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Sidlauskas BL, Mathur S, Aydoğan H, Monzyk FR, Black AN. Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish. BMC Ecol Evol 2024; 24:2. [PMID: 38177987 PMCID: PMC10765885 DOI: 10.1186/s12862-023-02191-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024] Open
Abstract
Foskett Spring in Oregon's desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace's recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population's surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate that persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5000 within Foskett Spring, though Ne in the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada's Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace fewer than 1000 years ago, much more recently than previously suspected and possibly coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.
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Affiliation(s)
- Brian L Sidlauskas
- Department of Fisheries, Wildlife and Conservation Sciences, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331, USA.
| | - Samarth Mathur
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W 12th Ave, Columbus, OH, 43210, USA
| | - Hakan Aydoğan
- Department of Fisheries, Wildlife and Conservation Sciences, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331, USA
| | - Fred R Monzyk
- Oregon Department of Fish and Wildlife, Corvallis Research Lab, 28655 OR-34, Corvallis, OR, 97333, USA
| | - Andrew N Black
- Center for Quantitative Life Sciences, Oregon State University, 2750 SW Campus Way, Corvallis, OR, 97331, USA
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2
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Finger AJ, Benjamin A, Crookshanks C, Campbell MA, Sağlam İK. Broad‐ and fine‐scale structure across the distribution of the relict dace (
Relictus solitarius
) in the Great Basin desert,
USA. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Amanda J. Finger
- Department of Animal Science University of California Davis California USA
| | - Alyssa Benjamin
- Department of Animal Science University of California Davis California USA
| | | | | | - İsmail K. Sağlam
- Department of Molecular Biology and Genetics Koç University Istanbul Turkey
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3
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Black AN, Willoughby JR, Brüniche-Olsen A, Pierce BL, DeWoody JA. The endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation. Mol Ecol Resour 2021; 21:2520-2532. [PMID: 34137170 DOI: 10.1111/1755-0998.13447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/30/2022]
Abstract
The White Sands pupfish (Cyprinodon tularosa), endemic to New Mexico in Southwestern North America, is of conservation concern due in part to invasive species, chemical pollution, and groundwater withdrawal. Herein, we developed a draft reference genome and use it to provide biological insights into the evolution and conservation of C. tularosa. We used our assembly to localize microsatellite markers previously used to demarcate evolutionary significant units (ESU), quantified genomic divergence and transposable element profiles between species, and compared C. tularosa genomic diversity related species. Our de novo assembly of PacBio Sequel II error-corrected reads resulted in a 1.08 Gb draft genome with a contig N50 of 1.4 Mb and 25,260 annotated protein coding genes, including 95% of the expected Actinopterygii conserved complete single-copy orthologues. Many of the C. tularosa microsatellite markers used for conservation assessments fell within, or near, genes and exhibited a pattern of increased heterozygosity near genic areas compared to those in intergenic regions. Nuclear alignments between these two species revealed 193 genes contained in rapidly diverging tracts; transposable element profiles were largely concordant and suggest a shared, rapid expansion of LINE and Gypsy elements. Genome-wide heterozygosity was markedly lower in C. tularosa compared to estimates from other related species, probably because of smaller long-term effective population sizes constrained by their isolated and limited habitat. Overall, these inferences provide new insights into C. tularosa that should help inform future management efforts.
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Affiliation(s)
- Andrew N Black
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
| | - Janna R Willoughby
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA.,School of Forestry and Wildlife Sciences, Auburn University, Auburn, USA
| | - Anna Brüniche-Olsen
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Brian L Pierce
- Natural Resources Institute, Texas A&M University, College Station, Texas, USA
| | - J Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
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4
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Peek RA, O'Rourke SM, Miller MR. Flow modification associated with reduced genetic health of a river‐breeding frog,
Rana boylii. Ecosphere 2021. [DOI: 10.1002/ecs2.3496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Ryan A. Peek
- Center for Watershed Sciences University of California Davis California95616USA
| | - Sean M. O'Rourke
- Department of Animal Science University of California Davis California95616USA
| | - Michael R. Miller
- Department of Animal Science University of California Davis California95616USA
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5
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Hedin M, Foldi S, Rajah-Boyer B. Evolutionary divergences mirror Pleistocene paleodrainages in a rapidly-evolving complex of oasis-dwelling jumping spiders (Salticidae, Habronattus tarsalis). Mol Phylogenet Evol 2020; 144:106696. [DOI: 10.1016/j.ympev.2019.106696] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/14/2019] [Accepted: 11/27/2019] [Indexed: 10/25/2022]
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6
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Lema SC. Hormones, developmental plasticity, and adaptive evolution: Endocrine flexibility as a catalyst for 'plasticity-first' phenotypic divergence. Mol Cell Endocrinol 2020; 502:110678. [PMID: 31830511 DOI: 10.1016/j.mce.2019.110678] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
Abstract
Explaining how populations adapt to environments is among the foremost objectives of evolutionary theory. Over generations, natural selection impels the phenotypic distribution of a population based on individual variation in phenotype and fitness. However, environmental conditions can also shape how individuals develop within their lifetime to influence which phenotypes are expressed in a population. It has been proposed that such environmentally-initiated phenotypic variation - also termed developmental plasticity - may enable adaptive evolution under some scenarios. As dynamic regulators of development and phenotypic expression, hormones are important physiological mediators of developmental plasticity. Patterns of hormone secretion, hormone transport, and the sensitivity of tissues to hormones can each be altered by environmental conditions, and understanding how endocrine regulation shapes phenotypic development in an ecologically-relevant context has much to contribute toward clarifying the role of plasticity in evolutionary adaptation. This article explores how the environmental sensitivity of endocrine regulation may facilitate 'plasticity-first' evolution by generating phenotypic variants that precede adaptation to altered or novel environments. Predictions arising from 'plasticity-first' evolution are examined in the context of thyroid hormone mediation of morphological plasticity in Cyprinodon pupfishes from the Death Valley region of California and Nevada, USA. This clade of extremophile fishes diversified morphologically over the last ~20,000 years, and observations that some populations experienced contemporary phenotypic differentiation under recent habitat change provide evidence that hormone-mediate plasticity preceded genetic assimilation of morphology in one of the region's species: the Devils Hole pupfish, Cyprinodon diabolis. This example illustrates how conceptualizing hormones not only as regulators of homeostasis, but also as developmental intermediaries between environment conditions and phenotypic variation at the individual-, population-, and species-levels can enrich our understanding of endocrine regulation both as a facilitator of phenotypic change under shifting environments, and as important proximate mechanisms that may initiate 'plasticity-first' evolutionary adaptation.
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Affiliation(s)
- Sean C Lema
- Biological Sciences Department, Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA, 93407, USA.
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7
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Peek RA, Bedwell M, O'Rourke SM, Goldberg C, Wengert GM, Miller MR. Hybridization between two parapatric ranid frog species in the northern Sierra Nevada, California, USA. Mol Ecol 2019; 28:4636-4647. [DOI: 10.1111/mec.15236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Ryan A. Peek
- Center for Watershed Sciences University of California Davis CA USA
- Department of Animal Science University of California Davis CA USA
| | - Mallory Bedwell
- School of the Environment Washington State University Pullman WA USA
| | - Sean M. O'Rourke
- Department of Animal Science University of California Davis CA USA
| | - Caren Goldberg
- School of the Environment Washington State University Pullman WA USA
| | | | - Michael R. Miller
- Center for Watershed Sciences University of California Davis CA USA
- Department of Animal Science University of California Davis CA USA
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8
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Smith CT, Von Bargen J, DeHaan PW, Scheerer P, Meeuwig MH. Genetic structure and the history of chub in the Alvord Basin. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01148-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Lencer ES, McCune AR. An embryonic staging series up to hatching for Cyprinodon variegatus: An emerging fish model for developmental, evolutionary, and ecological research. J Morphol 2018; 279:1559-1578. [PMID: 30368863 DOI: 10.1002/jmor.20870] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/17/2018] [Accepted: 06/22/2018] [Indexed: 11/08/2022]
Abstract
Using multiple taxa to research development is necessary for making general conclusions about developmental patterns and mechanisms. We present a staging series for Cyprinodon variegatus as a basis for further study of the developmental biology of fishes in the genus Cyprinodon and for comparative work on teleost fishes beyond the standard models. Cyprinodon are small, euryhaline fishes, widely distributed in fresh, brackish, and hypersaline waters of southern and eastern North America. Cyprinodontids are closely related to fundulids, providing a comparative reference point to the embryological model, Fundulus heteroclitus. Ecologists and evolutionary biologists commonly study Cyprinodon, and we have been using Cyprinodon to study skull variation and its genetic basis among closely related species. We divided embryonic development of C. variegatus into 34 morphologically identifiable stages. We reference our staging series to that already defined for a related model species, Oryzias latipes (medaka) that is studied by a large community of researchers. We provide a description of the early chondrogenesis and ossification of skull and caudal fin bones during the latter stages of embryonic development. We show that Cyprinodon are tractable for studying development. Eggs can be obtained easily from breeding pairs and our study provides a staging system to facilitate future developmental studies.
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Affiliation(s)
- Ezra S Lencer
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
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10
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Sağlam İK, Baumsteiger J, Smith MJ, Linares-Casenave J, Nichols AL, O'Rourke SM, Miller MR. Best available science still supports an ancient common origin of Devils Hole and Devils Hole pupfish. Mol Ecol 2018; 27:839-842. [PMID: 29442386 DOI: 10.1111/mec.14502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/20/2017] [Indexed: 11/27/2022]
Abstract
The age of DHP and how pupfish colonized Devils Hole have always been a topic of interest. Recently, two different publications (Martin, Crawford, Turner, & Simons, & Sağlam et al., ) tackled this issue using genomic data sets and demographic models but came to widely different conclusions. In their comment, Martin and Höhne () argue that our results (Sağlam et al., ) were misleading because we used inappropriate calibration information and biased a priori assumptions. They then re-analysed our data using a "biologically informed" mutation rate prior and concluded that our data support a much younger age of DHP (12.6 kya) as opposed to 60 kya reported in our study. Below we will summarize why their arguments do not hold up and explore some of the inconsistencies between their claims and what was actually presented in our study. Furthermore, we will demonstrate their re-analyses provide no new information compared to what was presented in our original manuscript and reinforce our estimate of a 60 kya divergence of DHP as outweighing competing hypotheses.
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Affiliation(s)
- İsmail K Sağlam
- Department of Animal Science, University of California, Davis, CA, USA.,Department of Biology, Ecological Sciences Research Laboratories, Hacettepe University, Ankara, Turkey
| | - Jason Baumsteiger
- Department of Animal Science, University of California, Davis, CA, USA.,Center for Watershed Sciences, University of California, Davis, CA, USA
| | - Matt J Smith
- Abernathy Fish Technology Center, U.S. Fish and Wildlife Service, Longview, WA, USA
| | | | - Andrew L Nichols
- Center for Watershed Sciences, University of California, Davis, CA, USA
| | - Sean M O'Rourke
- Department of Animal Science, University of California, Davis, CA, USA
| | - Michael R Miller
- Department of Animal Science, University of California, Davis, CA, USA.,Center for Watershed Sciences, University of California, Davis, CA, USA
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11
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Benjamin A, Sağlam İK, Mahardja B, Hobbs J, Hung TC, Finger AJ. Use of single nucleotide polymorphisms identifies backcrossing and species misidentifications among three San Francisco estuary osmerids. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1048-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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12
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Baumsteiger J, Moyle PB, Aguilar A, O’Rourke SM, Miller MR. Genomics clarifies taxonomic boundaries in a difficult species complex. PLoS One 2017; 12:e0189417. [PMID: 29232403 PMCID: PMC5726641 DOI: 10.1371/journal.pone.0189417] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/24/2017] [Indexed: 11/19/2022] Open
Abstract
Efforts to taxonomically delineate species are often confounded with conflicting information and subjective interpretation. Advances in genomic methods have resulted in a new approach to taxonomic identification that stands to greatly reduce much of this conflict. This approach is ideal for species complexes, where divergence times are recent (evolutionarily) and lineages less well defined. The California Roach/Hitch fish species complex is an excellent example, experiencing a convoluted geologic history, diverse habitats, conflicting species designations and potential admixture between species. Here we use this fish complex to illustrate how genomics can be used to better clarify and assign taxonomic categories. We performed restriction-site associated DNA (RAD) sequencing on 255 Roach and Hitch samples collected throughout California to discover and genotype thousands of single nucleotide polymorphism (SNPs). Data were then used in hierarchical principal component, admixture, and FST analyses to provide results that consistently resolved a number of ambiguities and provided novel insights across a range of taxonomic levels. At the highest level, our results show that the CA Roach/Hitch complex should be considered five species split into two genera (4 + 1) as opposed to two species from distinct genera (1 +1). Subsequent levels revealed multiple subspecies and distinct population segments within identified species. At the lowest level, our results indicate Roach from a large coastal river are not native but instead introduced from a nearby river. Overall, this study provides a clear demonstration of the power of genomic methods for informing taxonomy and serves as a model for future studies wishing to decipher difficult species questions. By allowing for systematic identification across multiple scales, taxonomic structure can then be tied to historical and contemporary ecological, geographic or anthropogenic factors.
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Affiliation(s)
- Jason Baumsteiger
- Center for Watershed Sciences, University of California, Davis, United States of America
- Department of Animal Sciences, University of California, Davis, United States of America
- * E-mail: (JB); (MM)
| | - Peter B. Moyle
- Center for Watershed Sciences, University of California, Davis, United States of America
- Department of Wildlife, Fisheries, and Conservation Biology, University of California, Davis, United States of America
| | - Andres Aguilar
- Department of Biological Sciences, California State University, Los Angeles, United States of America
| | - Sean M. O’Rourke
- Department of Animal Sciences, University of California, Davis, United States of America
| | - Michael R. Miller
- Center for Watershed Sciences, University of California, Davis, United States of America
- Department of Animal Sciences, University of California, Davis, United States of America
- * E-mail: (JB); (MM)
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13
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Martin CH, Höhna S. New evidence for the recent divergence of Devil's Hole pupfish and the plausibility of elevated mutation rates in endangered taxa. Mol Ecol 2017; 27:831-838. [DOI: 10.1111/mec.14404] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 08/18/2017] [Accepted: 09/15/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Christopher H. Martin
- Department of Biology; University of North Carolina at Chapel Hill; Chapel Hill NC USA
| | - Sebastian Höhna
- Department of Integrative Biology; University of California; Berkeley CA USA
- Department of Statistics; University of California; Berkeley CA USA
- Division of Evolutionary Biology; Ludwig-Maximilians-Universität; München Germany
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15
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Corbett King A, Reed JM. Successful population establishment from small introductions appears to be less common than believed. PeerJ 2016; 4:e2440. [PMID: 27688964 PMCID: PMC5036100 DOI: 10.7717/peerj.2440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 08/13/2016] [Indexed: 11/22/2022] Open
Abstract
Although small populations are at high risk of extinction, there are regular reports in the scientific literature of purported small, isolated, persistent populations. One source of evidence of the viability of small populations comes from the alleged successful introduction of species to areas outside their original range from introductions of few individuals. We reviewed the examples from introduction compendia on deliberate translocations of birds, and the original sources, to identify and evaluate purported examples of successful establishments from small introductions. We found 23 purportedly successful introductions from few (<30) individuals. After assessing original sources, we found that two of the claims were substantiated; the rest were ambiguous or could be rejected as examples, primarily due to a lack of evidence in original sources of the number of birds released and because of supplemental individuals from other releases, releases in nearby regions, and the possibility of natural invasion. Our results suggest that reports of successful establishment of birds from introductions of few individuals have been overstated. These results strengthen the relationship previously reported between propagule pressure and likelihood of establishment, and support the lack of viability of small populations presumed by population theory. We suggest that analyses of introduction failure and success would benefit from excluding studies where introduction effort is unknown or unreliably documented.
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Affiliation(s)
- Alyssa Corbett King
- Department of Biology, Tufts University, Medford, MA, USA; Current affiliation: The School for Field Studies, Beverly, MA, USA
| | - J Michael Reed
- Department of Biology, Tufts University , Medford , MA , USA
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