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Marabuto E, Nunes MS, Martins R, Mendes R, Moreira-Pinhal TC, Raimundo J, Seabra SG, Paulo OS. Integrative analysis reveals the divergence and speciation between sister Sooty Copper butterflies Lycaena bleusei and L. tityrus. Mol Phylogenet Evol 2023; 180:107699. [PMID: 36621583 DOI: 10.1016/j.ympev.2022.107699] [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: 06/10/2020] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/07/2023]
Abstract
The comparison of closely related taxa is cornerstone in biology, as understanding mechanisms leading up to differentiation in relation to extant shared characters are powerful tools in interpreting the evolutionary process. Hotspots of biodiversity such as the west-Mediterranean, where many lineages meet are ideal grounds to study these processes. We set to explore the interesting example of Sooty Copper butterflies: widespread Eurasian Lycaena tityrus (Poda, 1761) comes into contact in Iberia with closely related and local endemic, L. bleusei (Oberthür, 1884), which hasn't always been considered a distinct species. An integrative analysis was designed, combining the use of extensive molecular data (five genes), geometric morphometrics analyses, verified and up-to-date distribution data, and environmental niche modelling, aimed at deciphering their true relationship, their placement within European Lycaena and trace their evolutionary history. We revealed several levels of differentiation: L. bleusei and L. tityrus appear to be reciprocally monophyletic independent gene-pools, distinct in all genes analysed, having mutually diverged 4.8 Ma ago. L. tityrus but not L. bleusei, further displays a genetic structure compatible with several glacial refugia, where populations assignable to infraspecific taxa surface. Conversely, L. bleusei shows a loss in mtDNA diversity in relation to nuDNA. Morphological analyses differentiate both species according to size and shape but also discriminate strong seasonal and sexual traits and a geographical phenotype segregation in L. tityrus. Finally, updated distribution and its modelling for current and glacial timeframes reveal both species respond differently to environmental variables, defining a mostly parapatric distribution and an overlapping belt where sympatry was recovered. During the last glacial maximum, a wider expansion in L. bleusei distribution explains current isolated populations. Our study highlights the importance of gathering several lines of evidence when deciphering the relationships between closely related populations in the fringe of cryptic species realm.
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Affiliation(s)
- Eduardo Marabuto
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Current affiliation: Leibniz Institute fir the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn & Senckenberg Natural History Collections, Dresden, Germany.
| | - Miguel S Nunes
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Renata Martins
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Current affiliation: Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Golm, 14476 Potsdam, Germany
| | - Raquel Mendes
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Tatiana C Moreira-Pinhal
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Associação BioLiving, Rua do Outeiro, 3850-635 Frossos, Albergaria-a-Velha, Portugal
| | - João Raimundo
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Sofia G Seabra
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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2
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Humeau L, Le Corre M, Reynolds SJ, Wearn C, Hennicke JC, Russell JC, Gomard Y, Magalon H, Pinet P, Gélin P, Couzi F, Bemanaja E, Tatayah V, Ousseni B, Rocamora G, Talbot P, Shah N, Bugoni L, Da Silva D, Jaeger A. Genetic structuring among colonies of a pantropical seabird: Implication for subspecies validation and conservation. Ecol Evol 2020; 10:11886-11905. [PMID: 33209258 PMCID: PMC7663974 DOI: 10.1002/ece3.6635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 01/17/2023] Open
Abstract
Investigations of the genetic structure of populations over the entire range of a species yield valuable information about connectivity among populations. Seabirds are an intriguing taxon in this regard because they move extensively when not breeding, facilitating intermixing of populations, but breed consistently on the same isolated islands, restricting gene flow among populations. The degree of genetic structuring of populations varies extensively among seabird species but they have been understudied in their tropical ranges. Here, we address this across a broad spatial scale by using microsatellite and mitochondrial data to explore the population connectivity of 13 breeding populations representing the six subspecies of the white-tailed tropicbird (Phaethon lepturus) in the Atlantic, Indian, and Pacific Oceans. Our primary aim was to identify appropriate conservation units for this little known species. Three morphometric characters were also examined in the subspecies. We found a clear pattern of population structuring with four genetic groups. The most ancient and the most isolated group was in the northwestern Atlantic Ocean. The South Atlantic populations and South Mozambique Channel population on Europa were genetically isolated and may have had a common ancestor. Birds from the Indo-Pacific region showed unclear and weak genetic differentiation. This structuring was most well defined from nuclear and mtDNA markers but was less well resolved by morphological data. The validity of classifying white-tailed tropicbirds into six distinct subspecies is discussed in light of our new findings. From a conservation standpoint our results highlight that the three most threatened conservation units for this species are the two subspecies of the tropical North and South Atlantic Oceans and that of Europa Island in the Indian Ocean.
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Affiliation(s)
- Laurence Humeau
- UMR PVBMTUniversité de La RéunionCIRADSaint‐Denis Cedex 9La RéunionFrance
| | - Matthieu Le Corre
- UMR ENTROPIEUniversité de La RéunionIRDCNRSSaint‐Denis Cedex 9La RéunionFrance
| | - Silas James Reynolds
- Centre for OrnithologySchool of BiosciencesCollege of Life & Environmental SciencesUniversity of BirminghamBirminghamUK
- Army Ornithological Society (AOS)c/o Prince Consort LibraryAldershotHampshireUK
| | - Colin Wearn
- Royal Air Force Ornithological Society (RAFOS)Royal Air Force HeadquartersBuckinghamshireUK
| | - Janos C. Hennicke
- Department of Ecology and ConservationBiocentre GrindelUniversity of HamburgHamburgGermany
- Centre d'Etudes Biologiques de ChizéCEBC‐CNRSVilliers‐en‐BoisFrance
| | - James C. Russell
- UMR ENTROPIEUniversité de La RéunionIRDCNRSSaint‐Denis Cedex 9La RéunionFrance
- School of Biological Sciences and Department of StatisticsUniversity of AucklandAucklandNew Zealand
| | - Yann Gomard
- UMR PIMITCNRSINSERMIRDUniversité de La RéunionPlateforme Technologique CYROISainte‐ClotildeLa RéunionFrance
| | - Hélène Magalon
- UMR ENTROPIEUniversité de La RéunionIRDCNRSSaint‐Denis Cedex 9La RéunionFrance
| | - Patrick Pinet
- UMR ENTROPIEUniversité de La RéunionIRDCNRSSaint‐Denis Cedex 9La RéunionFrance
- Parc National de La RéunionLa Plaine des PalmistesLa RéunionFrance
| | - Pauline Gélin
- UMR ENTROPIEUniversité de La RéunionIRDCNRSSaint‐Denis Cedex 9La RéunionFrance
| | | | - Etienne Bemanaja
- Centre National de Recherches Océanographiques (CNRO)Nosy BeMadagascar
| | | | | | - Gérard Rocamora
- Island Conservation SocietyMahéSeychelles
- Island Biodiversity and Conservation centreUniversity of SeychellesMahéSeychelles
| | | | - Nirmal Shah
- Nature SeychellesThe Center for Environment and EducationMahéSeychelles
| | - Leandro Bugoni
- Instituto de Ciências BiológicasUniversidade Federal do Rio Grande (FURG)Rio GrandeBrazil
| | - Denis Da Silva
- UMR PVBMTUniversité de La RéunionCIRADSaint‐Denis Cedex 9La RéunionFrance
| | - Audrey Jaeger
- UMR ENTROPIEUniversité de La RéunionIRDCNRSSaint‐Denis Cedex 9La RéunionFrance
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Yao L, Witt K, Li H, Rice J, Salinas NR, Martin RD, Huerta-Sánchez E, Malhi RS. Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:21-33. [PMID: 32643146 PMCID: PMC8329942 DOI: 10.1002/ajpa.24099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVES Long-tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long-tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long-tailed macaques using low-coverage nuclear DNA (nDNA) data from museum specimens. METHODS We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long-tailed macaque museum specimens from localities throughout Southeast Asia. RESULTS We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades within M. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island-living individuals, including those from southern Sumatra. CONCLUSIONS Overall, we demonstrate that low-coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.
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Affiliation(s)
- Lu Yao
- American Museum of Natural History, New York, New York, USA
| | - Kelsey Witt
- Brown University, Providence, Rhode Island, USA
- University of California Merced, Merced, California, USA
| | - Hongjie Li
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan Rice
- University of California Merced, Merced, California, USA
| | - Nelson R Salinas
- American Museum of Natural History, New York, New York, USA
- Instituto de Hidrología, Metereología y Estudios Ambientales IDEAM, Bogotá, Colombia
| | - Robert D Martin
- The Field Museum of Natural History, Chicago, Illinois, USA
- University of Zürich, Zürich, Switzerland
| | | | - Ripan S Malhi
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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Murtskhvaladze M, Tarkhnishvili D, Anderson CL, Kotorashvili A. Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection. PLoS One 2020; 15:e0233680. [PMID: 32511235 PMCID: PMC7279592 DOI: 10.1371/journal.pone.0233680] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 05/11/2020] [Indexed: 11/18/2022] Open
Abstract
We generated a phylogeny for Caucasian rock lizards (Darevskia), and included six other families of true lizards (Lacertini), based on complete mitochondrial genome analysis. Next-generation sequencing (NGS) of genomic DNA was used to obtain 16 new mitogenomes of Darevskia. These, along with 35 sequences downloaded from GenBank: genera Darevskia, Zootoca, Podarcis, Phoenicolacerta, Takydromus, Lacerta, and Eremias-were used in the analysis. All four analytical methods (Bayesian Inference, BI; Maximum Likelihood, ML; Maximum Parsimony, MP; and Neighbor-Joining, NJ) showed almost congruent intra-generic topologies for Darevskia and other lizard genera. However, ML and NJ methods on one side, and BI and MP methods on the other harvested conflicting phylogenies. The ML/NJ topology supports earlier published separation of Darevskia into three mitochondrial clades (Murphy, Fu, Macculloch, Darevsky, and Kupinova, 2000), but BI and MP topologies support that the basal branching occurred between D. parvula from the western Lesser Caucasus and the rest of Darevskia. All topologies altered the phylogenetic position of some individual species, including D. daghestanica, D. derjugini, and D. chlorogaster. Reanalysis after excluding four saturated genes from the data set, and excluding genus Eremias gives fully convergent topologies. The most basal branching for true lizards was between Far Eastern Takydromus and the Western Eurasian genera (BI). Comparing phylogenetic performance of individual genes relative to whole mitogenome data, concatenated 16S RNA (the least saturated gene in our analyses) and Cytochrome b genes generate a robust phylogeny that is fully congruent with that based on the complete mitogenome.
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Affiliation(s)
- Marine Murtskhvaladze
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
- L. Sakvarelidze National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - David Tarkhnishvili
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
| | - Cort L. Anderson
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
| | - Adam Kotorashvili
- L. Sakvarelidze National Center for Disease Control and Public Health, Tbilisi, Georgia
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Kim JS, Park J, Fong JJ, Zhang YP, Li SR, Ota H, Min SH, Min MS, Park D. Genetic diversity and inferred dispersal history of the Schlegel's Japanese Gecko ( Gekko japonicus) in Northeast Asia based on population genetic analyses and paleo-species distribution modelling. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:120-130. [PMID: 32212876 DOI: 10.1080/24701394.2020.1742332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
To understand the genetic diversity and dispersal history of Schlegel's Japanese gecko (Gekko japonicus), we performed genetic analyses and paleo-species distributional modelling. For the genetic analysis, we analyzed mitochondrial DNA (mtDNA) (cytochrome b [Cytb] and NADH dehydrogenase 2 [ND2]) and seven microsatellite loci of 353 individuals from 11 populations (2 east coast China, 4 west and central coast Japan and 5 Korea). For the paleo-species distribution modelling, we used 432 occurrence data points (125 China, 291 Japan and 16 Korea) over the Pleistocene and Holocene. China is inferred to be the source population, which had higher genetic diversity (mtDNA) and more private alleles (mtDNA) compared to Japanese and Korean populations. Differences between the three counties were very small in the mtDNA haplotype network despite some genetic structure among the three countries. Microsatellite analysis inferred that genetic exchange has actively occurred among the Chinese, Japanese and Korean populations. Suitable habitats in Japan should have been plentiful by the mid-Holocene, but have only recently become available in Korea. These results suggest that dispersal of G. japonicus occurred after the Holocene warming from the east coast of China to the west and central coasts of Japan and Korea, and gene flow is actively occurring among the three countries.
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Affiliation(s)
- Jong-Sun Kim
- Division of Science Education, Kangwon National University, Chuncheon, Republic of Korea
| | - Jaejin Park
- Division of Science Education, Kangwon National University, Chuncheon, Republic of Korea
| | | | - Yong-Pu Zhang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, PR China
| | - Shu-Ran Li
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, PR China
| | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences, University of Hyogo, Sanda, Japan
| | - Sung-Hun Min
- Division of Science Education, Kangwon National University, Chuncheon, Republic of Korea
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Daesik Park
- Division of Science Education, Kangwon National University, Chuncheon, Republic of Korea
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Vörös J, Ursenbacher S, Jelić D. Population Genetic Analyses Using 10 New Polymorphic Microsatellite Loci Confirms Genetic Subdivision within the Olm, Proteus anguinus. J Hered 2019; 110:211-218. [PMID: 30576453 DOI: 10.1093/jhered/esy067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 12/19/2018] [Indexed: 11/13/2022] Open
Abstract
We provide a comparative population genetic study of the elusive amphibian, Proteus anguinus, by comparing the genetic diversity and divergence among 4 cave populations (96 individuals) sampled in the Dinaric Karst of Croatia. We developed 10 variable microsatellite markers using pyrosequencing and applied them to the 4 selected populations belonging to 4 different cave systems. The results showed strong genetic differentiation between the 4 caves corroborating with previous findings suggesting that Proteus might comprise several unrecognized taxa. Our results confirmed that gene flow should be high within the caves, whereas it is low between hydrographic systems since geological periods. Finally, we conclude that the high genetic subdivision suggests the necessity of treating the 4 studied Proteus populations as evolutionary significant units.
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Affiliation(s)
- Judit Vörös
- Department of Zoology, Hungarian Natural History Museum, Baross u., Hungary.,Laboratory for Molecular Taxonomy, Hungarian Natural History Museum, Ludovika-tér 2-6, Hungary
| | - Sylvain Ursenbacher
- Department of Environmental Science Section of Conservation Biology, University of Basel, Basel, Switzerland.,The info fauna, UniMail-Bâtiment G, Bellevaux, Neuchâtel, Switzerland
| | - Dušan Jelić
- The Croatian Institute for Biodiversity, BIOTA j.d.o.o., Zagreb, Maksimirska cesta, Croatia
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Querejeta M, Castresana J. Evolutionary history of the endemic water shrew Neomys anomalus: Recurrent phylogeographic patterns in semi-aquatic mammals of the Iberian Peninsula. Ecol Evol 2018; 8:10138-10146. [PMID: 30397453 PMCID: PMC6206195 DOI: 10.1002/ece3.4487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/27/2018] [Accepted: 08/08/2018] [Indexed: 11/10/2022] Open
Abstract
The Cabrera's water shrew (Neomys anomalus) is a small semi-aquatic mammal whose taxonomic status was recently elevated from subspecies to species; as a consequence of this change, this species is now endemic to the Iberian Peninsula. In this study, we looked at its evolutionary history by combining phylogeography, the spatial distribution of genetic diversity, and species distribution modeling. To perform these analyses, we used noninvasive samples collected across the species distribution range and sequenced partial mitochondrial cytochrome b and D-loop genes. Maximum-likelihood and Bayesian phylogenetic trees derived from these sequences indicated that N. anomalus is divided into two main phylogroups that correlate strongly with geography, with two contact zones between the groups that showed limited spatial mixing between them. River basins were responsible for only a small percentage of the structure of the genetic diversity of this species despite its riparian habitat. The nucleotide diversity variation map showed the highest genetic diversity to be in the north of the Iberian Peninsula. Finally, species distribution modeling allowed the inference of an optimal area during the Last Interglacial in the north of the Iberian Peninsula, and multiple glacial refugia during the Last Glacial Maximum. The phylogeographic pattern of N. anomalus is strikingly similar to that of another semi-aquatic Iberian mammal, the Pyrenean desman (Galemys pyrenaicus), revealing how Pleistocene glaciations could have had equivalent effects on species of similar ecology and distribution. This phylogeographic structure is consistent with N. anomalus having been isolated for long periods in multiple glacial refugia within the Iberian Peninsula, in agreement with the "refugia-within-refugia" hypothesis, and further supporting its status as a distinct species.
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Affiliation(s)
- Marina Querejeta
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- Bavarian State Collection of ZoologyMünchenGermany
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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da Silva M, Noll FB, e Castro ACMC. Phylogeographic analysis reveals high genetic structure with uniform phenotypes in the paper wasp Protonectarina sylveirae (Hymenoptera: Vespidae). PLoS One 2018. [PMID: 29538451 PMCID: PMC5851647 DOI: 10.1371/journal.pone.0194424] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Swarm-founding wasps are endemic and common representatives of neotropical fauna and compose an interesting social tribe of vespids, presenting both complex social characteristics and uncommon traits for a eusocial group, such as the absence of castes with distinct morphology. The paper wasp Protonectarina sylveirae (Saussure) presents a broad distribution from Brazil, Argentina and Paraguay, occurring widespread in the Atlantic rainforest and arboreal Caatinga, being absent in the Amazon region. Given the peculiar distribution among swarm-founding wasps, an integrative approach to reconstruct the evolutionary history of P. sylveirae in a spatial-temporal framework was performed to investigate: the presence of genetic structure and its relationship with the geography, the evolution of distinct morphologic lineages and the possible historical event(s) in Neotropical region, which could explain the observed phylogeographic pattern. Individuals of P. sylveirae were obtained from populations of 16 areas throughout its distribution for DNA extraction and amplification of mitochondrial genes 12S, 16S and COI. Analysis of genetic diversity, construction of haplotype net, analysis of population structure and dating analysis of divergence time were performed. A morphometric analysis was also performed using 8 measures of the body of the adult (workers) to test if there are morphological distinction among populations. Thirty-five haplotypes were identified, most of them exclusively of a group and a high population structure was found. The possibility of genetic divergence because of isolation by distance was rejected. Morphological analysis pointed to a great uniformity in phenotypes, with only a small degree of differentiation between populations of south and the remaining. Divergence time analysis showed a Middle/Late Miocene origin, a period where an extensive marine ingression occurred in South America. Divergence of haplogroups began from the Plio/Pleistocene boundary and the last glacial maximum most likely modeled the current distribution of species, even though it was not the cause of genetic breaks.
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Affiliation(s)
- Marjorie da Silva
- Departamento de Zoologia e Botânica, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista “Júlio de Mesquita Filho”, São José do Rio Preto, São Paulo, Brazil
- * E-mail:
| | - Fernando Barbosa Noll
- Departamento de Zoologia e Botânica, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista “Júlio de Mesquita Filho”, São José do Rio Preto, São Paulo, Brazil
| | - Adriana C. Morales-Corrêa e Castro
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, São Paulo, Brazil
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Abstract
Abstract
Conservation planning of threatened taxa relies upon accurate data on systematics, ecological traits and suitable habitats. The genus Gazella includes taxa with distinct morphologies and ecological traits, but close phylogenetic relationships. The North African Gazella cuvieri and Gazella leptoceros loderi share morphological and physiological characters but the former is darker and found in mountain areas, while the latter is lighter and associated with sand dunes. Here we aim to assess the genetic distinctiveness of these taxa, to characterize their ecological niches and to identify potential occurrence areas, by analysing 327 samples across North-West Africa. Phylogenetic analyses based on mitochondrial (CYTB) and five nuclear gene fragments (KCAS, LAC, SPTBN1, PRKCI and THYR) show that both taxa comprise a single monophyletic group. However, ecological niche-based modelling suggests that populations of these taxa occupy distinct geographic areas and specific environments. Predicted areas of sympatry were restricted, as a consequence of local sharp transitions in climatic traits. The lack of genetic differentiation between these taxa suggests they should be lumped into G. cuvieri, while ecological and morphological differences indicate they correspond to distinct ecotypes. Conservation planning of G. cuvieri should consider the preservation of both mountain and lowland ecotypes to maintain the overall adaptive potential of the species. This integrative approach provides valuable insights in identifying evolutionary units and should be extended to other gazelles.
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10
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Querejeta M, Fernández-González A, Romero R, Castresana J. Postglacial dispersal patterns and mitochondrial genetic structure of the Pyrenean desman ( Galemys pyrenaicus) in the northwestern region of the Iberian Peninsula. Ecol Evol 2017. [PMID: 28649358 PMCID: PMC5478051 DOI: 10.1002/ece3.3034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The genetic structure of small semiaquatic animals may be influenced by dispersal across both rivers and land. The relative importance of these two modes of dispersal may vary across different species and with ecological conditions and evolutionary periods. The Pyrenean desman (Galemys pyrenaicus) is an endemic mammal of the Iberian Peninsula with a strong phylogeographic structure and semiaquatic habits, thus making it an ideal model to study the effects of river and overland dispersal on its genetic structure. Thanks to different types of noninvasive samples, we obtained an extensive sampling of the Pyrenean desman from the northwestern region of the Iberian Peninsula and sequenced two mitochondrial DNA fragments. We then analyzed, using an isolation‐by‐distance approach, the correlation between phylogenetic distances and geographical distances measured along both river networks and land to infer the relative importance of river and overland dispersal. We found that the correlations in the whole area and in a large basin were consistent with an effect of overland dispersal, which may be due to the postglacial colonization of new territories using terrestrial corridors and, possibly, a more extensive fluvial network that may have been present during the Holocene. However, in a small basin, likely to be less influenced by the impact of ancient postglacial dispersal, the correlations suggested significant overall effects of both overland and river dispersal, as expected for a semiaquatic mammal. Therefore, different scales and geographical regions reflect different aspects of the evolutionary history and ecology of this semiaquatic species using this isolation‐by‐distance method. The results we obtained may have crucial implications for the conservation of the Pyrenean desman because they reinforce the importance of interbasin dispersal for this species in the studied area and the need to protect the whole riverine ecosystem, including rivers, upland streams and terrestrial corridors between basins.
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Affiliation(s)
- Marina Querejeta
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra) Barcelona Spain
| | | | - Rafael Romero
- Calle Presidente Salvador Allende 13 Santiago de Compostela Spain
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra) Barcelona Spain
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Gutiérrez-Rodríguez J, Barbosa AM, Martínez-Solano Í. Integrative inference of population history in the Ibero-Maghrebian endemic Pleurodeles waltl (Salamandridae). Mol Phylogenet Evol 2017; 112:122-137. [PMID: 28454930 DOI: 10.1016/j.ympev.2017.04.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 03/01/2017] [Accepted: 04/04/2017] [Indexed: 11/16/2022]
Abstract
Inference of population histories from the molecular signatures of past demographic processes is challenging, but recent methodological advances in species distribution models and their integration in time-calibrated phylogeographic studies allow detailed reconstruction of complex biogeographic scenarios. We apply an integrative approach to infer the evolutionary history of the Iberian ribbed newt (Pleurodeles waltl), an Ibero-Maghrebian endemic with populations north and south of the Strait of Gibraltar. We analyzed an extensive multilocus dataset (mitochondrial and nuclear DNA sequences and ten polymorphic microsatellite loci) and found a deep east-west phylogeographic break in Iberian populations dating back to the Plio-Pleistocene. This break is inferred to result from vicariance associated with the formation of the Guadalquivir river basin. In contrast with previous studies, North African populations showed exclusive mtDNA haplotypes, and formed a monophyletic clade within the Eastern Iberian lineage in the mtDNA genealogy. On the other hand, microsatellites failed to recover Moroccan populations as a differentiated genetic cluster. This is interpreted to result from post-divergence gene flow based on the results of IMA2 and Migrate analyses. Thus, Moroccan populations would have originated after overseas dispersal from the Iberian Peninsula in the Pleistocene, with subsequent gene flow in more recent times, implying at least two trans-marine dispersal events. We modeled the distribution of the species and of each lineage, and projected these models back in time to infer climatically favourable areas during the mid-Holocene, the last glacial maximum (LGM) and the last interglacial (LIG), to reconstruct more recent population dynamics. We found minor differences in climatic favourability across lineages, suggesting intraspecific niche conservatism. Genetic diversity was significantly correlated with the intersection of environmental favourability in the LIG and LGM, indicating that populations of P. waltl are genetically more diverse in regions that have remained environmentally favourable through the last glacial cycle, particularly southern Iberia and northern Morocco. This study provides novel insights into the relative roles of geology and climate on the biogeography of a biodiversity hotspot.
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Affiliation(s)
| | - A Márcia Barbosa
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/InBIO) - Universidade de Évora, 7004-516 Évora, Portugal
| | - Íñigo Martínez-Solano
- Museo Nacional de Ciencias Naturales, CSIC, c/ José Gutiérrez Abascal, 2, 28006 Madrid, Spain; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, s/n, 13071 Ciudad Real, Spain; CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, R. Padre Armando Quintas, 4485-661 Vairão, Portugal; Ecology, Evolution, and Development Group, Department of Wetland Ecology, Doñana Biological Station, CSIC, c/ Américo Vespucio, s/n, 41092 Seville, Spain.
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12
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Ball SE, Bovero S, Sotgiu G, Tessa G, Angelini C, Bielby J, Durrant C, Favelli M, Gazzaniga E, Garner TWJ. Islands within an island: Population genetic structure of the endemic Sardinian newt, Euproctus platycephalus. Ecol Evol 2017; 7:1190-1211. [PMID: 28303189 PMCID: PMC5306002 DOI: 10.1002/ece3.2665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/21/2016] [Indexed: 12/04/2022] Open
Abstract
The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus. Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change. We have demonstrated a clear hierarchy of structure across genetically divergent and spatially distinct subpopulations. Divergence between three main mountain regions dominated genetic partitioning with both markers. Mitochondrial phylogeography revealed a deep division dating to ca. 1 million years ago (Mya), isolating the northern region, and further differentiation between the central and southern regions ca. 0.5 Mya, suggesting an association with Pleistocene severe glacial oscillations. Our findings are consistent with a model of southward range expansion during glacial periods, with postglacial range retraction to montane habitat and subsequent genetic isolation. Microsatellite markers revealed further strong population structure, demonstrating significant divergence within the central region, and partial differentiation within the south. The northern population showed reduced genetic diversity. Discordance between mitochondrial and microsatellite markers at this scale indicated a further complexity of population structure, in keeping with male-biased dispersal and female philopatry. Our study underscores the need to elucidate cryptic population structure in the ecology and conservation strategies for endangered island-restricted amphibians, especially in the context of disease and climate change.
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Affiliation(s)
- Sarah E. Ball
- Institute of ZoologyThe Zoological Society of LondonLondonUK
| | - Stefano Bovero
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Giuseppe Sotgiu
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Giulia Tessa
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
- Dipartimento di Scienze della Vita e Biologia dei SistemiUniversita degli Studi di TorinoTorinoItaly
| | - Claudio Angelini
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Jon Bielby
- Institute of ZoologyThe Zoological Society of LondonLondonUK
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | | | - Marco Favelli
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Enrico Gazzaniga
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
| | - Trenton W. J. Garner
- Institute of ZoologyThe Zoological Society of LondonLondonUK
- Zirichiltaggi S. W. C. Non‐profit Association for Wildlife ConservationSassariItaly
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13
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Juhásová L, Králová-Hromadová I, Bazsalovicsová E, Minárik G, Štefka J, Mikulíček P, Pálková L, Pybus M. Population structure and dispersal routes of an invasive parasite, Fascioloides magna, in North America and Europe. Parasit Vectors 2016; 9:547. [PMID: 27737705 PMCID: PMC5064932 DOI: 10.1186/s13071-016-1811-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/22/2016] [Indexed: 02/04/2023] Open
Abstract
Background Fascioloides magna (Trematoda: Fasciolidae) is an important liver parasite of a wide range of free-living and domestic ruminants; it represents a remarkable species due to its large spatial distribution, invasive character, and potential to colonize new territories. The present study provides patterns of population genetic structure and admixture in F. magna across all enzootic regions in North America and natural foci in Europe, and infers migratory routes of the parasite on both continents. Methods In total, 432 individuals from five North American enzootic regions and three European foci were analysed by 11 microsatellite loci. Genetic data were evaluated by several statistical approaches: (i) the population genetic structure of F. magna was inferred using program STRUCTURE; (ii) the genetic interrelationships between populations were analysed by PRINCIPAL COORDINATES ANALYSIS; and (iii) historical dispersal routes in North America and recent invasion routes in Europe were explored using MIGRATE. Results The analysis of dispersal routes of the parasite in North America revealed west-east and south-north lineages that partially overlapped in the central part of the continent, where different host populations historically met. The exact origin of European populations of F. magna and their potential translocation routes were determined. Flukes from the first European focus, Italy, were related to F. magna from northern Pacific coast, while parasites from the Czech focus originated from south-eastern USA, particularly South Carolina. The Danube floodplain forests (third and still expanding focus) did not display relationship with any North American population; instead the Czech origin of the Danube population was indicated. A serial dilution of genetic diversity along the dispersion route across central and eastern Europe was observed. The results of microsatellite analyses were compared to previously acquired outputs from mitochondrial haplotype data and correlated with past human-directed translocations and natural migration of the final cervid hosts of F. magna. Conclusions The present study revealed a complex picture of the population genetic structure and interrelationships of North American and European populations, global distribution and migratory routes of F. magna and an origin of European foci. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1811-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ludmila Juhásová
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 040 01, Košice, Slovakia
| | - Ivica Králová-Hromadová
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 040 01, Košice, Slovakia.
| | - Eva Bazsalovicsová
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 040 01, Košice, Slovakia
| | - Gabriel Minárik
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 842 15, Bratislava, Slovakia.,Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08, Bratislava, Slovakia.,Geneton Ltd, Ilkovičova 3, 841 04, Bratislava, Slovakia
| | - Jan Štefka
- Biology Centre CAS, Institute of Parasitology and Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Peter Mikulíček
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 842 15, Bratislava, Slovakia
| | - Lenka Pálková
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08, Bratislava, Slovakia
| | - Margo Pybus
- Alberta Fish and Wildlife Division and Department of Biological Sciences, University of Alberta, 6909-116 St, Edmonton, AB, T6H 4P2, Canada
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14
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15
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Pereira RJ, Martínez-Solano I, Buckley D. Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander. Mol Ecol 2016; 25:1551-65. [DOI: 10.1111/mec.13575] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/11/2016] [Accepted: 02/01/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Ricardo J. Pereira
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
| | - Iñigo Martínez-Solano
- Instituto de Investigación en Recursos Cinegéticos (IREC-UCLM-CSIC-JCCM); Ronda de Toledo, s/n 13005 Ciudad Real Spain
- Ecology, Evolution and Development Group; Department of Wetland Ecology; Estación Biológica de Doñana (EBD-CSIC); Avenida Américo Vespucio, s/n 41092 Sevilla Spain
| | - David Buckley
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales MNCN-CSIC; c/José Gutiérrez Abascal 2 28006 Madrid Spain
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16
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Stojak J, Wójcik JM, Ruczyńska I, Searle JB, McDevitt AD. Contrasting and congruent patterns of genetic structuring in two Microtus vole species using museum specimens. MAMMAL RES 2016. [DOI: 10.1007/s13364-015-0260-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Janda M, Matos-Maraví P, Borovanska M, Zima J, Youngerman E, Pierce NE. Phylogeny and population genetic structure of the ant genus Acropyga (Hymenoptera : Formicidae) in Papua New Guinea. INVERTEBR SYST 2016. [DOI: 10.1071/is14050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Spatial isolation and geological history are important factors in the diversification and population differentiation of species. Here we describe distributional patterns of ants in the genus Acropyga across Papua New Guinea (PNG), a highly biodiverse but little-studied region. We estimate phylogenetic relationships among currently recognised species of Acropyga and assess population genetic structure of the widespread species, A. acutiventris, across lowland areas of the island. We find that species of Acropyga present in PNG diversified during the Pliocene, between six and two million years ago. Most species now exhibit a patchy distribution that does not show a strong signal of geological history. However, the population genetic structure of the widespread species A. acutiventris has been influenced by geography, habitat association and, possibly, historical habitat fragmentation. There is a significant effect of isolation-by-distance within continuous lowland forest, and proximity to Australia has had a larger impact in structuring populations of A. acutiventris in PNG than has the Central Papuan Cordillera. This study is the first to describe population genetic patterns of an ant species in Papua New Guinea.
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18
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Phylogeography of the arid-adapted Malagasy bullfrog, Laliostoma labrosum, influenced by past connectivity and habitat stability. Mol Phylogenet Evol 2015; 92:11-24. [DOI: 10.1016/j.ympev.2015.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 12/21/2022]
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19
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Edwards SV, Shultz AJ, Campbell-Staton SC. Next-generation sequencing and the expanding domain of phylogeography. FOLIA ZOOLOGICA 2015. [DOI: 10.25225/fozo.v64.i3.a2.2015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Scott V. Edwards
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
| | - Allison J. Shultz
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
| | - Shane C. Campbell-Staton
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
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20
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Chávez-Galarza J, Henriques D, Johnston JS, Carneiro M, Rufino J, Patton JC, Pinto MA. Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome-wide nuclear variations provide support for secondary contact from historical refugia. Mol Ecol 2015; 24:2973-92. [PMID: 25930679 DOI: 10.1111/mec.13223] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 04/16/2015] [Accepted: 04/21/2015] [Indexed: 12/30/2022]
Abstract
Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of taxa, and the Iberian honey bee is no exception. Surveys of genetic variation in the Iberian honey bee are among the most extensive for any honey bee subspecies. From these, differential and complex patterns of diversity have emerged, which have yet to be fully resolved. Here, we used a genome-wide data set of 309 neutrally tested single nucleotide polymorphisms (SNPs), scattered across the 16 honey bee chromosomes, which were genotyped in 711 haploid males. These SNPs were analysed along with an intergenic locus of the mtDNA, to reveal historical patterns of population structure across the entire range of the Iberian honey bee. Overall, patterns of population structure inferred from nuclear loci by multiple clustering approaches and geographic cline analysis were consistent with two major clusters forming a well-defined cline that bisects Iberia along a northeastern-southwestern axis, a pattern that remarkably parallels that of the mtDNA. While a mechanism of primary intergradation or isolation by distance could explain the observed clinal variation, our results are more consistent with an alternative model of secondary contact between divergent populations previously isolated in glacial refugia, as proposed for a growing list of other Iberian taxa. Despite current intense honey bee management, human-mediated processes have seemingly played a minor role in shaping Iberian honey bee genetic structure. This study highlights the complexity of the Iberian honey bee patterns and reinforces the importance of Iberia as a reservoir of Apis mellifera diversity.
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Affiliation(s)
- Julio Chávez-Galarza
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal.,Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Dora Henriques
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal.,Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA
| | - Miguel Carneiro
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - José Rufino
- Polytechnic Institute of Bragança, 5301-857, Bragança, Portugal
| | - John C Patton
- Department of Forestry and Natural Resources, Purdue University, 715 W State St., West Lafayette, IN, 4797-2061, USA
| | - M Alice Pinto
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal
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21
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Zinenko O, Stümpel N, Mazanaeva L, Bakiev A, Shiryaev K, Pavlov A, Kotenko T, Kukushkin O, Chikin Y, Duisebayeva T, Nilson G, Orlov NL, Tuniyev S, Ananjeva NB, Murphy RW, Joger U. Mitochondrial phylogeny shows multiple independent ecological transitions and northern dispersion despite of Pleistocene glaciations in meadow and steppe vipers (Vipera ursinii and Vipera renardi). Mol Phylogenet Evol 2015; 84:85-100. [DOI: 10.1016/j.ympev.2014.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 10/20/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
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22
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Khanyile KS, Dzomba EF, Muchadeyi FC. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa. Front Genet 2015; 6:13. [PMID: 25691890 PMCID: PMC4315093 DOI: 10.3389/fgene.2015.00013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 01/11/2015] [Indexed: 11/14/2022] Open
Abstract
Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective population sizes particularly in the conservation flocks. The utility and limitations of the iselect chicken SNP60K in village chicken populations is discussed.
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Affiliation(s)
- Khulekani S Khanyile
- Biotechnology Platform, Agricultural Research Council Pretoria, South Africa ; Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal Pietermaritzburg, South Africa
| | - Edgar F Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal Pietermaritzburg, South Africa
| | - Farai C Muchadeyi
- Biotechnology Platform, Agricultural Research Council Pretoria, South Africa
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23
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Macher JN, Rozenberg A, Pauls SU, Tollrian R, Wagner R, Leese F. Assessing the phylogeographic history of the montane caddisfly Thremma gallicum using mitochondrial and restriction-site-associated DNA (RAD) markers. Ecol Evol 2015; 5:648-62. [PMID: 25691988 PMCID: PMC4328769 DOI: 10.1002/ece3.1366] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 11/17/2014] [Indexed: 12/24/2022] Open
Abstract
Repeated Quaternary glaciations have significantly shaped the present distribution and diversity of several European species in aquatic and terrestrial habitats. To study the phylogeography of freshwater invertebrates, patterns of intraspecific variation have been examined primarily using mitochondrial DNA markers that may yield results unrepresentative of the true species history. Here, population genetic parameters were inferred for a montane aquatic caddisfly, Thremma gallicum, by sequencing a 658-bp fragment of the mitochondrial CO1 gene, and 12,514 nuclear RAD loci. T. gallicum has a highly disjunct distribution in southern and central Europe, with known populations in the Cantabrian Mountains, Pyrenees, Massif Central, and Black Forest. Both datasets represented rangewide sampling of T. gallicum. For the CO1 dataset, this included 352 specimens from 26 populations, and for the RAD dataset, 17 specimens from eight populations. We tested 20 competing phylogeographic scenarios using approximate Bayesian computation (ABC) and estimated genetic diversity patterns. Support for phylogeographic scenarios and diversity estimates differed between datasets with the RAD data favouring a southern origin of extant populations and indicating the Cantabrian Mountains and Massif Central populations to represent highly diverse populations as compared with the Pyrenees and Black Forest populations. The CO1 data supported a vicariance scenario (north-south) and yielded inconsistent diversity estimates. Permutation tests suggest that a few hundred polymorphic RAD SNPs are necessary for reliable parameter estimates. Our results highlight the potential of RAD and ABC-based hypothesis testing to complement phylogeographic studies on non-model species.
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Affiliation(s)
- Jan-Niklas Macher
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University BochumUniversitätsstraße 150, 44801, Bochum, Germany
| | - Andrey Rozenberg
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University BochumUniversitätsstraße 150, 44801, Bochum, Germany
| | - Steffen U Pauls
- Biodiversity and Climate Research Centre (BiK-F)Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für NaturforschungSenckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Ralph Tollrian
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University BochumUniversitätsstraße 150, 44801, Bochum, Germany
| | - Rüdiger Wagner
- Working Group Limnology, University of KasselHeinrich-Plett-Straße 30, 34132, Kassel, Germany
- Max Planck Institute for Evolutionary BiologyAugust-Thienemann-Straße 2, 24306, Plön, Germany
| | - Florian Leese
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University BochumUniversitätsstraße 150, 44801, Bochum, Germany
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24
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First estimates of genetic diversity for the highly endangered giant sable antelope using a set of 57 microsatellites. EUR J WILDLIFE RES 2015. [DOI: 10.1007/s10344-014-0880-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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25
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Kumar G, Kocour M, Kunal SP. Mitochondrial DNA variation and phylogenetic relationships among five tuna species based on sequencing of D-loop region. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1976-80. [PMID: 25329285 DOI: 10.3109/19401736.2014.971313] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In order to assess the DNA sequence variation and phylogenetic relationship among five tuna species (Auxis thazard, Euthynnus affinis, Katsuwonus pelamis, Thunnus tonggol, and T. albacares) out of all four tuna genera, partial sequences of the mitochondrial DNA (mtDNA) D-loop region were analyzed. The estimate of intra-specific sequence variation in studied species was low, ranging from 0.027 to 0.080 [Kimura's two parameter distance (K2P)], whereas values of inter-specific variation ranged from 0.049 to 0.491. The longtail tuna (T. tonggol) and yellowfin tuna (T. albacares) were found to share a close relationship (K2P = 0.049) while skipjack tuna (K. pelamis) was most divergent studied species. Phylogenetic analysis using Maximum-Likelihood (ML) and Neighbor-Joining (NJ) methods supported the monophyletic origin of Thunnus species. Similarly, phylogeny of Auxis and Euthynnus species substantiate the monophyly. However, results showed a distinct origin of K. pelamis from genus Thunnus as well as Auxis and Euthynnus. Thus, the mtDNA D-loop region sequence data supports the polyphyletic origin of tuna species.
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Affiliation(s)
- Girish Kumar
- a South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice , Vodnany , Czech Republic and
| | - Martin Kocour
- a South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice , Vodnany , Czech Republic and
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Leung MY, Paszkowski C, Russell A. Genetic structure of the endangered Greater Short-horned Lizard (Phrynosoma hernandesi) in Canada: evidence from mitochondrial and nuclear genes. CAN J ZOOL 2014. [DOI: 10.1139/cjz-2014-0079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The northern edge of the range of the Greater Short-horned Lizard (Phrynosoma hernandesi Girard, 1858) occurs in western Canada, where the species has “endangered” status and exhibits a patchy distribution. Phylogenetic inference and genetic analyses were employed to investigate the genetic structure of P. hernandesi throughout its Canadian range. One nuclear and two mitochondrial DNA genes were sequenced from 94 lizard tail tips. Overall, sequences from lizards from both Alberta and Saskatchewan displayed very little variability, and the consistent clustering of all the P. hernandesi mitochondrial and nuclear DNA sequences from Canada in both phylogenetic and population genetic analyses is consistent with the lizards from all sampled localities having originated from a single glacial refugium, and with being, until recently (or currently) interconnected genetically. The genetic data obtained so far furnish no information useful for interpreting the species’ present-day patchy distribution patterns or for formulating conservation strategies.
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Affiliation(s)
- M.N.-Y. Leung
- Department of Biological Sciences, University of Calgary, 2500 University Drive Northwest, Calgary, AB T2N 1N4, Canada
| | - C.A. Paszkowski
- Department of Biological Sciences, University of Alberta, 116 Street and 85th Avenue, Edmonton, AB T6G 2R3, Canada
| | - A.P. Russell
- Department of Biological Sciences, University of Calgary, 2500 University Drive Northwest, Calgary, AB T2N 1N4, Canada
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Godinho R, López-Bao JV, Castro D, Llaneza L, Lopes S, Silva P, Ferrand N. Real-time assessment of hybridization between wolves and dogs: combining noninvasive samples with ancestry informative markers. Mol Ecol Resour 2014; 15:317-28. [PMID: 25132482 DOI: 10.1111/1755-0998.12313] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 07/26/2014] [Accepted: 07/28/2014] [Indexed: 01/17/2023]
Abstract
Wolves and dogs provide a paradigmatic example of the ecological and conservation implications of hybridization events between wild and domesticated forms. However, our understanding of such implications has been traditionally hampered by both high genetic similarity and the difficulties in obtaining tissue samples (TS), which limit our ability to assess ongoing hybridization events. To assess the occurrence and extension of hybridization in a pack of wolf-dog hybrids in northwestern Iberia, we compared the power of 52 nuclear markers implemented on TS with a subset of 13 ancestry informative markers (AIMs) typed in noninvasive samples (NIS). We demonstrate that the 13 AIMs are as accurate as the 52 markers that were chosen without regard to the power to differentiate between wolves and dogs, also having the advantage of being rapidly screened on NIS. The efficiency of AIMs significantly outperformed ten random sets of similar size and an additional commercial set of 18 markers. Bayesian clustering analysis implemented on AIMs and NIS identified nine hybrids, two wolves and two dogs. Four hybrids were unambiguously assigned to F1xWolf backcrosses. Our approach (AIMs + NIS) overcomes previous difficulties related to sample availability and informative power of markers, allowing a quick identification of wolf-dog hybrids in the first phases of hybridization episodes. This provides managers with a reliable tool to evaluate hybridization and estimate the success of their actions. This approach may be easily adapted for other pairs of wild/domesticated species, thus improving our understanding of the introgression of domestication genes into natural populations.
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Affiliation(s)
- Raquel Godinho
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
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McLean CA, Stuart-Fox D, Moussalli A. Phylogeographic structure, demographic history and morph composition in a colour polymorphic lizard. J Evol Biol 2014; 27:2123-37. [DOI: 10.1111/jeb.12464] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 07/14/2014] [Accepted: 07/21/2014] [Indexed: 12/22/2022]
Affiliation(s)
- C. A. McLean
- Department of Zoology; The University of Melbourne; Parkville Vic. Australia
- Sciences Department; Museum Victoria; Carlton Gardens Vic. Australia
| | - D. Stuart-Fox
- Department of Zoology; The University of Melbourne; Parkville Vic. Australia
| | - A. Moussalli
- Sciences Department; Museum Victoria; Carlton Gardens Vic. Australia
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Sagonas K, Poulakakis N, Lymberakis P, Parmakelis A, Pafilis P, Valakos ED. Molecular systematics and historical biogeography of the green lizards (Lacerta) in Greece: Insights from mitochondrial and nuclear DNA. Mol Phylogenet Evol 2014; 76:144-54. [DOI: 10.1016/j.ympev.2014.03.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 02/24/2014] [Accepted: 03/14/2014] [Indexed: 10/25/2022]
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Dool SE, Puechmaille SJ, Dietz C, Juste J, Ibáñez C, Hulva P, Roué SG, Petit EJ, Jones G, Russo D, Toffoli R, Viglino A, Martinoli A, Rossiter SJ, Teeling EC. Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers. Mol Ecol 2014; 22:4055-70. [PMID: 23889545 DOI: 10.1111/mec.12373] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 01/03/2023]
Abstract
The demographic history of Rhinolophus hipposideros (lesser horseshoe bat) was reconstructed across its European, North African and Middle-Eastern distribution prior to, during and following the most recent glaciations by generating and analysing a multimarker data set. This data set consisted of an X-linked nuclear intron (Bgn; 543 bp), mitochondrial DNA (cytb-tRNA-control region; 1630 bp) and eight variable microsatellite loci for up to 373 individuals from 86 localities. Using this data set of diverse markers, it was possible to determine the species' demography at three temporal stages. Nuclear intron data revealed early colonization into Europe from the east, which pre-dates the Quaternary glaciations. The mtDNA data supported multiple glacial refugia across the Mediterranean, the largest of which were found in the Ibero-Maghreb region and an eastern location (Anatolia/Middle East)-that were used by R. hipposideros during the most recent glacial cycles. Finally, microsatellites provided the most recent information on these species' movements since the Last Glacial Maximum and suggested that lineages that had diverged into glacial refugia, such as in the Ibero-Maghreb region, have remained isolated. These findings should be used to inform future conservation management strategies for R. hipposideros and show the power of using a multimarker data set for phylogeographic studies.
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Affiliation(s)
- Serena E Dool
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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Pimvichai P, Enghoff H, Panha S. Molecular phylogeny of the Thyropygus allevatus group of giant millipedes and some closely related groups. Mol Phylogenet Evol 2013; 71:170-83. [PMID: 24269316 DOI: 10.1016/j.ympev.2013.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 10/21/2013] [Accepted: 11/11/2013] [Indexed: 11/25/2022]
Abstract
Giant cylindrical millipedes of the family Harpagophoridae, especially species of the genus Thyropygus, are broadly distributed in Thailand and nearby countries. They show a great deal of variation in body size, color patterns and gonopodal characters. Phylogenetic analyses of 26 nominate species from six genera in the subfamilies Harpagophorinae and Rhynchoproctinae, as well as nine new morphotypes (regarded as new species), were performed with the DNA sequences from two mitochondrial gene fragments (16S rRNA and COI). The genus Thyropygus (Harpagophorinae) was recovered as monophyletic under all analyses, whilst the representatives of Rhynchoproctinae also formed a monophyletic group. However, the analyses suggested that the tribe Gonoplectini should be elevated to a separate subfamily, Gonoplectinae. The molecular analyses were largely (but not totally) congruent with, and so supported the usefulness of, gonopodal characters for the classification and identification of harpagophorid millipedes, and additionally supported previous studies on the delimitation of species and subgroups. This is the first molecular study inside the family Harpagophoridae and provides the basis for further studies of the evolutionary processes and biogeographic patterns of millipedes in Southeast Asia.
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Affiliation(s)
- Piyatida Pimvichai
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Henrik Enghoff
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Bidegaray-Batista L, Ferrández MÁ, Arnedo MA. Winter is coming: Miocene and Quaternary climatic shifts shaped the diversification of Western-MediterraneanHarpactocrates(Araneae, Dysderidae) spiders. Cladistics 2013; 30:428-446. [DOI: 10.1111/cla.12054] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2013] [Indexed: 01/26/2023] Open
Affiliation(s)
- Leticia Bidegaray-Batista
- Institut de Recerca de la Biodiversitat and Departament de Biologia Animal; Universitat de Barcelona; Av. Diagonal 643 Barcelona 08028 Spain
| | - Miguel Á. Ferrández
- Sociedad para el Estudio y la Conservación de las Arañas; c/Villafranca 24, 1_C Madrid 28028 Spain
| | - Miquel A. Arnedo
- Institut de Recerca de la Biodiversitat and Departament de Biologia Animal; Universitat de Barcelona; Av. Diagonal 643 Barcelona 08028 Spain
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Monasterio C, Shoo LP, Salvador A, Iraeta P, Díaz JA. High temperature constrains reproductive success in a temperate lizard: implications for distribution range limits and the impacts of climate change. J Zool (1987) 2013. [DOI: 10.1111/jzo.12057] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. Monasterio
- Dpto. de Zoología y Antropología Física (Vertebrados); Facultad de Biología; Universidad Complutense; Madrid Spain
| | - L. P. Shoo
- Wilson Conservation Ecology Lab; School of Biological Sciences; University of Queensland; St. Lucia Qld Australia
| | - A. Salvador
- Dpto. de Ecología Evolutiva; Museo Nacional de Ciencias Naturales; CSIC; Madrid Spain
| | - P. Iraeta
- Dpto. de Zoología y Antropología Física (Vertebrados); Facultad de Biología; Universidad Complutense; Madrid Spain
| | - J. A. Díaz
- Dpto. de Zoología y Antropología Física (Vertebrados); Facultad de Biología; Universidad Complutense; Madrid Spain
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Milá B, Surget-Groba Y, Heulin B, Gosá A, Fitze PS. Multilocus phylogeography of the common lizard Zootoca vivipara at the Ibero-Pyrenean suture zone reveals lowland barriers and high-elevation introgression. BMC Evol Biol 2013; 13:192. [PMID: 24021154 PMCID: PMC3847509 DOI: 10.1186/1471-2148-13-192] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 09/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The geographic distribution of evolutionary lineages and the patterns of gene flow upon secondary contact provide insight into the process of divergence and speciation. We explore the evolutionary history of the common lizard Zootoca vivipara (= Lacerta vivipara) in the Iberian Peninsula and test the role of the Pyrenees and the Cantabrian Mountains in restricting gene flow and driving lineage isolation and divergence. We also assess patterns of introgression among lineages upon secondary contact, and test for the role of high-elevation trans-mountain colonisations in explaining spatial patterns of genetic diversity. We use mtDNA sequence data and genome-wide AFLP loci to reconstruct phylogenetic relationships among lineages, and measure genetic structure. RESULTS The main genetic split in mtDNA corresponds generally to the French and Spanish sides of the Pyrenees as previously reported, in contrast to genome-wide AFLP data, which show a major division between NW Spain and the rest. Both types of markers support the existence of four distinct and geographically congruent genetic groups, which are consistent with major topographic barriers. Both datasets reveal the presence of three independent contact zones between lineages in the Pyrenean region, one in the Basque lowlands, one in the low-elevation mountains of the western Pyrenees, and one in the French side of the central Pyrenees. The latter shows genetic evidence of a recent, high-altitude trans-Pyrenean incursion from Spain into France. CONCLUSIONS The distribution and age of major lineages is consistent with a Pleistocene origin and a role for both the Pyrenees and the Cantabrian Mountains in driving isolation and differentiation of Z. vivipara lineages at large geographic scales. However, mountain ranges are not always effective barriers to dispersal, and have not prevented a recent high-elevation trans-Pyrenean incursion that has led to asymmetrical introgression among divergent lineages. Cytonuclear discordance in patterns of genetic structure and introgression at contact zones suggests selection may be involved at various scales. Suture zones are important areas for the study of lineage formation and speciation, and our results show that biogeographic barriers can yield markedly different phylogeographic patterns in different vertebrate and invertebrate taxa.
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Affiliation(s)
- Borja Milá
- National Museum of Natural Sciences, Spanish Research Council (CSIC), José Gutiérrez Abascal 2, Madrid 28006, Spain
| | - Yann Surget-Groba
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, P. R China
| | - Benoît Heulin
- Station Biologique, CNRS UMR 6553, Paimpont 35380, France
| | - Alberto Gosá
- Herpetology Department, Sociedad de Ciencias Aranzadi, San Sebastián 20014, Spain
| | - Patrick S Fitze
- National Museum of Natural Sciences, Spanish Research Council (CSIC), José Gutiérrez Abascal 2, Madrid 28006, Spain
- ARAID Foundation, Zaragoza 50004, Spain
- Instituto Pirenaico de Ecología (IPE-CSIC), Jaca 22700, Spain
- Université de Lausanne, Department of Ecology and Evolution (DEE), Biophore, Lausanne 1015, Switzerland
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Causes and evolutionary consequences of population subdivision of an Iberian mountain lizard, Iberolacerta monticola. PLoS One 2013; 8:e66034. [PMID: 23762459 PMCID: PMC3676366 DOI: 10.1371/journal.pone.0066034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 05/06/2013] [Indexed: 11/30/2022] Open
Abstract
Aim The study of the factors that influence population connectivity and spatial distribution of genetic variation is crucial for understanding speciation and for predicting the effects of landscape modification and habitat fragmentation, which are considered severe threats to global biodiversity. This dual perspective is obtained from analyses of subalpine mountain species, whose present distribution may have been shaped both by cyclical climate changes over ice ages and anthropogenic perturbations of their habitats. Here, we examine the phylogeography, population structure and genetic diversity of the lacertid lizard Iberolacerta monticola, an endemism considered to be facing a high risk of extinction in several populations. Location Northwestern quadrant of the Iberian Peninsula. Methods We analyzed the mtDNA variation at the control region (454 bp) and the cytochrome b (598 bp) loci, as well as at 10 nuclear microsatellite loci from 17 populations throughout the distribution range of the species. Results According to nuclear markers, most sampling sites are defined as distinct, genetically differentiated populations, and many of them show traces of recent bottlenecks. Mitochondrial data identify a relatively old, geographically restricted lineage, and four to six younger geographically vicariant sister clades, whose origin may be traced back to the mid-Pleistocene revolution, with several subclades possibly associated to the mid-Bruhnes transition. Geographic range fragmentation of one of these clades, which includes lowland sites, is very recent, and most likely due to the accelerated loss of Atlantic forests by human intervention. Main Conclusions Altogether, the data fit a “refugia within refugia” model, some lack of pattern uniformity notwithstanding, and suggest that these mountains might be the cradles of new species of Iberolacerta. However, the changes operated during the Holocene severely compromise the long-term survival of those genetic lineages more exposed to the anthropogenic perturbations of their habitats.
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Igea J, Aymerich P, Fernández-González A, González-Esteban J, Gómez A, Alonso R, Gosálbez J, Castresana J. Phylogeography and postglacial expansion of the endangered semi-aquatic mammal Galemys pyrenaicus. BMC Evol Biol 2013; 13:115. [PMID: 23738626 PMCID: PMC3682870 DOI: 10.1186/1471-2148-13-115] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/28/2013] [Indexed: 01/20/2023] Open
Abstract
Background Species with strict ecological requirements may provide new insights into the forces that shaped the geographic variation of genetic diversity. The Pyrenean desman, Galemys pyrenaicus, is a small semi-aquatic mammal that inhabits clean streams of the northern half of the Iberian Peninsula and is endangered in most of its geographic range, but its genetic structure is currently unknown. While the stringent ecological demands derived from its aquatic habitat might have caused a partition of the genetic diversity among river basins, Pleistocene glaciations would have generated a genetic pattern related to glacial refugia. Results To study the relative importance of historical and ecological factors in the genetic structure of G. pyrenaicus, we used mitochondrial and intronic sequences of specimens covering most of the species range. We show, first, that the Pyrenean desman has very low levels of genetic diversity compared to other mammals. In addition, phylogenetic and dating analyses of the mitochondrial sequences reveal a strong phylogeographic structure of a Middle Pleistocene origin, suggesting that the main lineages arose during periods of glacial isolation. Furthermore, both the spatial distribution of nuclear and mitochondrial diversity and the results of species distribution modeling suggest the existence of a major glacial refugium in the northwestern part of the Iberian Peninsula. Finally, the main mitochondrial lineages show a striking parapatric distribution without any apparent exchange of mitochondrial haplotypes between the lineages that came into secondary contact (although with certain permeability to nuclear genes), indicating incomplete mixing after the post-glacial recolonization. On the other hand, when we analyzed the partition of the genetic diversity among river basins, the Pyrenean desman showed a lower than expected genetic differentiation among main rivers. Conclusions The analysis of mitochondrial and intronic markers in G. pyrenaicus showed the predominant effects of Pleistocene glaciations on the genetic structure of this species, while the distribution of the genetic diversity was not greatly influenced by the main river systems. These results and, particularly, the discovery of a marked phylogeographic structure, may have important implications for the conservation of the Pyrenean desman.
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Affiliation(s)
- Javier Igea
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37, Barcelona 08003, Spain
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Mammella MA, Martin FN, Cacciola SO, Coffey MD, Faedda R, Schena L. Analyses of the population structure in a global collection of Phytophthora nicotianae isolates inferred from mitochondrial and nuclear DNA sequences. PHYTOPATHOLOGY 2013; 103:610-22. [PMID: 23384862 DOI: 10.1094/phyto-10-12-0263-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Genetic variation within the heterothallic cosmopolitan plant pathogen Phytophthora nicotianae was determined in 96 isolates from a wide range of hosts and geographic locations by characterizing four mitochondrial (10% of the genome) and three nuclear loci. In all, 52 single-nucleotide polymorphisms (SNPs) (an average of 1 every 58 bp) and 313 sites with gaps representing 5,450 bases enabled the identification of 50 different multilocus mitochondrial haplotypes. Similarly, 24 SNPs (an average of 1 every 69 bp), with heterozygosity observed at each locus, were observed in three nuclear regions (hyp, scp, and β-tub) differentiating 40 multilocus nuclear genotypes. Both mitochondrial and nuclear markers revealed a high level of dispersal of isolates and an inconsistent geographic structuring of populations. However, a specific association was observed for host of origin and genetic grouping with both nuclear and mitochondrial sequences. In particular, the majority of citrus isolates from Italy, California, Florida, Syria, Albania, and the Philippines clustered in the same mitochondrial group and shared at least one nuclear allele. A similar association was also observed for isolates recovered from Nicotiana and Solanum spp. The present study suggests an important role of nursery populations in increasing genetic recombination within the species and the existence of extensive phenomena of migration of isolates that have been likely spread worldwide with infected plant material.
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Affiliation(s)
- Marco A Mammella
- Dipartimento di Agraria, Università degli Studi Mediterranea, Località Feo di Vito, 89122 Reggio Calabria, Italy
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Sauer J, Oldeland J, Hausdorf B. Continuing fragmentation of a widespread species by geographical barriers as initial step in a land snail radiation on crete. PLoS One 2013; 8:e62569. [PMID: 23658748 PMCID: PMC3641037 DOI: 10.1371/journal.pone.0062569] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/23/2013] [Indexed: 11/18/2022] Open
Abstract
The phylogeographic structure of the land snail Xerocrassa mesostena on Crete inferred from AFLP markers and mitochondrial cox1 sequences can be explained by three mechanisms: gene flow restriction, population expansion and leptokurtic dispersal. Gene flow restriction by geographic barriers caused subdivision of the gene pool into distinct clusters. Population expansion was probably facilitated by deforestation of Crete in the postglacial. Newly available areas were colonized by leptokurtic dispersal, i.e. slow active expansion resulting in isolation by distance within the clusters and occasional long distance dispersal events that resulted in departures from the isolation by distance model. Less than one percent of the AFLP markers show correlations with environmental variables. Random phylogeographic breaks in the distribution of the mitochondrial haplotype groups indicate that single locus markers, especially mitochondrial DNA, might result in a misleading picture of the phylogeographic structure of a species. Restriction of gene flow between metapopulations caused by geographical barriers can interact with sexual selection resulting in the differentiation of these metapopulations into separate species without noticeable ecological differentiation. Evidence for gene flow between parapatrically distributed evolutionary units representing different stages of the speciation process suggests that the ongoing process of fragmentation of the X. mesostena complex might be an example for parapatric speciation. The lack of ecological differentiation between these units confirms theoretical predictions that divergent selection for local adaptation is not required for rapid speciation.
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Affiliation(s)
- Jan Sauer
- Department of Chemical Ecology, University of Bielefeld, Bielefeld, Germany
- Zoological Museum, University of Hamburg, Hamburg, Germany
| | - Jens Oldeland
- Biodiversity, Evolution and Ecology of Plants, Biozentrum Klein Flottbek, University of Hamburg, Hamburg, Germany
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Grechko VV. The problems of molecular phylogenetics with the example of squamate reptiles: Mitochondrial DNA markers. Mol Biol 2013. [DOI: 10.1134/s0026893313010056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Diversity of tuco-tucos (Ctenomys, Rodentia) in the Northeastern wetlands from Argentina: mitochondrial phylogeny and chromosomal evolution. Genetica 2012; 140:125-36. [DOI: 10.1007/s10709-012-9664-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 06/22/2012] [Indexed: 10/28/2022]
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Neiva J, Pearson GA, Valero M, Serrão EA. Fine-scale genetic breaks driven by historical range dynamics and ongoing density-barrier effects in the estuarine seaweed Fucus ceranoides L. BMC Evol Biol 2012; 12:78. [PMID: 22672720 PMCID: PMC3483196 DOI: 10.1186/1471-2148-12-78] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 05/14/2012] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Factors promoting the emergence of sharp phylogeographic breaks include restricted dispersal, habitat discontinuity, physical barriers, disruptive selection, mating incompatibility, genetic surfing and secondary contact. Disentangling the role of each in any particular system can be difficult, especially when species are evenly distributed across transition zones and dispersal barriers are not evident. The estuarine seaweed Fucus ceranoides provides a good example of highly differentiated populations along its most persistent distributional range at the present rear edge of the species distribution, in NW Iberia. Intrinsic dispersal restrictions are obvious in this species, but have not prevented F. ceranoides from vastly expanding its range northwards following the last glaciation, implying that additional factors are responsible for the lack of connectivity between neighbouring southern populations. In this study we analyze 22 consecutive populations of F. ceranoides along NW Iberia to investigate the processes generating and maintaining the observed high levels of regional genetic divergence. RESULTS Variation at seven microsatellite loci and at mtDNA spacer sequences was concordant in revealing that Iberian F. ceranoides is composed of three divergent genetic clusters displaying nearly disjunct geographical distributions. Structure and AFC analyses detected two populations with an admixed nuclear background. Haplotypic diversity was high in the W sector and very low in the N sector. Within each genetic cluster, population structure was also pervasive, although shallower. CONCLUSIONS The deep divergence between sectors coupled with the lack of support for a role of oceanographic barriers in defining the location of breaks suggested 1) that the parapatric genetic sectors result from the regional reassembly of formerly vicariant sub-populations, and 2) that the genetic discontinuities at secondary contact zones (and elsewhere) are maintained despite normal migration rates. We conclude that colonization and immigration, as sources of gene-flow, have very different genetic effects. Migration between established populations is effectively too low to prevent their differentiation by drift or to smooth historical differences inherited from the colonization process. F. ceranoides, but possibly low-dispersal species in general, appear to be unified to a large extent by historical, non-equilibrium processes of extinction and colonization, rather than by contemporary patterns of gene flow.
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Affiliation(s)
- João Neiva
- Centro de Ciências do Mar, Centro de Investigação Marinha e Ambiental - Laboratório Associado, Universidade do Algarve, Gambelas, Faro, 8005-139, Portugal
- Unité Mixte de Recherche 7144, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Station Biologique de Roscoff, Place Georges-Teissier, BP 74, Roscoff Cedex, 29682, France
| | - Gareth A Pearson
- Centro de Ciências do Mar, Centro de Investigação Marinha e Ambiental - Laboratório Associado, Universidade do Algarve, Gambelas, Faro, 8005-139, Portugal
| | - Myriam Valero
- Unité Mixte de Recherche 7144, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie, Station Biologique de Roscoff, Place Georges-Teissier, BP 74, Roscoff Cedex, 29682, France
| | - Ester A Serrão
- Centro de Ciências do Mar, Centro de Investigação Marinha e Ambiental - Laboratório Associado, Universidade do Algarve, Gambelas, Faro, 8005-139, Portugal
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BARATA MAFALDA, PERERA ANA, MARTÍNEZ-FREIRÍA FERNANDO, HARRIS DJAMES. Cryptic diversity within the Moroccan endemic day geckos Quedenfeldtia (Squamata: Gekkonidae): a multidisciplinary approach using genetic, morphological and ecological data. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01903.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Martínez-Solano Í, Peralta-García A, Jockusch EL, Wake DB, Vázquez-Domínguez E, Parra-Olea G. Molecular systematics of Batrachoseps (Caudata, Plethodontidae) in southern California and Baja California: Mitochondrial-nuclear DNA discordance and the evolutionary history of B. major. Mol Phylogenet Evol 2012; 63:131-49. [DOI: 10.1016/j.ympev.2011.12.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 12/20/2011] [Accepted: 12/28/2011] [Indexed: 11/16/2022]
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Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape. Mol Phylogenet Evol 2012; 62:87-96. [DOI: 10.1016/j.ympev.2011.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 09/01/2011] [Accepted: 09/11/2011] [Indexed: 11/22/2022]
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MATTOCCIA MARCO, MARTA SILVIO, ROMANO ANTONIO, SBORDONI VALERIO. Phylogeography of an Italian endemic salamander (genus Salamandrina): glacial refugia, postglacial expansions, and secondary contact. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01747.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Miraldo A, Hewitt GM, Paulo OS, Emerson BC. Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones. BMC Evol Biol 2011; 11:170. [PMID: 21682856 PMCID: PMC3141430 DOI: 10.1186/1471-2148-11-170] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 06/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Iberian Peninsula is recognized as an important refugial area for species survival and diversification during the climatic cycles of the Quaternary. Recent phylogeographic studies have revealed Iberia as a complex of multiple refugia. However, most of these studies have focused either on species with narrow distributions within the region or species groups that, although widely distributed, generally have a genetic structure that relates to pre-Quaternary cladogenetic events. In this study we undertake a detailed phylogeographic analysis of the lizard species, Lacerta lepida, whose distribution encompasses the entire Iberian Peninsula. We attempt to identify refugial areas, recolonization routes, zones of secondary contact and date demographic events within this species. RESULTS Results support the existence of 6 evolutionary lineages (phylogroups) with a strong association between genetic variation and geography, suggesting a history of allopatric divergence in different refugia. Diversification within phylogroups is concordant with the onset of the Pleistocene climatic oscillations. The southern regions of several phylogroups show a high incidence of ancestral alleles in contrast with high incidence of recently derived alleles in northern regions. All phylogroups show signs of recent demographic and spatial expansions. We have further identified several zones of secondary contact, with divergent mitochondrial haplotypes occurring in narrow zones of sympatry. CONCLUSIONS The concordant patterns of spatial and demographic expansions detected within phylogroups, together with the high incidence of ancestral haplotypes in southern regions of several phylogroups, suggests a pattern of contraction of populations into southern refugia during adverse climatic conditions from which subsequent northern expansions occurred. This study supports the emergent pattern of multiple refugia within Iberia but adds to it by identifying a pattern of refugia coincident with the southern distribution limits of individual evolutionary lineages. These areas are important in terms of long-term species persistence and therefore important areas for conservation.
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Affiliation(s)
- Andreia Miraldo
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7J, UK.
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DING LI, GAN XIAONI, HE SHUNPING, ZHAO ERMI. A phylogeographic, demographic and historical analysis of the short-tailed pit viper (Gloydius brevicaudus): evidence for early divergence and late expansion during the Pleistocene. Mol Ecol 2011; 20:1905-22. [DOI: 10.1111/j.1365-294x.2011.05060.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Melo-Ferreira J, Alves PC, Rocha J, Ferrand N, Boursot P. Interspecific X-chromosome and mitochondrial DNA introgression in the Iberian hare: selection or allele surfing? Evolution 2011; 65:1956-68. [PMID: 21729051 DOI: 10.1111/j.1558-5646.2011.01261.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introgression from a resident species into an invading one is predicted to occur through the demographic process of "allele surfing," and to particularly affect genomic regions transmitted by the lower migrating sex, such as mtDNA. This could explain that northern Iberian populations of Lepus granatensis harbor high frequencies of mtDNA from L. timidus, an arctic hare it replaced there after deglaciation. We report that variation of introgressed timidus-like mtDNA reflects several predicted effects of this process: increasing frequency and diversity in the direction of expansion, strong perpendicular phylogeographic structure and signs of postglacial demographic growth. However, demographic inferences for the granatensis and timidus-like mtDNA lineages suggest the latter may have outcompeted the former in northern Iberia. Autosomal introgression occurs at low frequencies and species-wide rather than only in the north. If this difference with mtDNA resulted from sex-biased migration, an intermediate pattern should prevail for the X-chromosome, but we report species-wide and high-frequency introgression of an X-fragment. Either selection favored this ubiquitous X-introgression, or more complex postglacial expansion patterns prevailed, with different consequences depending on the genomic and geographic region. This illustrates the difficulty of distinguishing demographic and selective effects and the need for genome and species-wide based demographic models.
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Affiliation(s)
- José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
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Hausdorf B, Wilkens H, Strecker U. Population genetic patterns revealed by microsatellite data challenge the mitochondrial DNA based taxonomy of Astyanax in Mexico (Characidae, Teleostei). Mol Phylogenet Evol 2011; 60:89-97. [PMID: 21419231 DOI: 10.1016/j.ympev.2011.03.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 03/03/2011] [Accepted: 03/08/2011] [Indexed: 11/24/2022]
Abstract
Astyanax has become an important model system for evolutionary studies of cave animals. We investigated correlations of population genetic patterns revealed by microsatellite data and phylogeographic patterns shown by mitochondrial DNA sequences in Mexican cave and surface fish of the genus Astyanax (Characidae, Teleostei) to improve the understanding of the colonization history of this neotropical fish in Central and North America and to assess a recent taxonomic classification. The distribution of nuclear genotypes is not congruent with that of the mitochondrial clades. Admixture analyses suggest there has been nuclear gene flow between populations defined by different mitochondrial clades. The microsatellite data indicate that there was mitochondrial capture of a cave population from adjacent populations. Furthermore, gene flow also occurred between populations belonging to different nuclear genotypic clusters. This indicates that neither the nuclear genotypic clusters nor the mitochondrial clades represent independent evolutionary units, although the mitochondrial divergences are high and in a range usually characteristic for different fish species. This conclusion is supported by the presence of morphologically intermediate forms. Our analyses show that the Trans-Mexican Volcanic Belt limited gene flow, but has been crossed by Astyanax several times. In Yucatán, where obvious geographic barriers are missing, the incongruence between the distribution of nuclear and mitochondrial markers reflects random colonization events caused by inundations or marine transgressions resulting in random phylogeographic breaks. Thus, conclusions about the phylogeographic history and even more about the delimitation of species should not be based on single genetic markers.
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Affiliation(s)
- Bernhard Hausdorf
- Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
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When selection deceives phylogeographic interpretation: The case of the Mediterranean house gecko, Hemidactylus turcicus (Linnaeus, 1758). Mol Phylogenet Evol 2011; 58:365-73. [DOI: 10.1016/j.ympev.2010.12.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 12/08/2010] [Accepted: 12/10/2010] [Indexed: 11/22/2022]
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