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Vlček J, Miláček M, Vinkler M, Štefka J. Effect of population size and selection on Toll-like receptor diversity in populations of Galápagos mockingbirds. J Evol Biol 2023; 36:109-120. [PMID: 36398499 DOI: 10.1111/jeb.14121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/25/2022] [Accepted: 09/10/2022] [Indexed: 11/19/2022]
Abstract
The interactions of evolutionary forces are difficult to analyse in free-living populations. However, when properly understood, they provide valuable insights into evolutionary biology and conservation genetics. This is particularly important for the interplay of genetic drift and natural selection in immune genes that confer resistance to disease. The Galápagos Islands are inhabited by four closely related species of mockingbirds (Mimus spp.). We used 12 different-sized populations of Galápagos mockingbirds and one population of their continental relative northern mockingbird (Mimus polyglottos) to study the effects of genetic drift on the molecular evolution of immune genes, the Toll-like receptors (TLRs: TLR1B, TLR4 and TLR15). We found that neutral genetic diversity was positively correlated with island size, indicating an important effect of genetic drift. However, for TLR1B and TLR4, there was little correlation between functional (e.g., protein) diversity and island size, and protein structural properties were largely conserved, indicating only a limited effect of genetic drift on molecular phenotype. By contrast, TLR15 was less conserved and even its putative functional polymorphism correlated with island size. The patterns observed for the three genes suggest that genetic drift does not necessarily dominate selection even in relatively small populations, but that the final outcome depends on the degree of selection constraint that is specific for each TLR locus.
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Affiliation(s)
- Jakub Vlček
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Zoology, University of South Bohemia in České Budějovice Faculty of Science, České Budějovice, Czech Republic.,Department of Botany, Charles University Faculty of Science, Prague, Czech Republic
| | - Matěj Miláček
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Zoology, University of South Bohemia in České Budějovice Faculty of Science, České Budějovice, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Charles University Faculty of Science, Prague, Czech Republic
| | - Jan Štefka
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Zoology, University of South Bohemia in České Budějovice Faculty of Science, České Budějovice, Czech Republic
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2
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Snead AA, Alda F. Time-Series Sequences for Evolutionary Inferences. Integr Comp Biol 2022; 62:1771-1783. [PMID: 36104153 DOI: 10.1093/icb/icac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/05/2023] Open
Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
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3
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Portinha B, Avril A, Bernasconi C, Helanterä H, Monaghan J, Seifert B, Sousa VC, Kulmuni J, Nouhaud P. Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges. Mol Ecol 2022; 31:3416-3431. [PMID: 35460311 PMCID: PMC9320829 DOI: 10.1111/mec.16481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, for example, when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species Formica polyctena and F. aquilonia. We performed whole-genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent-based approach. Our analyses always supported a scenario of divergence with gene flow, suggesting that divergence started in the Pleistocene (c. 500 kya) and occurred with continuous asymmetrical gene flow from F. aquilonia to F. polyctena until a recent time, when migration became negligible (2-19 kya). However, we found support for contemporary gene flow in a sympatric pair from Finland, where the species hybridise, but no signature of recent bidirectional gene flow elsewhere. Overall, our results suggest that divergence histories reconstructed from a few individuals may be applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is spatially heterogeneous.
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Affiliation(s)
- Beatriz Portinha
- Organismal & Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
- cE3cCentre for Ecology, Evolution and Environmental changesFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Amaury Avril
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | | | | | | | | | - Vitor C. Sousa
- cE3cCentre for Ecology, Evolution and Environmental changesFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Jonna Kulmuni
- Organismal & Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
- Tvärminne Zoological StationUniversity of HelsinkiHankoFinland
| | - Pierre Nouhaud
- Organismal & Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
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4
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Cohen O, Ram Y, Hadany L, Gafny S, Geffen E. Annual climatic fluctuations and short-term genetic variation in the eastern spadefoot toad. Sci Rep 2021; 11:13514. [PMID: 34188104 PMCID: PMC8241830 DOI: 10.1038/s41598-021-92696-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 06/10/2021] [Indexed: 11/15/2022] Open
Abstract
In addition to variations on the spatial scale, short- and long-term temporal variations, too, can impose intense selection on the overall genetic diversity and composition of a population. We hypothesized that the allelic composition in populations of the eastern spadefoot toad (Pelobates syriacus) would change among successive years in accordance with the short-term changes in environmental conditions. Surprisingly, the effect of short-term climate fluctuations on genetic composition have rarely been addressed in the literature, and to our knowledge the effect of annual climatic fluctuations have not been considered meaningful. Our findings show that climatic variation among successive years, primarily the amount of rainfall and rainy days, can significantly alter both microsatellite allelic composition and diversity. We suggest that environmental (i.e. fluctuating) selection is differential across the globe, and that its intensity is expected to be greatest in regions where short-term climatic conditions are least stable.
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Affiliation(s)
- Orly Cohen
- School of Zoology, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Yoav Ram
- School of Zoology, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Lilach Hadany
- School of Plant Sciences and Food Security, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Sarig Gafny
- Faculty of Marine Sciences, Ruppin Academic Center, 40297, Michmoret, Israel
| | - Eli Geffen
- School of Zoology, Tel Aviv University, 69978, Tel Aviv, Israel.
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5
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Colombelli‐Négrel D, Kleindorfer S. Behavioural response to songs between genetically diverged allopatric populations of Darwin's small tree finch in the Galápagos. J Evol Biol 2021; 34:816-829. [PMID: 33714212 PMCID: PMC8251970 DOI: 10.1111/jeb.13783] [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: 05/08/2020] [Revised: 02/01/2021] [Accepted: 03/03/2021] [Indexed: 11/26/2022]
Abstract
Empirical data that identify contemporary mechanisms of divergence shed light on how species could multiply. In this study, we measured population genetic structure, song syllable diversity and response to simulated intruder song in Darwin's small tree finch (Camarhynchus parvulus) on Santa Cruz and Floreana Islands, Galápagos archipelago. Our aim was to test whether the magnitude of contemporary behavioural response in resident birds was consistent with patterns of genetic or cultural differences between populations. We analysed genetic structure and the occurrence of song syllable types, and experimentally measured the response of resident birds to intruder bird song from different geographical origin (i.e., island) or syllable type. We discovered a weak signal of population genetic structure between Santa Cruz and Floreana Islands. Although some song syllables occurred on both islands, others were unique to each island; Santa Cruz Island males used more unique syllables than Floreana Island males. Both Santa Cruz and Floreana resident males discriminated their response towards a simulated intruder song based on the geographical origin of the intruder song, but not on the syllable type sung by the intruder. We conclude that the populations are diverging in genetic and cultural traits and identified a signal of contemporary behavioural response that could maintain divergence upon secondary contact.
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Affiliation(s)
| | - Sonia Kleindorfer
- College of Science and EngineeringFlinders UniversityAdelaideSouth AustraliaAustralia
- Konrad Lorenz Research Centre for Behaviour and CognitionDepartment of Behavioural and Cognitive BiologyUniversity of ViennaViennaAustria
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6
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Cambrone C, Cézilly F, Wattier R, Eraud C, Bezault E. Levels of genetic differentiation and gene flow between four populations of the Scaly-naped Pigeon, Patagioenas squamosa: implications for conservation. STUDIES ON NEOTROPICAL FAUNA AND ENVIRONMENT 2021. [DOI: 10.1080/01650521.2021.1878765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Christopher Cambrone
- Biologie des Organismes et Écosystèmes Aquatiques (BOREA) UMR MNHN/SU/UNICAEN/UA/CNRS/IRD/UA, Université des Antilles, Pointe à Pitre, Guadeloupe (F.W.I)
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
- Caribaea Initiative, Université des Antilles, Pointe-à-Pitre, Guadeloupe
| | - Frank Cézilly
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
- Caribaea Initiative, Université des Antilles, Pointe-à-Pitre, Guadeloupe
- Université d’Etat d’Haïti, Port-au-Prince, Haiti
| | - Rémi Wattier
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne-Franche Comté, Dijon, France
| | - Cyril Eraud
- Office Français de la Biodiversité, Unité Avifaune Migratrice, Chizé, France
| | - Etienne Bezault
- Biologie des Organismes et Écosystèmes Aquatiques (BOREA) UMR MNHN/SU/UNICAEN/UA/CNRS/IRD/UA, Université des Antilles, Pointe à Pitre, Guadeloupe (F.W.I)
- Caribaea Initiative, Université des Antilles, Pointe-à-Pitre, Guadeloupe
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7
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Fleischer R, Risely A, Hoeck PEA, Keller LF, Sommer S. Mechanisms governing avian phylosymbiosis: Genetic dissimilarity based on neutral and MHC regions exhibits little relationship with gut microbiome distributions of Galápagos mockingbirds. Ecol Evol 2020; 10:13345-13354. [PMID: 33304542 PMCID: PMC7713960 DOI: 10.1002/ece3.6934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/14/2020] [Accepted: 09/28/2020] [Indexed: 01/01/2023] Open
Abstract
The gut microbiome of animals, which serves important functions but can also contain potential pathogens, is to varying degrees under host genetic control. This can generate signals of phylosymbiosis, whereby gut microbiome composition matches host phylogenetic structure. However, the genetic mechanisms that generate phylosymbiosis and the scale at which they act remain unclear. Two non-mutually exclusive hypotheses are that phylosymbiosis is driven by immunogenetic regions such as the major histocompatibility complex (MHC) controlling microbial composition, or by spatial structuring of neutral host genetic diversity via founder effects, genetic drift, or isolation by distance. Alternatively, associations between microbes and host phylogeny may be generated by their spatial autocorrelation across landscapes, rather than the direct effects of host genetics. In this study, we collected MHC, microsatellite, and gut microbiome data from separate individuals belonging to the Galápagos mockingbird species complex, which consists of four allopatrically distributed species. We applied multiple regression with distance matrices and Bayesian inference to test for correlations between average genetic and microbiome similarity across nine islands for which all three levels of data were available. Clustering of individuals by species was strongest when measured with microsatellite markers and weakest for gut microbiome distributions, with intermediate clustering of MHC allele frequencies. We found that while correlations between island-averaged gut microbiome composition and both microsatellite and MHC dissimilarity existed across species, these relationships were greatly weakened when accounting for geographic distance. Overall, our study finds little support for large-scale control of gut microbiome composition by neutral or adaptive genetic regions across closely related bird phylogenies, although this does not preclude the possibility that host genetics shapes gut microbiome at the individual level.
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Affiliation(s)
- Ramona Fleischer
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | - Alice Risely
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | | | - Lukas F. Keller
- Zoological MuseumUniversity of ZurichZurichSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
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8
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Affiliation(s)
- Naoyuki Nakahama
- Institute of Natural and Environmental Sciences, University of Hyogo Sanda City Japan
- The Museum of Nature and Human Activities, Hyogo Sanda City Japan
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9
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Víquez‐R L, Fleischer R, Wilhelm K, Tschapka M, Sommer S. Jumping the green wall: The use of PNA-DNA clamps to enhance microbiome sampling depth in wildlife microbiome research. Ecol Evol 2020; 10:11779-11786. [PMID: 33145000 PMCID: PMC7593133 DOI: 10.1002/ece3.6814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/12/2020] [Accepted: 08/24/2020] [Indexed: 01/04/2023] Open
Abstract
As microbiome research moves away from model organisms to wildlife, new challenges for microbiome high-throughput sequencing arise caused by the variety of wildlife diets. High levels of contamination are commonly observed emanating from the host (mitochondria) or diet (chloroplast). Such high contamination levels affect the overall sequencing depth of wildlife samples thus decreasing statistical power and leading to poor performance in downstream analysis. We developed an amplification protocol utilizing PNA-DNA clamps to maximize the use of resources and to increase the sampling depth of true microbiome sequences in samples with high levels of plastid contamination. We chose two study organisms, a bat (Leptonyteris yerbabuenae) and a bird (Mimus parvulus), both relying on heavy plant-based diets that sometimes lead to traces of plant-based fecal material producing high contamination signals from chloroplasts and mitochondria. On average, our protocol yielded a 13-fold increase in bacterial sequence amplification compared with the standard protocol (Earth Microbiome Protocol) used in wildlife research. For both focal species, we were able to increase significantly the percentage of sequences available for downstream analyses after the filtering of plastids and mitochondria. Our study presents the first results obtained by using PNA-DNA clamps to block the PCR amplification of chloroplast and mitochondrial DNA from the diet in the gut microbiome of wildlife. The method involves a cost-effective molecular technique instead of the filtering out of unwanted sequencing reads. As 33% and 26% of birds and bats, respectively, have a plant-based diet, the tool that we present here will optimize the sequencing and analysis of wild microbiomes.
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Affiliation(s)
- Luis Víquez‐R
- Institute for Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | - Ramona Fleischer
- Institute for Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | - Kerstin Wilhelm
- Institute for Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | - Marco Tschapka
- Institute for Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
- Smithsonian Tropical Research InstituteBalboaPanama
| | - Simone Sommer
- Institute for Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
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10
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Vlček J, Štefka J. Association between louse abundance and MHC II supertypes in Galápagos mockingbirds. Parasitol Res 2020; 119:1597-1605. [PMID: 32006226 DOI: 10.1007/s00436-020-06617-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/22/2020] [Indexed: 01/30/2023]
Abstract
Major histocompatibility complex class II (MHC II) is an essential molecule triggering the adaptive immune response by the presentation of pathogens to helper T cells. The association between individual MHC II variants and various parasites has become a frequent finding in studies of vertebrate populations. However, although bird ectoparasites have a significant effect on their host's fitness, and the host's immune system can regulate ectoparasitic infections, no study has yet investigated the association between MHC II polymorphism and ectoparasite infection in the populations of free-living birds. Here, we test whether an association exists between the abundance of a chewing louse (Myrsidea nesomimi) and MHC II polymorphism of its hosts, the Galápagos mockingbirds (Mimus). We have found that the presence of two MHC II supertypes (functionally differentiated clusters) was significantly associated with louse abundance. This pattern supports the theory that a co-evolutionary interaction stands behind the maintenance of MHC polymorphism. Moreover, we have found a positive correlation between louse abundance and heterophil/lymphocyte ratio (an indicator of immunological stress) that serves as an additional piece of evidence that ectoparasite burden is affected by immunological state of Galápagos mockingbirds.
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Affiliation(s)
- Jakub Vlček
- Institute of Parasitology, Biology Centre CAS, Branišovská 1160/31, 37005, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia, Branišovská, 1760, České Budějovice, Czech Republic.
| | - Jan Štefka
- Institute of Parasitology, Biology Centre CAS, Branišovská 1160/31, 37005, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská, 1760, České Budějovice, Czech Republic
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11
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Greenhorn JE, Bowman J, Wilson PJ. Genetic monitoring suggests increasing structure following recolonization by fishers. J Wildl Manage 2018. [DOI: 10.1002/jwmg.21495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Janet E. Greenhorn
- Environmental and Life Sciences Graduate Program; Trent University; 2140 East Bank Drive Peterborough ON K9L 0G2 Canada
| | - Jeff Bowman
- Wildlife Research and Monitoring Section; Ontario Ministry of Natural Resources and Forestry; 2140 East Bank Drive Peterborough ON K9L 0G2 Canada
| | - Paul J. Wilson
- Department of Biology; Trent University; 2140 East Bank Drive Peterborough ON K9L 0G2 Canada
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12
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Mikula P, Csanády A, Hromada M. A critical evaluation of the exotic bird collection of the Šariš Museum in Bardejov, Slovakia. Zookeys 2018:105-118. [PMID: 30150879 PMCID: PMC6108285 DOI: 10.3897/zookeys.776.24462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/18/2018] [Indexed: 12/17/2022] Open
Abstract
A collection of exotic birds deposited in the Šariš Museum in Bardejov (SMB), Slovakia, has not been evaluated critically since their deposition. We assessed the accuracy of identification of 465 bird specimens deposited in SMB with native distributions outside of Slovakia. Specimens belonged to 322 species of 82 families and 26 orders. Of the specimen represented, 34 belonged to species considered as ‘near-threatened’ (7.3%), 16 as ‘vulnerable’ (3.4%) and one as ‘endangered’ (0.2%). The SMB collection holds 10 of 28 extant Cuban endemic species and another 11 species endemic to the Caribbean archipelago. Even among birds that are relatively easy to identify, many specimens were identified incorrectly or species identification was missing. Of 465 specimens evaluated, 95 (20.4%) were identified incorrectly or were missing species identification, and another 79 (17%) were identified correctly, but their names have changed over time due to taxonomic shift, thus they required correction.
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Affiliation(s)
- Peter Mikula
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 43 Praha 2, Czech Republic Charles University Praha Czech Republic
| | - Alexander Csanády
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, 17. novembra 1, 080 01 Prešov, Slovakia University of Prešov Prešov Slovakia
| | - Martin Hromada
- Laboratory and Museum of Evolutionary Ecology, Department of Ecology, Faculty of Humanities and Natural Sciences, University of Presov, 17. novembra 15, 080 01 Prešov, Slovakia University of Zielona Gora Zielona Gora Poland.,Faculty of Biological Sciences, University of Zielona Góra, Prof. Z. Szafrana 1, 65-516 Zielona Góra, Poland Charles University Praha Czech Republic
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13
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The Hitchhiker Wave: Non-native Small Terrestrial Vertebrates in the Galapagos. UNDERSTANDING INVASIVE SPECIES IN THE GALAPAGOS ISLANDS 2018. [DOI: 10.1007/978-3-319-67177-2_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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Fessl B, Heimpel GE, Causton CE. Invasion of an Avian Nest Parasite, Philornis downsi, to the Galapagos Islands: Colonization History, Adaptations to Novel Ecosystems, and Conservation Challenges. DISEASE ECOLOGY 2018. [DOI: 10.1007/978-3-319-65909-1_9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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15
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Floreana Island re-colonization potential of the Galápagos short-eared owl (Asio flammeus galapagoensis). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1007-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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A century of temporal stability of genetic diversity in wild bumblebees. Sci Rep 2016; 6:38289. [PMID: 27917908 PMCID: PMC5137105 DOI: 10.1038/srep38289] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/07/2016] [Indexed: 11/23/2022] Open
Abstract
Since the 1950s, bumblebee (Bombus) species are showing a clear decline worldwide. Although many plausible drivers have been hypothesized, the cause(s) of this phenomenon remain debated. Here, genetic diversity in recent versus historical populations of bumblebee species was investigated by selecting four currently restricted and four currently widespread species. Specimens from five locations in Belgium were genotyped at 16 microsatellite loci, comparing historical specimens (1913–1915) with recent ones (2013–2015). Surprisingly, our results showed temporal stability of genetic diversity in the restricted species. Furthermore, both historical and recent populations of restricted species showed a significantly lower genetic diversity than found in populations of co-occurring widespread species. The difference in genetic diversity between species was thus already present before the alleged recent drivers of bumblebee decline could have acted (from the 1950’s). These results suggest that the alleged drivers are not directly linked with the genetic variation of currently declining bumblebee populations. A future sampling in the entire distribution range of these species will infer if the observed link between low genetic diversity and population distribution on the Belgium scale correlates with species decline on a global scale.
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17
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Vlček J, Hoeck PEA, Keller LF, Wayhart JP, Dolinová I, Štefka J. Balancing selection and genetic drift create unusual patterns of MHCIIβ variation in Galápagos mockingbirds. Mol Ecol 2016; 25:4757-72. [PMID: 27545344 DOI: 10.1111/mec.13807] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 07/28/2016] [Accepted: 08/08/2016] [Indexed: 01/01/2023]
Abstract
The extracellular subunit of the major histocompatibility complex MHCIIβ plays an important role in the recognition of pathogens and the initiation of the adaptive immune response of vertebrates. It is widely accepted that pathogen-mediated selection in combination with neutral micro-evolutionary forces (e.g. genetic drift) shape the diversity of MHCIIβ, but it has proved difficult to determine the relative effects of these forces. We evaluated the effect of genetic drift and balancing selection on MHCIIβ diversity in 12 small populations of Galápagos mockingbirds belonging to four different species, and one larger population of the Northern mockingbird from the continental USA. After genotyping MHCIIβ loci by high-throughput sequencing, we applied a correlational approach to explore the relationships between MHCIIβ diversity and population size by proxy of island size. As expected when drift predominates, we found a positive effect of population size on the number of MHCIIβ alleles present in a population. However, the number of MHCIIβ alleles per individual and number of supertypes were not correlated with population size. This discrepancy points to an interesting feature of MHCIIβ diversity dynamics: some levels of diversity might be shaped by genetic drift while others are independent and possibly maintained by balancing selection.
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Affiliation(s)
- Jakub Vlček
- Biology Centre CAS, Branišovská 31, 37005, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1670, České Budějovice, Czech Republic
| | - Paquita E A Hoeck
- Institute for Conservation Research, San Diego Zoo Global, 15600 San Pasqual Valley Road, Escondido, CA, 92027, USA
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jessica P Wayhart
- Institute for Conservation Research, San Diego Zoo Global, 15600 San Pasqual Valley Road, Escondido, CA, 92027, USA
| | - Iva Dolinová
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec, Czech Republic
| | - Jan Štefka
- Biology Centre CAS, Branišovská 31, 37005, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia, Branišovská 1670, České Budějovice, Czech Republic.
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18
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Bozzuto C, Hoeck PEA, Bagheri HC, Keller LF. Modelling different reintroduction strategies for the critically endangered Floreana mockingbird. Anim Conserv 2016. [DOI: 10.1111/acv.12299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. Bozzuto
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - P. E. A. Hoeck
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - H. C. Bagheri
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - L. F. Keller
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
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Harradine EL, Andrew ME, Thomas JW, How RA, Schmitt LH, Spencer PBS. Importance of dispersal routes that minimize open-ocean movement to the genetic structure of island populations. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:1704-1714. [PMID: 26171679 DOI: 10.1111/cobi.12555] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/23/2015] [Indexed: 06/04/2023]
Abstract
Islands present a unique scenario in conservation biology, offering refuge yet imposing limitations on insular populations. The Kimberley region of northwestern Australia has more than 2500 islands that have recently come into focus as substantial conservation resources. It is therefore of great interest for managers to understand the driving forces of genetic structure of species within these island archipelagos. We used the ubiquitous bar-shouldered skink (Ctenotus inornatus) as a model species to represent the influence of landscape factors on genetic structure across the Kimberley islands. On 41 islands and 4 mainland locations in a remote area of Australia, we genotyped individuals across 18 nuclear (microsatellite) markers. Measures of genetic differentiation and diversity were used in two complementary analyses. We used circuit theory and Mantel tests to examine the influence of the landscape matrix on population connectivity and linear regression and model selection based on Akaike's information criterion to investigate landscape controls on genetic diversity. Genetic differentiation between islands was best predicted with circuit-theory models that accounted for the large difference in resistance to dispersal between land and ocean. In contrast, straight-line distances were unrelated to either resistance distances or genetic differentiation. Instead, connectivity was determined by island-hopping routes that allow organisms to minimize the distance of difficult ocean passages. Island populations of C. inornatus retained varying degrees of genetic diversity (NA = 1.83 - 7.39), but it was greatest on islands closer to the mainland, in terms of resistance-distance units. In contrast, genetic diversity was unrelated to island size. Our results highlight the potential for islands to contribute to both theoretical and applied conservation, provide strong evidence of the driving forces of population structure within undisturbed landscapes, and identify the islands most valuable for conservation based on their contributions to gene flow and genetic diversity.
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Affiliation(s)
- E L Harradine
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| | - M E Andrew
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| | - J W Thomas
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| | - R A How
- School of Anatomy, Physiology & Human Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - L H Schmitt
- School of Anatomy, Physiology & Human Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - P B S Spencer
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
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20
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Kahilainen A, Puurtinen M, Kotiaho JS. Conservation implications of species–genetic diversity correlations. Glob Ecol Conserv 2014. [DOI: 10.1016/j.gecco.2014.10.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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21
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Illera JC, Palmero AM, Laiolo P, Rodríguez F, Moreno ÁC, Navascués M. Genetic, morphological, and acoustic evidence reveals lack of diversification in the colonization process in an island bird. Evolution 2014; 68:2259-74. [PMID: 24749863 DOI: 10.1111/evo.12429] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 03/30/2014] [Accepted: 03/31/2014] [Indexed: 11/28/2022]
Abstract
Songbirds with recently (i.e., early Holocene) founded populations are suitable models for studying incipient differentiation in oceanic islands. On such systems each colonization event represents a different evolutionary episode that can be studied by addressing sets of diverging phenotypic and genetic traits. We investigate the process of early differentiation in the spectacled warbler (Sylvia conspicillata) in 14 populations separated by sea barriers from three Atlantic archipelagos and from continental regions spanning from tropical to temperate latitudes. Our approach involved the study of sexual acoustic signals, morphology, and genetic data. Mitochondrial DNA did not provide clear population structure. However, microsatellites analyses consistently identified two genetic groups, albeit without correspondence to subspecies classification and little correspondence to geography. Coalescent analyses showed significant evidence for gene flow between the two genetic groups. Discriminant analyses could not correctly assign morphological or acoustic traits to source populations. Therefore, although theory predicting that in isolated populations genetic, morphological, or acoustic traits can lead to radiation, we have strikingly failed to document differentiation on these attributes in a resident passerine throughout three oceanic archipelagos.
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Affiliation(s)
- Juan Carlos Illera
- Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Campus of Mieres, Research Building, 5th Floor, C/Gonzalo Gutiérrez Quirós, s/n, 33600 Mieres, Asturias, Spain; Island Ecology and Evolution Research Group, IPNA, CSIC, 38206 La Laguna, Tenerife, Canary Islands, Spain. ,
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22
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Segelbacher G, Strand TM, Quintela M, Axelsson T, Jansman HAH, Koelewijn HP, Höglund J. Analyses of historical and current populations of black grouse in Central Europe reveal strong effects of genetic drift and loss of genetic diversity. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0610-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Genetic differentiation over a short water barrier in the Brazilian tanager, Ramphocelus bresilius (Passeriformes: Thraupidae) an endemic species of the Atlantic forest, Brazil. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0607-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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24
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Morgan K, McGaughran A, Ganeshan S, Herrmann M, Sommer RJ. Landscape and oceanic barriers shape dispersal and population structure in the island nematodePristionchus pacificus. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12255] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Katy Morgan
- Department of Evolutionary Biology; Max Planck Institute for Developmental Biology; Spemannstr. 37 Tübingen Germany
| | - Angela McGaughran
- Department of Evolutionary Biology; Max Planck Institute for Developmental Biology; Spemannstr. 37 Tübingen Germany
| | | | - Matthias Herrmann
- Department of Evolutionary Biology; Max Planck Institute for Developmental Biology; Spemannstr. 37 Tübingen Germany
| | - Ralf J. Sommer
- Department of Evolutionary Biology; Max Planck Institute for Developmental Biology; Spemannstr. 37 Tübingen Germany
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25
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Spurgin LG, Illera JC, Jorgensen TH, Dawson DA, Richardson DS. Genetic and phenotypic divergence in an island bird: isolation by distance, by colonization or by adaptation? Mol Ecol 2014; 23:1028-39. [PMID: 24447303 DOI: 10.1111/mec.12672] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/30/2013] [Accepted: 01/08/2014] [Indexed: 02/02/2023]
Abstract
Discerning the relative roles of adaptive and nonadaptive processes in generating differences among populations and species, as well as how these processes interact, is a fundamental aim in biology. Both genetic and phenotypic divergence across populations can be the product of limited dispersal and gradual genetic drift across populations (isolation by distance), of colonization history and founder effects (isolation by colonization) or of adaptation to different environments preventing migration between populations (isolation by adaptation). Here, we attempt to differentiate between these processes using island populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three Atlantic archipelagos. Using microsatellite markers and approximate Bayesian computation, we reveal that the northward colonization of this species ca. 8500 years ago resulted in genetic bottlenecks in the colonized archipelagos. We then show that high levels of genetic structure exist across archipelagos and that these are consistent with a pattern of isolation by colonization, but not with isolation by distance or adaptation. Finally, we show that substantial morphological divergence also exists and that this is strongly concordant with patterns of genetic structure and bottleneck history, but not with environmental differences or geographic distance. Overall, our data suggest that founder effects are responsible for both genetic and phenotypic changes across archipelagos. Our findings provide a rare example of how founder effects can persist over evolutionary timescales and suggest that they may play an important role in the early stages of speciation.
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Affiliation(s)
- Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK; Behavioural Ecology and Self-organization, Centre for Ecological and Evolutionary Studies, University of Groningen, 9700 CC, Groningen, The Netherlands; NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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Monceau K, Cézilly F, Moreau J, Motreuil S, Wattier R. Colonisation and diversification of the Zenaida Dove (Zenaida aurita) in the Antilles: phylogeography, contemporary gene flow and morphological divergence. PLoS One 2013; 8:e82189. [PMID: 24349217 PMCID: PMC3861367 DOI: 10.1371/journal.pone.0082189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 10/22/2013] [Indexed: 11/19/2022] Open
Abstract
Caribbean avifaunal biogeography has been mainly studied based on mitochondrial DNA. Here, we investigated both past and recent island differentiation and micro-evolutionary changes in the Zenaida Dove (Zenaida aurita) based on combined information from one mitochondrial (Cytochrome c Oxydase subunit I, COI) and 13 microsatellite markers and four morphological characters. This Caribbean endemic and abundant species has a large distribution, and two subspecies are supposed to occur: Z. a. zenaida in the Greater Antilles (GA) and Z. a. aurita in the Lesser Antilles (LA). Doves were sampled on two GA islands (Puerto Rico and the British Virgin Islands) and six LA islands (Saint Barthélemy, Guadeloupe, Les Saintes, Martinique, Saint Lucia and Barbados). Eleven COI haplotypes were observed that could be assembled in two distinct lineages, with six specific to GA, four to LA, the remaining one occurring in all islands. However, the level of divergence between those two lineages was too moderate to fully corroborate the existence of two subspecies. Colonisation of the studied islands appeared to be a recent process. However, both phenotypic and microsatellite data suggest that differentiation is already under way between all of them, partly associated with the existence of limited gene flow. No isolation by distance was observed. Differentiation for morphological traits was more pronounced than for neutral markers. These results suggest that despite recent colonisation, genetic drift and/or restricted gene flow are promoting differentiation for neutral markers. Variation in selective pressures between islands may explain the observed phenotypic differentiation.
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Affiliation(s)
- Karine Monceau
- Université de Bourgogne, UMR CNRS 6282 Biogéosciences, Equipe Ecologie Evolutive, Dijon, France
| | - Frank Cézilly
- Université de Bourgogne, UMR CNRS 6282 Biogéosciences, Equipe Ecologie Evolutive, Dijon, France
- Institut Universitaire de France, France
| | - Jérôme Moreau
- Université de Bourgogne, UMR CNRS 6282 Biogéosciences, Equipe Ecologie Evolutive, Dijon, France
| | - Sébastien Motreuil
- Université de Bourgogne, UMR CNRS 6282 Biogéosciences, Equipe Ecologie Evolutive, Dijon, France
| | - Rémi Wattier
- Université de Bourgogne, UMR CNRS 6282 Biogéosciences, Equipe Ecologie Evolutive, Dijon, France
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Levin II, Zwiers P, Deem SL, Geest EA, Higashiguchi JM, Iezhova TA, Jiménez-Uzcátegui G, Kim DH, Morton JP, Perlut NG, Renfrew RB, Sari EHR, Valkiunas G, Parker PG. Multiple lineages of Avian malaria parasites (Plasmodium) in the Galapagos Islands and evidence for arrival via migratory birds. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2013; 27:1366-1377. [PMID: 24033638 DOI: 10.1111/cobi.12127] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 04/06/2013] [Indexed: 06/02/2023]
Abstract
Haemosporidian parasites in the genus Plasmodium were recently detected through molecular screening in the Galapagos Penguin (Spheniscus mendiculus). We summarized results of an archipelago-wide screen of 3726 endemic birds representing 22 species for Plasmodium spp. through a combination of molecular and microscopy techniques. Three additional Plasmodium lineages were present in Galapagos. Lineage A-infected penguins, Yellow Warblers (Setophaga petechia aureola), and one Medium Ground Finch (Geospiza fortis) and was detected at multiple sites in multiple years [corrected]. The other 3 lineages were each detected at one site and at one time; apparently, they were transient infections of parasites not established on the archipelago. No gametocytes were found in blood smears of infected individuals; thus, endemic Galapagos birds may be dead-end hosts for these Plasmodium lineages. Determining when and how parasites and pathogens arrive in Galapagos is key to developing conservation strategies to prevent and mitigate the effects of introduced diseases. To assess the potential for Plasmodium parasites to arrive via migratory birds, we analyzed blood samples from 438 North American breeding Bobolinks (Dolichonyx oryzivorus), the only songbird that regularly migrates through Galapagos. Two of the ephemeral Plasmodium lineages (B and C) found in Galapagos birds matched parasite sequences from Bobolinks. Although this is not confirmation that Bobolinks are responsible for introducing these lineages, evidence points to higher potential arrival rates of avian pathogens than previously thought. Linajes Múltiples de Parásitos de Malaria Aviar (Plasmodium) en las Islas Galápagos y Evidencia de su Arribo por Medio de Aves Migratorias.
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Affiliation(s)
- I I Levin
- Department of Biology, University of Missouri-St. Louis, One University Blvd, St. Louis, MO, 63121, U.S.A.; Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, One University Blvd, St. Louis, MO, 63121, U.S.A.; WildCare Institute, Saint Louis Zoo, St. Louis, MO, 63110, U.S.A..
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28
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Habel JC, Husemann M, Finger A, Danley PD, Zachos FE. The relevance of time series in molecular ecology and conservation biology. Biol Rev Camb Philos Soc 2013; 89:484-92. [DOI: 10.1111/brv.12068] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 09/21/2013] [Accepted: 09/24/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Jan C. Habel
- Department of Ecology and Ecosystem Management; Technische Universität München; Hans-Carl-von-Carlowitz-Platz D-85350 Freising-Weihenstephan Germany
| | - Martin Husemann
- Biology Department; Baylor University, One Bear Place 97388; Waco TX 76798 U.S.A
| | - Aline Finger
- Genetics and Conservation; Royal Botanic Garden Edinburgh, 20A Inverleith Row; Edinburgh EH3 5LR U.K
| | - Patrick D. Danley
- Biology Department; Baylor University, One Bear Place 97388; Waco TX 76798 U.S.A
| | - Frank E. Zachos
- Natural History Museum Vienna, Burgring 7; 1010 Vienna Austria
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29
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Kuhn K, Schwenk K, Both C, Canal D, Johansson US, van der Mije S, Töpfer T, Päckert M. Differentiation in neutral genes and a candidate gene in the pied flycatcher: using biological archives to track global climate change. Ecol Evol 2013; 3:4799-814. [PMID: 24363905 PMCID: PMC3867912 DOI: 10.1002/ece3.855] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/25/2013] [Accepted: 09/25/2013] [Indexed: 11/11/2022] Open
Abstract
Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes.
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Affiliation(s)
- Kerstin Kuhn
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Ecology and Evolution, Johann Wolfgang Goethe-UniversitätMax-von-Laue-Straße 13, Frankfurt am Main, D-60438, Germany
| | - Klaus Schwenk
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Institute of Environmental Sciences, University of Koblenz-LandauFortstraße 7, Landau in der Pfalz, 76829, Germany
| | - Christiaan Both
- Centre for Ecological and Evolutionary Studies (CEES), University of GroningenPO Box 11103, Groningen, 9700 CC, The Netherlands
| | - David Canal
- Department of Evolutionary Ecology, Estación Biológica de Doñana, CSICAv. Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Ulf S Johansson
- Department of Zoology, Swedish Museum of Natural HistoryPO Box 50007, Stockholm, SE 10405, Sweden
| | | | - Till Töpfer
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Museum of Zoology, Senckenberg Natural History CollectionsKönigsbrücker Landstraße 159, Dresden, D-01109, Germany
| | - Martin Päckert
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Museum of Zoology, Senckenberg Natural History CollectionsKönigsbrücker Landstraße 159, Dresden, D-01109, Germany
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Nietlisbach P, Wandeler P, Parker PG, Grant PR, Grant BR, Keller LF, Hoeck PEA. Hybrid ancestry of an island subspecies of Galápagos mockingbird explains discordant gene trees. Mol Phylogenet Evol 2013; 69:581-92. [PMID: 23906599 DOI: 10.1016/j.ympev.2013.07.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/17/2013] [Accepted: 07/18/2013] [Indexed: 11/28/2022]
Abstract
Introgression of genes through hybridization has been proposed to be an important driver of speciation, but in animals this has been shown only in relatively few cases until recently. Additionally, introgressive hybridization among non-sister species leads to a change in the gene tree topology of the concerned loci and thus complicates phylogenetic reconstruction. However, such cases of ancient introgression have been very difficult to demonstrate in birds. Here, we present such an example in an island bird subspecies, the Genovesa mockingbird (Mimus parvulus bauri). We assessed phylogenetic relationships and population structure among mockingbirds of the Galápagos archipelago using mitochondrial and nuclear DNA sequences, autosomal microsatellites, and morphological measurements. Mitochondrial haplotypes of Genovesa mockingbirds clustered closely with the haplotypes from two different species, San Cristóbal (M. melanotis) and Española (M. macdonaldi) mockingbirds. The same pattern was found for some haplotypes of two nuclear gene introns, while the majority of nuclear haplotypes of Genovesa mockingbirds were shared with other populations of the same species (M. parvulus). At 26 autosomal microsatellites, Genovesa mockingbirds grouped with other M. parvulus populations. This pattern shows that Genovesa mockingbirds contain mitochondria and some autosomal alleles that have most likely introgressed from M. melanotis into a largely M. parvulus background, making Genovesa mockingbirds a lineage of mixed ancestry, possibly undergoing speciation. Consistent with this hypothesis, mockingbirds on Genovesa are more clearly differentiated morphologically from other M. parvulus populations than M. melanotis is from M. parvulus.
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Affiliation(s)
- Pirmin Nietlisbach
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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Gomez-Uchida D, Palstra FP, Knight TW, Ruzzante DE. Contemporary effective population and metapopulation size (N e and meta-N e): comparison among three salmonids inhabiting a fragmented system and differing in gene flow and its asymmetries. Ecol Evol 2013; 3:569-80. [PMID: 23532448 PMCID: PMC3605847 DOI: 10.1002/ece3.485] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 12/14/2012] [Accepted: 12/24/2012] [Indexed: 11/15/2022] Open
Abstract
We estimated local and metapopulation effective sizes ([Formula: see text] and meta-[Formula: see text]) for three coexisting salmonid species (Salmo salar, Salvelinus fontinalis, Salvelinus alpinus) inhabiting a freshwater system comprising seven interconnected lakes. First, we hypothesized that [Formula: see text] might be inversely related to within-species population divergence as reported in an earlier study (i.e., FST: S. salar> S. fontinalis> S. alpinus). Using the approximate Bayesian computation method implemented in ONeSAMP, we found significant differences in [Formula: see text] ([Formula: see text]) between species, consistent with a hierarchy of adult population sizes ([Formula: see text]). Using another method based on a measure of linkage disequilibrium (LDNE: [Formula: see text]), we found more finite [Formula: see text] values for S. salar than for the other two salmonids, in line with the results above that indicate that S. salar exhibits the lowest [Formula: see text] among the three species. Considering subpopulations as open to migration (i.e., removing putative immigrants) led to only marginal and non-significant changes in [Formula: see text], suggesting that migration may be at equilibrium between genetically similar sources. Second, we hypothesized that meta-[Formula: see text] might be significantly smaller than the sum of local [Formula: see text]s (null model) if gene flow is asymmetric, varies among subpopulations, and is driven by common landscape features such as waterfalls. One 'bottom-up' or numerical approach that explicitly incorporates variable and asymmetric migration rates showed this very pattern, while a number of analytical models provided meta-[Formula: see text] estimates that were not significantly different from the null model or from each other. Our study of three species inhabiting a shared environment highlights the importance and utility of differentiating species-specific and landscape effects, not only on dispersal but also in the demography of wild populations as assessed through local [Formula: see text]s and meta-[Formula: see text]s and their relevance in ecology, evolution and conservation.
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Levin II, Parker PG. Philopatry drives genetic differentiation in an island archipelago: comparative population genetics of Galapagos Nazca boobies (Sula granti) and great frigatebirds (Fregata minor). Ecol Evol 2012; 2:2775-87. [PMID: 23170212 PMCID: PMC3501629 DOI: 10.1002/ece3.386] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 08/21/2012] [Accepted: 08/27/2012] [Indexed: 11/09/2022] Open
Abstract
Seabirds are considered highly mobile, able to fly great distances with few apparent barriers to dispersal. However, it is often the case that seabird populations exhibit strong population genetic structure despite their potential vagility. Here we show that Galapagos Nazca booby (Sula granti) populations are substantially differentiated, even within the small geographic scale of this archipelago. On the other hand, Galapagos great frigatebird (Fregata minor) populations do not show any genetic structure. We characterized the genetic differentiation by sampling five colonies of both species in the Galapagos archipelago and analyzing eight microsatellite loci and three mitochondrial genes. Using an F-statistic approach on the multilocus data, we found significant differentiation between nearly all island pairs of Nazca booby populations and a Bayesian clustering analysis provided support for three distinct genetic clusters. Mitochondrial DNA showed less differentiation of Nazca booby colonies; only Nazca boobies from the island of Darwin were significantly differentiated from individuals throughout the rest of the archipelago. Great frigatebird populations showed little to no evidence for genetic differentiation at the same scale. Only two island pairs (Darwin - Wolf, N. Seymour - Wolf) were significantly differentiated using the multilocus data, and only two island pairs had statistically significant φ(ST) values (N. Seymour - Darwin, N. Seymour - Wolf) according to the mitochondrial data. There was no significant pattern of isolation by distance for either species calculated using both markers. Seven of the ten Nazca booby migration rates calculated between island pairs were in the south or southeast to north or northwest direction. The population differentiation found among Galapagos Nazca booby colonies, but not great frigatebird colonies, is most likely due to differences in natal and breeding philopatry.
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Affiliation(s)
- Iris I Levin
- Department of Biology, University of Missouri - St. Louis, One University Blvd. St. Louis, Missouri, 63121 ; Whitney R. Harris World Ecology Center, University of Missouri - St. Louis, One University Blvd. St. Louis, Missouri, 63121
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Lovette IJ, Arbogast BS, Curry RL, Zink RM, Botero CA, Sullivan JP, Talaba AL, Harris RB, Rubenstein DR, Ricklefs RE, Bermingham E. Phylogenetic relationships of the mockingbirds and thrashers (Aves: Mimidae). Mol Phylogenet Evol 2012; 63:219-29. [DOI: 10.1016/j.ympev.2011.07.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Revised: 06/03/2011] [Accepted: 07/11/2011] [Indexed: 10/17/2022]
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Bijlsma R, Loeschcke V. Genetic erosion impedes adaptive responses to stressful environments. Evol Appl 2011; 5:117-29. [PMID: 25568035 PMCID: PMC3353342 DOI: 10.1111/j.1752-4571.2011.00214.x] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 10/11/2011] [Indexed: 11/26/2022] Open
Abstract
Biodiversity is increasingly subjected to human-induced changes of the environment. To persist, populations continually have to adapt to these often stressful changes including pollution and climate change. Genetic erosion in small populations, owing to fragmentation of natural habitats, is expected to obstruct such adaptive responses: (i) genetic drift will cause a decrease in the level of adaptive genetic variation, thereby limiting evolutionary responses; (ii) inbreeding and the concomitant inbreeding depression will reduce individual fitness and, consequently, the tolerance of populations to environmental stress. Importantly, inbreeding generally increases the sensitivity of a population to stress, thereby increasing the amount of inbreeding depression. As adaptation to stress is most often accompanied by increased mortality (cost of selection), the increase in the ‘cost of inbreeding’ under stress is expected to severely hamper evolutionary adaptive processes. Inbreeding thus plays a pivotal role in this process and is expected to limit the probability of genetically eroded populations to successfully adapt to stressful environmental conditions. Consequently, the dynamics of small fragmented populations may differ considerably from large nonfragmented populations. The resilience of fragmented populations to changing and deteriorating environments is expected to be greatly decreased. Alleviating inbreeding depression, therefore, is crucial to ensure population persistence.
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Affiliation(s)
- R Bijlsma
- Population and Conservation Genetics, University of Groningen, Center for Life Sciences Groningen, The Netherlands ; Theoretical Biology, University of Groningen, Center for Life Sciences Groningen, The Netherlands
| | - Volker Loeschcke
- Department of Biosciences, Ecology and Genetics, Aarhus University Aarhus C, Denmark
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Štefka J, Hoeck PEA, Keller LF, Smith VS. A hitchhikers guide to the Galápagos: co-phylogeography of Galápagos mockingbirds and their parasites. BMC Evol Biol 2011; 11:284. [PMID: 21966954 PMCID: PMC3209464 DOI: 10.1186/1471-2148-11-284] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 10/03/2011] [Indexed: 01/11/2023] Open
Abstract
Background Parasites are evolutionary hitchhikers whose phylogenies often track the evolutionary history of their hosts. Incongruence in the evolutionary history of closely associated lineages can be explained through a variety of possible events including host switching and host independent speciation. However, in recently diverged lineages stochastic population processes, such as retention of ancestral polymorphism or secondary contact, can also explain discordant genealogies, even in fully co-speciating taxa. The relatively simple biogeographic arrangement of the Galápagos archipelago, compared with mainland biomes, provides a framework to identify stochastic and evolutionary informative components of genealogic data in these recently diverged organisms. Results Mitochondrial DNA sequences were obtained for four species of Galápagos mockingbirds and three sympatric species of ectoparasites - two louse and one mite species. These data were complemented with nuclear EF1α sequences in selected samples of parasites and with information from microsatellite loci in the mockingbirds. Mitochondrial sequence data revealed differences in population genetic diversity between all taxa and varying degrees of topological congruence between host and parasite lineages. A very low level of genetic variability and lack of congruence was found in one of the louse parasites, which was excluded from subsequent joint analysis of mitochondrial data. The reconciled multi-species tree obtained from the analysis is congruent with both the nuclear data and the geological history of the islands. Conclusions The gene genealogies of Galápagos mockingbirds and two of their ectoparasites show strong phylogeographic correlations, with instances of incongruence mostly explained by ancestral genetic polymorphism. A third parasite genealogy shows low levels of genetic diversity and little evidence of co-phylogeny with their hosts. These differences can mostly be explained by variation in life-history characteristics, primarily host specificity and dispersal capabilities. We show that pooling genetic data from organisms living in close ecological association reveals a more accurate phylogeographic history for these taxa. Our results have implications for the conservation and taxonomy of Galápagos mockingbirds and their parasites.
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Affiliation(s)
- Jan Štefka
- Entomology Department, Natural History Museum, Cromwell Road, SW7 5BD London, UK.
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Parker PG, Buckles EL, Farrington H, Petren K, Whiteman NK, Ricklefs RE, Bollmer JL, Jiménez-Uzcátegui G. 110 years of Avipoxvirus in the Galapagos Islands. PLoS One 2011; 6:e15989. [PMID: 21249151 PMCID: PMC3020966 DOI: 10.1371/journal.pone.0015989] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 12/02/2010] [Indexed: 12/04/2022] Open
Abstract
The role of disease in regulating populations is controversial, partly owing to the absence of good disease records in historic wildlife populations. We examined birds collected in the Galapagos Islands between 1891 and 1906 that are currently held at the California Academy of Sciences and the Zoologisches Staatssammlung Muenchen, including 3973 specimens representing species from two well-studied families of endemic passerine birds: finches and mockingbirds. Beginning with samples collected in 1899, we observed cutaneous lesions consistent with Avipoxvirus on 226 (6.3%) specimens. Histopathology and viral genotyping of 59 candidate tissue samples from six islands showed that 21 (35.6%) were positive for Avipoxvirus, while alternative diagnoses for some of those testing negative by both methods were feather follicle cysts, non-specific dermatitis, or post mortem fungal colonization. Positive specimens were significantly nonrandomly distributed among islands both for mockingbirds (San Cristobal vs. Espanola, Santa Fe and Santa Cruz) and for finches (San Cristobal and Isabela vs. Santa Cruz and Floreana), and overall highly significantly distributed toward islands that were inhabited by humans (San Cristobal, Isabela, Floreana) vs. uninhabited at the time of collection (Santa Cruz, Santa Fe, Espanola), with only one positive individual on an uninhabited island. Eleven of the positive specimens sequenced successfully were identical at four diagnostic sites to the two canarypox variants previously described in contemporary Galapagos passerines. We conclude that this virus was introduced late in 1890′s and was dispersed among islands by a variety of mechanisms, including regular human movements among colonized islands. At present, this disease represents an ongoing threat to the birds on the Galapagos Islands.
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Affiliation(s)
- Patricia G Parker
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, United States of America.
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Mathys BA, Lockwood JL. Contemporary morphological diversification of passerine birds introduced to the Hawaiian archipelago. Proc Biol Sci 2011; 278:2392-400. [PMID: 21208954 DOI: 10.1098/rspb.2010.2302] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Species that have been introduced to islands experience novel and strong selection pressures after establishment. There is evidence that exotic species diverge from their native source populations; further, a few studies have demonstrated adaptive divergence across multiple exotic populations of a single species. Exotic birds provide a good study system, as they have been introduced to many locations worldwide, and we often know details concerning the propagule origin, time of introduction, and dynamics of establishment and dispersal within the introduced range. These data make them especially conducive to the examination of contemporary evolution. Island faunas have received intense scrutiny, therefore we have expectations concerning the patterns of diversification for exotic species. We examine six passerine bird species that were introduced to the Hawaiian archipelago less than 150 years ago. We find that five of these show morphological divergence among islands from the time since they were established. We demonstrate that some of this divergence cannot be accounted for by genetic drift, and therefore we must consider adaptive evolution to explain it. We also evaluate evolutionary divergence rates and find that these species are diverging at similar rates to those found in published studies of contemporary evolution in native species.
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Affiliation(s)
- Blake A Mathys
- Natural Sciences and Mathematics, The Richard Stockton College of New Jersey, PO Box 195, Pomona, NJ 08240, USA.
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Abzhanov A. Darwin's Galapagos finches in modern biology. Philos Trans R Soc Lond B Biol Sci 2010; 365:1001-7. [PMID: 20194163 DOI: 10.1098/rstb.2009.0321] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One of the classic examples of adaptive radiation under natural selection is the evolution of 15 closely related species of Darwin's finches (Passeriformes), whose primary diversity lies in the size and shape of their beaks. Since Charles Darwin and other members of the Beagle expedition collected these birds on the Galápagos Islands in 1835 and introduced them to science, they have been the subjects of intense research. Many biology textbooks use Darwin's finches to illustrate a variety of topics of evolutionary theory, such as speciation, natural selection and niche partitioning. Today, as this Theme Issue illustrates, Darwin's finches continue to be a very valuable source of biological discovery. Certain advantages of studying this group allow further breakthroughs in our understanding of changes in recent island biodiversity, mechanisms of speciation and hybridization, evolution of cognitive behaviours, principles of beak/jaw biomechanics as well as the underlying developmental genetic mechanisms in generating morphological diversity. Our objective was to bring together some of the key workers in the field of ecology and evolutionary biology who study Darwin's finches or whose studies were inspired by research on Darwin's finches. Insights provided by papers collected in this Theme Issue will be of interest to a wide audience.
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Affiliation(s)
- Arhat Abzhanov
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
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Hoeck PEA, Beaumont MA, James KE, Grant RB, Grant PR, Keller LF. Saving Darwin's muse: evolutionary genetics for the recovery of the Floreana mockingbird. Biol Lett 2009; 6:212-5. [PMID: 19923141 DOI: 10.1098/rsbl.2009.0778] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The distribution of mockingbird species among the Galápagos Islands prompted Charles Darwin to question, for the first time in writing, the 'stability of species'. Some 50 years after Darwin's visit, however, the endemic Floreana mockingbird (Mimus trifasciatus) had become extinct on Floreana Island and, today, only two small populations survive on two satellite islets. As Darwin noted, rarity often precedes extinction. To avert extinction, plans are being developed to reintroduce M. trifasciatus to Floreana. Here, we integrate evolutionary thinking and conservation practice using coalescent analyses and genetic data from contemporary and museum samples, including two collected by Darwin and Robert Fitzroy on Floreana in 1835. Our microsatellite results show substantial differentiation between the two extant populations, but our coalescence-based modelling does not indicate long, independent evolutionary histories. One of the populations is highly inbred, but both harbour unique alleles present on Floreana in 1835, suggesting that birds from both islets should be used to establish a single, mixed population on Floreana. Thus, Darwin's mockingbird specimens not only revealed to him a level of variation that suggested speciation following geographical isolation but also, more than 170 years later, return important information to their place of origin for the conservation of their conspecifics.
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Affiliation(s)
- Paquita E A Hoeck
- Zoological Museum, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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