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Kaya S, Kabasakal B, Erdoğan A. Geographic Genetic Structure of Alectoris chukar in Türkiye: Post-LGM-Induced Hybridization and Human-Mediated Contaminations. BIOLOGY 2023; 12:biology12030401. [PMID: 36979093 PMCID: PMC10045126 DOI: 10.3390/biology12030401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/19/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Türkiye is considered an important evolutionary area for Chukar partridge (Alectoris chukar), since it is both a potential ancestral area and a diversification center for the species. Using 2 mitochondrial (Cty-b and D-loop) and 13 polymorphic microsatellite markers, we investigated the geographic genetic structure of A. chukar populations to determine how past climatic fluctuations and human activities have shaped the gene pool of this species in Türkiye. Our results indicate, firstly, that only A. chukar of the genus Alectoris is present in Türkiye (Anatolia and Thrace), with no natural or artificial gene flow from congenerics. Secondly, the geographic genetic structure of the species in Türkiye has been shaped by topographic heterogeneity, Pleistocene climatic fluctuations, and artificial transport by humans. Third, there appears to be three genetic clusters: Thracian, Eastern, and Western. Fourth, the post-LGM demographic expansion of the Eastern and Western populations has formed a hybrid zone in Central Anatolia (~8 kyBP). Fifth, the rate of China clade-B contamination in Türkiye is about 8% in mtDNA and about 12% in nuDNA, with the Southeastern Anatolian population having the highest contamination. Sixth, the Thracian population was the most genetically distinct, with the lowest genetic diversity and highest level of inbreeding and no China clad-B contamination. These results can contribute to the conservation regarding A. chukar populations, especially the Thracian population.
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Affiliation(s)
- Sarp Kaya
- First and Emergency Aid Programme, Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur 15030, Turkey
| | - Bekir Kabasakal
- Department of Biology, Akdeniz University, Antalya 07058, Turkey
- Anesthesia Programme, Department of Medical Services and Techniques, Vocational School of Health Services, Antalya Bilim University, Antalya 07190, Turkey
- Correspondence:
| | - Ali Erdoğan
- Department of Biology, Akdeniz University, Antalya 07058, Turkey
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Uvizl M, Benda P. Intraspecific Variation of Myotis emarginatus (Chiroptera: Vespertilionidae) Inferred from Mitochondrial and Nuclear Genetic Markers. ACTA CHIROPTEROLOGICA 2022. [DOI: 10.3161/15081109acc2021.23.2.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Marek Uvizl
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44 Praha 2, Czech Republic
| | - Petr Benda
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44 Praha 2, Czech Republic
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Vine C, Teeling EC, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan J, Quail MA, McCarthy SA, Howe K, Torrance J, Wood J, Pelan S, Sims Y, Challis R, Threlfall J, Mead D, Blaxter M. The genome sequence of the common pipistrelle, Pipistrellus pipistrellus Schreber 1774. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16895.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present a genome assembly from an individual female Pipistrellus pipistrellus (the common pipistrelle; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence is 1.76 gigabases in span. The majority of the assembly is scaffolded into 21 chromosomal pseudomolecules, with the X sex chromosome assembled.
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Queirós J, Acevedo P, Santos JPV, Barasona J, Beltran-Beck B, González-Barrio D, Armenteros JA, Diez-Delgado I, Boadella M, Fernandéz de Mera I, Ruiz-Fons JF, Vicente J, de la Fuente J, Gortázar C, Searle JB, Alves PC. Red deer in Iberia: Molecular ecological studies in a southern refugium and inferences on European postglacial colonization history. PLoS One 2019; 14:e0210282. [PMID: 30620758 PMCID: PMC6324796 DOI: 10.1371/journal.pone.0210282] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/19/2018] [Indexed: 01/31/2023] Open
Abstract
The red deer (Cervus elaphus) is a widespread wild ungulate in Europe that has suffered strong anthropogenic impacts over their distribution during the last centuries, but also at the present time, due its economic importance as a game species. Here we focus on the evolutionary history of the red deer in Iberia, one of the three main southern refugial areas for temperate species in Europe, and addressed the hypothesis of a cryptic refugia at higher latitudes during the Last Glacial Maximum (LGM). A total of 911 individuals were sampled, genotyped for 34 microsatellites specifically developed for red deer and sequenced for a fragment of 670 bp of the mitochondrial (mtDNA) D-loop. The results were combined with published mtDNA sequences, and integrated with species distribution models and historical European paleo-distribution data, in order to further examine the alternative glacial refugial models and the influence of cryptic refugia on European postglacial colonization history. Clear genetic differentiation between Iberian and European contemporary populations was observed at nuclear and mtDNA levels, despite the mtDNA haplotypes central to the phylogenetic network are present across western Europe (including Iberia) suggesting a panmictic population in the past. Species distribution models, fossil records and genetic data support a timing of divergence between Iberian and European populations that overlap with the LGM. A notable population structure was also found within the Iberian Peninsula, although several populations displayed high levels of admixture as a consequence of recent red deer translocations. Five D-loop sub-lineages were found in Iberia that belong to the Western European mtDNA lineage, while there were four main clusters based on analysis of nuclear markers. Regarding glacial refugial models, our findings provide detailed support for the hypothesis that red deer may have persisted in cryptic northern refugia in western Europe during the LGM, most likely in southern France, southern Ireland, or in a region between them (continental shelf), and these regions were the source of individuals during the European re-colonization. This evidence heightens the importance of conserving the high mitochondrial and nuclear diversity currently observed in Iberian populations.
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Affiliation(s)
- João Queirós
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- * E-mail:
| | - Pelayo Acevedo
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - João P. V. Santos
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- Departamento de Biologia & CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Jose Barasona
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Beatriz Beltran-Beck
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - David González-Barrio
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose A. Armenteros
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Iratxe Diez-Delgado
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Mariana Boadella
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- SABIOtec. Ed. Polivalente UCLM, Ciudad Real, Spain
| | - Isabel Fernandéz de Mera
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose F. Ruiz-Fons
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Joaquin Vicente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose de la Fuente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States of America
| | - Christian Gortázar
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jeremy B. Searle
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Paulo C. Alves
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- Wildlife Biology Program, University of Montana, Missoula, MT, United States of America
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Najafi N, Akmali V, Sharifi M. Historical explanation of genetic variation in the Mediterranean horseshoe bat Rhinolophus euryale (Chiroptera: Rhinolophidae) inferred from mitochondrial cytochrome-b and D-loop genes in Iran. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:135-147. [PMID: 29697024 DOI: 10.1080/24701394.2018.1463375] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Molecular phylogeography and species distribution modelling (SDM) suggest that late Quaternary glacial cycles have portrayed a significant role in structuring current population genetic structure and diversity. Based on phylogenetic relationships using Bayesian inference and maximum likelihood of 535 bp mtDNA (D-loop) and 745 bp mtDNA (Cytb) in 62 individuals of the Mediterranean Horseshoe Bat, Rhinolophus euryale, from 13 different localities in Iran we identified two subspecific populations with differing population genetic structure distributed in southern Zagros Mts. and northern Elburz Mts. Analysis of molecular variance (AMOVA) obtained from D-loop sequences indicates that 21.18% of sequence variation is distributed among populations and 10.84% within them. Moreover, a degree of genetic subdivision, mainly attributable to the existence of significant variance among the two regions is shown (θCT = 0.68, p = .005). The positive and significant correlation between geographic and genetic distances (R2 = 0.28, r = 0.529, p = .000) is obtained following controlling for environmental distance. Spatial distribution of haplotypes indicates that marginal population of the species in southern part of the species range have occupied this section as a glacial refugia. However, this genetic variation, in conjunction with results of the SDM shows a massive postglacial range expansion for R. euryale towards higher latitudes in Iran.
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Affiliation(s)
- Nargess Najafi
- a Department of Biology, Faculty of Science , Razi University , Kermanshah , Iran
| | - Vahid Akmali
- a Department of Biology, Faculty of Science , Razi University , Kermanshah , Iran
| | - Mozafar Sharifi
- a Department of Biology, Faculty of Science , Razi University , Kermanshah , Iran
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Kindler C, Graciá E, Fritz U. Extra-Mediterranean glacial refuges in barred and common grass snakes (Natrix helvetica, N. natrix). Sci Rep 2018; 8:1821. [PMID: 29379101 PMCID: PMC5788984 DOI: 10.1038/s41598-018-20218-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/16/2018] [Indexed: 11/30/2022] Open
Abstract
Extra-Mediterranean glacial refugia of thermophilic biota, in particular in northern latitudes, are controversial. In the present study we provide genetic evidence for extra-Mediterranean refugia in two species of grass snake. The refuge of a widely distributed western European lineage of the barred grass snake (Natrix helvetica) was most likely located in southern France, outside the classical refuges in the southern European peninsulas. One genetic lineage of the common grass snake (N. natrix), distributed in Scandinavia, Central Europe and the Balkan Peninsula, had two distinct glacial refuges. We show that one was located in the southern Balkan Peninsula. However, Central Europe and Scandinavia were not colonized from there, but from a second refuge in Central Europe. This refuge was located in between the northern ice sheet and the Alpine glaciers of the last glaciation and most likely in a permafrost region. Another co-distributed genetic lineage of N. natrix, now massively hybridizing with the aforementioned lineage, survived the last glaciation in a structured refuge in the southern Balkan Peninsula, according to the idea of 'refugia-within-refugia'. It reached Central Europe only very recently. This study reports for the first time the glacial survival of a thermophilic egg-laying reptile species in Central Europe.
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Affiliation(s)
- Carolin Kindler
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | - Eva Graciá
- Ecology Area, Department of Applied Biology, Miguel Hernández University, Av. de la Universidad, Torreblanca, 03202, Elche, Spain
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany.
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Nusová G, šemeláková M, paučulovÁ L, Uhrin M, Kañuch P. Haplotype diversity in common pipistrelle’s mass hibernacula from central Europe. Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Dool SE, Puechmaille SJ, Foley NM, Allegrini B, Bastian A, Mutumi GL, Maluleke TG, Odendaal LJ, Teeling EC, Jacobs DS. Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera). Mol Phylogenet Evol 2016; 97:196-212. [PMID: 26826601 DOI: 10.1016/j.ympev.2016.01.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 01/22/2023]
Abstract
Despite many studies illustrating the perils of utilising mitochondrial DNA in phylogenetic studies, it remains one of the most widely used genetic markers for this purpose. Over the last decade, nuclear introns have been proposed as alternative markers for phylogenetic reconstruction. However, the resolution capabilities of mtDNA and nuclear introns have rarely been quantified and compared. In the current study we generated a novel ∼5kb dataset comprising six nuclear introns and a mtDNA fragment. We assessed the relative resolution capabilities of the six intronic fragments with respect to each other, when used in various combinations together, and when compared to the traditionally used mtDNA. We focused on a major clade in the horseshoe bat family (Afro-Palaearctic clade; Rhinolophidae) as our case study. This old, widely distributed and speciose group contains a high level of conserved morphology. This morphological stasis renders the reconstruction of the phylogeny of this group with traditional morphological characters complex. We sampled multiple individuals per species to represent their geographic distributions as best as possible (122 individuals, 24 species, 68 localities). We reconstructed the species phylogeny using several complementary methods (partitioned Maximum Likelihood and Bayesian and Bayesian multispecies-coalescent) and made inferences based on consensus across these methods. We computed pairwise comparisons based on Robinson-Foulds tree distance metric between all Bayesian topologies generated (27,000) for every gene(s) and visualised the tree space using multidimensional scaling (MDS) plots. Using our supported species phylogeny we estimated the ancestral state of key traits of interest within this group, e.g. echolocation peak frequency which has been implicated in speciation. Our results revealed many potential cryptic species within this group, even in taxa where this was not suspected a priori and also found evidence for mtDNA introgression. We demonstrated that by using just two introns one can recover a better supported species tree than when using the mtDNA alone, despite the shorter overall length of the combined introns. Additionally, when combining any single intron with mtDNA, we showed that the result is highly similar to the mtDNA gene tree and far from the true species tree and therefore this approach should be avoided. We caution against the indiscriminate use of mtDNA in phylogenetic studies and advocate for pilot studies to select nuclear introns. The selection of marker type and number is a crucial step that is best based on critical examination of preliminary or previously published data. Based on our findings and previous publications, we recommend the following markers to recover phylogenetic relationships between recently diverged taxa (<20 My) in bats and other mammals: ACOX2, COPS7A, BGN, ROGDI and STAT5A.
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Affiliation(s)
- Serena E Dool
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa; Zoological Institute and Museum, University of Greifswald, Soldmann-Straße 14, D-17487 Greifswald, Germany.
| | - Sebastien J Puechmaille
- Zoological Institute and Museum, University of Greifswald, Soldmann-Straße 14, D-17487 Greifswald, Germany; Midi-Pyrénées bat group (CREN-GCMP), Toulouse, France; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Nicole M Foley
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - Anna Bastian
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Gregory L Mutumi
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Tinyiko G Maluleke
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Lizelle J Odendaal
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - David S Jacobs
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
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Andriollo T, Naciri Y, Ruedi M. Two Mitochondrial Barcodes for one Biological Species: The Case of European Kuhl's Pipistrelles (Chiroptera). PLoS One 2015; 10:e0134881. [PMID: 26241944 PMCID: PMC4524706 DOI: 10.1371/journal.pone.0134881] [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: 04/16/2015] [Accepted: 07/14/2015] [Indexed: 11/18/2022] Open
Abstract
The Kuhl's pipistrelle (Pipistrellus kuhlii) is a Western Palaearctic species of bat that exhibits several deeply divergent mitochondrial lineages across its range. These lineages could represent cryptic species or merely ancient polymorphism, but no nuclear markers have been studied so far to properly assess the taxonomic status of these lineages. We examined here two lineages occurring in Western Europe, and used both mitochondrial and nuclear markers to measure degrees of genetic isolation between bats carrying them. The sampling focused on an area of strict lineage sympatry in Switzerland but also included bats from further south, in North Africa. All individuals were barcoded for the COI gene to identify their mitochondrial lineages and five highly polymorphic microsatellite loci were used to cluster them according to their nuclear genotypes. Despite this low number of nuclear markers, all North African nuclear genotypes were grouped in a highly distinct subpopulation when compared with European samples sharing the same mitochondrial barcodes. The reverse situation prevailed in Switzerland where bats carrying distinct barcodes had similar nuclear genotypes. There was a weak east/west nuclear structure of populations, but this was independent of mitochondrial lineages as bats carrying either variant were completely admixed. Thus, the divergent mitochondrial barcodes present in Western Europe do not represent cryptic species, but are part of a single biological species. We argue that these distinct barcodes evolved in allopatry and came recently into secondary contact in an area of admixture north of the Alps. Historical records from this area and molecular dating support such a recent bipolar spatial expansion. These results also highlight the need for using appropriate markers before claiming the existence of cryptic species based on highly divergent barcodes.
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Affiliation(s)
- Tommy Andriollo
- Muséum d’histoire naturelle de la Ville de Genève, BP 6434, 1211 Geneva 6, Switzerland
- Université de Genève, Faculté des Sciences, Section de biologie, 1211 Geneva 4, Switzerland
- * E-mail:
| | - Yamama Naciri
- Université de Genève, Faculté des Sciences, Section de biologie, 1211 Geneva 4, Switzerland
- Conservatoire et Jardin botaniques de la Ville de Genève and University of Geneva, BP 60, 1292 Chambésy, Geneva, Switzerland
| | - Manuel Ruedi
- Muséum d’histoire naturelle de la Ville de Genève, BP 6434, 1211 Geneva 6, Switzerland
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