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Dzul MC, Kendall WL, Yackulic CB, Van Haverbeke DR, Mackinnon P, Young K, Pillow MJ, Thomas J. Estimating migration timing and abundance in partial migratory systems by integrating continuous antenna detections with physical captures. J Anim Ecol 2024; 93:796-811. [PMID: 38561901 DOI: 10.1111/1365-2656.14076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/09/2024] [Indexed: 04/04/2024]
Abstract
Many populations migrate between two different habitats (e.g. wintering/foraging to breeding area, mainstem-tributary, river-lake, river-ocean, river-side channel) as part of their life history. Detection technologies, such as passive integrated transponder (PIT) antennas or sonic receivers, can be placed at boundaries between habitats (e.g. near the confluence of rivers) to detect migratory movements of marked animals. Often, these detection systems have high detection probabilities and detect many individuals but are limited in their ability to make inferences about abundance because only marked individuals can be detected. Here, we introduce a mark-recapture modelling approach that uses detections from a double-array PIT antenna system to imply movement directionality from arrays and estimate migration timing. Additionally, when combined with physical captures, the model can be used to estimate abundances for both migratory and non-migratory groups and help quantify partial migration. We first test our approach using simulation, and results indicate our approach displayed negligible bias for total abundance (less than ±1%) and slight biases for state-specific abundance estimates (±1%-6%). We fit our model to array detections and physical captures of three native fishes (humpback chub [Gila cypha], flannelmouth sucker [Catostomus latipinnis] and bluehead sucker [Catostomus discobolus]) in the Little Colorado River (LCR) in Grand Canyon, AZ, a system that exhibits partial migration (i.e. includes residents and migrants). Abundance estimates from our model confirm that, for all three species, migratory individuals are much more numerous than residents. There was little difference in movement timing between 2021 (a year without preceding winter/spring floods) and 2022 (a year with a small flood occurring in early April). In both years, flannelmouth sucker arrived in mid-March whereas humpback chub and bluehead sucker arrivals occurred early- to mid-April. With humpback chub and flannelmouth sucker, movement timing was influenced by body size so that large individuals were more likely to arrive early compared to smaller individuals. With more years of data, this model framework could be used to evaluate ecological questions pertaining to flow cues and movement timing or intensity, relative trends in migrants versus residents and ecological drivers of skipped spawning.
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Affiliation(s)
- M C Dzul
- Southwest Biological Science Center, U.S. Geological Survey, Grand Canyon Monitoring and Research Center, Flagstaff, Arizona, USA
| | - W L Kendall
- Colorado Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, Colorado State University, Fort Collins, Colorado, USA
| | - C B Yackulic
- Southwest Biological Science Center, U.S. Geological Survey, Grand Canyon Monitoring and Research Center, Flagstaff, Arizona, USA
| | - D R Van Haverbeke
- U.S. Fish and Wildlife Service, Arizona Fish and Wildlife Conservation Office, Flagstaff, Arizona, USA
| | - P Mackinnon
- Department of Watershed Sciences, Utah State University, Logan, Utah, USA
| | - K Young
- U.S. Fish and Wildlife Service, Arizona Fish and Wildlife Conservation Office, Flagstaff, Arizona, USA
| | - M J Pillow
- U.S. Fish and Wildlife Service, Arizona Fish and Wildlife Conservation Office, Flagstaff, Arizona, USA
| | - J Thomas
- Southwest Biological Science Center, U.S. Geological Survey, Grand Canyon Monitoring and Research Center, Flagstaff, Arizona, USA
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2
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Osborne MJ, Archdeacon TP, Yackulic CB, Dudley RK, Caeiro-Dias G, Turner TF. Genetic erosion in an endangered desert fish during a megadrought despite long-term supportive breeding. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14154. [PMID: 37489292 DOI: 10.1111/cobi.14154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/08/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023]
Abstract
Human water use combined with a recent megadrought have reduced river and stream flow through the southwest United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande silvery minnow (Hybognathus amarus). This species is subject to boom-and-bust population dynamics, under which large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We used demographic and genetic data from wild and hatchery individuals to examine the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's d = 1.34) and remained low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size based on linkage disequilibrium (LD Ne ) were positively associated (r = 0.53) with wild abundance and total abundance, but as the proportion of hatchery-origin spawners increased, LD Ne declined (r = -0.55). Megadrought limited wild spawner abundance and precluded refreshment of hatchery brood stocks with wild fish; hence, we predict a riverine population increasingly dominated by hatchery-origin individuals and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas P Archdeacon
- U.S. Fish and Wildlife Service, New Mexico Fish and Wildlife Conservation Office, Albuquerque, New Mexico, USA
| | - Charles B Yackulic
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, Arizona, USA
| | - Robert K Dudley
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
- American Southwest Ichthyological Researchers, Albuquerque, New Mexico, USA
| | - Guilherme Caeiro-Dias
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
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3
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Bonjour SM, Gido KB, McKinstry MC, Cathcart CN, Bogaard MR, Dzul M, Healy BD, Hooley-Underwood ZE, Rogowski DL, Yackulic CB. Migration timing and tributary use of spawning flannelmouth sucker (Catostomus latipinnis). JOURNAL OF FISH BIOLOGY 2023; 103:1144-1162. [PMID: 37495557 DOI: 10.1111/jfb.15509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 07/28/2023]
Abstract
Spawning phenology and associated migrations of fishes are often regulated by factors such as temperature and stream discharge, but flow regulation of mainstem rivers coupled with climate change might disrupt these cues and affect fitness. Flannelmouth sucker (Catostomus latipinnis) persisting in heavily modified river networks are known to spawn in tributaries that might provide better spawning habitat than neighboring mainstem rivers subject to habitat degradation (e.g., embedded sediments, altered thermal regimes, and disconnected floodplains). PIT tag data and radio telemetry were used to quantify the timing and duration of flannelmouth sucker tributary spawning migrations in relation to environmental cues in McElmo Creek, a tributary of the San Juan River in the American Southwest. We also tested the extent of the tributary migration and assessed mainstem movements prior to and after tributary migrations. Additionally, multiyear data sets of PIT detections from other tributaries in the Colorado River basin were used to quantify interannual and cross-site variation in the timing of flannelmouth sucker spawning migrations in relation to environmental cues. The arrival and residence times of fish spawning in McElmo Creek varied among years, with earlier migration and a 3-week increase in residence time in relatively wet years compared to drier years. Classification tree analysis suggested a combination of discharge- and temperature-determined arrival timing. Of fish PIT tagged in the fall, 56% tagged within 10 km of McElmo Creek spawned in the tributary the following spring, as did 60% of radio-tagged fish, with a decline in its use corresponding to increased distance of tagging location. A broader analysis of four tributaries in the Colorado River basin, including McElmo Creek, found photoperiod and temperature of tributary and mainstem rivers were the most important variables in determining migration timing, but tributary and mainstem discharge also aided in classification success. The largest tributary, the Little Colorado River, had more residential fish or fish that stayed for longer periods (median = 30 days), whereas McElmo Creek fish stayed an average of just 10 days in 2022. Our results generally suggest that higher discharge, across years or across sites, results in extended use of tributaries by flannelmouth suckers. Conservation actions that limit water extraction and maintain natural flow regimes in tributaries, while maintaining open connection with mainstem rivers, may benefit migratory species, including flannelmouth suckers.
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Affiliation(s)
- Sophia M Bonjour
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Keith B Gido
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Mark C McKinstry
- Upper Colorado Regional Office, U.S. Bureau of Reclamation, Salt Lake City, Utah, USA
| | - Charles N Cathcart
- Alaska Department of Fish and Game, Alaska Freshwater Fish Inventory, Anchorage, Alaska, USA
| | - Matthew R Bogaard
- Washington Department of Fish and Wildlife, Washington, District of Columbia, USA
| | - Maria Dzul
- U.S. Geological Survey, Southwest Biological Science Center, Grand Canyon Monitoring and Research Center, Flagstaff, Arizona, USA
| | - Brian D Healy
- U.S. Geological Survey, Eastern Ecological Science Center at Patuxent Research Refuge, Laurel, Maryland, USA
| | | | | | - Charles B Yackulic
- U.S. Geological Survey, Southwest Biological Science Center, Grand Canyon Monitoring and Research Center, Flagstaff, Arizona, USA
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4
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Healy BD, Budy P, Yackulic CB, Murphy BP, Schelly RC, McKinstry MC. Exploring metapopulation-scale suppression alternatives for a global invader in a river network experiencing climate change. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e13993. [PMID: 36047692 PMCID: PMC10107352 DOI: 10.1111/cobi.13993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/07/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Invasive species can dramatically alter ecosystems, but eradication is difficult, and suppression is expensive once they are established. Uncertainties in the potential for expansion and impacts by an invader can lead to delayed and inadequate suppression, allowing for establishment. Metapopulation viability models can aid in planning strategies to improve responses to invaders and lessen invasive species' impacts, which may be particularly important under climate change. We used a spatially explicit metapopulation viability model to explore suppression strategies for ecologically damaging invasive brown trout (Salmo trutta), established in the Colorado River and a tributary in Grand Canyon National Park. Our goals were to estimate the effectiveness of strategies targeting different life stages and subpopulations within a metapopulation; quantify the effectiveness of a rapid response to a new invasion relative to delaying action until establishment; and estimate whether future hydrology and temperature regimes related to climate change and reservoir management affect metapopulation viability and alter the optimal management response. Our models included scenarios targeting different life stages with spatially varying intensities of electrofishing, redd destruction, incentivized angler harvest, piscicides, and a weir. Quasi-extinction (QE) was obtainable only with metapopulation-wide suppression targeting multiple life stages. Brown trout population growth rates were most sensitive to changes in age 0 and large adult mortality. The duration of suppression needed to reach QE for a large established subpopulation was 12 years compared with 4 with a rapid response to a new invasion. Isolated subpopulations were vulnerable to suppression; however, connected tributary subpopulations enhanced metapopulation persistence by serving as climate refuges. Water shortages driving changes in reservoir storage and subsequent warming would cause brown trout declines, but metapopulation QE was achieved only through refocusing and increasing suppression. Our modeling approach improves understanding of invasive brown trout metapopulation dynamics, which could lead to more focused and effective invasive species suppression strategies and, ultimately, maintenance of populations of endemic fishes.
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Affiliation(s)
- Brian D. Healy
- Department of Watershed Sciences and the Ecology CenterUtah State UniversityLoganUtahUSA
- Native Fish Ecology and Conservation Program, Division of Science and Resource ManagementGrand Canyon National Park, National Park ServiceFlagstaffArizonaUSA
| | - Phaedra Budy
- U.S. Geological Survey, Utah Cooperative Fish and Wildlife Research Unit, Department of Watershed SciencesUtah State UniversityLoganUtahUSA
| | - Charles. B. Yackulic
- U.S. Geological Survey, Southwest Biological Science CenterGrand Canyon Monitoring and Research CenterFlagstaffArizonaUSA
| | - Brendan P. Murphy
- School of Environmental ScienceSimon Fraser UniversityVancouverBritish ColumbiaCanada
| | - Robert C. Schelly
- Native Fish Ecology and Conservation Program, Division of Science and Resource ManagementGrand Canyon National Park, National Park ServiceFlagstaffArizonaUSA
| | - Mark C. McKinstry
- Upper Colorado Regional OfficeU.S. Bureau of ReclamationSalt Lake CityUtahUSA
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5
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Yackulic CB, Archdeacon TP, Valdez RA, Hobbs M, Porter MD, Lusk J, Tanner A, Gonzales EJ, Lee DY, Haggerty GM. Quantifying flow and nonflow management impacts on an endangered fish by integrating data, research, and expert opinion. Ecosphere 2022. [DOI: 10.1002/ecs2.4240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Charles B. Yackulic
- Southwest Biological Science Center U.S. Geological Survey Flagstaff Arizona USA
| | - Thomas P. Archdeacon
- New Mexico Fish & Wildlife Conservation Office U.S. Fish & Wildlife Service Albuquerque New Mexico USA
| | | | - Monika Hobbs
- Albuquerque Bernalillo County Water Utility Authority Albuquerque New Mexico USA
| | - Michael D. Porter
- U.S. Army Corps of Engineers, Albuquerque District Albuquerque New Mexico USA
| | - Joel Lusk
- Environment & Lands Division U.S. Bureau of Reclamation, Albuquerque Area Office Albuquerque New Mexico USA
| | - Ashley Tanner
- Caesar Kleberg Wildlife Research Institute Texas A&M University‐Kingsville Kingsville Texas USA
| | - Eric J. Gonzales
- Environment & Lands Division U.S. Bureau of Reclamation, Albuquerque Area Office Albuquerque New Mexico USA
| | - Debbie Y. Lee
- Western EcoSystems Technology, Inc. Albuquerque New Mexico USA
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Healy BD, Budy P, Conner MM, Omana Smith EC. Life and death in a dynamic environment: Invasive trout, floods, and intraspecific drivers of translocated populations. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022. [PMID: 35403769 DOI: 10.6084/m9.figshare.c.5805593.v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Understanding the relative strengths of intrinsic and extrinsic factors regulating populations is a long-standing focus of ecology and critical to advancing conservation programs for imperiled species. Conservation could benefit from an increased understanding of factors influencing vital rates (somatic growth, recruitment, survival) in small, translocated populations, which is lacking owing to difficulties in long-term monitoring of rare species. Translocations, here defined as the transfer of wild-captured individuals from source populations to new habitats, are widely used for species conservation, but outcomes are often minimally monitored, and translocations that are monitored often fail. To improve our understanding of how translocated populations respond to environmental variation, we developed and tested hypotheses related to intrinsic (density dependent) and extrinsic (introduced rainbow trout Oncorhynchus mykiss, stream flow and temperature regime) causes of vital rate variation in endangered humpback chub (Gila cypha) populations translocated to Colorado River tributaries in the Grand Canyon (GC), USA. Using biannual recapture data from translocated populations over 10 years, we tested hypotheses related to seasonal somatic growth, and recruitment and population growth rates with linear mixed-effects models and temporal symmetry mark-recapture models. We combined data from recaptures and resights of dispersed fish (both physical captures and continuously recorded antenna detections) from throughout GC to test survival hypotheses, while accounting for site fidelity, using joint live-recapture/live-resight models. While recruitment only occurred in one site, which also drove population growth (relative to survival), evidence supported hypotheses related to density dependence in growth, survival, and recruitment, and somatic growth and recruitment were further limited by introduced trout. Mixed-effects models explained between 67% and 86% of the variation in somatic growth, which showed increased growth rates with greater flood-pulse frequency during monsoon season. Monthly survival was 0.56-0.99 and 0.80-0.99 in the two populations, with lower survival during periods of higher intraspecific abundance and low flood frequency. Our results suggest translocations can contribute toward the recovery of large-river fishes, but continued suppression of invasive fishes to enhance recruitment may be required to ensure population resilience. Furthermore, we demonstrate the importance of flooding to population demographics in food-depauperate, dynamic, invaded systems.
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Affiliation(s)
- Brian D Healy
- Department of Watershed Sciences and the Ecology Center, Utah State University, Logan, Utah, USA
- Native Fish Ecology and Conservation Program, Division of Science and Resource Management, Grand Canyon National Park, National Park Service, Flagstaff, Arizona, USA
| | - Phaedra Budy
- Department of Watershed Sciences and the Ecology Center, Utah State University, Logan, Utah, USA
- United States Geological Survey, Utah Cooperative Fish and Wildlife Research Unit, Department of Watershed Sciences, Utah State University, Logan, Utah, USA
| | - Mary M Conner
- Department of Wildland Resources and the Ecology Center, Utah State University, Logan, Utah, USA
| | - Emily C Omana Smith
- Native Fish Ecology and Conservation Program, Division of Science and Resource Management, Grand Canyon National Park, National Park Service, Flagstaff, Arizona, USA
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7
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Healy BD, Budy P, Conner MM, Omana Smith EC. Life and death in a dynamic environment: Invasive trout, floods, and intraspecific drivers of translocated populations. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2635. [PMID: 35403769 PMCID: PMC9541007 DOI: 10.1002/eap.2635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 01/25/2022] [Accepted: 02/24/2022] [Indexed: 05/14/2023]
Abstract
Understanding the relative strengths of intrinsic and extrinsic factors regulating populations is a long-standing focus of ecology and critical to advancing conservation programs for imperiled species. Conservation could benefit from an increased understanding of factors influencing vital rates (somatic growth, recruitment, survival) in small, translocated populations, which is lacking owing to difficulties in long-term monitoring of rare species. Translocations, here defined as the transfer of wild-captured individuals from source populations to new habitats, are widely used for species conservation, but outcomes are often minimally monitored, and translocations that are monitored often fail. To improve our understanding of how translocated populations respond to environmental variation, we developed and tested hypotheses related to intrinsic (density dependent) and extrinsic (introduced rainbow trout Oncorhynchus mykiss, stream flow and temperature regime) causes of vital rate variation in endangered humpback chub (Gila cypha) populations translocated to Colorado River tributaries in the Grand Canyon (GC), USA. Using biannual recapture data from translocated populations over 10 years, we tested hypotheses related to seasonal somatic growth, and recruitment and population growth rates with linear mixed-effects models and temporal symmetry mark-recapture models. We combined data from recaptures and resights of dispersed fish (both physical captures and continuously recorded antenna detections) from throughout GC to test survival hypotheses, while accounting for site fidelity, using joint live-recapture/live-resight models. While recruitment only occurred in one site, which also drove population growth (relative to survival), evidence supported hypotheses related to density dependence in growth, survival, and recruitment, and somatic growth and recruitment were further limited by introduced trout. Mixed-effects models explained between 67% and 86% of the variation in somatic growth, which showed increased growth rates with greater flood-pulse frequency during monsoon season. Monthly survival was 0.56-0.99 and 0.80-0.99 in the two populations, with lower survival during periods of higher intraspecific abundance and low flood frequency. Our results suggest translocations can contribute toward the recovery of large-river fishes, but continued suppression of invasive fishes to enhance recruitment may be required to ensure population resilience. Furthermore, we demonstrate the importance of flooding to population demographics in food-depauperate, dynamic, invaded systems.
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Affiliation(s)
- Brian D. Healy
- Department of Watershed Sciences and the Ecology CenterUtah State UniversityLoganUtahUSA
- Native Fish Ecology and Conservation Program, Division of Science and Resource ManagementGrand Canyon National Park, National Park ServiceFlagstaffArizonaUSA
| | - Phaedra Budy
- Department of Watershed Sciences and the Ecology CenterUtah State UniversityLoganUtahUSA
- United States Geological Survey, Utah Cooperative Fish and Wildlife Research Unit, Department of Watershed SciencesUtah State UniversityLoganUtahUSA
| | - Mary M. Conner
- Department of Wildland Resources and the Ecology CenterUtah State UniversityLoganUtahUSA
| | - Emily C. Omana Smith
- Native Fish Ecology and Conservation Program, Division of Science and Resource ManagementGrand Canyon National Park, National Park ServiceFlagstaffArizonaUSA
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8
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Wheeler KG, Udall B, Wang J, Kuhn E, Salehabadi H, Schmidt JC. What will it take to stabilize the Colorado River? Science 2022; 377:373-375. [PMID: 35862535 DOI: 10.1126/science.abo4452] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A continuation of the current 23-year-long drought will require difficult decisions to prevent further decline.
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Affiliation(s)
- Kevin G Wheeler
- Environmental Change Institute, University of Oxford, Oxford, UK.,Water Balance Consulting, Boulder, CO, USA
| | - Brad Udall
- Colorado Water Center, Colorado State University, Fort Collins, CO, USA
| | - Jian Wang
- Utah Water Research Laboratory and Department of Civil and Environmental Engineering, Utah State University, Logan, UT, USA
| | | | - Homa Salehabadi
- Utah Water Research Laboratory and Department of Civil and Environmental Engineering, Utah State University, Logan, UT, USA
| | - John C Schmidt
- Center for Colorado River Studies, Department of Watershed Sciences, Utah State University, Logan, UT, USA
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Chafin TK, Regmi B, Douglas MR, Edds DR, Wangchuk K, Dorji S, Norbu P, Norbu S, Changlu C, Khanal GP, Tshering S, Douglas ME. Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210727. [PMID: 34729207 PMCID: PMC8548808 DOI: 10.1098/rsos.210727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The recurrence of similar evolutionary patterns within different habitats often reflects parallel selective pressures acting upon either standing or independently occurring genetic variation to produce a convergence of phenotypes. This interpretation (i.e. parallel divergences within adjacent streams) has been hypothesized for drainage-specific morphological 'ecotypes' observed in polyploid snowtrout (Cyprinidae: Schizothorax). However, parallel patterns of differential introgression during secondary contact are a viable alternative hypothesis. Here, we used ddRADseq (N = 35 319 de novo and N = 10 884 transcriptome-aligned SNPs), as derived from Nepali/Bhutanese samples (N = 48 each), to test these competing hypotheses. We first employed genome-wide allelic depths to derive appropriate ploidy models, then a Bayesian approach to yield genotypes statistically consistent under the inferred expectations. Elevational 'ecotypes' were consistent in geometric morphometric space, but with phylogenetic relationships at the drainage level, sustaining a hypothesis of independent emergence. However, partitioned analyses of phylogeny and admixture identified subsets of loci under selection that retained genealogical concordance with morphology, suggesting instead that apparent patterns of morphological/phylogenetic discordance are driven by widespread genomic homogenization. Here, admixture occurring in secondary contact effectively 'masks' previous isolation. Our results underscore two salient factors: (i) morphological adaptations are retained despite hybridization and (ii) the degree of admixture varies across tributaries, presumably concomitant with underlying environmental or anthropogenic factors.
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Affiliation(s)
- Tyler K. Chafin
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder 80309, USA
| | - Binod Regmi
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- National Institute of Arthritis, Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Marlis R. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - David R. Edds
- Department of Biological Sciences, Emporia State University, Emporia, KS 66801, USA
| | - Karma Wangchuk
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Sonam Dorji
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Pema Norbu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Sangay Norbu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Changlu Changlu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Gopal Prasad Khanal
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Singye Tshering
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Michael E. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
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Yackulic CB, Van Haverbeke DR, Dzul M, Bair L, Young KL. Assessing the population impacts and cost‐effectiveness of a conservation translocation. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.13908] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Charles B. Yackulic
- U.S. Geological Survey Southwest Biological Science Center Grand Canyon Monitoring and Research Center Flagstaff AZ USA
| | | | - Maria Dzul
- U.S. Geological Survey Southwest Biological Science Center Grand Canyon Monitoring and Research Center Flagstaff AZ USA
| | - Lucas Bair
- U.S. Geological Survey Southwest Biological Science Center Grand Canyon Monitoring and Research Center Flagstaff AZ USA
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