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Martin AM, Johnson JA, Berry RB, Carling M, Martínez Del Rio C. Contrasting Genomic Diversity and Inbreeding Levels Among Two Closely Related Falcon Species With Overlapping Geographic Distributions. Mol Ecol 2024:e17549. [PMID: 39400432 DOI: 10.1111/mec.17549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 09/01/2024] [Accepted: 09/26/2024] [Indexed: 10/15/2024]
Abstract
Genomic resources are valuable to examine historical demographic patterns and their effects to better inform management and conservation of threatened species. We evaluated population trends and genome-wide variation in the near-threatened Orange-breasted Falcon (Falco deiroleucus) and its more common sister species, the Bat Falcon (F. rufigularis), to explore how the two species differ in genomic diversity as influenced by their contrasting long-term demographic histories. We generated and aligned whole genome resequencing data for 12 Orange-breasted Falcons and 9 Bat Falcons to an annotated Gyrfalcon (F. rusticolus) reference genome that retained approximately 22.4 million biallelic autosomal SNPs (chromosomes 1-22). Our analyses indicated much lower genomic diversity in Orange-breasted Falcons compared to Bat Falcons. All sampled Orange-breasted Falcons were significantly more inbred than the sampled Bat Falcons, with values similar to those observed in island-mainland species comparisons. The distribution of runs of homozygosity showed variation suggesting long-term low population size and the possibility of bottlenecks in Orange-breasted Falcons contrasting with consistently larger populations in Bat Falcons. Analysis of genetic load suggests that Orange-breasted Falcons are less likely to experience inbreeding depression than Bat Falcons due to reduced inbreeding load but are at elevated risk from fixation of deleterious gene variants and perhaps a reduced adaptive potential. These genomic analyses highlight differences in the historical demography of two closely related species that have influenced their current genomic diversity and should result in differing strategies for their continued conservation.
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Affiliation(s)
- Audrey M Martin
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
| | | | | | - Matthew Carling
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
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2
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Johnson JA, Athrey G, Anderson CM, Bell DA, Dixon A, Kumazawa Y, Maechtle T, Meeks GW, Mindell D, Nakajima K, Novak B, Talbot S, White C, Zhan X. Whole-genome survey reveals extensive variation in genetic diversity and inbreeding levels among peregrine falcon subspecies. Ecol Evol 2023; 13:e10347. [PMID: 37484928 PMCID: PMC10361364 DOI: 10.1002/ece3.10347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023] Open
Abstract
In efforts to prevent extinction, resource managers are often tasked with increasing genetic diversity in a population of concern to prevent inbreeding depression or improve adaptive potential in a changing environment. The assumption that all small populations require measures to increase their genetic diversity may be unwarranted, and limited resources for conservation may be better utilized elsewhere. We test this assumption in a case study focused on the peregrine falcon (Falco peregrinus), a cosmopolitan circumpolar species with 19 named subspecies. We used whole-genome resequencing to generate over two million single nucleotide polymorphisms (SNPs) from multiple individuals of all peregrine falcon subspecies. Our analyses revealed extensive variation among subspecies, with many island-restricted and nonmigratory populations possessing lower overall genomic diversity, elevated inbreeding coefficients (F ROH)-among the highest reported, and extensive runs of homozygosity (ROH) compared to mainland and migratory populations. Similarly, the majority of subspecies that are either nonmigratory or restricted to islands show a much longer history of low effective population size (N e). While mutational load analyses indicated an increased proportion of homozygous-derived deleterious variants (i.e., drift load) among nonmigrant and island populations compared to those that are migrant or reside on the mainland, no significant differences in the proportion of heterozygous deleterious variants (i.e., inbreeding load) was observed. Our results provide evidence that high levels of inbreeding may not be an existential threat for some populations or taxa. Additional factors such as the timing and severity of population declines are important to consider in management decisions about extinction potential.
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Affiliation(s)
- Jeff A. Johnson
- Department of Biological SciencesUniversity of North TexasDentonTexasUSA
- Wolf Creek Operating FoundationWolfWyomingUSA
| | - Giridhar Athrey
- Department of Poultry Science & Faculty of Ecology and Evolutionary BiologyTexas A&M UniversityCollege StationTexasUSA
| | | | - Douglas A. Bell
- East Bay Regional Park DistrictOaklandCaliforniaUSA
- California Academy of SciencesSan FranciscoCaliforniaUSA
| | - Andrew Dixon
- The Mohamed Bin Zayed Raptor Conservation FundAbu DhabiUnited Arab Emirates
- International Wildlife ConsultantsCarmarthenUK
| | - Yoshinori Kumazawa
- Research Center for Biological DiversityNagoya City UniversityNagoyaJapan
| | | | - Garrett W. Meeks
- Department of Biological SciencesUniversity of North TexasDentonTexasUSA
| | - David Mindell
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Keiya Nakajima
- Research Center for Biological DiversityNagoya City UniversityNagoyaJapan
- The Japan Falconiformes CenterOwariasahiJapan
| | - Ben Novak
- Revive & RestoreSausalitoCaliforniaUSA
| | - Sandra Talbot
- Far Northwestern Institute of Art and ScienceAnchorageAlaskaUSA
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3
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Belokon MM, Belokon YS, Nechaeva AV, Sylvestrov NA, Sarychev EI, Beme IR. Genetic Identification and Relationship Analysis of Captive Breeding Falcons. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422060023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Massively parallel sequencing and capillary electrophoresis of a novel panel of falcon STRs: Concordance with minisatellite DNA profiles from historical wildlife crime. Forensic Sci Int Genet 2021; 54:102550. [PMID: 34174583 PMCID: PMC8430417 DOI: 10.1016/j.fsigen.2021.102550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022]
Abstract
Birds of prey have suffered persecution for centuries through trapping, shooting, poisoning and theft from the wild to meet the demand from egg collectors and falconers; they were also amongst the earliest beneficiaries of DNA testing in wildlife forensics. Here we report the identification and characterisation of 14 novel tetramer, pentamer and hexamer short tandem repeat (STR) markers which can be typed either by capillary electrophoresis or massively parallel sequencing (MPS) and apply them to historical casework samples involving 49 peregrine falcons, 30 of which were claimed to be the captively bred offspring of nine pairs. The birds were initially tested in 1994 with a multilocus DNA fingerprinting probe, a sex test and eight single-locus minisatellite probes (SLPs) demonstrating that 23 birds were unrelated to the claimed parents. The multilocus and SLP approaches were highly discriminating but extremely time consuming and required microgram quantities of high molecular weight DNA and the use of radioisotopes. The STR markers displayed between 2 and 21 alleles per locus (mean = 7.6), lengths between 140 and 360 bp, and heterozygosities from 0.4 to 0.93. They produced wholly concordant conclusions with similar discrimination power but in a fraction of the time using a hundred-fold less DNA and with standard forensic equipment. Furthermore, eleven of these STRs were amplified in a single reaction and typed using MPS on the Illumina MiSeq platform revealing eight additional alleles (three with variant repeat structures and five solely due to flanking SNPs) across four loci. This approach gave a random match probability of < 1E-9, and a parental pair false inclusion probability of < 1E-5, with a further ten-fold reduction in the amount of DNA required (~3 ng) and the potential to analyse mixed samples. These STRs will be of value in monitoring wild populations of these key indicator species as well as for testing captive breeding claims and establishing a database of captive raptors. They have the potential to resolve complex cases involving trace, mixed and degraded samples from raptor persecution casework representing a significant advance over the previously applied methods.
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Puchała KO, Nowak-Życzyńska Z, Sielicki S, Olech W. Assessment of the Genetic Potential of the Peregrine Falcon ( Falco peregrinus peregrinus) Population Used in the Reintroduction Program in Poland. Genes (Basel) 2021; 12:genes12050666. [PMID: 33946707 PMCID: PMC8145731 DOI: 10.3390/genes12050666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/16/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
Microsatellite DNA analysis is a powerful tool for assessing population genetics. The main aim of this study was to assess the genetic potential of the peregrine falcon population covered by the restitution program. We characterized individuals from breeders that set their birds for release into the wild and birds that have been reintroduced in previous years. This was done using a well-known microsatellite panel designed for the peregrine falcon containing 10 markers. We calculated the genetic distance between individuals and populations using the UPGMA (unweighted pair group method with arithmetic mean) method and then performed a Principal Coordinates Analysis (PCoA) and constructed phylogenetic trees, to visualize the results. In addition, we used the Bayesian clustering method, assuming 1-15 hypothetical populations, to find the model that best fit the data. Units were segregated into groups regardless of the country of origin, and the number of alleles and observed heterozygosity were different in different breeding groups. The wild and captive populations were grouped independent of the original population.
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Affiliation(s)
- Karol O. Puchała
- Department of Animal Genetics and Conservation, Warsaw University of Life Sciences, 02-787 Warszawa, Poland; (Z.N.-Ż.); (W.O.)
- Correspondence:
| | - Zuzanna Nowak-Życzyńska
- Department of Animal Genetics and Conservation, Warsaw University of Life Sciences, 02-787 Warszawa, Poland; (Z.N.-Ż.); (W.O.)
| | | | - Wanda Olech
- Department of Animal Genetics and Conservation, Warsaw University of Life Sciences, 02-787 Warszawa, Poland; (Z.N.-Ż.); (W.O.)
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6
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Conservation genetics of regionally extinct peregrine falcons (Falco peregrinus) and unassisted recovery without genetic bottleneck in southern England. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01324-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Franke A, Falk K, Hawkshaw K, Ambrose S, Anderson DL, Bente PJ, Booms T, Burnham KK, Ekenstedt J, Fufachev I, Ganusevich S, Johansen K, Johnson JA, Kharitonov S, Koskimies P, Kulikova O, Lindberg P, Lindström BO, Mattox WG, McIntyre CL, Mechnikova S, Mossop D, Møller S, Nielsen ÓK, Ollila T, Østlyngen A, Pokrovsky I, Poole K, Restani M, Robinson BW, Rosenfield R, Sokolov A, Sokolov V, Swem T, Vorkamp K. Status and trends of circumpolar peregrine falcon and gyrfalcon populations. AMBIO 2020; 49:762-783. [PMID: 31858488 PMCID: PMC6989710 DOI: 10.1007/s13280-019-01300-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/23/2019] [Accepted: 11/18/2019] [Indexed: 05/26/2023]
Abstract
The peregrine falcon (Falco peregrinus) and the gyrfalcon (Falco rusticolus) are top avian predators of Arctic ecosystems. Although existing monitoring efforts are well established for both species, collaboration of activities among Arctic scientists actively involved in research of large falcons in the Nearctic and Palearctic has been poorly coordinated. Here we provide the first overview of Arctic falcon monitoring sites, present trends for long-term occupancy and productivity, and summarize information describing abundance, distribution, phenology, and health of the two species. We summarize data for 24 falcon monitoring sites across the Arctic, and identify gaps in coverage for eastern Russia, the Arctic Archipelago of Canada, and East Greenland. Our results indicate that peregrine falcon and gyrfalcon populations are generally stable, and assuming that these patterns hold beyond the temporal and spatial extents of the monitoring sites, it is reasonable to suggest that breeding populations at broader scales are similarly stable. We have highlighted several challenges that preclude direct comparisons of Focal Ecosystem Components (FEC) attributes among monitoring sites, and we acknowledge that methodological problems cannot be corrected retrospectively, but could be accounted for in future monitoring. Despite these drawbacks, ample opportunity exists to establish a coordinated monitoring program for Arctic-nesting raptor species that supports CBMP goals.
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Affiliation(s)
- Alastair Franke
- Department of Biological Sciences, University of Alberta, CW 405, Biological Sciences Bldg., Edmonton, AB T6G 2E9 Canada
- Arctic Raptor Project, P.O. Box 626, Rankin Inlet, NT X0C 0G0 Canada
| | | | - Kevin Hawkshaw
- Department of Renewable Resources, University of Alberta, Edmonton, Canada
| | | | | | | | | | | | | | - Ivan Fufachev
- Arctic Research Station of Institute of Plant and Animal Ecology Ural Branch, Russian Academy of Sciences, Zelenaya Gorka Str., 21, Labytnangi, Yamal-Nenets Autonomous District Russia 629400
| | - Sergey Ganusevich
- Center for Rescue of Wild Animals (Independent Non-profit Organization), Moscow, Russia
| | | | - Jeff A. Johnson
- Department of Biological Sciences, Advanced Environmental Research Institute, University of North Texas, 1155 Union Circle, #310559, Denton, TX 76203 USA
| | | | | | - Olga Kulikova
- Institute of Biological Problems of the North, 18 Portovaya Street, Magadan, Russia 685000
| | - Peter Lindberg
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden
| | | | - William G. Mattox
- Conservation Research Foundation, 702 S. Spelman Ln, Meridian, ID USA
| | | | - Svetlana Mechnikova
- I. M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Trubetskaya 8, Moscow, Russia
| | | | - Søren Møller
- Roskilde University, P.O. Box 260, 4000 Roskilde, Denmark
| | | | - Tuomo Ollila
- Metsähallitus, Parks and Wildlife Finland, Rovaniemi, Finland
| | | | - Ivan Pokrovsky
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315 Radolfzell, Germany
- Laboratory of Ornithology, Institute of Biological Problems of the North FEB RAS, 18 Portovaya Str., Magadan, Russia 685000
- Arctic Research Station, Institute of Plant & Animal Ecology, UD RAS, 21 Zelyonaya Gorka, Labytnangi, Russia 629400
| | - Kim Poole
- Aurora Wildlife Research, Nelson, Canada
| | | | | | | | - Aleksandr Sokolov
- Arctic Research Station of Institute of Plant and Animal Ecology Ural Branch, Russian Academy of Sciences, Zelenaya Gorka Str., 21, Labytnangi, Yamal-Nenets Autonomous District Russia 629400
| | - Vasiliy Sokolov
- Institute of Plant and Animal Ecology Ural Branch, Russian Academy of Sciences, Ekaterinburg, Russia
| | - Ted Swem
- U.S. Fish and Wildlife Service, Alaska, USA
| | - Katrin Vorkamp
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
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Wilcox JJS, Boissinot S, Idaghdour Y. Falcon genomics in the context of conservation, speciation, and human culture. Ecol Evol 2019; 9:14523-14537. [PMID: 31938538 PMCID: PMC6953694 DOI: 10.1002/ece3.5864] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/11/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
Here, we review the diversity, evolutionary history, and genomics of falcons in the context of their conservation and interactions with humans, and provide a perspective on how new genomic approaches may be applied to expand our knowledge of these topics. For millennia, humans and falcons (genus Falco) have developed unique relationships through falconry, religious rituals, conservation efforts, and human lifestyle transitions. From an evolutionary perspective, falcons remain an enigma. Having experienced several recent radiations, they have reached an unparalleled and almost global distribution, with an intrageneric species richness that is roughly an order of magnitude higher than typical within their family (Falconidae) and across other birds (Phylum: Aves). This diversity has evolved in the context of unusual genomic architecture that includes unique chromosomal rearrangements, relatively low chromosome counts, extremely low microdeletion rates, and high levels of nuclear mitochondrial DNA segments (NUMTs). These genomic peculiarities combine with high levels of ecological and organismal diversity and a legacy of human interactions to make falcons obvious candidates for evolutionary studies, providing unique research opportunities in common topics, including chromosomal evolution, the mechanics of speciation, local adaptation, domestication, and urban adaptation.
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Affiliation(s)
- Justin J. S. Wilcox
- Center for Genomics & Systems BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Stéphane Boissinot
- Center for Genomics & Systems BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
- Program in BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Youssef Idaghdour
- Center for Genomics & Systems BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
- Program in BiologyNew York University Abu DhabiAbu DhabiUnited Arab Emirates
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Talbot SL, Sage GK, Sonsthagen SA, Gravley MC, Swem T, Williams JC, Longmire JL, Ambrose S, Flamme MJ, Lewis SB, Phillips L, Anderson C, White CM. Intraspecific evolutionary relationships among peregrine falcons in western North American high latitudes. PLoS One 2017; 12:e0188185. [PMID: 29149202 PMCID: PMC5693296 DOI: 10.1371/journal.pone.0188185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/02/2017] [Indexed: 11/22/2022] Open
Abstract
Subspecies relationships within the peregrine falcon (Falco peregrinus) have been long debated because of the polytypic nature of melanin-based plumage characteristics used in subspecies designations and potential differentiation of local subpopulations due to philopatry. In North America, understanding the evolutionary relationships among subspecies may have been further complicated by the introduction of captive bred peregrines originating from non-native stock, as part of recovery efforts associated with mid 20th century population declines resulting from organochloride pollution. Alaska hosts all three nominal subspecies of North American peregrine falcons–F. p. tundrius, anatum, and pealei–for which distributions in Alaska are broadly associated with nesting locales within Arctic, boreal, and south coastal maritime habitats, respectively. Unlike elsewhere, populations of peregrine falcon in Alaska were not augmented by captive-bred birds during the late 20th century recovery efforts. Population genetic differentiation analyses of peregrine populations in Alaska, based on sequence data from the mitochondrial DNA control region and fragment data from microsatellite loci, failed to uncover genetic distinction between populations of peregrines occupying Arctic and boreal Alaskan locales. However, the maritime subspecies, pealei, was genetically differentiated from Arctic and boreal populations, and substructured into eastern and western populations. Levels of interpopulational gene flow between anatum and tundrius were generally higher than between pealei and either anatum or tundrius. Estimates based on both marker types revealed gene flow between augmented Canadian populations and unaugmented Alaskan populations. While we make no attempt at formal taxonomic revision, our data suggest that peregrine falcons occupying habitats in Alaska and the North Pacific coast of North America belong to two distinct regional groupings–a coastal grouping (pealei) and a boreal/Arctic grouping (currently anatum and tundrius)–each comprised of discrete populations that are variously intra-regionally connected.
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Affiliation(s)
- Sandra L. Talbot
- U.S. Geological Survey Alaska Science Center, Anchorage, Alaska, United States of America
- * E-mail:
| | - George K. Sage
- U.S. Geological Survey Alaska Science Center, Anchorage, Alaska, United States of America
| | - Sarah A. Sonsthagen
- U.S. Geological Survey Alaska Science Center, Anchorage, Alaska, United States of America
| | - Meg C. Gravley
- U.S. Geological Survey Alaska Science Center, Anchorage, Alaska, United States of America
| | - Ted Swem
- Fairbanks Fish and Wildlife Field Office, U. S. Fish and Wildlife Service, Fairbanks, Alaska, United States of America
| | - Jeffrey C. Williams
- Alaska Maritime National Wildlife Refuge, U. S. Fish and Wildlife Service, Homer, Alaska, United States of America
| | - Jonathan L. Longmire
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Skip Ambrose
- Fairbanks Fish and Wildlife Field Office, U. S. Fish and Wildlife Service, Fairbanks, Alaska, United States of America
| | - Melanie J. Flamme
- Yukon-Charley River National Preserve and Gates of the Arctic National Park and Preserve, National Park Service, Fairbanks, Alaska, United States of America
| | - Stephen B. Lewis
- Migratory Bird Management, U. S. Fish and Wildlife Service, Juneau, Alaska, United States of America
| | - Laura Phillips
- Alaska Regional Office, National Park Service, Anchorage, Alaska, United States of America
| | | | - Clayton M. White
- Department of Plant and Wildlife Sciences and Monte L. Bean Life Science Museum, Brigham Young University, Provo, Utah, United States of America
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Bernos TA, Fraser DJ. Spatiotemporal relationship between adult census size and genetic population size across a wide population size gradient. Mol Ecol 2016; 25:4472-87. [DOI: 10.1111/mec.13790] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 07/21/2016] [Accepted: 07/26/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Thaїs A. Bernos
- Department of Biology; Concordia University; 7141 rue Sherbrooke Ouest Montréal Québec Canada H4B1R6
| | - Dylan J. Fraser
- Department of Biology; Concordia University; 7141 rue Sherbrooke Ouest Montréal Québec Canada H4B1R6
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Seegar WS, Yates MA, Doney GE, Jenny JP, Seegar TCM, Perkins C, Giovanni M. Migrating Tundra Peregrine Falcons accumulate polycyclic aromatic hydrocarbons along Gulf of Mexico following Deepwater Horizon oil spill. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:1102-1111. [PMID: 25794559 DOI: 10.1007/s10646-015-1450-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/12/2015] [Indexed: 06/04/2023]
Abstract
Monitoring internal crude oil exposure can assist the understanding of associated risks and impacts, as well as the effectiveness of restoration efforts. Under the auspices of a long-term monitoring program of Tundra Peregrine Falcons (Falco peregrinus tundrius) at Assateague (Maryland) and South Padre Islands (Texas), we measured the 16 parent (unsubstituted) polycyclic aromatic hydrocarbons (PAHs), priority pollutants identified by the United States Environmental Protection Agency and components of crude oil, in peripheral blood cells of migrating Peregrine Falcons from 2009 to 2011. The study was designed to assess the spatial and temporal trends of crude oil exposure associated with the 2010 Deepwater Horizon (DWH) oil spill which started 20 April 2010 and was capped on 15 July of that year. Basal PAH blood distributions were determined from pre-DWH oil spill (2009) and unaffected reference area sampling. This sentinel species, a predator of shorebirds and seabirds during migration, was potentially exposed to residual oil from the spill in the northern Gulf of Mexico. Results demonstrate an increased incidence (frequency of PAH detection and blood concentrations) of PAH contamination in 2010 fall migrants sampled along the Texas Gulf Coast, declining to near basal levels in 2011. Kaplan-Meier peak mean ∑PAH blood concentration estimates varied with age (Juveniles-16.28 ± 1.25, Adults-5.41 ± 1.10 ng/g, wet weight) and PAHs detected, likely attributed to the discussed Tundra Peregrine natural history traits. Increased incidence of fluorene, pyrene and anthracene, with the presence of alkylated PAHs in peregrine blood suggests an additional crude oil source after DWH oil spill. The analyses of PAHs in Peregrine Falcon blood provide a convenient repeatable method, in conjunction with ongoing banding efforts, to monitoring crude oil contamination in this avian predator.
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12
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Fuchs J, Johnson JA, Mindell DP. Rapid diversification of falcons (Aves: Falconidae) due to expansion of open habitats in the Late Miocene. Mol Phylogenet Evol 2015; 82 Pt A:166-82. [DOI: 10.1016/j.ympev.2014.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/22/2014] [Accepted: 08/10/2014] [Indexed: 10/24/2022]
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Neuditschko M, Khatkar MS, Raadsma HW. NetView: a high-definition network-visualization approach to detect fine-scale population structures from genome-wide patterns of variation. PLoS One 2012; 7:e48375. [PMID: 23152744 PMCID: PMC3485224 DOI: 10.1371/journal.pone.0048375] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 09/25/2012] [Indexed: 02/06/2023] Open
Abstract
High-throughput sequencing and single nucleotide polymorphism (SNP) genotyping can be used to infer complex population structures. Fine-scale population structure analysis tracing individual ancestry remains one of the major challenges. Based on network theory and recent advances in SNP chip technology, we investigated an unsupervised network clustering method called Super Paramagnetic Clustering (Spc). When applied to whole-genome marker data it identifies the natural divisions of groups of individuals into population clusters without use of prior ancestry information. Furthermore, we optimised an analysis pipeline called NetView, a high-definition network visualization, starting with computation of genetic distance, followed clustering using Spc and finally visualization of clusters with Cytoscape. We compared NetView against commonly used methodologies including Principal Component Analyses (PCA) and a model-based algorithm, Admixture, on whole-genome-wide SNP data derived from three previously described data sets: simulated (2.5 million SNPs, 5 populations), human (1.4 million SNPs, 11 populations) and cattle (32,653 SNPs, 19 populations). We demonstrate that individuals can be effectively allocated to their correct population whilst simultaneously revealing fine-scale structure within the populations. Analyzing the human HapMap populations, we identified unexpected genetic relatedness among individuals, and population stratification within the Indian, African and Mexican samples. In the cattle data set, we correctly assigned all individuals to their respective breeds and detected fine-scale population sub-structures reflecting different sample origins and phenotypes. The NetView pipeline is computationally extremely efficient and can be easily applied on large-scale genome-wide data sets to assign individuals to particular populations and to reproduce fine-scale population structures without prior knowledge of individual ancestry. NetView can be used on any data from which a genetic relationship/distance between individuals can be calculated.
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Affiliation(s)
- Markus Neuditschko
- Reprogen-Animal Bioscience, Faculty of Veterinary Science, University of Sydney, Camden, New South Wales, Australia.
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14
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Wilson AS, Marra PP, Fleischer RC. Temporal patterns of genetic diversity in Kirtland's warblers (Dendroica kirtlandii), the rarest songbird in North America. BMC Ecol 2012; 12:8. [PMID: 22726952 PMCID: PMC3430571 DOI: 10.1186/1472-6785-12-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 05/25/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kirtland's warblers are the rarest songbird species in North America, rarity due in part to a reliance on early successional Jack Pine forests. Habitat loss due to fire suppression led to population declines to fewer than 200 males during the 1970s. Subsequent conservation management has allowed the species to recover to over 1700 males by 2010. In this study, we directly examine the impact that low population sizes have had on genetic variation in Kirtland's warblers. We compare the molecular variation of samples collected in Oscoda County, Michigan across three time periods: 1903-1912, 1929-1955 and 2008-2009. RESULTS In a hierarchical rarified sample of 20 genes and one time period, allelic richness was highest in 1903-1912 sample (A(R) = 5.96), followed by the 1929-1955 sample (A(R) = 5.74), and was lowest in the 2008-2009 sample (A(R) = 5.54). Heterozygosity measures were not different between the 1929-1955 and 2008-2009 samples, but were lower in the 1903-1912 sample. Under some models, a genetic bottleneck signature was present in the 1929-1955 and 2008-2009 samples but not in the 1903-1912 sample. CONCLUSIONS We suggest that these temporal genetic patterns are the result of the declining Kirtland's warbler population compressing into available habitat and a consequence of existing at low numbers for several decades.
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Affiliation(s)
- Amy S Wilson
- Migratory Bird Center, Smithsonian Conservation Biology Institute, 3001 Connecticut Ave N.W, Washington, DC, 20008, USA
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, 3001 Connecticut Ave N.W, Washington, DC, 20008, USA
| | - Peter P Marra
- Migratory Bird Center, Smithsonian Conservation Biology Institute, 3001 Connecticut Ave N.W, Washington, DC, 20008, USA
| | - Robert C Fleischer
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, 3001 Connecticut Ave N.W, Washington, DC, 20008, USA
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Raeymaekers JAM, Lens L, Van den Broeck F, Van Dongen S, Volckaert FAM. Quantifying population structure on short timescales. Mol Ecol 2012; 21:3458-73. [PMID: 22646231 DOI: 10.1111/j.1365-294x.2012.05628.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Quantifying the contribution of the various processes that influence population genetic structure is important, but difficult. One of the reasons is that no single measure appropriately quantifies all aspects of genetic structure. An increasing number of studies is analysing population structure using the statistic D, which measures genetic differentiation, next to G(ST) , which quantifies the standardized variance in allele frequencies among populations. Few studies have evaluated which statistic is most appropriate in particular situations. In this study, we evaluated which index is more suitable in quantifying postglacial divergence between three-spined stickleback (Gasterosteus aculeatus) populations from Western Europe. Population structure on this short timescale (10 000 generations) is probably shaped by colonization history, followed by migration and drift. Using microsatellite markers and anticipating that D and G(ST) might have different capacities to reveal these processes, we evaluated population structure at two levels: (i) between lowland and upland populations, aiming to infer historical processes; and (ii) among upland populations, aiming to quantify contemporary processes. In the first case, only D revealed clear clusters of populations, putatively indicative of population ancestry. In the second case, only G(ST) was indicative for the balance between migration and drift. Simulations of colonization and subsequent divergence in a hierarchical stepping stone model confirmed this discrepancy, which becomes particularly strong for markers with moderate to high mutation rates. We conclude that on short timescales, and across strong clines in population size and connectivity, D is useful to infer colonization history, whereas G(ST) is sensitive to more recent demographic events.
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Affiliation(s)
- Joost A M Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. Deberiotstraat, 32, B-3000 Leuven, Belgium.
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