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Hay NM, Windham MD, Mandáková T, Lysak MA, Hendriks KP, Mummenhoff K, Lens F, Pryer KM, Bailey CD. A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets. AMERICAN JOURNAL OF BOTANY 2023; 110:e16226. [PMID: 37561651 DOI: 10.1002/ajb2.16226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
PREMISE Although Boechera (Boechereae, Brassicaceae) has become a plant model system for both ecological genomics and evolutionary biology, all previous phylogenetic studies have had limited success in resolving species relationships within the genus. The recent effective application of sequence data from target enrichment approaches to resolve the evolutionary relationships of several other challenging plant groups prompted us to investigate their usefulness in Boechera and Boechereae. METHODS To resolve the phylogeny of Boechera and closely related genera, we utilized the Hybpiper pipeline to analyze two combined bait sets: Angiosperms353, with broad applicability across flowering plants; and a Brassicaceae-specific bait set designed for use in the mustard family. Relationships for 101 samples representing 81 currently recognized species were inferred from a total of 1114 low-copy nuclear genes using both supermatrix and species coalescence methods. RESULTS Our analyses resulted in a well-resolved and highly supported phylogeny of the tribe Boechereae. Boechereae is divided into two major clades, one comprising all western North American species of Boechera, the other encompassing the eight other genera of the tribe. Our understanding of relationships within Boechera is enhanced by the recognition of three core clades that are further subdivided into robust regional species complexes. CONCLUSIONS This study presents the first broadly sampled, well-resolved phylogeny for most known sexual diploid Boechera. This effort provides the foundation for a new phylogenetically informed taxonomy of Boechera that is crucial for its continued use as a model system.
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Affiliation(s)
- Nikolai M Hay
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - Michael D Windham
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kasper P Hendriks
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, Osnabrück, D-49076, Germany
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, Osnabrück, D-49076, Germany
| | - Frederic Lens
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - C Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
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2
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Mauro AA, Shah AA, Martin PR, Ghalambor CK. An Integrative Perspective on the Mechanistic Basis of Context Dependent Species Interactions. Integr Comp Biol 2022; 62:164-178. [PMID: 35612972 DOI: 10.1093/icb/icac055] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/10/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
It has long been known that the outcome of species interactions depends on the environmental context in which they occur. Climate change research has sparked a renewed interest in context dependent species interactions because rapidly changing abiotic environments will cause species interactions to occur in novel contexts and researchers must incorporate this in their predictions of species' responses to climate change. Here we argue that predicting how the environment will alter the outcome of species interactions requires an integrative biology approach that focuses on the traits, mechanisms, and processes that bridge disciplines such as physiology, biomechanics, ecology, and evolutionary biology. Specifically, we advocate for quantifying how species differ in their tolerance and performance to both environmental challenges independent of species interactions, and in interactions with other species as a function of the environment. Such an approach increases our understanding of the mechanisms underlying outcomes of species interactions across different environmental contexts. This understanding will in turn help determine how the outcome of species interactions affects the relative abundance and distribution of the interacting species in nature. A general theme that emerges from this perspective is that species are unable to maintain high levels of performance across different environmental contexts because of trade-offs between physiological tolerance to environmental challenges and performance in species interactions. Thus, an integrative biology paradigm that focuses on the trade-offs across environments, the physiological mechanisms involved, and how the ecological context impacts the outcome of species interactions provides a stronger framework to understand why species interactions are context dependent.
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Affiliation(s)
- Alexander A Mauro
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA 94720
| | - Alisha A Shah
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI, USA
| | - Paul R Martin
- Department of Biology, Queens University, Kingston, ON, Canada
| | - Cameron K Ghalambor
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway.,Department of Biology, Colorado State University, Fort Collins, CO 80523.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523
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3
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Alexander JM, Atwater DZ, Colautti RI, Hargreaves AL. Effects of species interactions on the potential for evolution at species' range limits. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210020. [PMID: 35184598 PMCID: PMC8859514 DOI: 10.1098/rstb.2021.0020] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Species’ ranges are limited by both ecological and evolutionary constraints. While there is a growing appreciation that ecological constraints include interactions among species, like competition, we know relatively little about how interactions contribute to evolutionary constraints at species' niche and range limits. Building on concepts from community ecology and evolutionary biology, we review how biotic interactions can influence adaptation at range limits by impeding the demographic conditions that facilitate evolution (which we term a ‘demographic pathway to adaptation’), and/or by imposing evolutionary trade-offs with the abiotic environment (a ‘trade-offs pathway’). While theory for the former is well-developed, theory for the trade-offs pathway is not, and empirical evidence is scarce for both. Therefore, we develop a model to illustrate how fitness trade-offs along biotic and abiotic gradients could affect the potential for range expansion and niche evolution following ecological release. The model shows that which genotypes are favoured at species' range edges can depend strongly on the biotic context and the nature of fitness trade-offs. Experiments that characterize trade-offs and properly account for biotic context are needed to predict which species will expand their niche or range in response to environmental change. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.
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Affiliation(s)
- Jake M Alexander
- Institute of Integrative Biology, ETH Zurich, Universitätsstrasse 16, 8092 Zurich, Switzerland
| | - Daniel Z Atwater
- Biology Department, Earlham College, 801 National Rd. W, Richmond, IN 47374, USA
| | - Robert I Colautti
- Biology Department, Queen's University, 116 Barrie, St. Kingston, ON, Canada, K7 L 3N6
| | - Anna L Hargreaves
- Department of Biology, McGill University, 1205 Dr Penfield Av, Montreal, QC, Canada H3A 1B1
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4
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Mauro AA, Torres-Dowdall J, Marshall CA, Ghalambor CK. A genetically based ecological trade-off contributes to setting a geographic range limit. Ecol Lett 2021; 24:2739-2749. [PMID: 34636129 DOI: 10.1111/ele.13900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/07/2021] [Accepted: 09/14/2021] [Indexed: 12/19/2022]
Abstract
Understanding the ecological factors that shape geographic range limits and the evolutionary constraints that prevent populations from adaptively evolving beyond these limits is an unresolved question. Here, we investigated why the euryhaline fish, Poecila reticulata, is confined to freshwater within its native range, despite being tolerant of brackish water. We hypothesised that competitive interactions with a close relative, Poecilia picta, in brackish water prevents P. reticulata from colonising brackish water. Using a combination of field transplant, common garden breeding, and laboratory behaviour experiments, we find support for this hypothesis, as P. reticulata are behaviourally subordinate and have lower survival in brackish water with P. picta. We also found a negative genetic correlation between P. reticulata growth in brackish water versus freshwater in the presence of P. picta, suggesting a genetically based trade-off between salinity tolerance and competitive ability could constrain adaptive evolution at the range limit.
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Affiliation(s)
- Alexander A Mauro
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Craig A Marshall
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Cameron K Ghalambor
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA.,Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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5
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Bontrager M, Usui T, Lee-Yaw JA, Anstett DN, Branch HA, Hargreaves AL, Muir CD, Angert AL. Adaptation across geographic ranges is consistent with strong selection in marginal climates and legacies of range expansion. Evolution 2021; 75:1316-1333. [PMID: 33885152 DOI: 10.1111/evo.14231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/14/2021] [Indexed: 12/27/2022]
Abstract
Every species experiences limits to its geographic distribution. Some evolutionary models predict that populations at range edges are less well adapted to their local environments due to drift, expansion load, or swamping gene flow from the range interior. Alternatively, populations near range edges might be uniquely adapted to marginal environments. In this study, we use a database of transplant studies that quantify performance at broad geographic scales to test how local adaptation, site quality, and population quality change from spatial and climatic range centers toward edges. We find that populations from poleward edges perform relatively poorly, both on average across all sites (15% lower population quality) and when compared to other populations at home (31% relative fitness disadvantage), consistent with these populations harboring high genetic load. Populations from equatorial edges also perform poorly on average (18% lower population quality) but, in contrast, outperform foreign populations (16% relative fitness advantage), suggesting that populations from equatorial edges have strongly adapted to unique environments. Finally, we find that populations from sites that are thermally extreme relative to the species' niche demonstrate strong local adaptation, regardless of their geographic position. Our findings indicate that both nonadaptive processes and adaptive evolution contribute to variation in adaptation across species' ranges.
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Affiliation(s)
- Megan Bontrager
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Current Address: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada
| | - Takuji Usui
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Julie A Lee-Yaw
- Department of Biological Sciences, University of Lethbridge, Lethbridge, T1K 3M4, Canada
| | - Daniel N Anstett
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Haley A Branch
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | | | - Christopher D Muir
- School of Life Sciences, University of Hawaii, Honolulu, Hawaii, 96822, United States
| | - Amy L Angert
- Departments of Botany and Zoology and the Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
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6
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Angert AL, Bontrager MG, Ågren J. What Do We Really Know About Adaptation at Range Edges? ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-012120-091002] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent theory and empirical evidence have provided new insights regarding how evolutionary forces interact to shape adaptation at stable and transient range margins. Predictions regarding trait divergence at leading edges are frequently supported. However, declines in fitness at and beyond edges show that trait divergence has sometimes been insufficient to maintain high fitness, so identifying constraints to adaptation at range edges remains a key challenge. Indirect evidence suggests that range expansion may be limited by adaptive genetic variation, but direct estimates of genetic constraints at and beyond range edges are still scarce. Sequence data suggest increased genetic load in edge populations in several systems, but its causes and fitness consequences are usually poorly understood. The balance between maladaptive and positive effects of gene flow on fitness at range edges deserves further study. It is becoming increasingly clear that characterizations about degree of adaptation based solely on geographical peripherality are unsupported.
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Affiliation(s)
- Amy L. Angert
- Departments of Botany and Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Megan G. Bontrager
- Department of Evolution and Ecology, University of California, Davis, California 95616, USA
| | - Jon Ågren
- Department of Ecology and Genetics, Uppsala University, SE-752 36 Uppsala, Sweden
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7
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Mauro AA, Ghalambor CK. Trade-offs, Pleiotropy, and Shared Molecular Pathways: A Unified View of Constraints on Adaptation. Integr Comp Biol 2020; 60:332-347. [DOI: 10.1093/icb/icaa056] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Synopsis
The concept of trade-offs permeates our thinking about adaptive evolution because they are exhibited at every level of biological organization, from molecular and cellular processes to organismal and ecological functions. Trade-offs inevitably arise because different traits do not occur in isolation, but instead are imbedded within complex, integrated systems that make up whole organisms. The genetic and mechanistic underpinning of trade-offs can be found in the pleiotropic nodes that occur in the biological pathways shared between traits. Yet, often trade-offs are only understood as statistical correlations, limiting the ability to evaluate the interplay between how selection and constraint interact during adaptive evolution. Here, we first review the classic paradigms in which physiologists and evolutionary biologists have studied trade-offs and highlight the ways in which network and molecular pathway approaches unify these paradigms. We discuss how these approaches allow researchers to evaluate why trade-offs arise and how selection can act to overcome trait correlations and evolutionary constraints. We argue that understanding how the conserved molecular pathways are shared between different traits and functions provides a conceptual framework for evolutionary biologists, physiologists, and molecular biologists to meaningfully work together toward the goal of understanding why correlations and trade-offs occur between traits. We briefly highlight the melanocortin system and the hormonal control of osmoregulation as two case studies where an understanding of shared molecular pathways reveals why trade-offs occur between seemingly unrelated traits. While we recognize that applying such approaches poses challenges and limitations particularly in the context of natural populations, we advocate for the view that focusing on the biological pathways responsible for trade-offs provides a unified conceptual context accessible to a broad range of integrative biologists.
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Affiliation(s)
- Alexander A Mauro
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Cameron K Ghalambor
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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