1
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Tsai WLE, Escalona M, Garrett KL, Terrill RS, Sahasrabudhe R, Nguyen O, Beraut E, Seligmann W, Fairbairn CW, Harrigan RJ, McCormack JE, Alfaro ME, Smith TB, Bay RA. A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia). J Hered 2024; 115:317-325. [PMID: 38401156 PMCID: PMC11081134 DOI: 10.1093/jhered/esae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/16/2024] [Indexed: 02/26/2024] Open
Abstract
The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.
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Affiliation(s)
- Whitney L E Tsai
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, United States
| | - Kimball L Garrett
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, United States
| | - Ryan S Terrill
- Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States
| | - Colin W Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States
| | - Ryan J Harrigan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
| | - John E McCormack
- Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
| | - Thomas B Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
| | - Rachael A Bay
- Department of Evolution and Ecology, University of California, Davis, CA 95616, United States
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2
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Barr K, Bossu CM, Bay RA, Anderson EC, Belthoff J, Trulio LA, Chromczak D, Wisinski CL, Smith TB, Ruegg KC. Genetic and environmental drivers of migratory behavior in western burrowing owls and implications for conservation and management. Evol Appl 2023; 16:1889-1900. [PMID: 38143900 PMCID: PMC10739168 DOI: 10.1111/eva.13600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 12/26/2023] Open
Abstract
Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, with the former being genetically structured and the latter exhibiting no signs of structure. Among resident populations, we observed significantly higher genetic differentiation, significant isolation-by-distance, and significantly elevated inbreeding. Among migratory breeding groups, on the other hand, we observed lower genetic differentiation, no isolation-by-distance, and substantially lower inbreeding. Using genotype-environment association analysis, we find significant evidence for relationships between migratory phenotypes (i.e., migrant versus resident) and environmental variation associated with cold temperatures during the winter and barren, open habitats. In the regions of the genome most differentiated between migrants and residents, we find significant enrichment for genes associated with the metabolism of fats. This may be linked to the increased pressure on migrants to process and store fats more efficiently in preparation for and during migration. Our results provide a significant contribution toward understanding the evolution of migratory behavior and vital insight into ongoing conservation and management efforts for the western burrowing owl.
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Affiliation(s)
- Kelly Barr
- Center for Tropical ResearchInstitute of the Environment and Sustainability, University of California, Los AngelesLos AngelesCaliforniaUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Christen M. Bossu
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Rachael A. Bay
- Department of Evolution and EcologyUniversity of California, DavisDavisCaliforniaUSA
| | - Eric C. Anderson
- Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Jim Belthoff
- Raptor Research Center and Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Lynne A. Trulio
- Department of Environmental StudiesSan José State UniversitySan JoseCaliforniaUSA
| | - Debra Chromczak
- Burrowing Owl Researcher & ConsultantRiegelsvillePennsylvaniaUSA
| | | | - Thomas B. Smith
- Center for Tropical ResearchInstitute of the Environment and Sustainability, University of California, Los AngelesLos AngelesCaliforniaUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Kristen C. Ruegg
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
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3
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Adams NE, Bandivadekar RR, Battey CJ, Clark MW, Epperly K, Ruegg K, Tell LA, Bay RA. Widespread gene flow following range expansion in Anna's hummingbird. Mol Ecol 2023. [PMID: 36934423 DOI: 10.1111/mec.16928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/28/2023] [Accepted: 03/08/2023] [Indexed: 03/20/2023]
Abstract
Anthropogenic changes have altered the historical distributions of many North American taxa. As environments shift, ecological and evolutionary processes can combine in complex ways to either stimulate or inhibit range expansion. Here we examine the role of evolution in a rapid range expansion whose ecological context has been well-documented, Anna's Hummingbird (Calypte anna). Previous work suggests that the C. anna range expansion is the result of an ecological release facilitated by human-mediated environmental changes, where access to new food sources have allowed further filling of the abiotic niche. We examine the role of gene flow and adaptation during range expansion from their native California breeding range, north into Canada and east into New Mexico and Texas, USA. Using low coverage whole genome sequencing we found high genetic diversity, low divergence, and little evidence of selection on the northern and eastern expansion fronts. Additionally, there are no clear barriers to gene flow across the native and expanded range. The lack of selective signals between core and expanded ranges could reflect i) an absence of novel selection pressure in the expanded range (supporting the ecological release hypothesis), ii) swamping of adaptive variation due to high gene flow, or iii) limitations of genome scans for detecting small shifts in allele frequencies across many loci. Nevertheless, our results provide an example where strong selection is not apparent during a rapid, contemporary range shift.
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Affiliation(s)
- Nicole E Adams
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Ruta R Bandivadekar
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - C J Battey
- Myriad Genetics, South San Francisco, CA
| | - Michael W Clark
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Kevin Epperly
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Kristen Ruegg
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Lisa A Tell
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Rachael A Bay
- Department of Evolution and Ecology, University of California, Davis, CA, USA
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4
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Schiebelhut LM, Grosberg RK, Stachowicz JJ, Bay RA. Genomic responses to parallel temperature gradients in the eelgrass Zostera marina in adjacent bays. Mol Ecol 2023; 32:2835-2849. [PMID: 36814144 DOI: 10.1111/mec.16899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/05/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
The extent of parallel genomic responses to similar selective pressures depends on a complex array of environmental, demographic, and evolutionary forces. Laboratory experiments with replicated selective pressures yield mixed outcomes under controlled conditions and our understanding of genomic parallelism in the wild is limited to a few well-established systems. Here, we examine genomic signals of selection in the eelgrass Zostera marina across temperature gradients in adjacent embayments. Although we find many genomic regions with signals of selection within each bay there is very little overlap in signals of selection at the SNP level, despite most polymorphisms being shared across bays. We do find overlap at the gene level, potentially suggesting multiple mutational pathways to the same phenotype. Using polygenic models we find that some sets of candidate SNPs are able to predict temperature across both bays, suggesting that small but parallel shifts in allele frequencies may be missed by independent genome scans. Together, these results highlight the continuous rather than binary nature of parallel evolution in polygenic traits and the complexity of evolutionary predictability.
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Affiliation(s)
- Lauren M Schiebelhut
- Life and Environmental Sciences, University of California, Merced, California, USA
| | - Richard K Grosberg
- Department of Evolution and Ecology, University of California, Davis, California, USA
| | - John J Stachowicz
- Department of Evolution and Ecology, University of California, Davis, California, USA
| | - Rachael A Bay
- Department of Evolution and Ecology, University of California, Davis, California, USA
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5
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Alvarado AH, Bossu CM, Harrigan RJ, Bay RA, Nelson ARP, Smith TB, Ruegg KC. Genotype‐environment associations across spatial scales reveal the importance of putative adaptive genetic variation in divergence. Evol Appl 2022; 15:1390-1407. [PMID: 36187181 PMCID: PMC9488676 DOI: 10.1111/eva.13444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/04/2022] [Indexed: 12/01/2022] Open
Abstract
Identifying areas of high evolutionary potential is a judicious strategy for developing conservation priorities in the face of environmental change. For wide‐ranging species occupying heterogeneous environments, the evolutionary forces that shape distinct populations can vary spatially. Here, we investigate patterns of genomic variation and genotype–environment associations in the hermit thrush (Catharus guttatus), a North American songbird, at broad (across the breeding range) and narrow spatial scales (at a hybrid zone). We begin by building a genoscape or map of genetic variation across the breeding range and find five distinct genetic clusters within the species, with the greatest variation occurring in the western portion of the range. Genotype–environment association analyses indicate higher allelic turnover in the west than in the east, with measures of temperature surfacing as key predictors of putative adaptive genomic variation rangewide. Since broad patterns detected across a species' range represent the aggregate of many locally adapted populations, we investigate whether our broadscale analysis is consistent with a finer scale analysis. We find that top rangewide temperature‐associated loci vary in their clinal patterns (e.g., steep clines vs. fixed allele frequencies) across a hybrid zone in British Columbia, suggesting that the environmental predictors and the associated candidate loci identified in the rangewide analysis are of variable importance in this particular region. However, two candidate loci exhibit strong concordance with the temperature gradient in British Columbia, suggesting a potential role for temperature‐related barriers to gene flow and/or temperature‐driven ecological selection in maintaining putative local adaptation. This study demonstrates how patterns identified at the broad (macrogeographic) scale can be validated by investigating genotype–environment correlations at the local (microgeographic) scale. Furthermore, our results highlight the importance of considering the spatial distribution of putative adaptive variation when assessing population‐level sensitivity to climate change and other stressors.
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Affiliation(s)
- Allison H. Alvarado
- Biology Department California State University Channel Islands Camarillo CA USA
| | - Christen M. Bossu
- Center for Tropical Research, Institute of Environment and Sustainability University of California Los Angeles CA USA
- Department of Biology Colorado State University Fort Collins CO USA
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of Environment and Sustainability University of California Los Angeles CA USA
| | - Rachael A. Bay
- Department of Evolution and Ecology University of California Davis CA USA
| | | | - Thomas B. Smith
- Center for Tropical Research, Institute of Environment and Sustainability University of California Los Angeles CA USA
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | - Kristen C. Ruegg
- Department of Biology Colorado State University Fort Collins CO USA
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6
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Rose NH, Bay RA, Morikawa MK, Thomas L, Sheets EA, Palumbi SR. Genomic analysis of distinct bleaching tolerances among cryptic coral species. Proc Biol Sci 2021; 288:20210678. [PMID: 34641729 DOI: 10.1098/rspb.2021.0678] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Reef-building coral species are experiencing an unprecedented decline owing to increasing frequency and intensity of marine heatwaves and associated bleaching-induced mortality. Closely related species from the Acropora hyacinthus species complex differ in heat tolerance and in their association with heat-tolerant symbionts. We used low-coverage full genome sequencing of 114 colonies monitored across the 2015 bleaching event in American Samoa to determine the genetic differences among four cryptic species (termed HA, HC, HD and HE) that have diverged in these species traits. Cryptic species differed strongly at thousands of single nucleotide polymorphisms across the genome which are enriched for amino acid changes in the bleaching-resistant species HE. In addition, HE also showed two particularly divergent regions with strong signals of differentiation. One approximately 220 kb locus, HES1, contained the majority of fixed differences in HE. A second locus, HES2, was fixed in HE but polymorphic in the other cryptic species. Surprisingly, non-HE individuals with HE-like haplotypes at HES2 were more likely to bleach. At both loci, HE showed particular sequence similarity to a congener, Acropora millepora. Overall, resilience to bleaching during the third global bleaching event was strongly structured by host cryptic species, buoyed by differences in symbiont associations between these species.
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Affiliation(s)
- Noah H Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Rachael A Bay
- Department of Evolution and Ecology, University of California, Davis, CA, USA.,Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Megan K Morikawa
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Luke Thomas
- The UWA Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia.,Australian Institute of Marine Science, Perth, Western Australia, Australia.,Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
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7
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Ruegg K, Anderson EC, Somveille M, Bay RA, Whitfield M, Paxton EH, Smith TB. Linking climate niches across seasons to assess population vulnerability in a migratory bird. Glob Chang Biol 2021; 27:3519-3531. [PMID: 33844878 DOI: 10.1111/gcb.15639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Global loss of biodiversity has placed new urgency on the need to understand factors regulating species response to rapid environmental change. While specialists are often less resilient to rapid environmental change than generalists, species-level analyses may obscure the extent of specialization when locally adapted populations vary in climate tolerances. Until recently, quantification of the degree of climate specialization in migratory birds below the species level was hindered by a lack of genomic and tracking information, but recent technological advances have helped to overcome these barriers. Here we take a genome-wide genetic approach to mapping population-specific migratory routes and quantifying niche breadth within genetically distinct populations of a migratory bird, the willow flycatcher (Empidonax traillii), which exhibits variation in the severity of population declines across its breeding range. While our sample size is restricted to the number of genetically distinct populations within the species, our results support the idea that locally adapted populations of the willow flycatcher with narrow climatic niches across seasons are already federally listed as endangered or in steep decline, while populations with broader climatic niches have remained stable in recent decades. Overall, this work highlights the value of quantifying niche breadth within genetically distinct groups across time and space when attempting to understand the factors that facilitate or constrain the response of locally adapted populations to rapid environmental change.
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Affiliation(s)
| | - Eric C Anderson
- Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | | | - Rachael A Bay
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
| | | | - Eben H Paxton
- U.S. Geological Survey Pacific Island Ecosystems Research Center, Hawaii National Park, HI, USA
| | - Thomas B Smith
- Department of Ecology and Evolutionary Biology and Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
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8
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Somveille M, Bay RA, Smith TB, Marra PP, Ruegg KC. A general theory of avian migratory connectivity. Ecol Lett 2021; 24:1848-1858. [PMID: 34173311 DOI: 10.1111/ele.13817] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 04/19/2021] [Accepted: 05/03/2021] [Indexed: 01/13/2023]
Abstract
Birds exhibit a remarkable array of seasonal migrations. Despite much research describing migratory behaviour, the underlying forces driving how a species' breeding and wintering populations redistribute each year, that is, migratory connectivity, remain largely unknown. Here, we test the hypothesis that birds migrate in a way that minimises energy expenditure while considering intraspecific competition for energy acquisition, by developing a modelling framework that simulates an optimal redistribution of individuals between breeding and wintering areas. Using 25 species across the Americas, we find that the model accurately predicts empirical migration patterns, and thus offers a general explanation for migratory connectivity based on first ecological and energetic principles. Our model provides a strong basis for exploring additional processes underlying the ecology and evolution of migration, but also a framework for predicting how migration impacts local adaptation across seasons and how environmental change may affect population dynamics in migratory species.
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Affiliation(s)
- Marius Somveille
- Department of Biology, Colorado State University, Fort Collins, CO, USA.,Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Rachael A Bay
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Thomas B Smith
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California, Los Angeles, CA, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Peter P Marra
- Department of Biology and McCourt School of Public Policy, Georgetown University, DC, USA
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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9
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Barr K, Beichman AC, Kalhori P, Rajbhandary J, Bay RA, Ruegg K, Smith TB. Persistent panmixia despite extreme habitat loss and population decline in the threatened tricolored blackbird ( Agelaius tricolor). Evol Appl 2021; 14:674-684. [PMID: 33767743 PMCID: PMC7980274 DOI: 10.1111/eva.13147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/18/2020] [Accepted: 10/01/2020] [Indexed: 01/25/2023] Open
Abstract
Habitat loss and alteration has driven many species into decline, often to the point of requiring protection and intervention to avert extinction. Genomic data provide the opportunity to inform conservation and recovery efforts with details about vital evolutionary processes with a resolution far beyond that of traditional genetic approaches. The tricolored blackbird (Agelaius tricolor) has suffered severe losses during the previous century largely due to anthropogenic impacts on their habitat. Using a dataset composed of a whole genome paired with reduced representation libraries (RAD-Seq) from samples collected across the species' range, we find evidence for panmixia using multiple methods, including PCA (no geographic clustering), admixture analyses (ADMIXTURE and TESS conclude K = 1), and comparisons of genetic differentiation (average FST = 0.029). Demographic modeling approaches recovered an ancient decline that had a strong impact on genetic diversity but did not detect any effect from the known recent decline. We also did not detect any evidence for selection, and hence adaptive variation, at any site, either geographic or genomic. These results indicate that species continues to have high vagility across its range despite population decline and habitat loss and should be managed as a single unit.
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Affiliation(s)
- Kelly Barr
- Center for Tropical ResearchInstitute of the Environment and SustainabilityUniversity of California, Los AngelesLos AngelesCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Annabel C. Beichman
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Pooneh Kalhori
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Jasmine Rajbhandary
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Rachael A. Bay
- Department of Evolution and EcologyUniversity of California, DavisDavisCAUSA
| | - Kristen Ruegg
- Department of BiologyColorado State UniversityFort CollinsCOUSA
| | - Thomas B. Smith
- Center for Tropical ResearchInstitute of the Environment and SustainabilityUniversity of California, Los AngelesLos AngelesCAUSA
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
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10
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Bay RA, Karp DS, Saracco JF, Anderegg WRL, Frishkoff LO, Wiedenfeld D, Smith TB, Ruegg K. Genetic variation reveals individual-level climate tracking across the annual cycle of a migratory bird. Ecol Lett 2021; 24:819-828. [PMID: 33594778 DOI: 10.1111/ele.13706] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 11/28/2022]
Abstract
For migratory species, seasonal movements complicate local climate adaptation, as it is unclear whether individuals track climate niches across the annual cycle. In the migratory songbird yellow warbler (Setophaga petechia), we find a correlation between individual-level wintering and breeding precipitation, but not temperature. Birds wintering in the driest regions of the Neotropics breed in the driest regions of North America. Individuals from drier regions also possess distinct morphologies and population responses to varying rainfall. We find a positive association between bill size and breeding season precipitation which, given documented climate-associated genomic variation, might reflect adaptation to local precipitation regimes. Relative abundance in the breeding range is linked to interannual fluctuations in precipitation, but the directionality of this response varies across geography. Together, our results suggest that variation in climate optima may exist across the breeding range of yellow warblers and provide a mechanism for selection across the annual cycle.
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Affiliation(s)
- Rachael A Bay
- Department of Evolution and Ecology, University of California Davis, Davis, CA, 95616, USA
| | - Daniel S Karp
- Department of Wildlife, Fish, and Conservation Biology, University of California Davis, Davis, CA, 95616, USA
| | - James F Saracco
- The Institute for Bird Populations, Petaluma, CA, 94952, USA
| | - William R L Anderegg
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Luke O Frishkoff
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | | | - Thomas B Smith
- Institute of the Environment and Sustainability and Department of Ecology and Evolution, University of California Los Angeles, Los Angeles, CA, 90024, USA
| | - Kristen Ruegg
- Department of Biology, Colorado State University, Fort Collins, CA, 80523, USA
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11
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Capblancq T, Fitzpatrick MC, Bay RA, Exposito-Alonso M, Keller SR. Genomic Prediction of (Mal)Adaptation Across Current and Future Climatic Landscapes. Annu Rev Ecol Evol Syst 2020. [DOI: 10.1146/annurev-ecolsys-020720-042553] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Signals of local adaptation have been found in many plants and animals, highlighting the heterogeneity in the distribution of adaptive genetic variation throughout species ranges. In the coming decades, global climate change is expected to induce shifts in the selective pressures that shape this adaptive variation. These changes in selective pressures will likely result in varying degrees of local climate maladaptation and spatial reshuffling of the underlying distributions of adaptive alleles. There is a growing interest in using population genomic data to help predict future disruptions to locally adaptive gene-environment associations. One motivation behind such work is to better understand how the effects of changing climate on populations’ short-term fitness could vary spatially across species ranges. Here we review the current use of genomic data to predict the disruption of local adaptation across current and future climates. After assessing goals and motivationsunderlying the approach, we review the main steps and associated statistical methods currently in use and explore our current understanding of the limits and future potential of using genomics to predict climate change (mal)adaptation.
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Affiliation(s)
- Thibaut Capblancq
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405, USA
| | - Matthew C. Fitzpatrick
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, Maryland 21532, USA
| | - Rachael A. Bay
- Department of Evolution and Ecology, University of California, Davis, California 95616, USA
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Stephen R. Keller
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405, USA
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12
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Affiliation(s)
- Rachael A Bay
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA.
| | - Leslie Guerrero
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
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13
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Bay RA, Taylor EB, Schluter D. Parallel introgression and selection on introduced alleles in a native species. Mol Ecol 2019; 28:2802-2813. [PMID: 30980778 DOI: 10.1111/mec.15097] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 12/15/2022]
Abstract
As humans cause the redistribution of species ranges, hybridization between previously allopatric species is on the rise. Such hybridization can have complex effects on overall fitness of native species as new allelic combinations are tested. Widespread species introductions provide a unique opportunity to study selection on introgressed alleles in independent, replicated populations. We examined selection on alleles that repeatedly introgressed from introduced rainbow trout (Oncorhynchus mykiss) into native westslope cutthroat trout (Oncorhynchus clarkii lewisi) populations in western Canada. We found that the degree of introgression of individual single nucleotide polymorphisms from the invasive species into the native is correlated between independent watersheds. A number of rainbow trout alleles have repeatedly swept to high frequency in native populations, suggesting parallel adaptive advantages. Using simulations, we estimated large selection coefficients up to 0.05 favoring several rainbow trout alleles in the native background. Although previous studies have found reduced hybrid fitness and genome-wide resistance to introgression in westslope cutthroat trout, our results suggest that some introduced genomic regions are strongly favored by selection. Our study demonstrates the utility of replicated introductions as case studies for understanding parallel adaptation and the interactions between selection and introgression across the genome. We suggest that understanding this variation, including consideration of beneficial alleles, can inform management strategies for hybridizing species.
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Affiliation(s)
- Rachael A Bay
- Department of Evolution and Ecology, University of California, Davis, Davis, California
| | - Eric B Taylor
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dolph Schluter
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Cunning R, Bay RA, Gillette P, Baker AC, Traylor-Knowles N. Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution. Sci Rep 2018; 8:16134. [PMID: 30382153 PMCID: PMC6208414 DOI: 10.1038/s41598-018-34459-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/19/2018] [Indexed: 12/22/2022] Open
Abstract
Comparative analysis of the expanding genomic resources for scleractinian corals may provide insights into the evolution of these organisms, with implications for their continued persistence under global climate change. Here, we sequenced and annotated the genome of Pocillopora damicornis, one of the most abundant and widespread corals in the world. We compared this genome, based on protein-coding gene orthology, with other publicly available coral genomes (Cnidaria, Anthozoa, Scleractinia), as well as genomes from other anthozoan groups (Actiniaria, Corallimorpharia), and two basal metazoan outgroup phlya (Porifera, Ctenophora). We found that 46.6% of P. damicornis genes had orthologs in all other scleractinians, defining a coral ‘core’ genome enriched in basic housekeeping functions. Of these core genes, 3.7% were unique to scleractinians and were enriched in immune functionality, suggesting an important role of the immune system in coral evolution. Genes occurring only in P. damicornis were enriched in cellular signaling and stress response pathways, and we found similar immune-related gene family expansions in each coral species, indicating that immune system diversification may be a prominent feature of scleractinian coral evolution at multiple taxonomic levels. Diversification of the immune gene repertoire may underlie scleractinian adaptations to symbiosis, pathogen interactions, and environmental stress.
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Affiliation(s)
- R Cunning
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA. .,Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, 1200 South Lake Shore Drive, Chicago, IL, 60605, USA.
| | - R A Bay
- Department of Evolution and Ecology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - P Gillette
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - A C Baker
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - N Traylor-Knowles
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.
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15
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Bay RA, Harrigan RJ, Buermann W, Underwood VL, Gibbs HL, Smith TB, Ruegg K. Response to Comment on "Genomic signals of selection predict climate-driven population declines in a migratory bird". Science 2018; 361:361/6401/eaat7279. [PMID: 30072513 DOI: 10.1126/science.aat7956] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/05/2018] [Indexed: 11/02/2022]
Abstract
Fitzpatrick et al discuss issues that they had with analyses and interpretation in our recent manuscript on genomic correlates of climate in yellow warblers. We provide evidence that our findings would not change with different analysis and maintain that our study represents a promising direction for integrating the potential for climate adaptation as one of many tools in conservation management.
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Affiliation(s)
- Rachael A Bay
- Institute for the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA. .,Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ryan J Harrigan
- Institute for the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Wolfgang Buermann
- Institute for the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Vinh Le Underwood
- Institute for the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology and Ohio Biodiversity Conservation Partnership, Ohio State University, Columbus, OH 43210, USA
| | - Thomas B Smith
- Institute for the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Kristen Ruegg
- Institute for the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
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Ruegg K, Bay RA, Anderson EC, Saracco JF, Harrigan RJ, Whitfield M, Paxton EH, Smith TB. Ecological genomics predicts climate vulnerability in an endangered southwestern songbird. Ecol Lett 2018; 21:1085-1096. [DOI: 10.1111/ele.12977] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/11/2017] [Accepted: 03/15/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Kristen Ruegg
- Center for Tropical Research; Institute for the Environment and Sustainability; University of California Los Angeles; Los Angeles CA 90095 USA
- Department of Ecology and Evolutionary Biology; University of California Santa Cruz; Santa Cruz CA 95060 USA
| | - Rachael A. Bay
- Center for Tropical Research; Institute for the Environment and Sustainability; University of California Los Angeles; Los Angeles CA 90095 USA
- Department of Evolution and Ecology; University of California Davis; One Shields Ave Davis CA 95616 USA
- Southwest Fisheries Science Center; National Marine Fisheries Service; 110 Shaffer Road Santa Cruz CA 95060 USA
| | - Eric C. Anderson
- Department of Evolution and Ecology; University of California Davis; One Shields Ave Davis CA 95616 USA
- Southwest Fisheries Science Center; National Marine Fisheries Service; 110 Shaffer Road Santa Cruz CA 95060 USA
| | - James F. Saracco
- The Institute for Bird Populations; PO Box 1346 Point Reyes Station CA 94956 USA
| | - Ryan J. Harrigan
- Center for Tropical Research; Institute for the Environment and Sustainability; University of California Los Angeles; Los Angeles CA 90095 USA
| | - Mary Whitfield
- Southern Sierra Research Station; P.O. Box 1316 Weldon CA 932883 USA
| | - Eben H. Paxton
- U.S. Geological Survey Pacific Island Ecosystems Research Center; Hawaii Volcano National Park; HI 96718
| | - Thomas B. Smith
- Center for Tropical Research; Institute for the Environment and Sustainability; University of California Los Angeles; Los Angeles CA 90095 USA
- Department of Ecology and Evolutionary Biology; University of California, Los Angeles; 621 Charles E. Young Drive South Los Angeles CA 90095 USA
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Bay RA, Harrigan RJ, Underwood VL, Gibbs HL, Smith TB, Ruegg K. Genomic signals of selection predict climate-driven population declines in a migratory bird. Science 2018; 359:83-86. [PMID: 29302012 DOI: 10.1126/science.aan4380] [Citation(s) in RCA: 213] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 11/16/2017] [Indexed: 01/18/2023]
Abstract
The ongoing loss of biodiversity caused by rapid climatic shifts requires accurate models for predicting species' responses. Despite evidence that evolutionary adaptation could mitigate climate change impacts, evolution is rarely integrated into predictive models. Integrating population genomics and environmental data, we identified genomic variation associated with climate across the breeding range of the migratory songbird, yellow warbler (Setophaga petechia). Populations requiring the greatest shifts in allele frequencies to keep pace with future climate change have experienced the largest population declines, suggesting that failure to adapt may have already negatively affected populations. Broadly, our study suggests that the integration of genomic adaptation can increase the accuracy of future species distribution models and ultimately guide more effective mitigation efforts.
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Affiliation(s)
- Rachael A Bay
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California-Los Angeles, Los Angeles, CA 90095, USA.,Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ryan J Harrigan
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Vinh Le Underwood
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology and Ohio Biodiversity Conservation Partnership, Ohio State University, Columbus, OH 43210, USA
| | - Thomas B Smith
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California-Los Angeles, Los Angeles, CA 90095, USA.,Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Kristen Ruegg
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California-Los Angeles, Los Angeles, CA 90095, USA.,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
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Bay RA, Ruegg K. Genomic islands of divergence or opportunities for introgression? Proc Biol Sci 2018; 284:rspb.2016.2414. [PMID: 28275143 DOI: 10.1098/rspb.2016.2414] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/10/2017] [Indexed: 11/12/2022] Open
Abstract
In animals, introgression between species is often perceived as the breakdown of reproductive isolating mechanisms, but gene flow between incipient species can also represent a source for potentially beneficial alleles. Recently, genome-wide datasets have revealed clusters of differentiated loci ('genomic islands of divergence') that are thought to play a role in reproductive isolation and therefore have reduced gene flow. We use simulations to further examine the evolutionary forces that shape and maintain genomic islands of divergence between two subspecies of the migratory songbird, Swainson's thrush (Catharus ustulatus), which have come into secondary contact since the last glacial maximum. We find that, contrary to expectation, gene flow is high within islands and is highly asymmetric. In addition, patterns of nucleotide diversity at highly differentiated loci suggest selection was more frequent in a single ecotype. We propose a mechanism whereby beneficial alleles spread via selective sweeps following a post-glacial demographic expansion in one subspecies and move preferentially across the hybrid zone. We find no evidence that genomic islands are the result of divergent selection or reproductive isolation, rather our results suggest that differentiated loci both within and outside islands could provide opportunities for adaptive introgression across porous species boundaries.
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Affiliation(s)
- Rachael A Bay
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA, USA
| | - Kristen Ruegg
- Center for Tropical Research, Institute for the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA, USA
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Rose NH, Bay RA, Morikawa MK, Palumbi SR. Polygenic evolution drives species divergence and climate adaptation in corals. Evolution 2017; 72:82-94. [DOI: 10.1111/evo.13385] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Noah H. Rose
- Hopkins Marine Station, Department of Biology; Stanford University; Pacific Grove California 93950
- Current Address: Department of Ecology and Evolutionary Biology; Princeton University; Princeton New Jersey
| | - Rachael A. Bay
- Institute of the Environment and Sustainability; University of California; Los Angeles California 90095
| | - Megan K. Morikawa
- Hopkins Marine Station, Department of Biology; Stanford University; Pacific Grove California 93950
| | - Stephen R. Palumbi
- Hopkins Marine Station, Department of Biology; Stanford University; Pacific Grove California 93950
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20
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Bay RA, Rose NH, Logan CA, Palumbi SR. Genomic models predict successful coral adaptation if future ocean warming rates are reduced. Sci Adv 2017; 3:e1701413. [PMID: 29109975 PMCID: PMC5665595 DOI: 10.1126/sciadv.1701413] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 10/10/2017] [Indexed: 05/02/2023]
Abstract
Population genomic surveys suggest that climate-associated genetic variation occurs widely across species, but whether it is sufficient to allow population persistence via evolutionary adaptation has seldom been quantified. To ask whether rapid adaptation in reef-building corals can keep pace with future ocean warming, we measured genetic variation at predicted warm-adapted loci and simulated future evolution and persistence in a high-latitude population of corals from Rarotonga, Cook Islands. Alleles associated with thermal tolerance were present but at low frequencies in this cooler, southerly locality. Simulations based on predicted ocean warming in Rarotonga showed rapid evolution of heat tolerance resulting in population persistence under mild warming scenarios consistent with low CO2 emission plans, RCP2.6 and RCP4.5. Under more severe scenarios, RCP6.0 and RCP8.5, adaptation was not rapid enough to prevent extinction. Population adaptation was faster for models based on smaller numbers of additive loci that determine thermal tolerance and for higher population growth rates. Finally, accelerated migration via transplantation of thermally tolerant individuals (1 to 5%/year) sped adaptation. These results show that cool-water corals can adapt to warmer oceans but only under mild scenarios resulting from international emissions controls. Incorporation of genomic data into models of species response to climate change offers a promising method for estimating future adaptive processes.
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Affiliation(s)
- Rachael A. Bay
- Department of Biology, Hopkins Marine Station of Stanford University, Pacific Grove, CA 93950, USA
- Corresponding author.
| | - Noah H. Rose
- Department of Biology, Hopkins Marine Station of Stanford University, Pacific Grove, CA 93950, USA
| | - Cheryl A. Logan
- School of Natural Sciences, California State University, Monterey Bay, Seaside, CA 93955, USA
| | - Stephen R. Palumbi
- Department of Biology, Hopkins Marine Station of Stanford University, Pacific Grove, CA 93950, USA
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21
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Bay RA, Arnegard ME, Conte GL, Best J, Bedford NL, McCann SR, Dubin ME, Chan YF, Jones FC, Kingsley DM, Schluter D, Peichel CL. Genetic Coupling of Female Mate Choice with Polygenic Ecological Divergence Facilitates Stickleback Speciation. Curr Biol 2017; 27:3344-3349.e4. [PMID: 29056455 DOI: 10.1016/j.cub.2017.09.037] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/12/2017] [Accepted: 09/15/2017] [Indexed: 11/28/2022]
Abstract
Ecological speciation with gene flow is widespread in nature [1], but it presents a conundrum: how are associations between traits under divergent natural selection and traits that contribute to assortative mating maintained? Theoretical models suggest that genetic mechanisms inhibiting free recombination between loci underlying these two types of traits (hereafter, "genetic coupling") can facilitate speciation [2-4]. Here, we perform a direct test for genetic coupling by mapping both divergent traits and female mate choice in a classic model of ecological speciation: sympatric benthic and limnetic threespine stickleback (Gasterosteus aculeatus). By measuring mate choice in F2 hybrid females, we allowed for recombination between loci underlying assortative mating and those under divergent ecological selection. In semi-natural mating arenas in which females had access to both benthic and limnetic males, we found that F2 females mated with males similar to themselves in body size and shape. In addition, we found two quantitative trait loci (QTLs) associated with female mate choice that also predicted female morphology along the benthic-limnetic trait axis. Furthermore, a polygenic genetic model that explains adaptation to contrasting benthic and limnetic feeding niches [5] also predicted F2 female mate choice. Together, these results provide empirical evidence that genetic coupling of assortative mating with traits under divergent ecological selection helps maintain species in the face of gene flow, despite a polygenic basis for adaptation to divergent environments.
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Affiliation(s)
- Rachael A Bay
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada; Institute of the Environment and Sustainability, University of California, Los Angeles, 619 Charles E. Young Drive #300, Los Angeles, CA 90024, USA
| | - Matthew E Arnegard
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada; Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Gina L Conte
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Jacob Best
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Nicole L Bedford
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Shaugnessy R McCann
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Matthew E Dubin
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Yingguang Frank Chan
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Felicity C Jones
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - David M Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
| | - Dolph Schluter
- Biodiversity Research Centre and Zoology Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Catherine L Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.
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Bay RA, Palumbi SR. Transcriptome predictors of coral survival and growth in a highly variable environment. Ecol Evol 2017; 7:4794-4803. [PMID: 28690808 PMCID: PMC5496549 DOI: 10.1002/ece3.2685] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 12/26/2022] Open
Abstract
Concern over rapid environmental shifts associated with climate change has led to a search for molecular markers of environmental tolerance. Climate-associated gene expression profiles exist for a number of systems, but have rarely been tied to fitness outcomes, especially in nonmodel organisms. We reciprocally transplanted corals between two backreef locations with more and less variable temperature regimes to disentangle effects of recent and native environment on survival and growth. Coral growth over 12 months was largely determined by local environment. Survival, however, was impacted by native environment; corals from the more variable environment had 22% higher survivorship. By contrast, corals native to the less variable environment had more variable survival. This might represent a "selective sieve" where poor survivors are filtered from the more stressful environment. We also find a potential fitness trade-off-corals with high survival under stressful conditions grew less in the more benign environment. Transcriptome samples taken a year before transplantation were used to examine gene expression patterns that predicted transplant survival and growth. Two separate clusters of coexpressed genes were predictive of survival in the two locations. Genes from these clusters are candidate biomarkers for predicting persistence of corals under future climate change scenarios.
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Affiliation(s)
- Rachael A. Bay
- Hopkins Marine StationStanford UniversityPacific GroveCAUSA
- Present address: Institute for the Environment and SustainabilityUCLALos AngelesCAUSA
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Bay RA, Rose N, Barrett R, Bernatchez L, Ghalambor CK, Lasky JR, Brem RB, Palumbi SR, Ralph P. Predicting Responses to Contemporary Environmental Change Using Evolutionary Response Architectures. Am Nat 2017; 189:463-473. [DOI: 10.1086/691233] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
Population response to environmental variation involves adaptation, acclimation, or both. For long-lived organisms, acclimation likely generates a faster response but is only effective if the rates and limits of acclimation match the dynamics of local environmental variation. In coral reef habitats, heat stress from extreme ocean warming can occur over several weeks, resulting in symbiont expulsion and widespread coral death. However, transcriptome regulation during short-term acclimation is not well understood. We examined acclimation during a 11-day experiment in the coral Acropora nana. We acclimated colonies to three regimes: ambient temperature (29 °C), increased stable temperature (31 °C), and variable temperature (29–33 °C), mimicking local heat stress conditions. Within 7–11 days, individuals acclimated to increased temperatures had higher tolerance to acute heat stress. Despite physiological changes, no gene expression changes occurred during acclimation before acute heat stress. However, we found strikingly different transcriptional responses to heat stress between acclimation treatments across 893 contigs. Across these contigs, corals acclimated to higher temperatures (31 °C or 29–33 °C) exhibited a muted stress response—the magnitude of expression change before and after heat stress was less than in 29 °C acclimated corals. Our results show that corals have a rapid phase of acclimation that substantially increases their heat resilience within 7 days and that alters their transcriptional response to heat stress. This is in addition to a previously observed longer term response, distinguishable by its shift in baseline expression, under nonstressful conditions. Such rapid acclimation may provide some protection for this species of coral against slow onset of warming ocean temperatures.
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Bay RA, Palumbi SR. Multilocus adaptation associated with heat resistance in reef-building corals. Curr Biol 2014; 24:2952-6. [PMID: 25454780 DOI: 10.1016/j.cub.2014.10.044] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/08/2014] [Accepted: 10/14/2014] [Indexed: 11/28/2022]
Abstract
The evolution of tolerance to future climate change depends on the standing stock of genetic variation for resistance to climate-related impacts, but genes contributing to climate tolerance in wild populations are poorly described in number and effect. Physiology and gene expression patterns have shown that corals living in naturally high-temperature microclimates are more resistant to bleaching because of both acclimation and fixed effects, including adaptation. To search for potential genetic correlates of these fixed effects, we genotyped 15,399 single nucleotide polymorphisms (SNPs) in 23 individual tabletop corals, Acropora hyacinthus, within a natural temperature mosaic in backreef lagoons on Ofu Island, American Samoa. Despite overall lack of population substructure, we identified 114 highly divergent SNPs as candidates for environmental selection, via multiple stringent outlier tests, and correlations with temperature. Corals from the warmest reef location had higher minor allele frequencies across these candidate SNPs, a pattern not seen for noncandidate loci. Furthermore, within backreef pools, colonies in the warmest microclimates had a higher number and frequency of alternative alleles at candidate loci. These data suggest mild selection for alternate alleles at many loci in these corals during high heat episodes and possible maintenance of extensive polymorphism through multilocus balancing selection in a heterogeneous environment. In this case, a natural population harbors a reservoir of alleles preadapted to high temperatures, suggesting potential for future evolutionary response to climate change.
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Affiliation(s)
- Rachael A Bay
- Department of Biology, Hopkins Marine Station of Stanford University, Pacific Grove, CA 93950, USA.
| | - Stephen R Palumbi
- Department of Biology, Hopkins Marine Station of Stanford University, Pacific Grove, CA 93950, USA
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26
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Abstract
Reef corals are highly sensitive to heat, yet populations resistant to climate change have recently been identified. To determine the mechanisms of temperature tolerance, we reciprocally transplanted corals between reef sites experiencing distinct temperature regimes and tested subsequent physiological and gene expression profiles. Local acclimatization and fixed effects, such as adaptation, contributed about equally to heat tolerance and are reflected in patterns of gene expression. In less than 2 years, acclimatization achieves the same heat tolerance that we would expect from strong natural selection over many generations for these long-lived organisms. Our results show both short-term acclimatory and longer-term adaptive acquisition of climate resistance. Adding these adaptive abilities to ecosystem models is likely to slow predictions of demise for coral reef ecosystems.
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Affiliation(s)
- Stephen R Palumbi
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA.
| | - Daniel J Barshis
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | - Nikki Traylor-Knowles
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
| | - Rachael A Bay
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA 93950, USA
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Abstract
Tigers (Panthera tigris), like many large carnivores, are threatened by anthropogenic impacts, primarily habitat loss and poaching. Current conservation plans for tigers focus on population expansion, with the goal of doubling census size in the next 10 years. Previous studies have shown that because the demographic decline was recent, tiger populations still retain a large amount of genetic diversity. Although maintaining this diversity is extremely important to avoid deleterious effects of inbreeding, management plans have yet to consider predictive genetic models. We used coalescent simulations based on previously sequenced mitochondrial fragments (n = 125) from 5 of 6 extant subspecies to predict the population growth needed to maintain current genetic diversity over the next 150 years. We found that the level of gene flow between populations has a large effect on the local population growth necessary to maintain genetic diversity, without which tigers may face decreases in fitness. In the absence of gene flow, we demonstrate that maintaining genetic diversity is impossible based on known demographic parameters for the species. Thus, managing for the genetic diversity of the species should be prioritized over the riskier preservation of distinct subspecies. These predictive simulations provide unique management insights, hitherto not possible using existing analytical methods.
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Affiliation(s)
- Rachael A Bay
- the Department of Biology, Stanford University, Stanford, CA 94305
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Bay RA, Bielawski JP. Recombination Detection Under Evolutionary Scenarios Relevant to Functional Divergence. J Mol Evol 2012; 73:273-86. [DOI: 10.1007/s00239-011-9473-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 11/07/2011] [Indexed: 12/01/2022]
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