Biology and Centre for Forest ResearchUniversité LavalQuébecQCCanada
- Direction de la Recherche ForestièreMinistère des Forêts, de la Faune et des Parc du QuébecQuébecQCCanada
| | - Jean Beaulieu
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative Biology and Centre for Forest ResearchUniversité LavalQuébecQCCanada
| | - Jean Bousquet
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative Biology and Centre for Forest ResearchUniversité LavalQuébecQCCanada
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5
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Million KM, Lively CM. Trans-specific polymorphism and the convergent evolution of supertypes in major histocompatibility complex class II genes in darters ( Etheostoma). Ecol Evol 2022; 12:e8485. [PMID: 36311547 PMCID: PMC9601779 DOI: 10.1002/ece3.8485] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/24/2022] Open
Abstract
Major Histocompatibility Complex (MHC) genes are one of the most polymorphic gene groups known in vertebrates. MHC genes also exhibit allelic variants that are shared among taxa, referred to as trans-specific polymorphism (TSP). The role that selection plays in maintaining such high diversity within species, as well as TSP, is an ongoing discussion in biology. In this study, we used deep-sequencing techniques to characterize MHC class IIb gene diversity in three sympatric species of darters. We found at least 5 copies of the MHC gene in darters, with 126 genetic variants encoding 122 unique amino acid sequences. We identified four supertypes based on the binding properties of proteins encoded by the sequences. Although each species had a unique pool of variants, many variants were shared between species pairs and across all three species. Phylogenetic analysis showed that the variants did not group together monophyletically based on species identity or on supertype. An expanded phylogenetic analysis showed that some darter alleles grouped together with alleles from other percid fishes. Our findings show that TSP occurs in darters, which suggests that balancing selection is acting at the genotype level. Supertypes, however, are most likely evolving convergently, as evidenced by the fact that alleles do not form monophyletic groups based on supertype. Our research demonstrates that selection may be acting differently on MHC genes at the genotype and supertype levels, selecting for the maintenance of high genotypic diversity while driving the convergent evolution of similar MHC phenotypes across different species.
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Affiliation(s)
- Kara M. Million
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
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6
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Cruz-Nicolás J, Villarruel-Arroyo A, Gernandt DS, Fonseca RM, Aguirre-Planter E, Eguiarte LE, Jaramillo-Correa JP. Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics. Mol Phylogenet Evol 2021; 160:107125. [PMID: 33636326 DOI: 10.1016/j.ympev.2021.107125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022]
Abstract
Constructing phylogenetic relationships among closely related species is a recurrent challenge in evolutionary biology, particularly for long-lived taxa with large effective population sizes and uncomplete reproductive isolation, like conifers. Conifers further have slow evolutionary rates, which raises the question of whether adaptive or non/adaptive processes were predominantly involved when they rapidly diversified after migrating from temperate regions into the tropical mountains. Indeed, fine-scale phylogenetic relationships within several conifer genus remain under debate. Here, we studied the phylogenetic relationships of endemic firs (Abies, Pinaceae) discontinuously distributed in the montane forests from the Southwestern United States to Guatemala, and addressed several hypotheses related to adaptive and non-adaptive radiations. We derived over 80 K SNPs from genotyping by sequencing (GBS) for 45 individuals of nine Mesoamerican species to perform phylogenetic analyses. Both Maximum Likelihood and quartets-inference phylogenies resulted in a well-resolved topology, showing a single fir lineage divided in four subgroups that coincided with the main mountain ranges of Mesoamerica; thus having important taxonomic implications. Such subdivision fitted a North-South isolation by distance framework, in which non-adaptive allopatric processes seemed the rule. Interestingly, several reticulations were observed within subgroups, especially in the central-south region, which may explain past difficulties for generating infrageneric phylogenies. Further evidence for non-adaptive processes was obtained from analyses of 21 candidate-gene regions, which exhibited diminishing values of πa/πs and Ka/Ks with latitude, thus indicating reduced efficiency of purifying selection towards the Equator. Our study indicates that non-adaptive allopatric processes may be key generators of species diversity and endemism in the tropics.
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Affiliation(s)
- Jorge Cruz-Nicolás
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - Alfredo Villarruel-Arroyo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, AP 70-233, Mexico City CDMX 04510, Mexico
| | - Rosa María Fonseca
- Laboratorio de Plantas Vasculares, Facultad de Ciencias, Universidad Nacional Autónoma de México, AP 70-282, Mexico City CDMX 04510, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - Juan P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico.
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7
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Menon M, Bagley JC, Page GFM, Whipple AV, Schoettle AW, Still CJ, Wehenkel C, Waring KM, Flores-Renteria L, Cushman SA, Eckert AJ. Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants. Commun Biol 2021; 4:160. [PMID: 33547394 PMCID: PMC7864969 DOI: 10.1038/s42003-020-01632-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 11/18/2020] [Indexed: 01/30/2023] Open
Abstract
Extant conifer species may be susceptible to rapid environmental change owing to their long generation times, but could also be resilient due to high levels of standing genetic diversity. Hybridisation between closely related species can increase genetic diversity and generate novel allelic combinations capable of fuelling adaptive evolution. Our study unravelled the genetic architecture of adaptive evolution in a conifer hybrid zone formed between Pinus strobiformis and P. flexilis. Using a multifaceted approach emphasising the spatial and environmental patterns of linkage disequilibrium and ancestry enrichment, we identified recently introgressed and background genetic variants to be driving adaptive evolution along different environmental gradients. Specifically, recently introgressed variants from P. flexilis were favoured along freeze-related environmental gradients, while background variants were favoured along water availability-related gradients. We posit that such mosaics of allelic variants within conifer hybrid zones will confer upon them greater resilience to ongoing and future environmental change and can be a key resource for conservation efforts.
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Affiliation(s)
- Mitra Menon
- grid.27860.3b0000 0004 1936 9684Department of Evolution and Ecology, University of California, Davis, CA USA
| | - Justin C. Bagley
- grid.257992.20000 0001 0019 1845Department of Biology, Jacksonville State University, Jacksonville, AL USA
| | - Gerald F. M. Page
- grid.4391.f0000 0001 2112 1969Forest Ecosystems and Society, Oregon State University, Corvallis, OR USA
| | - Amy V. Whipple
- grid.261120.60000 0004 1936 8040Department of Biological Sciences and Merriam Powel Center for Environmental Research, Northern Arizona University, Flagstaff, AZ USA
| | - Anna W. Schoettle
- grid.497401.f0000 0001 2286 5230Rocky Mountain Research Station, USDA Forest Service, Fort Collins, CO USA
| | - Christopher J. Still
- grid.4391.f0000 0001 2112 1969Forest Ecosystems and Society, Oregon State University, Corvallis, OR USA
| | - Christian Wehenkel
- grid.412198.70000 0000 8724 8383Instituto de Silvicultura e Industria de la Madera, Universidad Juarez del Estado de Durango, Durango, Mexico
| | - Kristen M. Waring
- grid.261120.60000 0004 1936 8040School of Forestry, Northern Arizona University, Flagstaff, AZ USA
| | - Lluvia Flores-Renteria
- grid.263081.e0000 0001 0790 1491Department of Biology, San Diego State University, San Diego, CA USA
| | - Samuel A. Cushman
- grid.472551.00000 0004 0404 3120Rocky Mountain Research Station, USDA Forest Service, Flagstaff, AZ USA
| | - Andrew J. Eckert
- grid.224260.00000 0004 0458 8737Department of Biology, Virginia Commonwealth University, Richmond, VA USA
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8
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Capblancq T, Butnor JR, Deyoung S, Thibault E, Munson H, Nelson DM, Fitzpatrick MC, Keller SR. Whole-exome sequencing reveals a long-term decline in effective population size of red spruce ( Picea rubens). Evol Appl 2020; 13:2190-2205. [PMID: 33005218 PMCID: PMC7513712 DOI: 10.1111/eva.12985] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/26/2020] [Accepted: 04/09/2020] [Indexed: 01/02/2023] Open
Abstract
Understanding the factors influencing the current distribution of genetic diversity across a species range is one of the main questions of evolutionary biology, especially given the increasing threat to biodiversity posed by climate change. Historical demographic processes such as population expansion or bottlenecks and decline are known to exert a predominant influence on past and current levels of genetic diversity, and revealing this demo-genetic history can have immediate conservation implications. We used a whole-exome capture sequencing approach to analyze polymorphism across the gene space of red spruce (Picea rubens Sarg.), an endemic and emblematic tree species of eastern North America high-elevation forests that are facing the combined threat of global warming and increasing human activities. We sampled a total of 340 individuals, including populations from the current core of the range in northeastern USA and southeastern Canada and from the southern portions of its range along the Appalachian Mountains, where populations occur as highly fragmented mountaintop "sky islands." Exome capture baits were designed from the closely relative white spruce (P. glauca Voss) transcriptome, and sequencing successfully captured most regions on or near our target genes, resulting in the generation of a new and expansive genomic resource for studying standing genetic variation in red spruce applicable to its conservation. Our results, based on over 2 million exome-derived variants, indicate that red spruce is structured into three distinct ancestry groups that occupy different geographic regions of its highly fragmented range. Moreover, these groups show small Ne , with a temporal history of sustained population decline that has been ongoing for thousands (or even hundreds of thousands) of years. These results demonstrate the broad potential of genomic studies for revealing details of the demographic history that can inform management and conservation efforts of nonmodel species with active restoration programs, such as red spruce.
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Affiliation(s)
| | - John R Butnor
- USDA Forest Service Southern Research Station University of Vermont Burlington VT USA
| | - Sonia Deyoung
- Department of Plant Biology University of Vermont Burlington VT USA
| | - Ethan Thibault
- Department of Plant Biology University of Vermont Burlington VT USA
| | - Helena Munson
- Department of Plant Biology University of Vermont Burlington VT USA
| | - David M Nelson
- Appalachian Laboratory University of Maryland Center for Environmental Science Frostburg MD USA
| | - Matthew C Fitzpatrick
- Appalachian Laboratory University of Maryland Center for Environmental Science Frostburg MD USA
| | - Stephen R Keller
- Department of Plant Biology University of Vermont Burlington VT USA
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9
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Li J, Milne RI, Ru D, Miao J, Tao W, Zhang L, Xu J, Liu J, Mao K. Allopatric divergence and hybridization withinCupressus chengiana(Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China. Mol Ecol 2020; 29:1250-1266. [DOI: 10.1111/mec.15407] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Jialiang Li
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Richard I. Milne
- Institute of Molecular Plant Sciences The University of Edinburgh Edinburgh UK
| | - Dafu Ru
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
| | - Jibin Miao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Wenjing Tao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Lei Zhang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Jingjing Xu
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Jianquan Liu
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Kangshan Mao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
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10
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Kou Y, Zhang L, Fan D, Cheng S, Li D, Hodel RGJ, Zhang Z. Evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae), in south-east China during the late Neogene: old lineage, young populations. ANNALS OF BOTANY 2020; 125:105-117. [PMID: 31765468 PMCID: PMC6948213 DOI: 10.1093/aob/mcz153] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/04/2019] [Accepted: 11/17/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS Many monotypic gymnosperm lineages in south-east China paradoxically remain in relict status despite long evolutionary histories and ample opportunities for allopatric speciation, but this paradox has received little attention and has yet to be resolved. Here, we address this issue by investigating the evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae). METHODS DNA sequences from two chloroplast regions and 14 nuclear loci were obtained for 134 samples. The demographic history was inferred and the contribution of isolation by environment (IBE) in patterning genetic divergence was compared with that of isolation by distance (IBD). KEY RESULTS Three genetic clusters were identified. Approximate Bayesian computation analyses showed that the three clusters diverged in the late Pliocene (~3.68 Ma) and two admixture events were detected. Asymmetric gene flow and similar population divergence times (~ 3.74 Ma) were characterized using the isolation with migration model. Neither IBD nor IBE contributed significantly to genetic divergence, and the contribution of IBE was much smaller than that of IBD. CONCLUSIONS These results suggest that several monotypic relict gymnosperm lineages like P. chienii in south-east China did not remain in situ and undiversified for millions of years. On the contrary, they have been evolving and the extant populations have become established more recently, having insufficient time to speciate. Our findings provide a new perspective for understanding the formation and evolution of the relict gymnosperm flora of China as well as of the Sino-Japanese Flora.
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Affiliation(s)
- Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Li Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Dezhu Li
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Richard G J Hodel
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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11
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Shen TT, Ran JH, Wang XQ. Phylogenomics disentangles the evolutionary history of spruces (Picea) in the Qinghai-Tibetan Plateau: Implications for the design of population genetic studies and species delimitation of conifers. Mol Phylogenet Evol 2019; 141:106612. [DOI: 10.1016/j.ympev.2019.106612] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 12/13/2022]
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12
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Shao CC, Shen TT, Jin WT, Mao HJ, Ran JH, Wang XQ. Phylotranscriptomics resolves interspecific relationships and indicates multiple historical out-of-North America dispersals through the Bering Land Bridge for the genus Picea (Pinaceae). Mol Phylogenet Evol 2019; 141:106610. [DOI: 10.1016/j.ympev.2019.106610] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/30/2019] [Accepted: 09/05/2019] [Indexed: 01/21/2023]
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13
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Hu YN, Zhao L, Buggs RJA, Zhang XM, Li J, Wang N. Population structure of Betula albosinensis and Betula platyphylla: evidence for hybridization and a cryptic lineage. ANNALS OF BOTANY 2019; 123:1179-1189. [PMID: 30916314 PMCID: PMC6612935 DOI: 10.1093/aob/mcz024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/15/2019] [Accepted: 02/05/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Differences in local abundance and ploidy level are predicted to impact the direction of introgression between species. Here, we tested these hypotheses on populations of Betula albosinensis (red birch) and Betula platyphylla (white birch) which were thought to differ in ploidy level, the former being tetraploid and the latter diploid. METHODS We sampled 391 birch individuals from nine localities in China, and classified them into species based on leaf morphology. Twelve nuclear microsatellite markers were genotyped in each sample, and analysed using principal coordinates analysis and STRUCTURE software. We compared the effects of two different methods of scoring polyploid genotypes on population genetic analyses. We analysed the effect of ploidy, local species abundance and latitude on levels of introgression between the species. KEY RESULTS Leaf morphology divided our samples into red and white birch, but genetic analyses unexpectedly revealed two groups within red birch, one of which was tetraploid, as expected, but the other of which appeared to have diploid microsatellite genotypes. Five individuals were identified as early-generation hybrids or backcrosses between white birch and red birch and five were identified between red birch and 'diploid' red birch. Cline analysis showed that levels of admixture were not significantly correlated with latitude. Estimated genetic differentiation among species was not significantly different between determined tetraploid and undetermined tetraploid genotypes. CONCLUSIONS Limited hybridization and gene flow have occurred between red birch and white birch. Relative species abundance and ploidy level do not impact the direction of introgression between them, as genetic admixture is roughly symmetrical. We unexpectedly found populations of apparently diploid red birch and this taxon may be a progenitor of allotetraploid red birch populations. Incomplete lineage sorting may explain patterns of genetic admixture between apparently diploid and allotetraploid red birch.
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Affiliation(s)
- Ya-Nan Hu
- College of Forestry, Shandong Agricultural University, Tai’an city, Shandong province, China
| | - Lei Zhao
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Richard J A Buggs
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Xue-Min Zhang
- Mulan-Weichang National Forestry Administration, Chengde, China
| | - Jun Li
- Mulan-Weichang National Forestry Administration, Chengde, China
| | - Nian Wang
- College of Forestry, Shandong Agricultural University, Tai’an city, Shandong province, China
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14
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Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada. Microbiol Resour Announc 2019; 8:8/23/e00381-19. [PMID: 31171622 PMCID: PMC6554609 DOI: 10.1128/mra.00381-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present the complete chloroplast genome sequence of white spruce (Picea glauca, genotype WS77111), a coniferous tree widespread in the boreal forests of North America. This sequence contributes to genomic and phylogenetic analyses of the Picea genus that are part of ongoing research to understand their adaptation to environmental stress.
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15
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Azaiez A, Pavy N, Gérardi S, Laroche J, Boyle B, Gagnon F, Mottet MJ, Beaulieu J, Bousquet J. A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies). BMC Genomics 2018; 19:942. [PMID: 30558528 PMCID: PMC6296092 DOI: 10.1186/s12864-018-5247-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species. RESULTS Targeted sequencing was achieved by capturing P. abies exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes. CONCLUSION The annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13 K genes distributed across the P. abies genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce.
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Affiliation(s)
- Aïda Azaiez
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jérôme Laroche
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Brian Boyle
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Marie-Josée Mottet
- Direction de la recherche forestière, Ministère des Forêts, de la Faune et des Parcs du Québec, 2700 Einstein, Québec, Québec G1P 3W8 Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
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16
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Dorsey BL, Gregory TJ, Sass C, Specht CD. Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae). AMERICAN JOURNAL OF BOTANY 2018; 105:1512-1530. [PMID: 30229556 DOI: 10.1002/ajb2.1149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/10/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Recent estimates of crown ages for cycad genera (Late Miocene) challenge us to consider what processes have produced the extant diversity of this ancient group in such relatively little time. Pleistocene climate change has driven major shifts in species distributions in Mexico and may have led to speciation in the genus Dioon by forcing populations to migrate up in elevation, thereby becoming separated by topography. METHODS We inferred orthologs from transcriptomes of five species and sequenced these in 42 individuals representing all Dioon species. From these data and published plastid sequences, we inferred dated species trees and lineage-specific diversification rates. KEY RESULTS Analyses of 84 newly sequenced nuclear orthologs and published plastid data confirm four major clades within Dioon, all of Pleistocene age. Gene tree analysis, divergence dates, and an increase in diversification rate support very recent and rapid divergence of extant taxa. CONCLUSIONS This study confirms the Pleistocene age of Dioon species and implicates Pleistocene climate change and established topography in lineage spitting. These results add to our understanding of the cycads as evolutionarily dynamic lineages, not relicts or evolutionary dead ends. We also find that well-supported secondary calibration points can be reliable in the absence of fossils. Our hypothesis of lineage splitting mediated by habitat shifts may be applicable to other taxa that are restricted to elevation specific ecotones.
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Affiliation(s)
- Brian L Dorsey
- The Huntington Library, Art Collections, and Botanical Gardens, San Marino, CA, 91108, USA
| | - Timothy J Gregory
- University of California Botanical Garden, 200 Centennial Drive, Berkeley, CA, 94720, USA
| | - Chodon Sass
- Department of Integrative Biology and the University and Jepson Herbaria, 431 Koshland Hall, University of California, Berkeley, CA, 94720, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, 412 Mann Library Building, Ithaca, New York, 14853, USA
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17
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De La Torre AR, Li Z, Van de Peer Y, Ingvarsson PK. Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants. Mol Biol Evol 2017; 34:1363-1377. [PMID: 28333233 PMCID: PMC5435085 DOI: 10.1093/molbev/msx069] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.
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Affiliation(s)
- Amanda R De La Torre
- Department of Plant Sciences, University of California-Davis, Davis, CA.,Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Zhen Li
- Department of Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, South Africa
| | - Pär K Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.,Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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18
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Pavy N, Lamothe M, Pelgas B, Gagnon F, Birol I, Bohlmann J, Mackay J, Isabel N, Bousquet J. A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:189-203. [PMID: 28090692 DOI: 10.1111/tpj.13478] [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: 10/27/2016] [Revised: 12/23/2016] [Accepted: 01/03/2017] [Indexed: 05/21/2023]
Abstract
Over the last decade, extensive genetic and genomic resources have been developed for the conifer white spruce (Picea glauca, Pinaceae), which has one of the largest plant genomes (20 Gbp). Draft genome sequences of white spruce and other conifers have recently been produced, but dense genetic maps are needed to comprehend genome macrostructure, delineate regions involved in quantitative traits, complement functional genomic investigations, and assist the assembly of fragmented genomic sequences. A greatly expanded P. glauca composite linkage map was generated from a set of 1976 full-sib progeny, with the positioning of 8793 expressed genes. Regions with significant low or high gene density were identified. Gene family members tended to be mapped on the same chromosomes, with tandemly arrayed genes significantly biased towards specific functional classes. The map was integrated with transcriptome data surveyed across eight tissues. In total, 69 clusters of co-expressed and co-localising genes were identified. A high level of synteny was found with pine genetic maps, which should facilitate the transfer of structural information in the Pinaceae. Although the current white spruce genome sequence remains highly fragmented, dozens of scaffolds encompassing more than one mapped gene were identified. From these, the relationship between genetic and physical distances was examined and the genome-wide recombination rate was found to be much smaller than most estimates reported for angiosperm genomes. This gene linkage map shall assist the large-scale assembly of the next-generation white spruce genome sequence and provide a reference resource for the conifer genomics community.
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Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, 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
| | - Betty Pelgas
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, 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
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanç Birol
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - John Mackay
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, 0X1 3RB, UK
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, 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
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
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Diversification of Bromelioideae (Bromeliaceae) in the Brazilian Atlantic rainforest: A case study in Aechmea subgenus Ortgiesia. Mol Phylogenet Evol 2016; 98:346-57. [PMID: 26957015 DOI: 10.1016/j.ympev.2016.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 12/26/2015] [Accepted: 03/01/2016] [Indexed: 11/21/2022]
Abstract
Aechmea subgenus Ortgiesia comprises ca. 20 species distributed in Brazil, Argentina, Paraguay, and Uruguay, with a center of diversity in the Brazilian Atlantic rainforest. We examined interspecific relationships of Ortgiesia based on Amplified Fragment Length Polymorphisms (AFLP). Ninety-six accessions belonging to 14 species of Ortgiesia were sampled, and genotyped with 11 AFLP primer combinations. The neighbor joining (NJ) tree depicted two main genetic groups within Aechmea subgenus Ortgiesia, and four subgroups. The NJ tree showed short internal branches, indicating an overall shallow genetic divergence among Ortgiesia species as expected for the recently radiated subfamily Bromelioideae. Our results suggest that hybridization and/or incomplete lineage sorting may have hampered the reconstruction of interspecific relationships in Aechmea subgenus Ortgiesia. The mapping of petal color (yellow, blue, pink, or white), inflorescence type (simple or compound), and inflorescence shape (ellipsoid, subcylindric, cylindric, or pyramidal) against the NJ tree indicated that these characters are of limited taxonomic use in Aechmea subgenus Ortgiesia due to homoplasy. An analysis of the current distribution of Ortgiesia identified the southern region of the Brazilian Atlantic rainforest, between latitudes of 26° and 27°S, as the center of diversity for the subgenus.
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Jackman SD, Warren RL, Gibb EA, Vandervalk BP, Mohamadi H, Chu J, Raymond A, Pleasance S, Coope R, Wildung MR, Ritland CE, Bousquet J, Jones SJM, Bohlmann J, Birol I. Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation. Genome Biol Evol 2015; 8:29-41. [PMID: 26645680 PMCID: PMC4758241 DOI: 10.1093/gbe/evv244] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors hundreds of mitochondria and plastids. Hence, assembly of the 123-kb plastid and 5.9-Mb mitochondrial genomes were accomplished by analyzing data sets primarily representing low coverage of the nuclear genome. The assembled organellar genomes were annotated for their coding genes, ribosomal RNA, and transfer RNA. Transcript abundances of the mitochondrial genes were quantified in three developmental tissues and five mature tissues using data from RNA-seq experiments. C-to-U RNA editing was observed in the majority of mitochondrial genes, and in four genes, editing events were noted to modify ACG codons to create cryptic AUG start codons. The informatics methodology presented in this study should prove useful to assemble organellar genomes of other plant species using whole-genome shotgun sequencing data.
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Affiliation(s)
- Shaun D Jackman
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Ewan A Gibb
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Benjamin P Vandervalk
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Hamid Mohamadi
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Justin Chu
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Anthony Raymond
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Stephen Pleasance
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Robin Coope
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Mark R Wildung
- School of Molecular Biosciences, Washington State University
| | - Carol E Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jean Bousquet
- Department of Forest and Environmental Genomics, Université Laval, Québec, QC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Joerg Bohlmann
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Inanç Birol
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada School of Computing Science, Simon Fraser University, Burnaby, BC, Canada Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
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21
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Mitochondrial introgression and complex biogeographic history of the genus Picea. Mol Phylogenet Evol 2015; 93:63-76. [DOI: 10.1016/j.ympev.2015.07.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 07/18/2015] [Accepted: 07/25/2015] [Indexed: 11/18/2022]
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22
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Hornoy B, Pavy N, Gérardi S, Beaulieu J, Bousquet J. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes. Genome Biol Evol 2015; 7:3269-85. [PMID: 26560341 PMCID: PMC4700950 DOI: 10.1093/gbe/evv218] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome. Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs. Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources.
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Affiliation(s)
- Benjamin Hornoy
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada Natural Resources Canada, Canadian Wood Fibre Centre, Québec City, QC, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada
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23
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Pavy N, Gagnon F, Deschênes A, Boyle B, Beaulieu J, Bousquet J. Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana). Mol Ecol Resour 2015; 16:588-98. [PMID: 26391535 DOI: 10.1111/1755-0998.12468] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 06/30/2015] [Accepted: 08/21/2015] [Indexed: 11/29/2022]
Abstract
Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programmes for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97,075 highly reliable in silico SNPs. These SNPs were distributed across 14,909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2% for in silico SNPs, compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications.
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Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - France Gagnon
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Astrid Deschênes
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Brian Boyle
- Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Natural Resources Canada, Canadian Wood Fibre Centre, 1055 Rue du P.E.P.S., PO Box 10380, Station Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, QC, G1V 0A6, Canada.,Institute of Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
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24
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de Lafontaine G, Prunier J, Gérardi S, Bousquet J. Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana×P. rubens). Mol Ecol 2015; 24:5229-47. [DOI: 10.1111/mec.13377] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/05/2015] [Accepted: 09/01/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Guillaume de Lafontaine
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Julien Prunier
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
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25
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Faurby S, Eiserhardt WL, Svenning J. Strong effects of variation in taxonomic opinion on diversification analyses. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12449] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Søren Faurby
- Section for Ecoinformatics & Biodiversity Department of Bioscience Aarhus University Ny Munkegade 114 DK‐8000 Aarhus C Denmark
| | - Wolf L. Eiserhardt
- Section for Ecoinformatics & Biodiversity Department of Bioscience Aarhus University Ny Munkegade 114 DK‐8000 Aarhus C Denmark
| | - Jens‐Christian Svenning
- Section for Ecoinformatics & Biodiversity Department of Bioscience Aarhus University Ny Munkegade 114 DK‐8000 Aarhus C Denmark
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26
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Warren RL, Keeling CI, Yuen MMS, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, Robertson G, Yang C, Boyle B, Hoffmann M, Weigel D, Nelson DR, Ritland C, Isabel N, Jaquish B, Yanchuk A, Bousquet J, Jones SJM, MacKay J, Birol I, Bohlmann J. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:189-212. [PMID: 26017574 DOI: 10.1111/tpj.12886] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/15/2015] [Indexed: 05/21/2023]
Abstract
White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.
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Affiliation(s)
- René L Warren
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Christopher I Keeling
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Anthony Raymond
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Greg A Taylor
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Benjamin P Vandervalk
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Hamid Mohamadi
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Daniel Paulino
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Readman Chiu
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Shaun D Jackman
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Gordon Robertson
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Chen Yang
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Margarete Hoffmann
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Carol Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Barry Jaquish
- British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Alvin Yanchuk
- British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Jean Bousquet
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - John MacKay
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Inanc Birol
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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27
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Li L, Sun Y, Zou J, Yue W, Wang X, Liu J. Origin and speciation of Picea schrenkiana and Piceasmithiana in the Center Asian Highlands and Himalayas. PLANT MOLECULAR BIOLOGY REPORTER 2015; 33:661-672. [PMID: 25999663 PMCID: PMC4432025 DOI: 10.1007/s11105-014-0774-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Elucidating the evolutionary history of current species diversity, especially trees with large effective population sizes and long generation times, is a complicated exercise confounded by gene flow and incomplete lineage sorting. In the present study, we aim to determine the origin and speciation of Picea schrenkiana and Picea smithiana using population genetic data from chloroplast (cp), mitochondrial (mt), and nuclear (nr) genomes. These two species occur in the Central Asian Highlands and Himalayas, respectively, where they are isolated from other Asian congeneric species by the Qinghai-Tibet Plateau (QTP) or adjacent deserts. Previous studies based on both morphological and molecular evidence suggest that they have contrasting phylogenetic relationships with Picea likiangensis or Picea wilsonii which are closely related and both located in the QTP. We examined genetic variation among 16 loci of three genomes from 30 populations of these four species. At both cpDNA loci and mtDNA loci, P. schrenkiana appeared to be closely related to P. likiangensis, although statistical support for this was weak. However, phylogenetic analyses and speciation tests based on the nuclear data from 11 loci provided evidence that P. schrenkiana and P. smithiana are sister species. These two species diverged around five million years ago (Mya) while the divergence between them and the P. likiangensis-P. wilsonii clade occurred about 18.4 Mya. We also detected gene flow accompanying these speciation events. Our results highlight the complex speciation histories of these alpine conifers due to interspecific gene flow and/or incomplete lineage sorting, and the importance of the early QTP uplifts in promoting the origin of these important conifer species in the Asian highlands.
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Affiliation(s)
- Lili Li
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Yongshuai Sun
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Jiabin Zou
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Wei Yue
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Xi Wang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
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28
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Wang B, Jiang B, Zhou Y, Su Y, Wang T. Higher substitution rates and lower dN/dS for the plastid genes in Gnetales than other gymnosperms. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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29
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Hao ZZ, Liu YY, Nazaire M, Wei XX, Wang XQ. Molecular phylogenetics and evolutionary history of sect. Quinquefoliae (Pinus): implications for Northern Hemisphere biogeography. Mol Phylogenet Evol 2015; 87:65-79. [PMID: 25800283 DOI: 10.1016/j.ympev.2015.03.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/24/2015] [Accepted: 03/14/2015] [Indexed: 01/15/2023]
Abstract
Climatic changes and tectonic events in the Cenozoic have greatly influenced the evolution and geographic distribution of the temperate flora. Such consequences should be most evident in plant groups that are ancient, widespread, and diverse. As one of the most widespread genera of trees, Pinus provides a good model for investigating the history of species diversification and biogeographic disjunction in the Northern Hemisphere. In this study, we reconstructed the phylogeny and investigated the evolutionary and biogeographic history of sect. Quinquefoliae (Pinus), a species-rich lineage disjunctly distributed in Asia, Europe and North America, based on complete taxon sampling and by using nine DNA fragments from chloroplast (cp), mitochondrial (mt) and nuclear genomes. The monophyly of the three subsections, Krempfianae, Gerardianae, and Strobus, is well-supported by cpDNA and nuclear gene phylogenies. However, neither subsect. Gerardianae nor subsect. Strobus forms a monophyletic group in the mtDNA phylogeny, in which sect. Quinquefoliae was divided into two major clades, one consisting of the North American and northeastern Asian species as well as the European P. peuce of subsect. Strobus, and the other comprising the remaining Eurasian species belonging to three subsections. The significant topological incongruence among the gene trees, in conjunction with divergence time estimation and ancestral area reconstruction, indicates that both ancient and relatively recent introgressive hybridization events occurred in the evolution of sect. Quinquefoliae, particularly in northeastern Asia and northwestern North America. In addition, the phylogenetic analysis suggests that the species of subsect. Strobus from subtropical eastern Asia and neighboring areas may have a single origin, although species non-monophyly is very widespread in the nuclear gene trees. Moreover, our study seems to support a Tethyan origin of sect. Quinquefoliae given the distributions and phylogenetic positions of subsects. Krempfianae and Gerardianae, and also highlights the importance of active mountain buildings and climatic changes during the Late Neogene in shaping the species diversity and geographic distribution of Pinus.
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Affiliation(s)
- Zhen-Zhen Hao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yan-Yan Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Mare Nazaire
- Rancho Santa Ana Botanic Garden, Claremont, CA 91711, USA
| | - Xiao-Xin Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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30
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Molecular proxies for climate maladaptation in a long-lived tree (Pinus pinaster Aiton, Pinaceae). Genetics 2014; 199:793-807. [PMID: 25549630 DOI: 10.1534/genetics.114.173252] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP-climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change.
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31
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Semiz A, Sen A. Cloning and expression of a CYP720B orthologue involved in the biosynthesis of diterpene resin acids in Pinus brutia. Mol Biol Rep 2014; 42:737-44. [PMID: 25394757 DOI: 10.1007/s11033-014-3822-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 11/08/2014] [Indexed: 12/08/2022]
Abstract
Cytochrome P450 monooxygenases mediate a broad range of oxidative reactions involved in the biosynthesis of both primary and secondary metabolites in plants. Until now, only two P450 genes, CYP720B1 from Pinus taeda and CYP720B4 from Picea sitchensis, have been functionally characterised and described in the literature. The purpose of this study was to describe the cloning and expression of CYP720B from Pinus brutia due to its suggested role in the synthesis of bioactive compounds used for chemical defence against insects. A PCR product of the P. brutia CYP720B gene was cloned into the pCR8/GW/TOPO cloning vector. After optimising the sequence for codon usage in yeast, it was transferred into the inducible expression vector pYES-DEST52 and transfected into the S. cerevisiae INVSc1 strain. Sequence analysis showed that the P. brutia CYP720B gene contains an open reading frame of 1,464 nucleotides, which encodes a 53,570 Da putative protein of 487 amino acid residues. The putative protein contains the classic heme-binding sequence motif that is conserved in all P450 enzymes. It shares 99 and 61% identity with the deduced amino acid sequences of CYP720B1 from Pinus taeda and CYP720B4 from Picea sitchensis, respectively. Recombinant CYP720B protein expression was confirmed using western blot analysis. Furthermore, recombinant CYP720B was functionally active, showing a Soret peak at approximately 448 nm in the reduced CO difference spectra. These data suggest that the cloned gene is an orthologue of CYP720B in P. brutia and might be involved in DRA biosynthesis.
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Affiliation(s)
- Asli Semiz
- Department of Biology, University of Pamukkale, Kinikli, 20070, Denizli, Turkey
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Gaudeul M, Gardner MF, Thomas P, Ennos RA, Hollingsworth PM. Evolutionary dynamics of emblematic Araucaria species (Araucariaceae) in New Caledonia: nuclear and chloroplast markers suggest recent diversification, introgression, and a tight link between genetics and geography within species. BMC Evol Biol 2014; 14:171. [PMID: 25189104 PMCID: PMC4182765 DOI: 10.1186/s12862-014-0171-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 07/23/2014] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND New Caledonia harbours a highly diverse and endemic flora, and 13 (out of the 19 worldwide) species of Araucaria are endemic to this territory. Their phylogenetic relationships remain largely unresolved. Using nuclear microsatellites and chloroplast DNA sequencing, we focused on five closely related Araucaria species to investigate among-species relationships and the distribution of within-species genetic diversity across New Caledonia. RESULTS The species could be clearly distinguished here, except A. montana and A. laubenfelsii that were not differentiated and, at most, form a genetic cline. Given their apparent morphological and ecological similarity, we suggested that these two species may be considered as a single evolutionary unit. We observed cases of nuclear admixture and incongruence between nuclear and chloroplast data, probably explained by introgression and shared ancestral polymorphism. Ancient hybridization was evidenced between A. biramulata and A. laubenfelsii in Mt Do, and is strongly suspected between A. biramulata and A. rulei in Mt Tonta. In both cases, extensive asymmetrical backcrossing eliminated the influence of one parent in the nuclear DNA composition. Shared ancestral polymorphism was also observed for cpDNA, suggesting that species diverged recently, have large effective sizes and/or that cpDNA experienced slow rates of molecular evolution. Within-species genetic structure was pronounced, probably because of low gene flow and significant inbreeding, and appeared clearly influenced by geography. This may be due to survival in distinct refugia during Quaternary climatic oscillations. CONCLUSIONS The study species probably diverged recently and/or are characterized by a slow rate of cpDNA sequence evolution, and introgression is strongly suspected. Within-species genetic structure is tightly linked with geography. We underline the conservation implications of our results, and highlight several perspectives.
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Wang N, Borrell JS, Bodles WJA, Kuttapitiya A, Nichols RA, Buggs RJA. Molecular footprints of the Holocene retreat of dwarf birch in Britain. Mol Ecol 2014; 23:2771-82. [PMID: 24762172 PMCID: PMC4237149 DOI: 10.1111/mec.12768] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/19/2014] [Accepted: 04/21/2014] [Indexed: 01/17/2023]
Abstract
Past reproductive interactions among incompletely isolated species may leave behind a trail of introgressed alleles, shedding light on historical range movements. Betula pubescens is a widespread native tetraploid tree species in Britain, occupying habitats intermediate to those of its native diploid relatives, B. pendula and B. nana. Genotyping 1134 trees from the three species at 12 microsatellite loci, we found evidence of introgression from both diploid species into B. pubescens, despite the ploidy difference. Surprisingly, introgression from B. nana, a dwarf species whose present range is highly restricted in northern, high-altitude peat bogs, was greater than introgression from B. pendula, which is morphologically similar to B. pubescens and has a substantially overlapping range. A cline of introgression from B. nana was found extending into B. pubescens populations far to the south of the current B. nana range. We suggest that this genetic pattern is a footprint of a historical decline and/or northwards shift in the range of B. nana populations due to climate warming in the Holocene. This is consistent with pollen records that show a broader, more southerly distribution of B. nana in the past. Ecological niche modelling predicts that B. nana is adapted to a larger range than it currently occupies, suggesting additional factors such as grazing and hybridization may have exacerbated its decline. We found very little introgression between B. nana and B. pendula, despite both being diploid, perhaps because their distributions in the past have rarely overlapped. Future conservation of B. nana may partly depend on minimization of hybridization with B. pubescens, and avoidance of planting B. pendula near B. nana populations.
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Affiliation(s)
- Nian Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
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Hinsinger DD, Gaudeul M, Couloux A, Bousquet J, Frascaria-Lacoste N. The phylogeography of Eurasian Fraxinus species reveals ancient transcontinental reticulation. Mol Phylogenet Evol 2014; 77:223-37. [PMID: 24795215 DOI: 10.1016/j.ympev.2014.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/14/2014] [Accepted: 04/18/2014] [Indexed: 01/16/2023]
Abstract
To investigate the biogeographical history of ashes species of the Eurasian section Fraxinus and to test the hypothesis of ancient reticulations, we sequenced nuclear DNA (nETS and nITS, 1075 bp) for 533 samples and scored AFLP for 63 samples of Eurasian ashes within the section Fraxinus. The nITS phylogeny retrieved the classical view of the evolution of the section, whereas nETS phylogeny indicated an unexpected separation of F. angustifolia in two paraphyletic groups, respectively found in southeastern Europe and in the other parts of the Mediterranean basin. In the nETS phylogeny, the former group was closely related to F. excelsior, whereas the later was closely related to F. mandshurica, a species which is restricted nowadays to northeastern Asia. This topological incongruence between the two loci indicated the occurrence of an ancient reticulation between European and Asian ash species. Several other ancient reticulation events between the two European species and the other species of the section were supported by the posterior predictive checking method. Some of these reticulation events would have occurred during the Miocene, when climatic variations may have lead these species to expand their distribution range and come into contact. The recurrent reticulations observed among Eurasian ash species indicate that they should be considered as conspecific taxa, with subspecific status for some groups. Altogether, the results of the present study provide a rare documented evidence for the occurrence of multiple ancient reticulations within a group of temperate tree taxa with modern disjunct distributions in Eurasia. These ancient reticulation events indicate that the speciation process is slow in ashes, necessitating long periods of geographical isolation. The implications for speciation processes in temperate trees with similar life history and reproductive biology are discussed.
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Affiliation(s)
- Damien D Hinsinger
- AgroParisTech, UMR 8079, 91405 Orsay, France; Centre national de la recherche scientifique, UMR 8079, 910405 Orsay, France; Université Paris-Sud, UMR 8079, F-91000 Orsay, France; Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
| | - Myriam Gaudeul
- Muséum National d'Histoire Naturelle, UMR CNRS 7205 'Origine, Structure et Evolution de la Biodiversité', 16 rue Buffon, CP 39, F-75005 Paris, France.
| | - Arnaud Couloux
- Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP 5706, F-91057 Evry Cedex, France.
| | - Jean Bousquet
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
| | - Nathalie Frascaria-Lacoste
- AgroParisTech, UMR 8079, 91405 Orsay, France; Centre national de la recherche scientifique, UMR 8079, 910405 Orsay, France; Université Paris-Sud, UMR 8079, F-91000 Orsay, France.
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DeGiorgio M, Syring J, Eckert AJ, Liston A, Cronn R, Neale DB, Rosenberg NA. An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines. BMC Evol Biol 2014; 14:67. [PMID: 24678701 PMCID: PMC4021425 DOI: 10.1186/1471-2148-14-67] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 02/10/2014] [Indexed: 12/26/2022] Open
Abstract
Background As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size. Results Here, using North American pines, we empirically evaluate the behavior of 24 strategies for species tree inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup species from subsection Strobus and three outgroup species from subsection Gerardianae, spanning ∼47 kilobases of sequence at 121 loci. Each “strategy” for inferring species trees consists of three features: a species tree construction method, a gene tree inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify tree characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce trees with similar features. We find that strategies that construct species trees using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a species to infer gene trees tend to produce estimates of species trees that contain clades present in trees estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct species trees tend to produce species tree estimates that contain clades that are not present in trees estimated by the Concatenation, RTC, SMRT, STAR, and STEAC methods, and that in general are more balanced than those inferred by these other strategies. Conclusions When constructing a species tree from a multilocus set of sequences, our observations provide a basis for interpreting differences in species tree estimates obtained via different approaches that have a two-stage structure in common, one step for gene tree estimation and a second step for species tree estimation. The methods explored here employ a number of distinct features of the data, and our analysis suggests that recovery of the same results from multiple methods that tend to differ in their patterns of inference can be a valuable tool for obtaining reliable estimates.
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Affiliation(s)
- Michael DeGiorgio
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
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Li L, Abbott RJ, Liu B, Sun Y, Li L, Zou J, Wang X, Miehe G, Liu J. Pliocene intraspecific divergence and Plio-Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai-Tibet Plateau. Mol Ecol 2014; 22:5237-55. [PMID: 24118118 DOI: 10.1111/mec.12466] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 07/04/2013] [Accepted: 07/17/2013] [Indexed: 11/30/2022]
Abstract
A knowledge of intraspecific divergence and range dynamics of dominant forest trees in response to past geological and climate change is of major importance to an understanding of their recent evolution and demography. Such knowledge is informative of how forests were affected by environmental factors in the past and may provide pointers to their response to future environmental change. However, genetic signatures of such historical events are often weak at individual loci due to large effective population sizes and long generation times of forest trees. This problem can be overcome by analysing genetic variation across multiple loci. We used this approach to examine intraspecific divergence and past range dynamics in the conifer Picea likiangensis, a dominant tree of forests occurring in eastern and southern areas of the Qinghai-Tibet Plateau (QTP). We sequenced 13 nuclear loci, two mitochondrial DNA regions and three plastid (chloroplast) DNA regions in 177 individuals sampled from 22 natural populations of this species, and tested the hypothesis that its evolutionary history was markedly affected by Pliocene QTP uplifts and Quaternary climatic oscillations. Consistent with the taxonomic delimitation of the three morphologically divergent varieties examined, all individuals clustered into three genetic groups with intervariety admixture detected in regions of geographical overlap. Divergence between varieties was estimated to have occurred within the Pliocene and ecological niche modelling based on 20 ecological variables suggested that niche differentiation was high. Furthermore, modelling of population-genetic data indicated that two of the varieties (var. rubescens and var. linzhiensis) expanded their population sizes after the largest Quaternary glaciation in the QTP, while expansion of the third variety (var. likiangensis) began prior to this, probably following the Pliocene QTP uplift. These findings point to the importance of geological and climatic changes during the Pliocene and Pleistocene as causes of intraspecific diversification and range shifts of dominant tree species in the QTP biodiversity hot spot region.
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Affiliation(s)
- Long Li
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Lanzhou University, Lanzhou 730000, Gansu, China
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Sun Y, Abbott RJ, Li L, Li L, Zou J, Liu J. Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai-Tibet Plateau: homoploid hybrid origin and Pleistocene expansion. Mol Ecol 2013; 23:343-59. [PMID: 26010556 DOI: 10.1111/mec.12599] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 11/20/2013] [Accepted: 11/20/2013] [Indexed: 01/29/2023]
Abstract
Hybridization and introgression can play an important role in speciation. Here, we examine their roles in the origin and evolution of Picea purpurea, a diploid spruce species occurring on the Qinghai-Tibet Plateau (QTP). Phylogenetic relationships and ecological differences between this species and its relatives, P. schrenkiana, P. likiangensis and P. wilsonii, are unclear. To clarify them, we surveyed sequence variation within and between them for 11 nuclear loci, three chloroplast (cp) and two mitochondrial (mt) DNA fragments, and examined their ecological requirements using ecological niche modelling. Initial analyses based on 11 nuclear loci rejected a close relationship between P. schrenkiana and P. purpurea. BP&P tests and ecological niche modelling indicated substantial divergence between the remaining three species and supported the species status of P. purpurea, which contained many private alleles as expected for a well-established species. Sequence variation for cpDNA and mtDNA suggested a close relationship between P. purpurea and P. wilsonii, while variation at the nuclear se1364 gene suggested P. purpurea was more closely related to P. likiangensis. Analyses of genetic divergence, Bayesian clustering and model comparison using approximate Bayesian computation (ABC) of nuclear (nr) DNA variation all supported the hypothesis that P. purpurea originated by homoploid hybrid speciation from P. wilsonii and P. likiangensis. The ABC analysis dated the origin of P. purpurea at the Pleistocene, and the estimated hybrid parameter indicated that 69% of its nuclear composition was contributed by P. likiangensis and 31% by P. wilsonii. Our results further suggested that during or immediately following its formation, P. purpurea was subject to organelle DNA introgression from P. wilsonii such that it came to possess both mtDNA and cpDNA of P. wilsonii. The estimated parameters indicated that following its origin, P. purpurea underwent an expansion during/after the largest Pleistocene glaciation recorded for the QTP.
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Affiliation(s)
- Yongshuai Sun
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China.,Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Richard J Abbott
- School of Biology, University of St Andrews, Mitchell Building, St Andrews, Fife, KY16 9TH, UK
| | - Lili Li
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Long Li
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Jiabin Zou
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, 730000, China
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Zou J, Sun Y, Li L, Wang G, Yue W, Lu Z, Wang Q, Liu J. Population genetic evidence for speciation pattern and gene flow between Picea wilsonii, P. morrisonicola and P. neoveitchii. ANNALS OF BOTANY 2013; 112:1829-44. [PMID: 24220103 PMCID: PMC3838563 DOI: 10.1093/aob/mct241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/30/2013] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS Genetic drift due to geographical isolation, gene flow and mutation rates together make it difficult to determine the evolutionary relationships of present-day species. In this study, population genetic data were used to model and decipher interspecific relationships, speciation patterns and gene flow between three species of spruce with similar morphology, Picea wilsonii, P. neoveitchii and P. morrisonicola. Picea wilsonii and P. neoveitchii occur from central to north-west China, where they have overlapping distributions. Picea morrisonicola, however, is restricted solely to the island of Taiwan and is isolated from the other two species by a long distance. METHODS Sequence variations were examined in 18 DNA fragments for 22 populations, including three fragments from the chloroplast (cp) genome, two from the mitochondrial (mt) genome and 13 from the nuclear genome. KEY RESULTS In both the cpDNA and the mtDNA, P. morrisonicola accumulated more species-specific mutations than the other two species. However, most nuclear haplotypes of P. morrisonicola were shared by P. wilsonii, or derived from the dominant haplotypes found in that species. Modelling of population genetic data supported the hypothesis that P. morrisonicola derived from P. wilsonii within the more recent past, most probably indicating progenitor-derivative speciation with a distinct bottleneck, although further gene flow from the progenitor to the derivative continued. In addition, the occurrence was detected of an obvious mtDNA introgression from P. neoveitchii to P. wilsonii despite their early divergence. CONCLUSIONS The extent of mutation, introgression and lineage sorting taking place during interspecific divergence and demographic changes in the three species had varied greatly between the three genomes. The findings highlight the complex evolutionary histories of these three Asian spruce species.
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Affiliation(s)
| | | | | | | | | | | | | | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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Hinsinger DD, Basak J, Gaudeul M, Cruaud C, Bertolino P, Frascaria-Lacoste N, Bousquet J. The phylogeny and biogeographic history of ashes (fraxinus, oleaceae) highlight the roles of migration and vicariance in the diversification of temperate trees. PLoS One 2013; 8:e80431. [PMID: 24278282 PMCID: PMC3837005 DOI: 10.1371/journal.pone.0080431] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 10/03/2013] [Indexed: 11/18/2022] Open
Abstract
The cosmopolitan genus Fraxinus, which comprises about 40 species of temperate trees and shrubs occupying various habitats in the Northern Hemisphere, represents a useful model to study speciation in long-lived angiosperms. We used nuclear external transcribed spacers (nETS), phantastica gene sequences, and two chloroplast loci (trnH-psbA and rpl32-trnL) in combination with previously published and newly obtained nITS sequences to produce a time-calibrated multi-locus phylogeny of the genus. We then inferred the biogeographic history and evolution of floral morphology. An early dispersal event could be inferred from North America to Asia during the Oligocene, leading to the diversification of the section Melioides sensus lato. Another intercontinental dispersal originating from the Eurasian section of Fraxinus could be dated from the Miocene and resulted in the speciation of F. nigra in North America. In addition, vicariance was inferred to account for the distribution of the other Old World species (sections Sciadanthus, Fraxinus and Ornus). Geographic speciation likely involving dispersal and vicariance could also be inferred from the phylogenetic grouping of geographically close taxa. Molecular dating suggested that the initial divergence of the taxonomical sections occurred during the middle and late Eocene and Oligocene periods, whereas diversification within sections occurred mostly during the late Oligocene and Miocene, which is consistent with the climate warming and accompanying large distributional changes observed during these periods. These various results underline the importance of dispersal and vicariance in promoting geographic speciation and diversification in Fraxinus. Similarities in life history, reproductive and demographic attributes as well as geographical distribution patterns suggest that many other temperate trees should exhibit similar speciation patterns. On the other hand, the observed parallel evolution and reversions in floral morphology would imply a major influence of environmental pressure. The phylogeny obtained and its biogeographical implications should facilitate future studies on the evolution of complex adaptive characters, such as habitat preference, and their possible roles in promoting divergent evolution in trees.
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Affiliation(s)
- Damien Daniel Hinsinger
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, AgroParisTech, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Centre national de la recherche scientifique, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Université Paris Sud, Orsay, France
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Jolly Basak
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Université Paris Sud, Orsay, France
| | - Myriam Gaudeul
- Unité mixte de recherche 7205 ‘Origine, Structure et Evolution de la Biodiversité’, Muséum National d'Histoire Naturelle, Paris, France
| | | | - Paola Bertolino
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, AgroParisTech, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Centre national de la recherche scientifique, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Université Paris Sud, Orsay, France
| | - Nathalie Frascaria-Lacoste
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, AgroParisTech, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Centre national de la recherche scientifique, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Université Paris Sud, Orsay, France
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec, Canada
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Bodare S, Stocks M, Yang JC, Lascoux M. Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola). Ecol Evol 2013; 3:3320-33. [PMID: 24223271 PMCID: PMC3797480 DOI: 10.1002/ece3.698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 06/26/2013] [Accepted: 06/27/2013] [Indexed: 11/08/2022] Open
Abstract
Taiwan spruce (Picea morrisonicola) is a vulnerable conifer species endemic to the island of Taiwan. A warming climate and competition from subtropical tree species has limited the range of Taiwan spruce to the higher altitudes of the island. Using seeds sampled from an area in the central mountain range of Taiwan, 15 nuclear loci were sequenced in order to measure genetic variation and to assess the long-term genetic stability of the species. Genetic diversity is low and comparable to other spruce species with limited ranges such as Picea breweriana, Picea chihuahuana, and Picea schrenkiana. Importantly, analysis using approximate Bayesian computation (ABC) provides evidence for a drastic decline in the effective population size approximately 0.3–0.5 million years ago (mya). We used simulations to show that this is unlikely to be a false-positive result due to the limited sample used here. To investigate the phylogenetic origin of Taiwan spruce, additional sequencing was performed in the Chinese spruce Picea wilsonii and combined with previously published data for three other mainland China species, Picea purpurea, Picea likiangensis, and P. schrenkiana. Analysis of population structure revealed that P. morrisonicola clusters most closely with P. wilsonii, and coalescent analyses using the program MIMAR dated the split to 4–8 mya, coincidental to the formation of Taiwan. Considering the population decrease that occurred after the split, however, led to a much more recent origin.
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Affiliation(s)
- Sofia Bodare
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University Uppsala, Sweden
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Quaternary population dynamics of an endemic conifer, Picea omorika, and their conservation implications. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0523-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Lockwood JD, Aleksić JM, Zou J, Wang J, Liu J, Renner SS. A new phylogeny for the genus Picea from plastid, mitochondrial, and nuclear sequences. Mol Phylogenet Evol 2013; 69:717-27. [PMID: 23871916 DOI: 10.1016/j.ympev.2013.07.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/21/2013] [Accepted: 07/05/2013] [Indexed: 11/30/2022]
Abstract
Studies over the past ten years have shown that the crown groups of most conifer genera are only about 15-25 Ma old. The genus Picea (spruces, Pinaceae), with around 35 species, appears to be no exception. In addition, molecular studies of co-existing spruce species have demonstrated frequent introgression. Perhaps not surprisingly therefore previous phylogenetic studies of species relationships in Picea, based mostly on plastid sequences, suffered from poor statistical support. We therefore generated mitochondrial, nuclear, and further plastid DNA sequences from carefully sourced material, striking a balance between alignability with outgroups and phylogenetic signal content. Motif duplications in mitochondrial introns were treated as characters in a stochastic Dollo model; molecular clock models were calibrated with fossils; and ancestral ranges were inferred under maximum likelihood. In agreement with previous findings, Picea diverged from its sister clade 180 million years ago (Ma), and the most recent common ancestor of today's spruces dates to 28 Ma. Different from previous analyses though, we find a large Asian clade, an American clade, and a Eurasian clade. Two expansions occurred from Asia to North America and several between Asia and Europe. Chinese P. brachytyla, American P. engelmannii, and Norway spruce, P. abies, are not monophyletic, and North America has ten, not eight species. Divergence times imply that Pleistocene refugia are unlikely to be the full explanation for the relationships between the European species and their East Asian relatives. Thus, northern Norway spruce may be part of an Asian species complex that diverged from the southern Norway spruce lineage in the Upper Miocene, some 6 Ma, which can explain the deep genetic gap noted in phylogeographic studies of Norway spruce. The large effective population sizes of spruces, and incomplete lineage sorting during speciation, mean that the interspecific relationships within each of the geographic clades require further studies, especially based on genomic information and population genetic data.
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Affiliation(s)
- Jared D Lockwood
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Strasse 67, 80638 Munich, Germany
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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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Pavy N, Gagnon F, Rigault P, Blais S, Deschênes A, Boyle B, Pelgas B, Deslauriers M, Clément S, Lavigne P, Lamothe M, Cooke JE, Jaramillo‐Correa JP, Beaulieu J, Isabel N, Mackay J, Bousquet J. Development of high‐density
SNP
genotyping arrays for white spruce (
P
icea glauca
) and transferability to subtropical and nordic congeners. Mol Ecol Resour 2013; 13:324-36. [DOI: 10.1111/1755-0998.12062] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/01/2012] [Accepted: 12/04/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
| | - France Gagnon
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
| | | | - Sylvie Blais
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
| | - Astrid Deschênes
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
| | - Brian Boyle
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
| | - Betty Pelgas
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre 1055 Rue du P.E.P.S., C.P. 10380 succ, Sainte‐Foy Québec Canada QC G1V 4C7
| | - Marie Deslauriers
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Wood Fibre Centre 1055 Rue du P.E.P.S., C.P. 10380 succ. Sainte‐Foy Québec Canada QC G1V 4C7
| | - Sébastien Clément
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Wood Fibre Centre 1055 Rue du P.E.P.S., C.P. 10380 succ. Sainte‐Foy Québec Canada QC G1V 4C7
| | - Patricia Lavigne
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre 1055 Rue du P.E.P.S., C.P. 10380 succ, Sainte‐Foy Québec Canada QC G1V 4C7
| | - Manuel Lamothe
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre 1055 Rue du P.E.P.S., C.P. 10380 succ, Sainte‐Foy Québec Canada QC G1V 4C7
| | - Janice E.K. Cooke
- Department of Biological Sciences CW405 Biological Sciences Building University of Alberta Edmonton Canada AB T6G 2E9
| | - Juan P. Jaramillo‐Correa
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Departamento de Ecología Evolutiva Instituto de Ecología Universidad Nacional Autónoma de México Apartado Postal 70‐275 México D.F. Mexico
| | - Jean Beaulieu
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Wood Fibre Centre 1055 Rue du P.E.P.S., C.P. 10380 succ. Sainte‐Foy Québec Canada QC G1V 4C7
| | - Nathalie Isabel
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre 1055 Rue du P.E.P.S., C.P. 10380 succ, Sainte‐Foy Québec Canada QC G1V 4C7
| | - John Mackay
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
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Pavy N, Pelgas B, Laroche J, Rigault P, Isabel N, Bousquet J. A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers. BMC Biol 2012; 10:84. [PMID: 23102090 PMCID: PMC3519789 DOI: 10.1186/1741-7007-10-84] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2012] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Seed plants are composed of angiosperms and gymnosperms, which diverged from each other around 300 million years ago. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the sheer size of their genomes represents a significant challenge for characterization, sequencing and assembling. RESULTS To gain insight into the macro-organisation and long-term evolution of the conifer genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical approach based on kernel density estimation to analyse gene density and identified seven gene-rich isochors. Groups of co-localizing genes were also found that were transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses of 157 gene families for which at least two duplicates were mapped on the spruce genome indicated that ancient gene duplicates shared by angiosperms and gymnosperms outnumbered conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organised in tandem arrays. Both high synteny and collinearity were also observed between the genomes of spruce and pine, two conifers that diverged more than 100 million years ago. CONCLUSIONS Taken together, these results indicate that much genomic evolution has occurred in the seed plant lineage before the split between gymnosperms and angiosperms, and that the pace of evolution of the genome macro-structure has been much slower in the gymnosperm lineage leading to extent conifers than that seen for the same period of time in flowering plants. This trend is largely congruent with the contrasted rates of diversification and morphological evolution observed between these two groups of seed plants.
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Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec G1V 0A6, Canada.
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Prunier J, Gérardi S, Laroche J, Beaulieu J, Bousquet J. Parallel and lineage-specific molecular adaptation to climate in boreal black spruce. Mol Ecol 2012; 21:4270-86. [PMID: 22805595 DOI: 10.1111/j.1365-294x.2012.05691.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In response to selective pressure, adaptation may follow different genetic pathways throughout the natural range of a species due to historical differentiation in standing genetic variation. Using 41 populations of black spruce (Picea mariana), the objectives of this study were to identify adaptive genetic polymorphisms related to temperature and precipitation variation across the transcontinental range of the species, and to evaluate the potential influence of historical events on their geographic distribution. Population structure was first inferred using 50 control nuclear markers. Then, 47 candidate gene SNPs identified in previous genome scans were tested for relationship with climatic factors using an F(ST) -based outlier method and regressions between allele frequencies and climatic variations. Two main intraspecific lineages related to glacial vicariance were detected at the transcontinental scale. Within-lineage analyses of allele frequencies allowed the identification of 23 candidate SNPs significantly related to precipitation and/or temperature variation, among which seven were common to both lineages, eight were specific to the eastern lineage and eight were specific to the western lineage. The implication of these candidate SNPs in adaptive processes was further supported by gene functional annotations. Multiple evidences indicated that the occurrence of lineage-specific adaptive SNPs was better explained by selection acting on historically differentiated gene pools rather than differential selection due to heterogeneity of interacting environmental factors and pleiotropic effects. Taken together, these findings suggest that standing genetic variation of potentially adaptive nature has been modified by historical events, hence affecting the outcome of recent selection and leading to different adaptive routes between intraspecific lineages.
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Affiliation(s)
- Julien Prunier
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Université Laval, Québec, Québec, Canada G1V 0A6
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Arca M, Hinsinger DD, Cruaud C, Tillier A, Bousquet J, Frascaria-Lacoste N. Deciduous trees and the application of universal DNA barcodes: a case study on the circumpolar Fraxinus. PLoS One 2012; 7:e34089. [PMID: 22479532 PMCID: PMC3313964 DOI: 10.1371/journal.pone.0034089] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 02/21/2012] [Indexed: 02/01/2023] Open
Abstract
The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA "universal" barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed.
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Affiliation(s)
- Mariangela Arca
- Université Paris Sud, UMR 8079, Orsay, France
- Centre national de la recherche scientifique, UMR 8079, Orsay, France
- AgroParisTech, UMR 8079, Orsay, France
| | - Damien Daniel Hinsinger
- Université Paris Sud, UMR 8079, Orsay, France
- Centre national de la recherche scientifique, UMR 8079, Orsay, France
- AgroParisTech, UMR 8079, Orsay, France
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt, Université Laval, Québec, Québec, Canada
| | | | - Annie Tillier
- Département systématique et évolution and Service de systématique moléculaire, Muséum national d'histoire naturelle, Paris, France
| | - Jean Bousquet
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt, Université Laval, Québec, Québec, Canada
| | - Nathalie Frascaria-Lacoste
- Université Paris Sud, UMR 8079, Orsay, France
- Centre national de la recherche scientifique, UMR 8079, Orsay, France
- AgroParisTech, UMR 8079, Orsay, France
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Buschiazzo E, Ritland C, Bohlmann J, Ritland K. Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evol Biol 2012; 12:8. [PMID: 22264329 PMCID: PMC3328258 DOI: 10.1186/1471-2148-12-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 01/20/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Comparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA collections for two conifers, Sitka spruce (Picea sitchensis) and loblolly pine (Pinus taeda), together with full genome sequences for two angiosperms, Arabidopsis thaliana and poplar (Populus trichocarpa), offer an opportunity to infer the evolutionary processes underlying thousands of orthologous protein-coding genes in gymnosperms compared with an angiosperm orthologue set. RESULTS Based upon pairwise comparisons of 3,723 spruce and pine orthologues, we found an average synonymous genetic distance (dS) of 0.191, and an average dN/dS ratio of 0.314. Using a fossil-established divergence time of 140 million years between spruce and pine, we extrapolated a nucleotide substitution rate of 0.68 × 10(-9) synonymous substitutions per site per year. When compared to angiosperms, this indicates a dramatically slower rate of nucleotide substitution rates in conifers: on average 15-fold. Coincidentally, we found a three-fold higher dN/dS for the spruce-pine lineage compared to the poplar-Arabidopsis lineage. This joint occurrence of a slower evolutionary rate in conifers with higher dN/dS, and possibly positive selection, showcases the uniqueness of conifer genome evolution. CONCLUSIONS Our results are in line with documented reduced nucleotide diversity, conservative genome evolution and low rates of diversification in conifers on the one hand and numerous examples of local adaptation in conifers on the other hand. We propose that reduced levels of nucleotide mutation in large and long-lived conifer trees, coupled with large effective population size, were the main factors leading to slow substitution rates but retention of beneficial mutations.
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Affiliation(s)
- Emmanuel Buschiazzo
- Department of Forest Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada.
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Singh BK, Thakur AK, Tiwari SK, Siddiqui SA, Singh VV, Rai PK. Transferability of Brassica-Derived Microsatellites to Related Genera and their Implications for Phylogenetic Analysis. NATIONAL ACADEMY SCIENCE LETTERS 2012. [DOI: 10.1007/s40009-011-0006-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Aguirre-Planter É, Jaramillo-Correa JP, Gómez-Acevedo S, Khasa DP, Bousquet J, Eguiarte LE. Phylogeny, diversification rates and species boundaries of Mesoamerican firs (Abies, Pinaceae) in a genus-wide context. Mol Phylogenet Evol 2012; 62:263-74. [DOI: 10.1016/j.ympev.2011.09.021] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 09/26/2011] [Accepted: 09/28/2011] [Indexed: 11/27/2022]
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