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Hoffmann G, Mátrai N, Bakonyi G, Vili N, Gyurácz J, Lenczl M, Kisfali P, Stranczinger S, Magonyi NM, Mátics E, Mátics R. Contrasting mtDNA and microsatellite data of great reed warbler Acrocephalus arundinaceus breeding populations on a small geographic scale. Biol Futur 2022; 73:445-453. [PMID: 35904714 DOI: 10.1007/s42977-022-00127-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/11/2022] [Indexed: 01/10/2023]
Abstract
The great reed warbler has two genetically distinguishable haplogroups: "Clade A" occurs in higher proportions in Western Europe and Kazakhstan, and colonised Europe and Asia from a refugium in South-West Europe; and "Clade B", which is more common in Eastern Europe, and colonised parts of Europe from a refugium in the Middle East. Our aims were (i) to analyse the rate of differentiation in Hungarian breeding populations in order to see whether European-scale pattern is visible or not on as a small scale as the territory of Hungary and (ii) to compare the results obtained with mtDNA sequencing and microsatellite markers. To analyse the genetic differentiation, the mtDNA control region II was sequenced in 68 adult breeding birds, and 51 were fingerprinted at 11 microsatellite loci, while both analyses were performed on 36 birds (a total of 83 birds). The microsatellite data gave a better resolution and represented the fine-scale pattern of the suspected recolonisation. The lack of genetic differentiation among the breeding populations based on mitochondrial data seems to support this finding, because the admixture of the clades in this particular geographic region obliterates differentiation. Accordingly, the Fst values from different branches are significantly based on microsatellite data only. The mtDNA methods only give reliable results when a geographic and ecological factor plays a role in the population subdivision, but in the case of an intermixing population larger-scale studies are needed.
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Affiliation(s)
- Gyula Hoffmann
- Department of General Zoology and Developmental Biology, University of Pécs, Ifjúság u. 6, Hungary, 7601, Pécs
- Hungarian Nature Research Society (HuNaReS), Vadvirág str. 5, Hungary, 8448, Ajka
| | - Norbert Mátrai
- Department of Genetics, Hungarian Institute for Forensic Sciences, Mosonyi str. 9, Hungary, 1087, Budapest.
- Hungarian Nature Research Society (HuNaReS), Vadvirág str. 5, Hungary, 8448, Ajka.
- Department of Zoology and Ecology, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Hungary, 2100, Gödöllő.
| | - Gábor Bakonyi
- Department of Zoology and Ecology, Hungarian University of Agriculture and Life Sciences, Páter Károly str. 1, Hungary, 2100, Gödöllő
| | - Nóra Vili
- Molecular Ecology Research Group, University of Veterinary Medicine, István str. 2, 1078, Budapest, Hungary
| | - József Gyurácz
- Department of Biology, Eötvös Loránd University, Savaria Campus, POB 170, Hungary, 9701, Szombathely
| | - Mihály Lenczl
- Institute of Isotopes CO., LTD, Konkoly Thege Miklós Rd. 29-33, Hungary, 1121, Budapest
| | - Péter Kisfali
- Department of Medical Genetics, University of Pécs, Szigeti Rd. 12, Hungary, 7624, Pécs
| | - Szilvia Stranczinger
- Department of Plant Biology, University of Pécs, Ifjúság Rd. 6, Hungary, 7624, Pécs
| | - Nóra Mária Magonyi
- Doctoral School of Biology and Sportbiology, University of Pécs, Ifjúság Rd. 6, Hungary, 7624, Pécs
- Hungarian Nature Research Society (HuNaReS), Vadvirág str. 5, Hungary, 8448, Ajka
| | - Erika Mátics
- Doctoral School of Biology and Sportbiology, University of Pécs, Ifjúság Rd. 6, Hungary, 7624, Pécs
- Hungarian Nature Research Society (HuNaReS), Vadvirág str. 5, Hungary, 8448, Ajka
| | - Róbert Mátics
- Hungarian Nature Research Society (HuNaReS), Vadvirág str. 5, Hungary, 8448, Ajka
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Cairns KM, Crowther MS, Nesbitt B, Letnic M. The myth of wild dogs in Australia: are there any out there? AUSTRALIAN MAMMALOGY 2022. [DOI: 10.1071/am20055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Hybridisation between wild and domestic canids is a global conservation and management issue. In Australia, dingoes are a distinct lineage of wild-living canid with a controversial domestication status. They are mainland Australia’s apex terrestrial predator. There is ongoing concern that the identity of dingoes has been threatened from breeding with domestic dogs, and that feral dogs have established populations in rural Australia. We collate the results of microsatellite DNA testing from 5039 wild canids to explore patterns of domestic dog ancestry in dingoes and observations of feral domestic dogs across the continent. Only 31 feral dogs were detected, challenging the perception that feral dogs are widespread in Australia. First generation dingo × dog hybrids were similarly rare, with only 27 individuals identified. Spatial patterns of genetic ancestry across Australia identified that dingo populations in northern, western and central Australia were largely free from domestic dog introgression. Our findings challenge the perception that dingoes are virtually extinct in the wild and that feral dogs are common. A shift in terminology from wild dog to dingo would better reflect the identity of these wild canids and allow more nuanced debate about the balance between conservation and management of dingoes in Australia.
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Cowles SA, Uy JAC. Rapid, complete reproductive isolation in two closely related
Zosterops
White‐eye bird species despite broadly overlapping ranges*. Evolution 2019; 73:1647-1662. [DOI: 10.1111/evo.13797] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 06/06/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Sarah A. Cowles
- Department of BiologyUniversity of Miami Coral Gables Florida 33146
| | - J. Albert C. Uy
- Department of BiologyUniversity of Miami Coral Gables Florida 33146
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Reifová R, Majerová V, Reif J, Ahola M, Lindholm A, Procházka P. Patterns of gene flow and selection across multiple species of Acrocephalus warblers: footprints of parallel selection on the Z chromosome. BMC Evol Biol 2016; 16:130. [PMID: 27311647 PMCID: PMC4910229 DOI: 10.1186/s12862-016-0692-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/25/2016] [Indexed: 01/11/2023] Open
Abstract
Background Understanding the mechanisms and selective forces leading to adaptive radiations and origin of biodiversity is a major goal of evolutionary biology. Acrocephalus warblers are small passerines that underwent an adaptive radiation in the last approximately 10 million years that gave rise to 37 extant species, many of which still hybridize in nature. Acrocephalus warblers have served as model organisms for a wide variety of ecological and behavioral studies, yet our knowledge of mechanisms and selective forces driving their radiation is limited. Here we studied patterns of interspecific gene flow and selection across three European Acrocephalus warblers to get a first insight into mechanisms of radiation of this avian group. Results We analyzed nucleotide variation at eight nuclear loci in three hybridizing Acrocephalus species with overlapping breeding ranges in Europe. Using an isolation-with-migration model for multiple populations, we found evidence for unidirectional gene flow from A. scirpaceus to A. palustris and from A. palustris to A. dumetorum. Gene flow was higher between genetically more closely related A. scirpaceus and A. palustris than between ecologically more similar A. palustris and A. dumetorum, suggesting that gradual accumulation of intrinsic barriers rather than divergent ecological selection are more efficient in restricting interspecific gene flow in Acrocephalus warblers. Although levels of genetic differentiation between different species pairs were in general not correlated, we found signatures of apparently independent instances of positive selection at the same two Z-linked loci in multiple species. Conclusions Our study brings the first evidence that gene flow occurred during Acrocephalus radiation and not only between sister species. Interspecific gene flow could thus be an important source of genetic variation in individual Acrocephalus species and could have accelerated adaptive evolution and speciation rate in this avian group by creating novel genetic combinations and new phenotypes. Independent instances of positive selection at the same loci in multiple species indicate an interesting possibility that the same loci might have contributed to reproductive isolation in several speciation events. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0692-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Radka Reifová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.
| | - Veronika Majerová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Prague, Czech Republic.,Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Markus Ahola
- Department of Biology, Section of Ecology, FI-20014 University of Turku, Turku, Finland.,Natural Resources Institute Finland, Itäinen Pitkäkatu 3, FI-20240, Turku, Finland
| | | | - Petr Procházka
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Ren G, Conti E, Salamin N. Phylogeny and biogeography of Primula sect. Armerina: implications for plant evolution under climate change and the uplift of the Qinghai-Tibet Plateau. BMC Evol Biol 2015; 15:161. [PMID: 26275399 PMCID: PMC4537560 DOI: 10.1186/s12862-015-0445-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The historical orogenesis and associated climatic changes of mountain areas have been suggested to partly account for the occurrence of high levels of biodiversity and endemism. However, their effects on dispersal, differentiation and evolution of many groups of plants are still unknown. In this study, we examined the detailed diversification history of Primula sect. Armerina, and used biogeographic analysis and macro-evolutionary modeling to investigate a series of different questions concerning the evolution of the geographical and ecological distribution of the species in this section. RESULTS We sequenced five chloroplast and one nuclear genes for species of Primula sect. Armerina. Neither chloroplast nor nuclear trees support the monophyly of the section. The major incongruences between the two trees occur among closely related species and may be explained by hybridization. Our dating analyses based on the chloroplast dataset suggest that this section began to diverge from its relatives around 3.55 million years ago, largely coinciding with the last major uplift of the Qinghai-Tibet Plateau (QTP). Biogeographic analysis supports the origin of the section in the Himalayan Mountains and dispersal from the Himalayas to Northeastern QTP, Western QTP and Hengduan Mountains. Furthermore, evolutionary models of ecological niches show that the two P. fasciculata clades have significantly different climatic niche optima and rates of niche evolution, indicating niche evolution under climatic changes and further providing evidence for explaining their biogeographic patterns. CONCLUSION Our results support the hypothesis that geologic and climatic events play important roles in driving biological diversification of organisms in the QTP area. The Pliocene uplift of the QTP and following climatic changes most likely promoted both the inter- and intraspecific divergence of Primula sect. Armerina. This study also illustrates how niche evolution under climatic changes influences biogeographic patterns.
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Affiliation(s)
- Guangpeng Ren
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland.
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, , Gansu, China.
| | - Elena Conti
- Institute for Systematic Botany, University of Zurich, Zollikerstrasse 107, 8008, ZURICH, Switzerland.
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland.
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Butler IA, Siletti K, Oxley PR, Kronauer DJC. Conserved microsatellites in ants enable population genetic and colony pedigree studies across a wide range of species. PLoS One 2014; 9:e107334. [PMID: 25244681 PMCID: PMC4170976 DOI: 10.1371/journal.pone.0107334] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/15/2014] [Indexed: 01/05/2023] Open
Abstract
Broadly applicable polymorphic genetic markers are essential tools for population genetics, and different types of markers have been developed for this purpose. Microsatellites have been employed as particularly polymorphic markers for over 20 years. However, PCR primers for microsatellite loci are often not useful outside the species for which they were designed. This implies that a new set of loci has to be identified and primers developed for every new study species. To overcome this constraint, we identified 45 conserved microsatellite loci based on the eight currently available ant genomes and designed primers for PCR amplification. Among these loci, we chose 24 for in-depth study in six species covering six different ant subfamilies. On average, 11.16 of these 24 loci were polymorphic and in Hardy-Weinberg equilibrium in any given species. The average number of alleles for these polymorphic loci within single populations of the different species was 4.59. This set of genetic markers will thus be useful for population genetic and colony pedigree studies across a wide range of ant species, supplementing the markers available for previously studied species and greatly facilitating the study of the many ant species lacking genetic markers. Our study shows that it is possible to develop microsatellite loci that are both conserved over a broad range of taxa, yet polymorphic within species. This should encourage researchers to develop similar tools for other large taxonomic groups.
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Affiliation(s)
- Ian A. Butler
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, New York, United States of America
- * E-mail:
| | - Kimberly Siletti
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, New York, United States of America
| | - Peter R. Oxley
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, New York, United States of America
| | - Daniel J. C. Kronauer
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, New York, United States of America
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Evidence of Hybridization between Common Gartersnakes (Thamnophis sirtalis) and Butler's Gartersnakes (Thamnophis butleri) in Wisconsin, USA. J HERPETOL 2013. [DOI: 10.1670/12-057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Dawson DA, Ball AD, Spurgin LG, Martín-Gálvez D, Stewart IRK, Horsburgh GJ, Potter J, Molina-Morales M, Bicknell AWJ, Preston SAJ, Ekblom R, Slate J, Burke T. High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species. BMC Genomics 2013; 14:176. [PMID: 23497230 PMCID: PMC3738869 DOI: 10.1186/1471-2164-14-176] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 02/19/2013] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient "off-the-shelf" markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility. RESULTS We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species. CONCLUSIONS When combined with previously described conserved loci, this new set of conserved markers will not only reduce the necessity and expense of microsatellite isolation for a wide range of genetic studies, including avian parentage and population analyses, but will also now enable comparisons of genetic diversity among different species (and populations) at the same set of loci, with no or reduced bias. Finally, the approach used here can be applied to other taxa in which appropriate genome sequences are available.
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Affiliation(s)
- Deborah A Dawson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Alexander D Ball
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Lewis G Spurgin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - David Martín-Gálvez
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Estación Experimental de Zonas Áridas (CSIC), Almería, E-04120, Spain
| | - Ian R K Stewart
- Department of Biology, University of Delaware, Newark, DE, 19716, USA
| | - Gavin J Horsburgh
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jonathan Potter
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mercedes Molina-Morales
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Departamento de Zoología, Universidad de Granada, Granada, E-18071, Spain
| | - Anthony W J Bicknell
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Plymouth University, Marine Biology and Ecology Research Centre, Davy Building, Drake Circus, Plymouth, PL4 8AA, UK
| | - Stephanie A J Preston
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert Ekblom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Department of Ecology and Genetics, Uppsala University, Norbyv. 18D, Uppsala, SE-75236, Sweden
| | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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