1
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Miller CV, Bossu CM, Sarraco JF, Toews DPL, Rushing CS, Roberto-Charron A, Tremblay JA, Chandler RB, DeSaix MG, Fiss CJ, Larkin JL, Haché S, Nebel S, Ruegg KC. Genomics-informed conservation units reveal spatial variation in climate vulnerability in a migratory bird. Mol Ecol 2024; 33:e17199. [PMID: 38018020 DOI: 10.1111/mec.17199] [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: 08/02/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023]
Abstract
Identifying genetic conservation units (CUs) in threatened species is critical for the preservation of adaptive capacity and evolutionary potential in the face of climate change. However, delineating CUs in highly mobile species remains a challenge due to high rates of gene flow and genetic signatures of isolation by distance. Even when CUs are delineated in highly mobile species, the CUs often lack key biological information about what populations have the most conservation need to guide management decisions. Here we implement a framework for CU identification in the Canada Warbler (Cardellina canadensis), a migratory bird species of conservation concern, and then integrate demographic modelling and genomic offset to guide conservation decisions. We find that patterns of whole genome genetic variation in this highly mobile species are primarily driven by putative adaptive variation. Identification of CUs across the breeding range revealed that Canada Warblers fall into two evolutionarily significant units (ESU), and three putative adaptive units (AUs) in the South, East, and Northwest. Quantification of genomic offset, a metric of genetic changes necessary to maintain current gene-environment relationships, revealed significant spatial variation in climate vulnerability, with the Northwestern AU being identified as the most vulnerable to future climate change. Alternatively, quantification of past population trends within each AU revealed the steepest population declines have occurred within the Eastern AU. Overall, we illustrate that genomics-informed CUs provide a strong foundation for identifying current and future regional threats that can be used to inform management strategies for a highly mobile species in a rapidly changing world.
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Affiliation(s)
- Caitlin V Miller
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Christen M Bossu
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - James F Sarraco
- The Institute for Bird Populations, Petaluma, California, USA
| | - David P L Toews
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Clark S Rushing
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
| | | | - Junior A Tremblay
- Wildlife Research Division, Environment and Climate Change Canada, Québec, Quebec, Canada
| | - Richard B Chandler
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
| | - Matthew G DeSaix
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Cameron J Fiss
- Department of Biology, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA
| | - Jeff L Larkin
- Department of Biology, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA
| | - Samuel Haché
- Canadian Wildlife Service, Environment Climate Change Canada, Yellowknife, Northwest Territories, Canada
| | | | - Kristen C Ruegg
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
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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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Bossu CM, Rodriguez M, Rayne C, Chromczak DA, Higgins PG, Trulio LA, Ruegg KC. Genomic approaches to mitigating genetic diversity loss in declining populations. Mol Ecol 2023; 32:5228-5240. [PMID: 37610278 DOI: 10.1111/mec.17109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023]
Abstract
The accelerating pace of global biodiversity loss is exacerbated by habitat fragmentation and subsequent inbreeding in small populations. To address this problem, conservation practitioners often turn to assisted breeding programmes with the aim of enhancing genetic diversity in declining populations. Although genomic information is infrequently included in these efforts, it has the potential to significantly enhance the success of such programmes. In this study, we showcase the value of genomic approaches for increasing genetic diversity in assisted breeding efforts, specifically focusing on a highly inbred population of Western burrowing owls. To maximize genetic diversity in the resulting offspring, we begin by creating an optimal pairing decision tree based on sex, kinship and patterns of homozygosity across the genome. To evaluate the effectiveness of our strategy, we compare genetic diversity, brood size and nestling success rates between optimized and non-optimized pairs. Additionally, we leverage recently discovered correlations between telomere length and fitness across species to investigate whether genomic optimization could have long-term fitness benefits. Our results indicate that pairing individuals with contrasting patterns of homozygosity across the genome is an effective way to increase genetic diversity in offspring. Although short-term field-based metrics of success did not differ significantly between optimized and non-optimized pairs, offspring from optimized pairs had significantly longer telomeres, suggesting that genetic optimization can help reduce the risk of inbreeding depression. These findings underscore the importance of genomic tools for informing efforts to preserve the adaptive potential of small, inbred populations at risk of further decline.
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Affiliation(s)
- Christen M Bossu
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Marina Rodriguez
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Christine Rayne
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Debra A Chromczak
- Burrowing Owl Researcher & Consultant, Riegelsville, Pennsylvania, USA
| | | | - Lynne A Trulio
- Department of Environmental Studies, San José State University, San Jose, California, USA
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
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4
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DeSaix MG, Anderson EC, Bossu CM, Rayne CE, Schweizer TM, Bayly NJ, Narang DS, Hagelin JC, Gibbs HL, Saracco JF, Sherry TW, Webster MS, Smith TB, Marra PP, Ruegg KC. Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla). Mol Ecol 2023; 32:5528-5540. [PMID: 37706673 DOI: 10.1111/mec.17137] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/26/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate-Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.
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Affiliation(s)
- Matthew G DeSaix
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Eric C Anderson
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Santa Cruz, California, USA
- Department of Fisheries, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Christen M Bossu
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Christine E Rayne
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Teia M Schweizer
- Department of Fisheries, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Nicholas J Bayly
- SELVA Investigación para la conservación en el Neotropico, DG42A #20-37, Bogotá, Colombia
| | - Darshan S Narang
- Trinidad and Tobago Field Naturalists' Club, Port of Spain, Trinidad and Tobago
| | - Julie C Hagelin
- Threatened, Endangered and Diversity Program, Alaska Department of Fish and Game, Fairbanks, Alaska, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - James F Saracco
- The Institute for Bird Populations, Petaluma, California, USA
| | - Thomas W Sherry
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Michael S Webster
- Cornell Lab of Ornithology, Ithaca, New York, USA
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment & Sustainability, University of California Los Angeles, Los Angeles, California, USA
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Peter P Marra
- Department of Biology, Georgetown University, Washington, District of Columbia, USA
- McCourt School of Public Policy, Georgetown University, Washington, District of Columbia, USA
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
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5
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Turbek SP, Funk WC, Ruegg KC. Where to draw the line? Expanding the delineation of conservation units to highly mobile taxa. J Hered 2023; 114:300-311. [PMID: 36815497 DOI: 10.1093/jhered/esad011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 04/27/2022] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
Conservation units (CUs) are an essential tool for maximizing evolutionary potential and prioritizing areas across a species' range for protection when implementing conservation and management measures. However, current workflows for identifying CUs on the basis of neutral and adaptive genomic variation largely ignore information contained in patterns of isolation by distance (IBD), frequently the primary signal of population structure in highly mobile taxa, such as birds, bats, and marine organisms with pelagic larval stages. While individuals located on either end of a species' distribution may exhibit clear genetic, phenotypic, and ecological differences, IBD produces subtle changes in allele frequencies across space, making it difficult to draw clear boundaries for conservation purposes in the absence of discrete population structure. Here, we highlight potential pitfalls that arise when applying common methods for delineating CUs to continuously distributed organisms and review existing methods for detecting subtle breakpoints in patterns of IBD that can indicate barriers to gene flow in highly mobile taxa. In addition, we propose a new framework for identifying CUs in all organisms, including those characterized by continuous genomic differentiation, and suggest several possible ways to harness the information contained in patterns of IBD to guide conservation and management decisions.
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Affiliation(s)
- Sheela P Turbek
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Fort Collins, CO, United States
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6
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Funk ER, Spellman GM, Winker K, Withrow JJ, Ruegg KC, Taylor SA. The genetic basis of plumage coloration and elevation adaptation in a clade of recently diverged alpine and arctic songbirds. Evolution 2023; 77:705-717. [PMID: 36626815 DOI: 10.1093/evolut/qpac064] [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: 08/25/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023]
Abstract
Trait genetic architecture plays an important role in the probability that variation in that trait leads to divergence and speciation. In some cases, speciation may be driven by the generation of novel phenotypes through the recombination of genes associated with traits that are important for local adaptation or sexual selection. Here, we investigate the genetic basis of three plumage color traits, and one ecological trait, breeding elevation, in a recent avian radiation, the North American rosy-finches (Leucosticte spp.). We identify unique genomic regions associated with each trait and highlight 11 candidate genes. Among these are well-characterized melanogenesis genes, including Mitf and Tyrp1, and previously reported hypoxia-related genes including Egln1. Additionally, we use mitochondrial data to date the divergence of rosy-finch clades which appear to have diverged within the past 250 ky. Given the low levels of genome-wide differentiation among rosy-finch taxa, and evidence for extensive introgression in North America, plumage coloration and adaptation to high elevations have likely played large roles in generating the observed patterns of lineage divergence. The relative independence of these candidate regions across the genome suggests that recombination might have led to multiple phenotypes, and subsequent rosy-finch speciation, over short periods of time.
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Affiliation(s)
- Erik R Funk
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature and Science, Denver, CO, United States
| | - Kevin Winker
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Jack J Withrow
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
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7
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DeSaix MG, George TL, Seglund AE, Spellman GM, Zavaleta ES, Ruegg KC. Forecasting climate change response in an alpine specialist songbird reveals the importance of considering novel climate. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Matthew G. DeSaix
- Department of Biology Colorado State University Fort Collins Colorado USA
| | - T. Luke George
- Department of Fish, Wildlife, and Conservation Biology Colorado State University Fort Collins Colorado USA
| | | | - Garth M. Spellman
- Department of Zoology Denver Museum of Nature and Science Denver Colorado USA
| | - Erika S. Zavaleta
- Department of Ecology and Evolutionary Biology University of California Santa Cruz California USA
| | - Kristen C. Ruegg
- Department of Biology Colorado State University Fort Collins Colorado USA
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8
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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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9
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Bossu CM, Heath JA, Kaltenecker GS, Helm B, Ruegg KC. Clock-linked genes underlie seasonal migratory timing in a diurnal raptor. Proc Biol Sci 2022; 289:20212507. [PMID: 35506230 PMCID: PMC9069262 DOI: 10.1098/rspb.2021.2507] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/07/2022] [Indexed: 01/04/2023] Open
Abstract
Seasonal migration is a dynamic natural phenomenon that allows organisms to exploit favourable habitats across the annual cycle. While the morphological, physiological and behavioural changes associated with migratory behaviour are well characterized, the genetic basis of migration and its link to endogenous biological time-keeping pathways are poorly understood. Historically, genome-wide research has focused on genes of large effect, whereas many genes of small effect may work together to regulate complex traits like migratory behaviour. Here, we explicitly relax stringent outlier detection thresholds and, as a result, discover how multiple biological time-keeping genes are important to migratory timing in an iconic raptor species, the American kestrel (Falco sparverius). To validate the role of candidate loci in migratory timing, we genotyped kestrels captured across autumn migration and found significant associations between migratory timing and genetic variation in metabolic and light-input pathway genes that modulate biological clocks (top1, phlpp1, cpne4 and peak1). Further, we demonstrate that migrating individuals originated from a single panmictic source population, suggesting the existence of distinct early and late migratory genotypes (i.e. chronotypes). Overall, our results provide empirical support for the existence of a within-population-level polymorphism in genes underlying migratory timing in a diurnally migrating raptor.
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Affiliation(s)
- Christen M. Bossu
- Biology Department, Colorado State University, Fort Collins, CO 80521, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Julie A. Heath
- Raptor Research Center and Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Gregory S. Kaltenecker
- Intermountain Bird Observatory, Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Barbara Helm
- Department of Bird Migration, Swiss Ornithological Institute, 6204 Sempach, Switzerland
| | - Kristen C. Ruegg
- Biology Department, Colorado State University, Fort Collins, CO 80521, USA
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10
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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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11
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Sendell-Price AT, Ruegg KC, Robertson BC, Clegg SM. An island-hopping bird reveals how founder events shape genome-wide divergence. Mol Ecol 2021; 30:2495-2510. [PMID: 33826187 DOI: 10.1111/mec.15898] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/09/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022]
Abstract
When populations colonize new areas, both strong selection and strong drift can be experienced due to novel environments and small founding populations, respectively. Empirical studies have predominantly focused on the phenotype when assessing the role of selection, and limited neutral-loci when assessing founder-induced loss of diversity. Consequently, the extent to which processes interact to influence evolutionary trajectories is difficult to assess. Genomic-level approaches provide the opportunity to simultaneously consider these processes. Here, we examine the roles of selection and drift in shaping genomic diversity and divergence in historically documented sequential island colonizations by the silvereye (Zosterops lateralis). We provide the first empirical demonstration of the rapid appearance of highly diverged genomic regions following population founding, the position of which are highly idiosyncratic. As these regions rarely contained loci putatively under selection, it is most likely that these differences arise via the stochastic nature of the founding process. However, selection is required to explain rapid evolution of larger body size in insular silvereyes. Reconciling our genomic data with these phenotypic patterns suggests there may be many genomic routes to the island phenotype, which vary across populations. Finally, we show that accelerated divergence associated with multiple founding steps is the product of genome-wide rather than localized differences, and that diversity erodes due to loss of rare alleles. However, even multiple founder events do not result in divergence and diversity levels seen in evolutionary older subspecies, and therefore do not provide a shortcut to speciation as proposed by founder-effect speciation models.
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Affiliation(s)
- Ashley T Sendell-Price
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Kristen C Ruegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK.,Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK.,Environmental Futures Research Institute, Griffith University, Nathan, Qld, Australia
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12
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Ruegg KC, Harrigan RJ, Saracco JF, Smith TB, Taylor CM. A genoscape-network model for conservation prioritization in a migratory bird. Conserv Biol 2020; 34:1482-1491. [PMID: 32391608 DOI: 10.1111/cobi.13536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 03/01/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Migratory animals are declining worldwide and coordinated conservation efforts are needed to reverse current trends. We devised a novel genoscape-network model that combines genetic analyses with species distribution modeling and demographic data to overcome challenges with conceptualizing alternative risk factors in migratory species across their full annual cycle. We applied our method to the long distance, Neotropical migratory bird, Wilson's Warbler (Cardellina pusilla). Despite a lack of data from some wintering locations, we demonstrated how the results can be used to help prioritize conservation of breeding and wintering areas. For example, we showed that when genetic, demographic, and network modeling results were considered together it became clear that conservation recommendations will differ depending on whether the goal is to preserve unique genetic lineages or the largest number of birds per unit area. More specifically, if preservation of genetic lineages is the goal, then limited resources should be focused on preserving habitat in the California Sierra, Basin Rockies, or Coastal California, where the 3 most vulnerable genetic lineages breed, or in western Mexico, where 2 of the 3 most vulnerable lineages overwinter. Alternatively, if preservation of the largest number of individuals per unit area is the goal, then limited conservation dollars should be placed in the Pacific Northwest or Central America, where densities are estimated to be the highest. Overall, our results demonstrated the utility of adopting a genetically based network model for integrating multiple types of data across vast geographic scales and better inform conservation decision-making for migratory animals.
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Affiliation(s)
- Kristen C Ruegg
- Biology Department, Colorado State University, 251 W. Pitkins St, Fort Collins, CO, 80521, U.S.A
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E Young Drive East, Los Angeles, CA, 90095, U.S.A
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E Young Drive East, Los Angeles, CA, 90095, U.S.A
| | - James F Saracco
- The Institute for Bird Populations, PO Box 1346, Point Reyes Station, CA, 94956, U.S.A
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E Young Drive East, Los Angeles, CA, 90095, U.S.A
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, U.S.A
| | - Caz M Taylor
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Lindy Boggs Center, New Orleans, LA, 70118, U.S.A
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13
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Funk ER, Spellman GM, Winker K, Withrow JJ, Ruegg KC, Zavaleta E, Taylor SA. Phylogenomic Data Reveal Widespread Introgression Across the Range of an Alpine and Arctic Specialist. Syst Biol 2020; 70:527-541. [PMID: 32941630 DOI: 10.1093/sysbio/syaa071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 01/10/2023] Open
Abstract
Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. Although simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects of genetic drift and inbreeding, or localized selection. Although different signals can be difficult to separate, the application of high-throughput sequence data can provide the resolution necessary to distinguish many of these processes. We present whole-genome sequence data for an avian species group with an alpine and arctic tundra distribution to examine the role that different population genetic processes have played in their evolutionary history. Rosy-finches inhabit high elevation mountaintop sky islands and high-latitude island and continental tundra. They exhibit extensive plumage variation coupled with low levels of genetic variation. Additionally, the number of species within the complex is debated, making them excellent for studying the forces involved in the process of diversification, as well as an important species group in which to investigate species boundaries. Total genomic variation suggests a broadly continuous pattern of allele frequency changes across the mainland taxa of this group in North America. However, phylogenomic analyses recover multiple distinct, well supported, groups that coincide with previously described morphological variation and current species-level taxonomy. Tests of introgression using D-statistics and approximate Bayesian computation reveal significant levels of introgression between multiple North American taxa. These results provide insight into the balance between divergent and homogenizing population genetic processes and highlight remaining challenges in interpreting conflict between different types of analytical approaches with whole-genome sequence data. [ABBA-BABA; approximate Bayesian computation; gene flow; phylogenomics; speciation; whole-genome sequencing.].
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Affiliation(s)
- Erik R Funk
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St. 334 UCB, Boulder, CO 80309, USA
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature and Science, 2001 Colorado Blvd., Denver, CO 80205, USA
| | - Kevin Winker
- University of Alaska Museum, University of Alaska Fairbanks, 1962 Yukon Dr., Fairbanks, AK 99775, USA
| | - Jack J Withrow
- University of Alaska Museum, University of Alaska Fairbanks, 1962 Yukon Dr., Fairbanks, AK 99775, USA
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, 251 W Pitkin St., Fort Collins, CO 80521, USA
| | - Erika Zavaleta
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High St., Santa Cruz CA, 95064, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St. 334 UCB, Boulder, CO 80309, USA
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14
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Sendell-Price AT, Ruegg KC, Clegg SM. Rapid morphological divergence following a human-mediated introduction: the role of drift and directional selection. Heredity (Edinb) 2020; 124:535-549. [PMID: 32080374 PMCID: PMC7080774 DOI: 10.1038/s41437-020-0298-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 01/25/2023] Open
Abstract
Theory predicts that when populations are established by few individuals, random founder effects can facilitate rapid phenotypic divergence even in the absence of selective processes. However, empirical evidence from historically documented colonisations suggest that, in most cases, drift alone is not sufficient to explain the rate of morphological divergence. Here, using the human-mediated introduction of the silvereye (Zosterops lateralis) to French Polynesia, which represents a potentially extreme example of population founding, we reassess the potential for morphological shifts to arise via drift alone. Despite only 80 years of separation from their New Zealand ancestors, French Polynesian silvereyes displayed significant changes in body and bill size and shape, most of which could be accounted for by drift, without the need to invoke selection. However, signatures of selection at genes previously identified as candidates for bill size and body shape differences in a range of bird species, also suggests a role for selective processes in driving morphological shifts within this population. Twenty-four SNPs in our RAD-Seq dataset were also found to be strongly associated with phenotypic variation. Hence, even under population founding extremes, when it is difficult to reject drift as the sole mechanism based on rate tests of phenotypic shifts, the additional role of divergent natural selection in novel environments can be revealed at the level of the genome.
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Affiliation(s)
- Ashley T Sendell-Price
- Department of Zoology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Kristen C Ruegg
- Department of Zoology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, OX1 3PS, UK
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sonya M Clegg
- Department of Zoology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, OX1 3PS, UK
- Environmental Futures Research Institute, Griffith University, Queensland, 4111, Australia
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15
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Zhen Y, Harrigan RJ, Ruegg KC, Anderson EC, Ng TC, Lao S, Lohmueller KE, Smith TB. Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens). Mol Ecol 2017; 26:4966-4977. [PMID: 28752944 DOI: 10.1111/mec.14270] [Citation(s) in RCA: 26] [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: 02/08/2017] [Accepted: 06/28/2017] [Indexed: 01/08/2023]
Abstract
The little greenbul, a common rainforest passerine from sub-Saharan Africa, has been the subject of long-term evolutionary studies to understand the mechanisms leading to rainforest speciation. Previous research found morphological and behavioural divergence across rainforest-savannah transition zones (ecotones), and a pattern of divergence with gene flow suggesting divergent natural selection has contributed to adaptive divergence and ecotones could be important areas for rainforests speciation. Recent advances in genomics and environmental modelling make it possible to examine patterns of genetic divergence in a more comprehensive fashion. To assess the extent to which natural selection may drive patterns of differentiation, here we investigate patterns of genomic differentiation among populations across environmental gradients and regions. We find compelling evidence that individuals form discrete genetic clusters corresponding to distinctive environmental characteristics and habitat types. Pairwise FST between populations in different habitats is significantly higher than within habitats, and this differentiation is greater than what is expected from geographic distance alone. Moreover, we identified 140 SNPs that showed extreme differentiation among populations through a genomewide selection scan. These outliers were significantly enriched in exonic and coding regions, suggesting their functional importance. Environmental association analysis of SNP variation indicates that several environmental variables, including temperature and elevation, play important roles in driving the pattern of genomic diversification. Results lend important new genomic evidence for environmental gradients being important in population differentiation.
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Affiliation(s)
- Ying Zhen
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Ryan J Harrigan
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Kristen C Ruegg
- 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, Santa Cruz, CA, USA
| | - Eric C Anderson
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - Thomas C Ng
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Sirena Lao
- Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Thomas B Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA
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16
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Ruegg KC, Anderson EC, Harrigan RJ, Paxton KL, Kelly JF, Moore F, Smith TB. Genetic assignment with isotopes and habitat suitability (
gaiah
), a migratory bird case study. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12800] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Kristen C. Ruegg
- Center for Tropical Research, Institute of the Environment and Sustainability University of California, Los Angeles Los Angeles CA 90095‐1496 USA
- Department of Ecology and Evolutionary Biology University of California Santa Cruz CA 95064 USA
| | - Eric C. Anderson
- Fisheries Ecology Division, Southwest Fisheries Science Center National Marine Fisheries Service, NOAA Santa Cruz CA 95060 USA
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability University of California, Los Angeles Los Angeles CA 90095‐1496 USA
| | | | - Jeffrey F. Kelly
- Oklahoma Biological Survey University of Oklahoma Norman OK 73019 USA
- Department of Biology University of Oklahoma Norman OK 73019 USA
| | - Frank Moore
- Department of Biological Sciences University of Southern Mississippi Hattiesburg MS 39406 USA
| | - Thomas B. Smith
- Center for Tropical Research, Institute of the Environment and Sustainability University of California, Los Angeles Los Angeles CA 90095‐1496 USA
- Department of Ecology and Evolutionary Biology University of California Los Angles CA 90095 USA
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17
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Ruegg KC, Anderson EC, Paxton KL, Apkenas V, Lao S, Siegel RB, DeSante DF, Moore F, Smith TB. Mapping migration in a songbird using high-resolution genetic markers. Mol Ecol 2014; 23:5726-39. [DOI: 10.1111/mec.12977] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/17/2014] [Accepted: 10/20/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Kristen C. Ruegg
- Center for Tropical Research; Institute of the Environment and Sustainability; University of California, Los Angeles; La Kretz Hall Suite 300 619 Charles E. Young Dr. East Los Angeles CA 90095 USA
- Department of Ecology and Evolutionary Biology; University of California, Santa Cruz; Santa Cruz CA 95060 USA
| | - Eric C. Anderson
- Southwest Fisheries Science Center; National Marine Fisheries Service; 110 Shaffer Road Santa Cruz CA 95060 USA
- Department of Applied Mathematics and Statistics; University of California; Santa Cruz CA 95060 USA
| | - Kristina L. Paxton
- Department of Biological Sciences; University of Southern Mississippi; Hattiesburg MS 39406 USA
- Department of Biology; University of Hawaii; Hilo HI 96720 USA
| | - Vanessa Apkenas
- Southwest Fisheries Science Center; National Marine Fisheries Service; 110 Shaffer Road Santa Cruz CA 95060 USA
| | - Sirena Lao
- Center for Tropical Research; Institute of the Environment and Sustainability; University of California, Los Angeles; La Kretz Hall Suite 300 619 Charles E. Young Dr. East Los Angeles CA 90095 USA
| | - Rodney B. Siegel
- The Institute for Bird Populations; PO Box 1346 Point Reyes Station CA 94956 USA
| | - David F. DeSante
- The Institute for Bird Populations; PO Box 1346 Point Reyes Station CA 94956 USA
| | - Frank Moore
- Department of Biology; University of Hawaii; Hilo HI 96720 USA
| | - Thomas B. Smith
- Center for Tropical Research; Institute of the Environment and Sustainability; University of California, Los Angeles; La Kretz Hall Suite 300 619 Charles E. Young Dr. East Los Angeles CA 90095 USA
- Department of Ecology and Evolutionary Biology; University of California; Los Angles CA 90095 USA
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18
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Rundel CW, Wunder MB, Alvarado AH, Ruegg KC, Harrigan R, Schuh A, Kelly JF, Siegel RB, DeSante DF, Smith TB, Novembre J. Novel statistical methods for integrating genetic and stable isotope data to infer individual-level migratory connectivity. Mol Ecol 2013; 22:4163-4176. [DOI: 10.1111/mec.12393] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 04/27/2013] [Accepted: 05/03/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Colin W. Rundel
- Department of Statistical Sciences; Duke University; Durham NC 27708 USA
- Department of Statistics; University of California, Los Angeles; Los Angeles CA 90095 USA
| | - Michael B. Wunder
- Department of Integrative Biology; University of Colorado, Denver; Denver CO 80217 USA
| | - Allison H. Alvarado
- Center for Tropical Research Institute of 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; Los Angeles CA 90095 USA
| | - Kristen C. Ruegg
- Department of Integrative Biology; University of Colorado, Denver; Denver CO 80217 USA
- Department of Ecology and Evolutionary Biology; University of California, Santa Cruz; Santa Cruz CA 95064 USA
| | - Ryan Harrigan
- Center for Tropical Research Institute of the Environment and Sustainability; University of California, Los Angeles; Los Angeles CA 90095 USA
| | - Andrew Schuh
- Cooperative Institute for Research in the Atmosphere (CIRA); Fort Collins CO 80523 USA
| | - Jeffrey F. Kelly
- Oklahoma Biological Survey and Department of Biology; Ecology and Evolutionary Biology Program; University of Oklahoma; Norman OK 73019 USA
| | - Rodney B. Siegel
- The Institute for Bird Populations; Point Reyes Station CA 94956 USA
| | - David F. DeSante
- The Institute for Bird Populations; Point Reyes Station CA 94956 USA
| | - Thomas B. Smith
- Center for Tropical Research Institute of 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; Los Angeles CA 90095 USA
| | - John Novembre
- Department of Ecology and Evolutionary Biology; University of California, Los Angeles; Los Angeles CA 90095 USA
- Department of Human Genetics; Chicago IL 60637 USA
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19
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Abstract
Severe declines in megafauna worldwide illuminate the role of top predators in ecosystem structure. In the Antarctic, the Krill Surplus Hypothesis posits that the killing of more than 2 million large whales led to competitive release for smaller krill-eating species like the Antarctic minke whale. If true, the current size of the Antarctic minke whale population may be unusually high as an indirect result of whaling. Here, we estimate the long-term population size of the Antarctic minke whale prior to whaling by sequencing 11 nuclear genetic markers from 52 modern samples purchased in Japanese meat markets. We use coalescent simulations to explore the potential influence of population substructure and find that even though our samples are drawn from a limited geographic area, our estimate reflects ocean-wide genetic diversity. Using Bayesian estimates of the mutation rate and coalescent-based analyses of genetic diversity across loci, we calculate the long-term population size of the Antarctic minke whale to be 670,000 individuals (95% confidence interval: 374,000-1,150,000). Our estimate of long-term abundance is similar to, or greater than, contemporary abundance estimates, suggesting that managing Antarctic ecosystems under the assumption that Antarctic minke whales are unusually abundant is not warranted.
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Affiliation(s)
- Kristen C Ruegg
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA.
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20
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Abstract
Many migratory songbirds follow circuitous migratory routes instead of taking the shortest path between overwintering and breeding areas. Here, we study the migration patterns in Swainson's thrush (Catharus ustulatus), a neartic-neotropical migrant songbird, using molecular genetic approaches. This species is presently separated into genetically distinct coastal and continental populations that diverged during the Late Pleistocene (as indicated by molecular dating), yet appear to have retained ancestral patterns of migration. Low nucleotide diversity, a star-like haplotype phylogeny and unimodal mismatch distributions all support the hypothesis that both the coastal and the continental populations have undergone recent demographic expansions. Nearctic-neotropical banding and genetic data show nearly complete segregation of migratory routes and of overwintering locations: coastal populations migrate along the Pacific Coast to overwintering sites in Central America and Mexico, whereas continental populations migrate along an eastern route to overwintering sites in Panama and South America. Nearctic-neotropical banding data also show that continental birds north, northwest and east of this migratory divide fly thousands of miles east before turning south. We conclude that circuitous migration in the Swainson's thrush is an artefact of a Late Pleistocene range expansion.
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Affiliation(s)
- Kristen C Ruegg
- Center for Tropical Research and Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA
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