1
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Bensch S, Caballero-López V, Cornwallis CK, Sokolovskis K. The evolutionary history of "suboptimal" migration routes. iScience 2023; 26:108266. [PMID: 38026158 PMCID: PMC10663737 DOI: 10.1016/j.isci.2023.108266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/12/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Migratoriness in birds is evolutionary labile, with many examples of increasing or decreasing migration distances on the timescale of modern ornithology. In contrast, shifts of migration to more nearby wintering grounds seem to be a slow process. We examine the history of how Palearctic migratory landbirds have expanded their wintering ranges to include both tropical Africa and Asia, a process that has involved major shifts in migratory routes. We found that species with shorter migration distances and with resident populations in the Palearctic more often winter in both Africa and Asia. Our results suggest that changes in wintering grounds are not by long-distance migrant populations per se, but through historic intermediate populations that were less migratory from which long-distance migration evolved secondarily. The failure of long-distance migrants to shift migration direction to more nearby winter quarters indicates that major modifications to the migratory program may be difficult to evolve.
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Affiliation(s)
- Staffan Bensch
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, 22362 Lund, Sweden
| | - Violeta Caballero-López
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, 22362 Lund, Sweden
| | - Charlie K. Cornwallis
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, 22362 Lund, Sweden
| | - Kristaps Sokolovskis
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, 22362 Lund, Sweden
- Department of Biology, University of Turku, Vesilinnantie 5, 20500 Turku, Finland
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2
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Villsen K, Corse E, Meglécz E, Archambaud‐Suard G, Vignes H, Ereskovsky AV, Chappaz R, Dubut V. DNA metabarcoding suggests adaptive seasonal variation of individual trophic traits in a critically endangered fish. Mol Ecol 2022; 31:5889-5908. [PMID: 36125278 PMCID: PMC9828795 DOI: 10.1111/mec.16698] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
Dietary studies are critical for understanding foraging strategies and have important applications in conservation and habitat management. We applied a robust metabarcoding protocol to characterize the diet of the critically endangered freshwater fish Zingel asper (the Rhone streber). We conducted modelling and simulation analyses to identify and characterize some of the drivers of individual trophic trait variation in this species. We found that population density and ontogeny had minor effects on the trophic niche of Z. asper. Instead, our results suggest that the majority of trophic niche variation was driven by seasonal variation in ecological opportunity. The total trophic niche width of Z. asper seasonally expanded to include a broader range of prey. Furthermore, null model simulations revealed that the increase of between-individual variation in autumn indicates that Z. asper become more opportunistic relative to summer and spring, rather than being associated with a seasonal specialization of individuals. Overall, our results suggest an adaptive variation of individual trophic traits in Z. asper: the species mainly consumes a few ephemeropteran taxa (Baetis fuscatus and Ecdyonurus) but seems to be capable of adapting its foraging strategy to maintain its body condition. This study illustrates how metabarcoding data obtained from faeces can be validated and combined with individual-based modelling and simulation approaches to explore inter- and intrapopulational individual trophic traits variation and to test hypotheses in the conventional analytic framework of trophic ecology.
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Affiliation(s)
- Kurt Villsen
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
| | - Emmanuel Corse
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance,Centre Universitaire de Formation et de Recherche de Mayotte (CUFR)DembeniFrance,MARBEC, University of Montpellier, CNRS, Ifremer, IRDMontpellierFrance
| | - Emese Meglécz
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
| | | | - Hélène Vignes
- CIRAD, University of Montpellier, INRAE, Montpellier SupAgro, AGAPMontpellierFrance
| | - Alexander V. Ereskovsky
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance,St. Petersburg State UniversitySt. PetersburgRussia,Koltzov Institute of Developmental Biology of Russian Academy of SciencesMoscowRussia
| | - Rémi Chappaz
- INRAE, Aix Marseille Université, RECOVERAix‐en‐ProvenceFrance
| | - Vincent Dubut
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
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3
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Pârâu LG, Wink M. Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review. JOURNAL OF ORNITHOLOGY 2021; 162:937-959. [PMID: 34007780 PMCID: PMC8118378 DOI: 10.1007/s10336-021-01893-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 04/26/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
A plethora of studies have offered crucial insights in the phylogeographic status of Western Palearctic bird species. However, an overview integrating all this information and analyzing the combined results is still missing. In this study, we compiled all published peer-reviewed and grey literature available on the phylogeography of Western Palearctic bird species. Our literature review indicates a total number of 198 studies, with the overwhelming majority published as journal articles (n = 186). In total, these literature items offer information on 145 bird species. 85 of these species are characterized by low genetic differentiation, 46 species indicate genetic variation but no geographic structuring i.e. panmixia, while 14 species show geographically distinct lineages and haplotypes. Majority of bird species inhabiting the Western Palearctic display genetic admixture. The glaciation cycles in the past few million years were pivotal factors in shaping this situation: during warm periods many species expanded their distribution range to the north over wide areas of Eurasia; whereas, during ice ages most areas were no longer suitable and species retreated to refugia, where lineages mixed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10336-021-01893-x.
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Affiliation(s)
- Liviu G. Pârâu
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
- Present Address: SARS-CoV-2 Data Evaluation Office, Eurofins Genomics Europe Applied Genomics GmbH, Anzinger Straße 7a, 85560 Ebersberg, Germany
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
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4
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Rogalla S, Shawkey MD, Vanthournout B, D'Alba L. Thermoregulation and heat exchange in ospreys (Pandion haliaetus). J Therm Biol 2021; 96:102857. [PMID: 33627285 DOI: 10.1016/j.jtherbio.2021.102857] [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: 07/10/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 10/22/2022]
Abstract
The osprey (Pandion haliaetus) is a cosmopolitan and long-distant migrant, found at all thermal extremes ranging from polar to tropical climates. Since ospreys may have an unusually flexible thermal physiology due to their migration over, and use of, a wide range of habitats, they represent an interesting study system to explore thermoregulatory adaptations in a raptor. In this study, we investigated the efficiency of heat exchange between body and environment in ospreys using micro-computed tomography (μ-CT), infrared thermography and behavioral observations. μ-CT revealed that the osprey bill has its largest potential for heat exchange at the proximal bill region, where arteries are situated most closely under the surface. However, thermal images of 10 juvenile ospreys showed that the bill contributes to only 0.3% of the bird's total heat exchange. The long legs and protruding claws played a more prominent role as heat dissipation areas with a contribution of 6% and 7%, respectively. Operative thresholds, i.e. the ambient temperature below which heat is lost, were high (>38.5 °C) in these body parts. However, we found no indication of active regulation of heat exchange. Instead we observed multiple behavioral adaptations starting at relatively low ambient temperatures. At 26.3 °C ospreys had a 50% probability of showing panting behavior and above 27.9 °C they additionally spread their wings to enable heat dissipation from the less insulated ventral side. The thermal images revealed that at an ambient temperature of 32.1 °C ospreys had a 50% probability of developing a ≥2 °C and up to 7.5 °C colder stripe on the head, which was likely caused by cutaneous evaporation. Our observations suggest that ospreys more strongly rely on behavioral mechanisms than on active thermal windows to cope with heat stress. This study not only improves our understanding of the role of different body parts in ospreys' total heat exchange with the environment but further provides an insight about additional adaptations of this raptor to cope with heat stress.
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Affiliation(s)
- Svana Rogalla
- Evolution and Optics of Nanostructures Group, Department of Biology, University of Ghent, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Matthew D Shawkey
- Evolution and Optics of Nanostructures Group, Department of Biology, University of Ghent, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Bram Vanthournout
- Evolution and Optics of Nanostructures Group, Department of Biology, University of Ghent, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Liliana D'Alba
- Evolution and Optics of Nanostructures Group, Department of Biology, University of Ghent, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
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5
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Sato Y, Ogden R, Kishida T, Nakajima N, Maeda T, Inoue-Murayama M. Population history of the golden eagle inferred from whole-genome sequencing of three of its subspecies. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa068] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe application of evolutionary genetic research to investigate the potential for endangered species to adapt to changing environments is important for conservation biology. Effective population size (Ne) is informative for understanding adaptive potential as it refers to the genetic variation in breeding individuals who have contributed to contemporary and historic population diversity. We reconstruct fluctuations in Ne in three golden eagle subspecies (Japanese, Scottish, North American) using the pairwise sequential Markovian coalescent (PSMC) model based on whole-genome sequence data. Our results indicate the timing of subspeciation events and suggest significant ongoing demographic reductions since the start of the Last Glacial Period. Importantly, we find evidence for gene flow from continental populations into the ancestral Japanese population resulting in a short, sharp recovery in genetic diversity. Timing agrees with the palaeogeographic estimates of land bridge connections between the Japanese archipelago and Asian continent and matches a similar Ne spike in the Scottish population, but not in the North American population. Given contemporary declines in isolated Japanese and UK island populations, our study highlights a concerning loss of local genetic diversity, but also indicates the likely response of populations to genetic reinforcement from neighbouring subspecies, increasing management options and encouraging a range-wide species conservation approach.
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Affiliation(s)
- Yu Sato
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, Easter Bush Campus, University of Edinburgh, UK
| | - Takushi Kishida
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Museum of Natural and Environmental History, Shizuoka, Japan
| | - Nobuyoshi Nakajima
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan
| | - Taku Maeda
- Iwate Prefectural Research Institute for Environmental Sciences and Public Health, Morioka, Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan
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6
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Nagai K, Nakayama F, Tokita KI, Kawakami K. Genetic Structure and Diversity of Two Populations of the Eastern Buzzard ( Buteo japonicus japonicus and B. j. toyoshimai) in Japan. Zoolog Sci 2020; 36:471-478. [PMID: 31833318 DOI: 10.2108/zs190030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 06/05/2019] [Indexed: 11/17/2022]
Abstract
The nominotypical subspecies of the Eastern buzzard (Buteo japonicus japonicus; BJJ) is a common raptor inhabiting East Asia and Japan. Another subspecies, B. j. toyoshimai (BJT), inhabits only the Bonin Islands of the Ogasawara Islands, where there are only an estimated 85 breeding pairs. Because of this low population size, this subspecies is classified as endangered (class IB) in Japan. The aims of the present study were to examine genetic differences between BJJ and BJT, determine the genetic structure of the Eastern Buzzard, and assess genetic diversity within each subspecies. We sequenced 1526 bp within the control region of the mtDNA of 10 BJJ individuals during the breeding season in four sites; similarly, we sequenced 23 BJJ individuals during winter in three sites. We detected 24 haplotypes among the 33 individuals. In a similar analysis performed with 12 BJT individuals, three haplotypes were detected. The phylogenetic analysis showed that BJJ and BJT have diverged into distinct clades, supporting the genetic differentiation between the subspecies. Network and mismatch distribution analyses indicated that BJJ may have experienced population expansion. In addition, comparisons with other raptors revealed a high degree of genetic diversity in the BJJ population. In contrast, the genetic diversity of the BJT population is lower than that in other raptors. Our results indicated that it is necessary to protect BJT to prevent the reduction in its genetic diversity.
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Affiliation(s)
- Kazuya Nagai
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.,Research and Education Centre for Natural Sciences, Keio University, Yokohama, Kanagawa 223-8521, Japan,
| | | | - Ken-Ichi Tokita
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Kazuto Kawakami
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
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7
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Nebel C, Gamauf A, Haring E, Segelbacher G, Väli Ü, Villers A, Zachos FE. New insights into population structure of the European golden eagle (Aquila chrysaetos) revealed by microsatellite analysis. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz130] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractConnectivity between golden eagle (Aquila chrysaetos) populations is poorly understood. Field studies exploring natal dispersal suggest that this raptor is a philopatric species, but with the ability to roam far. However, little is known about the population structure of the species in Europe. Our study is based on 14 microsatellite loci and is complemented by new and previously published mitochondrial control region DNA data. The present dataset includes 121 eagles from Scotland, Norway, Finland, Estonia, the Mediterranean and Alpine regions. Our sampling focused on the Alpine and Mediterranean populations because both mitochondrial DNA (mtDNA) lineages found in golden eagles, the Holarctic and the Mediterranean, are known to co-occur there. Cluster analyses of nuclear DNA support a shallow split into northern and southern populations in Europe, similar to the distribution of the two mtDNA lineages, with the Holarctic lineage occurring in the north and the Mediterranean lineage predominating in the south. Additionally, Scotland shows significant differentiation and low relative migration levels that indicate isolation from the mainland populations. Alpine and Mediterranean golden eagles do not show nuclear structure corresponding to divergent mtDNA lineages. This indicates that the presence of northern Holarctic mitochondrial haplotypes in the Alps and the Mediterranean is attributable to past admixture rather than recent long-distance dispersal.
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Affiliation(s)
- Carina Nebel
- FitzPatrick Institute of African Ornithology, University of Cape Town, Cape Town, South Africa
- Natural History Museum Vienna, Vienna, Austria
| | - Anita Gamauf
- Natural History Museum Vienna, Vienna, Austria
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Elisabeth Haring
- Natural History Museum Vienna, Vienna, Austria
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | | | - Ülo Väli
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Alexandre Villers
- Centre d’Etudes Biologiques de Chizé, UMR7372, CNRS – Université de la Rochelle, Beauvoir sur Niort, France
- Section of Ecology, Department of Biology, University of Turku, Turku, Finland
- Unité Avifaune Migratrice, Office National de la Chasse et de la Faune Sauvage, Station de Chizé, Villiers-en-Bois, France
| | - Frank E Zachos
- Natural History Museum Vienna, Vienna, Austria
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
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8
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Duriez O, Peron G, Gremillet D, Sforzi A, Monti F. Migrating ospreys use thermal uplift over the open sea. Biol Lett 2019; 14:20180687. [PMID: 30958250 DOI: 10.1098/rsbl.2018.0687] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most large raptors on migration avoid crossing the sea because of the lack of atmospheric convection over temperate seas. The osprey Pandion haliaetus is an exception among raptors, since it can fly over several hundred kilometres of open water. We equipped five juvenile ospreys with GPS-Accelerometer-Magnetometer loggers. All birds were able to find and use thermal uplift while crossing the Mediterranean Sea, on average 7.5 times per 100 km, and could reach altitudes of 900 m above the sea surface. Their climb rate was 1.6 times slower than over land, and birds kept flapping most of the time while circling in the thermals, indicating that convections cells were weaker than over land. The frequency of thermal soaring was correlated with the difference between the sea surface and air temperature, indicating that atmospheric convection occurred when surface waters were warmer than the overlaying air. These observations help explain the transoceanic cosmopolitan distribution of osprey, and question the widely held assumption that water bodies represent strict barriers for large raptors.
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Affiliation(s)
- Olivier Duriez
- 1 Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, 1919 route de Mende, 34293 Montpellier , France
| | - Guillaume Peron
- 2 UMR CNRS 5558-LBBE 'Biométrie et Biologie Évolutive' , UCB Lyon 1-Bât. Grégor Mendel, 43 bd du 11 novembre 1918, 69622 Villeurbanne cedex , France
| | - David Gremillet
- 1 Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, 1919 route de Mende, 34293 Montpellier , France.,3 FitzPatrick Institute, DST/NRF Excellence Centre at the University of Cape Town , Rondebosch 7701 , South Africa
| | - Andrea Sforzi
- 4 Maremma Natural History Museum , Strada Corsini 5, 58100 Grosseto , Italy
| | - Flavio Monti
- 5 Department of Physical Sciences, Earth and Environment, University of Siena , Strada Laterina, 8, 53100 Siena , Italy
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9
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Corse E, Tougard C, Archambaud‐Suard G, Agnèse J, Messu Mandeng FD, Bilong Bilong CF, Duneau D, Zinger L, Chappaz R, Xu CC, Meglécz E, Dubut V. One-locus-several-primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies. Ecol Evol 2019; 9:4603-4620. [PMID: 31031930 PMCID: PMC6476781 DOI: 10.1002/ece3.5063] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 12/19/2022] Open
Abstract
In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets' complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [MOTUs] and variants). We then formalized the "one-locus-several-primer-sets" (OLSP) strategy, that is, the use of several primer sets that target the same locus (here the first part of the COI gene) and the same group of taxa (here invertebrates). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey-predator interactions.
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Affiliation(s)
- Emmanuel Corse
- Aix Marseille Univ, Avignon UnivCNRS, IRD, IMBEMarseilleFrance
- Agence de Recherche pour la Biodiversité à la Réunion (ARBRE)Saint‐Leu, La RéunionFrance
| | | | | | | | - Françoise D. Messu Mandeng
- Laboratory of Parasitology and Ecology, Departement of Animal Biology and PhysiologyUniversity of Yaoundé IYaoundéCameroon
| | - Charles F. Bilong Bilong
- Laboratory of Parasitology and Ecology, Departement of Animal Biology and PhysiologyUniversity of Yaoundé IYaoundéCameroon
| | - David Duneau
- Université Toulouse 3 Paul SabatierCNRS, ENSFEA, EDB (Laboratoire Évolution & Diversité Biologique)ToulouseFrance
| | - Lucie Zinger
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERMPSL Research UniversityParisFrance
| | - Rémi Chappaz
- Irstea, Aix Marseille Univ, RECOVERAix‐en‐ProvenceFrance
| | - Charles C.Y. Xu
- Redpath Museum and Department of BiologyMcGill UniversityMontréalQuebecCanada
| | - Emese Meglécz
- Aix Marseille Univ, Avignon UnivCNRS, IRD, IMBEMarseilleFrance
| | - Vincent Dubut
- Aix Marseille Univ, Avignon UnivCNRS, IRD, IMBEMarseilleFrance
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10
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Unravelling population processes over the Late Pleistocene driving contemporary genetic divergence in Palearctic buzzards. Mol Phylogenet Evol 2019; 134:269-281. [PMID: 30763758 DOI: 10.1016/j.ympev.2019.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 11/20/2022]
Abstract
Population range expansions and contractions as a response to climate and habitat change throughout the Quaternary are known to have contributed to complex phylogenetic and population genetic events. Speciation patterns and processes in Palearctic buzzards (genus Buteo) are a long-standing example of morphological and genetic data incongruence, attributed to panmixia, habitat range shifts, contact zones, and climate change. Here we assess the systematics, phylogeography and population genetic structure of three nominal species of Palearctic buzzards, Buteo buteo (including B. b. vulpinus), B. rufinus (including B. r. cirtensis) and B. hemilasius. Phylogenetic analyses inferred from mitochondrial data recover B. hemilasius as sister to the sister clades B. r. rufinus and B. buteo complex (B. b. buteo, B. b. vulpinus, but also including B. r. cirtensis). In contrast, we find an unresolved genetic delimitation inferred from four nuclear loci, suggesting an ancestral genetic pool for all species. Time-trees suggest population contractions and expansions throughout the Pleistocene, which likely reflect habitat change and contrasting ecological niche requirements between species. Microsatellite-based extended Bayesian skyline plots reveal relatively constant population sizes for B. hemilasius, B. r. rufinus, and B. b. vulpinus, in contrast to a dramatic population expansion in B. r. cirtensis within the last 3 kya. Overall, our study illustrates how complex population processes over the Late Pleistocene have shaped the patterns of genetic divergence in Palearctic buzzards, due to the joint effects of shared ancestral polymorphisms, population expansions and contractions, with hybridization at contact zones leading to admixture and introgression.
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11
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Nagai K, Iseki F, Azuma A. Analysis of the Genetic Diversity and Structure of the Grey-Faced Buzzard ( Butastur indicus) in Japan, Based on mtDNA. Zoolog Sci 2019; 36:17-22. [PMID: 31116534 DOI: 10.2108/zs180077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/23/2018] [Indexed: 11/17/2022]
Abstract
The grey-faced buzzard (Butastur indicus) is a raptor that inhabits East Asia, including Japan. Because the number of individuals has decreased by 75% over the last 40 years, this species is classified as vulnerable (VU) in Japan. In the present study, wesought to reveal the genetic structure of the Japanese grey-faced buzzard population at several breeding sites, and to assess the levels of genetic diversity within the Japanese population. We sequenced 555 bp of the mitochondrial DNA of 96 individuals sampled during the breeding season at 18 sites, and 11 individuals sampled during the winter season at one site. In total, 21 variable sites were found in the control region, and we detected 26 haplotypes among the 107 individuals. Fukuoka represented the core breeding area for grey-faced buzzards, as half of all haplotypes were detected there. Four unique haplotypes were detected in the overwintering area. The results of the network and mismatch distribution analyses indicated that the grey-faced buzzard has not experienced a genetic bottleneck in the past, but did experience recent population expansion. In addition, comparisons with other raptors revealed rich genetic diversity in the grey-faced buzzard population. Our results indicate that conservation of both breeding and wintering areas is important for the protection of the grey-faced buzzard.
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Affiliation(s)
- Kazuya Nagai
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.,Research and Education Centre for Natural Sciences, Keio University, Yokohama, Kanagawa 223-8521, Japan,
| | - Fumitaka Iseki
- Working group on Threatened Wildlife, Nakatsu, Oita 879-0122, Japan
| | - Atsuki Azuma
- Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
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12
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Uva V, Päckert M, Cibois A, Fumagalli L, Roulin A. Comprehensive molecular phylogeny of barn owls and relatives (Family: Tytonidae), and their six major Pleistocene radiations. Mol Phylogenet Evol 2018. [PMID: 29535030 DOI: 10.1016/j.ympev.2018.03.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The owl family Tytonidae comprises two genera: Phodilus, limited to the forests of central Africa and South-East Asia, and the ubiquitous Tyto. The genus Tyto is majorly represented by the cosmopolitan Common Barn Owl group, with more than 30 subspecies worldwide. Discrete differences in body size and plumage colouration have led to the classification of this family into many species and subspecies, but the taxonomic status and phylogenetic relationships between taxa remain unclear, and in some groups controversial. Although several previous studies attempted to resolve this problem, they have been limited in their taxonomic and geographical coverage, or have relied on restricted molecular evidence and low sample sizes. Based on the most comprehensive sampling to date (16 out of 17 Tyto species, and one out of three Phodilus species), a multi-locus approach using seven mitochondrial and two nuclear markers, and taking advantage of field data and museum collections available worldwide, our main questions in this study were: (1) what are the phylogenetic relationships and classification status of the whole family; (2) when and where did the most important speciation events occur? We confirm that the Common Barn Owl, Tyto alba is divided into three main evolutionary units: the American Barn Owl, T. furcata; the Western Barn Owl, T. alba; and the Eastern Barn Owl, T. javanica, and suggest a Late Miocene (ca. 6 mya) Australasian and African origin of the group. Our results are supported by fossil age information, given that the most recent common ancestor between the Tytonidae genera Phodilus and Tyto was probably from the Oligocene (ca. 28 mya) of Australasia. We finally reveal six major Pleistocene radiations of Tyto, all resulting in wide-range distributions.
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Affiliation(s)
- Vera Uva
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Martin Päckert
- Senckenberg Natural History Collections, Königsbrücker, Landstraße 159, 01109 Dresden, Germany.
| | - Alice Cibois
- Museum of Natural History of Geneva, Route de Managnou 1, 1208 Geneva, Switzerland.
| | - Luca Fumagalli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Rue du Bugnon 21, 1011 Lausanne, Switzerland.
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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Monti F, Duriez O, Dominici JM, Sforzi A, Robert A, Fusani L, Grémillet D. The price of success: integrative long-term study reveals ecotourism impacts on a flagship species at a UNESCO site. Anim Conserv 2018. [DOI: 10.1111/acv.12407] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- F. Monti
- CEFE; UMR 5175; CNRS; Université de Montpellier; Université Paul-Valéry Montpellier; EPHE; Montpellier Cedex 5 France
- Department of Life Sciences and Biotechnology; University of Ferrara; Ferrara Italy
- Department of Physical Sciences; Earth and Environment; University of Siena; Siena Italy
| | - O. Duriez
- CEFE; UMR 5175; CNRS; Université de Montpellier; Université Paul-Valéry Montpellier; EPHE; Montpellier Cedex 5 France
| | - J.-M. Dominici
- Réserve Naturelle Scandola; Parc Naturel Régional de Corse; Galeria France
| | - A. Sforzi
- Maremma Natural History Museum; Grosseto Italy
| | - A. Robert
- CEFE; UMR 5175; CNRS; Université de Montpellier; Université Paul-Valéry Montpellier; EPHE; Montpellier Cedex 5 France
| | - L. Fusani
- Department of Life Sciences and Biotechnology; University of Ferrara; Ferrara Italy
- Department of Cognitive Biology; University of Vienna; and Konrad Lorenz Institute of Ethology; University of Veterinary Medicine; Vienna Austria
| | - D. Grémillet
- CEFE; UMR 5175; CNRS; Université de Montpellier; Université Paul-Valéry Montpellier; EPHE; Montpellier Cedex 5 France
- FitzPatrick Institute; DST/NRF Centre of Excellence at the University of Cape Town; Rondebosch South Africa
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14
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Monti F, Delfour F, Arnal V, Zenboudji S, Duriez O, Montgelard C. Genetic connectivity among osprey populations and consequences for conservation: philopatry versus dispersal as key factors. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1058-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Savary R, Masclaux FG, Wyss T, Droh G, Cruz Corella J, Machado AP, Morton JB, Sanders IR. A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis. THE ISME JOURNAL 2018; 12:17-30. [PMID: 29027999 PMCID: PMC5739010 DOI: 10.1038/ismej.2017.153] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/20/2017] [Accepted: 08/21/2017] [Indexed: 11/26/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF; phylum Gomeromycota) associate with plants forming one of the most successful microbe-plant associations. The fungi promote plant diversity and have a potentially important role in global agriculture. Plant growth depends on both inter- and intra-specific variation in AMF. It was recently reported that an unusually large number of AMF taxa have an intercontinental distribution, suggesting long-distance gene flow for many AMF species, facilitated by either long-distance natural dispersal mechanisms or human-assisted dispersal. However, the intercontinental distribution of AMF species has been questioned because the use of very low-resolution markers may be unsuitable to detect genetic differences among geographically separated AMF, as seen with some other fungi. This has been untestable because of the lack of population genomic data, with high resolution, for any AMF taxa. Here we use phylogenetics and population genomics to test for intra-specific variation in Rhizophagus irregularis, an AMF species for which genome sequence information already exists. We used ddRAD sequencing to obtain thousands of markers distributed across the genomes of 81 R. irregularis isolates and related species. Based on 6 888 variable positions, we observed significant genetic divergence into four main genetic groups within R. irregularis, highlighting that previous studies have not captured underlying genetic variation. Despite considerable genetic divergence, surprisingly, the variation could not be explained by geographical origin, thus also supporting the hypothesis for at least one AMF species of widely dispersed AMF genotypes at an intercontinental scale. Such information is crucial for understanding AMF ecology, and how these fungi can be used in an environmentally safe way in distant locations.
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Affiliation(s)
- Romain Savary
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tania Wyss
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Germain Droh
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
- Laboratoire de Génétique, Unité de Formation et de Recherche en Biosciences, Université Félix Houphouet Boigny, Abidjan, Ivory Coast
| | - Joaquim Cruz Corella
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Ana Paula Machado
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Joseph B Morton
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Ian R Sanders
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
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16
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Corse E, Meglécz E, Archambaud G, Ardisson M, Martin JF, Tougard C, Chappaz R, Dubut V. A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies. Mol Ecol Resour 2017; 17:e146-e159. [PMID: 28776936 DOI: 10.1111/1755-0998.12703] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 07/17/2017] [Accepted: 07/25/2017] [Indexed: 11/30/2022]
Abstract
The main objective of this work was to develop and validate a robust and reliable "from-benchtop-to-desktop" metabarcoding workflow to investigate the diet of invertebrate-eaters. We applied our workflow to faecal DNA samples of an invertebrate-eating fish species. A fragment of the cytochrome c oxidase I (COI) gene was amplified by combining two minibarcoding primer sets to maximize the taxonomic coverage. Amplicons were sequenced by an Illumina MiSeq platform. We developed a filtering approach based on a series of nonarbitrary thresholds established from control samples and from molecular replicates to address the elimination of cross-contamination, PCR/sequencing errors and mistagging artefacts. This resulted in a conservative and informative metabarcoding data set. We developed a taxonomic assignment procedure that combines different approaches and that allowed the identification of ~75% of invertebrate COI variants to the species level. Moreover, based on the diversity of the variants, we introduced a semiquantitative statistic in our diet study, the minimum number of individuals, which is based on the number of distinct variants in each sample. The metabarcoding approach described in this article may guide future diet studies that aim to produce robust data sets associated with a fine and accurate identification of prey items.
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Affiliation(s)
- Emmanuel Corse
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, UMR IMBE, Marseille, France
| | - Emese Meglécz
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, UMR IMBE, Marseille, France
| | - Gaït Archambaud
- Irstea, UR RECOVER, Equipe FRESCHCO, Aix-en-Provence, France
| | | | | | - Christelle Tougard
- CNRS, Université de Montpellier, IRD, CIRAD, EPHE, UMR ISEM, Montpellier, France
| | - Rémi Chappaz
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, UMR IMBE, Marseille, France
| | - Vincent Dubut
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, UMR IMBE, Marseille, France
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17
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Aliabadian M, Alaei-Kakhki N, Mirshamsi O, Nijman V, Roulin A. Phylogeny, biogeography, and diversification of barn owls (Aves: Strigiformes). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12824] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mansour Aliabadian
- Department of Biology; Faculty of Science; Ferdowsi University of Mashhad; Mashhad 9177 9489 74 Iran
- Research Department of Zoological Innovations; Institute of Applied Zoology; Faculty of Science; Ferdowsi University of Mashhad; Mashhad 9177 9489 74 Iran
| | - Niloofar Alaei-Kakhki
- Department of Biology; Faculty of Science; Ferdowsi University of Mashhad; Mashhad 9177 9489 74 Iran
| | - Omid Mirshamsi
- Department of Biology; Faculty of Science; Ferdowsi University of Mashhad; Mashhad 9177 9489 74 Iran
- Research Department of Zoological Innovations; Institute of Applied Zoology; Faculty of Science; Ferdowsi University of Mashhad; Mashhad 9177 9489 74 Iran
| | - Vincent Nijman
- Department of Social Sciences; Oxford Brookes University; Oxford OX3 0BP UK
| | - Alexandre Roulin
- Department of Ecology and Evolution; University of Lausanne; Biophore Building; CH-1015 Lausanne Switzerland
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