1
|
Zhou Q, Karunarathne P, Andersson-Li L, Chen C, Opgenoorth L, Heer K, Piotti A, Vendramin GG, Nakvasina E, Lascoux M, Milesi P. Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles. Mol Ecol 2024; 33:e17495. [PMID: 39148357 DOI: 10.1111/mec.17495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 07/15/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
Most tree species underwent cycles of contraction and expansion during the Quaternary. These cycles led to an ancient and complex genetic structure that has since been affected by extensive gene flow and by strong local adaptation. The extent to which hybridization played a role in this multi-layered genetic structure is important to be investigated. To study the effect of hybridization on the joint population genetic structure of two dominant species of the Eurasian boreal forest, Picea abies and P. obovata, we used targeted resequencing and obtained around 480 K nuclear SNPs and 87 chloroplast SNPs in 542 individuals sampled across most of their distribution ranges. Despite extensive gene flow and a clear pattern of Isolation-by-Distance, distinct genetic clusters emerged, indicating the presence of barriers and corridors to migration. Two cryptic refugia located in the large hybrid zone between the two species played a critical role in shaping their current distributions. The two species repeatedly hybridized during the Pleistocene and the direction of introgression depended on latitude. Our study suggests that hybridization helped both species to overcome main shifts in their distribution ranges during glacial cycles and highlights the importance of considering whole species complex instead of separate entities to retrieve complex demographic histories.
Collapse
Affiliation(s)
- Qiujie Zhou
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
| | - Piyal Karunarathne
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
- Institute of Population Genetics, Heinrich-Heine University, Düsseldorf, Universitäts Straße 1, Düsseldorf, Germany
| | - Lili Andersson-Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska L2:02, Solna, Sweden
| | - Chen Chen
- Plant Pathology Group, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Lars Opgenoorth
- Department of Biology, Plant Ecology and Geobotany, Philipps-Universität Marburg, Marburg, Germany
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Katrin Heer
- Faculty of Environment and Natural Resources, Eva Mayr-Stihl Professorship for Forest Genetics, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
| | - Andrea Piotti
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | | | - Elena Nakvasina
- Department of Forestry and Forest Management, Northern (Arctic) Federal University Named after M.V. Lomonosov, Arkhangelsk, Russian Federation
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
| |
Collapse
|
2
|
Steenwyk JL, King N. The promise and pitfalls of synteny in phylogenomics. PLoS Biol 2024; 22:e3002632. [PMID: 38768403 PMCID: PMC11105162 DOI: 10.1371/journal.pbio.3002632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Reconstructing the tree of life remains a central goal in biology. Early methods, which relied on small numbers of morphological or genetic characters, often yielded conflicting evolutionary histories, undermining confidence in the results. Investigations based on phylogenomics, which use hundreds to thousands of loci for phylogenetic inquiry, have provided a clearer picture of life's history, but certain branches remain problematic. To resolve difficult nodes on the tree of life, 2 recent studies tested the utility of synteny, the conserved collinearity of orthologous genetic loci in 2 or more organisms, for phylogenetics. Synteny exhibits compelling phylogenomic potential while also raising new challenges. This Essay identifies and discusses specific opportunities and challenges that bear on the value of synteny data and other rare genomic changes for phylogenomic studies. Synteny-based analyses of highly contiguous genome assemblies mark a new chapter in the phylogenomic era and the quest to reconstruct the tree of life.
Collapse
Affiliation(s)
- Jacob L. Steenwyk
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Nicole King
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| |
Collapse
|
3
|
Sanderson BJ, Gambhir D, Feng G, Hu N, Cronk QC, Percy DM, Freaner FM, Johnson MG, Smart LB, Keefover-Ring K, Yin T, Ma T, DiFazio SP, Liu J, Olson MS. Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives. Syst Biol 2023; 72:1220-1232. [PMID: 37449764 DOI: 10.1093/sysbio/syad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 06/02/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023] Open
Abstract
Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a "spectacular failure" due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here, we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed the polyphyly of others. Using an fbranch analysis, we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix-Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Salix and Populus have played important roles in the diversification and diversity in these two genera.
Collapse
Affiliation(s)
- Brian J Sanderson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
- Department of Biology, West Virginia University, Morgantown, WV 26506,USA
| | - Diksha Gambhir
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Guanqiao Feng
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Nan Hu
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Quentin C Cronk
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Diana M Percy
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, New York 14456, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tongming Yin
- Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506,USA
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| |
Collapse
|
4
|
Grossfurthner LP, Milano ER, Hohenlohe PA, Waits LP, Richardson BA. Population structure and hybridization under contemporary and future climates in a heteroploid foundational shrub species ( Artemisia tridentata). FRONTIERS IN PLANT SCIENCE 2023; 14:1155868. [PMID: 37284723 PMCID: PMC10239881 DOI: 10.3389/fpls.2023.1155868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/20/2023] [Indexed: 06/08/2023]
Abstract
Current and past climatic changes can shift plant climatic niches, which may cause spatial overlap or separation between related taxa. The former often leads to hybridization and introgression, which may generate novel variation and influence the adaptive capacity of plants. An additional mechanism facilitating adaptations to novel environments and an important evolutionary driver in plants is polyploidy as the result of whole genome duplication. Artemisia tridentata (big sagebrush) is a landscape-dominating foundational shrub in the western United States which occupies distinct ecological niches, exhibiting diploid and tetraploid cytotypes. Tetraploids have a large impact on the species' landscape dominance as they occupy a preponderance of the arid spectrum of A. tridentata range. Three distinct subspecies are recognized, which co-occur in ecotones - the transition zone between two or more distinct ecological niches - allowing for hybridization and introgression. Here we assess the genomic distinctiveness and extent of hybridization among subspecies at different ploidies under both contemporary and predicted future climates. We sampled five transects throughout the western United States where a subspecies overlap was predicted using subspecies-specific climate niche models. Along each transect, we sampled multiple plots representing the parental and the potential hybrid habitats. We performed reduced representation sequencing and processed the data using a ploidy-informed genotyping approach. Population genomic analyses revealed distinct diploid subspecies and at least two distinct tetraploid gene pools, indicating independent origins of the tetraploid populations. We detected low levels of hybridization (2.5%) between the diploid subspecies, while we found evidence for increased admixture between ploidy levels (18%), indicating hybridization has an important role in the formation of tetraploids. Our analyses highlight the importance of subspecies co-occurrence within these ecotones to maintain gene exchange and potential formation of tetraploid populations. Genomic confirmations of subspecies in the ecotones support the subspecies overlap predicted by the contemporary climate niche models. However, future mid-century projections of subspecies niches predict a substantial loss in range and subspecies overlap. Thus, reductions in hybridization potential could affect new recruitment of genetically variable tetraploids that are vital to this species' ecological role. Our results underscore the importance of ecotone conservation and restoration.
Collapse
Affiliation(s)
- Lukas P. Grossfurthner
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, United States
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Elizabeth R. Milano
- Rocky Mountain Research Station, United States Department of Agriculture (USDA) Forest Service, Moscow, ID, United States
| | - Paul A. Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, United States
| | - Bryce A. Richardson
- Rocky Mountain Research Station, United States Department of Agriculture (USDA) Forest Service, Moscow, ID, United States
| |
Collapse
|
5
|
Whittemore AT, Miller RE. Dynamic properties of the pinyon pine syngameon. THE NEW PHYTOLOGIST 2023; 237:1943-1945. [PMID: 36652627 DOI: 10.1111/nph.18707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Alan T Whittemore
- Herbarium, Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
| | - Richard E Miller
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
- Flower Diversity Institute, Arvada, CO, 80003, USA
| |
Collapse
|