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Cisneros-Bernal AY, Rodríguez-Gómez F, Flores-Villela O, Fujita MK, Velasco JA, Fernández JA. Phylogeography supports lineage divergence for an endemic rattlesnake ( Crotalus ravus) of the Neotropical montane forest in the Trans-Mexican Volcanic Belt. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The formation of the Trans-Mexican Volcanic Belt (TMVB) and Pleistocene climatic fluctuations have been shown to influence the diversification of lineages and species distributed throughout central Mexico. In some taxa, however, evidence of lineage diversification is not easily recognized, as often is the case in reptiles. Here we present a phylogeographic study on a Mexican endemic rattlesnake species (Crotalus ravus), with the aim of understanding how distinct lineages are distributed across the TMVB. Genetic (mtDNA) and genomic (ddRADseq) data were generated from samples across the species’ range to evaluate phylogeographic structure, estimate phylogenetic relationships and divergence times, and perform environmental niche modeling (ENM). Both datasets recover strong phylogeographic structuring of two distinct lineages on an east-west axis, with an estimated Pleistocene divergence (~1.47 Myr). The ENM suggest that the distribution of the two lineages experienced expansion and reduction events throughout recent evolutionary time. We attribute the diversification of C. ravus lineages to geological events associated with the formation of the TMVB, as well as Quaternary climate changes, both of which have been previously recognized in co-distributed taxa in the TMVB. This work emphasizes the existence of cryptic diversification processes in a morphologically conserved species distributed in a region of complex climatic and orogenic heterogeneity.
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Affiliation(s)
- Antonio Yolocalli Cisneros-Bernal
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México , Circuito de los Posgrados S/N, coyoacán, 04510, Mexico City , Mexico
- Departamento de Biología Evolutiva, Universidad Nacional Autónoma de México, Mexico City , Circuito exterior, Ciudad Universitaria, Coyoacán, 04510 Mexico
- Totlok, A.C., Cerro del Agua, Integración Latinoamericana , Coyoacán, 04350, Mexico City , Mexico
| | - Flor Rodríguez-Gómez
- Departamento de Ingeniería Traslacional, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara , Blvd. Marcelino García Barragán 44430, Gadalajara, Jalisco , Mexico
| | - Oscar Flores-Villela
- Departamento de Biología Evolutiva, Universidad Nacional Autónoma de México, Mexico City , Circuito exterior, Ciudad Universitaria, Coyoacán, 04510 Mexico
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington , 501 S. Nedderman Drive 337 Life Science, Arlington, TX 76010-0498 , USA
| | - Julián A Velasco
- Instituto de Ciencias de la Atmósfera y Cambio Climático, Universidad Nacional Autónoma de México, Investigación Científica s/n, Ciudad Universitaria , Coyoacán, 04510 Mexico City , Mexico
| | - Jesús A Fernández
- Departamento de Recursos Naturales, Universidad Autónoma de Chihuahua , Periférico Francisco R. Almada km 1, Zootecnia 31415 Chihuahua , Mexico
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Benítez-Benítez C, Otero A, Ford KA, García-Moro P, Donadío S, Luceño M, Martín-Bravo S, Jiménez-Mejías P. An Evolutionary Study of Carex Subg. Psyllophorae (Cyperaceae) Sheds Light on a Strikingly Disjunct Distribution in the Southern Hemisphere, With Emphasis on Its Patagonian Diversification. FRONTIERS IN PLANT SCIENCE 2021; 12:735302. [PMID: 34819937 PMCID: PMC8606891 DOI: 10.3389/fpls.2021.735302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Carex subgenus Psyllophorae is an engaging study group due to its early diversification compared to most Carex lineages, and its remarkable disjunct distribution in four continents corresponding to three independent sections: sect. Psyllophorae in Western Palearctic, sect. Schoenoxiphium in Afrotropical region, and sect. Junciformes in South America (SA) and SW Pacific. The latter section is mainly distributed in Patagonia and the Andes, where it is one of the few Carex groups with a significant in situ diversification. We assess the role of historical geo-climatic events in the evolutionary history of the group, particularly intercontinental colonization events and diversification processes, with an emphasis on SA. We performed an integrative study using phylogenetic (four DNA regions), divergence times, diversification rates, biogeographic reconstruction, and bioclimatic niche evolution analyses. The crown age of subg. Psyllophorae (early Miocene) supports this lineage as one of the oldest within Carex. The diversification rate probably decreased over time in the whole subgenus. Geography seems to have played a primary role in the diversification of subg. Psyllophorae. Inferred divergence times imply a diversification scenario away from primary Gondwanan vicariance hypotheses and suggest long-distance dispersal-mediated allopatric diversification. Section Junciformes remained in Northern Patagonia since its divergence until Plio-Pleistocene glaciations. Andean orogeny appears to have acted as a northward corridor, which contrasts with the general pattern of North-to-South migration for temperate-adapted organisms. A striking niche conservatism characterizes the evolution of this section. Colonization of the SW Pacific took place on a single long-distance dispersal event from SA. The little ecological changes involved in the trans-Pacific disjunction imply the preadaptation of the group prior to the colonization of the SW Pacific. The high species number of the section results from simple accumulation of morphological changes (disparification), rather than shifts in ecological niche related to increased diversification rates (radiation).
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Affiliation(s)
- Carmen Benítez-Benítez
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Ana Otero
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL, United States
| | - Kerry A. Ford
- Allan Herbarium, Manaaki-Whenua Landcare Research, Lincoln, New Zealand
| | - Pablo García-Moro
- Department of Biology (Botany), Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Sabina Donadío
- Instituto de Botánica Darwinion (ANCEFN-CONICET), San Isidro, Argentina
| | - Modesto Luceño
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Santiago Martín-Bravo
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Pedro Jiménez-Mejías
- Department of Biology (Botany), Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
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Cordero RD, Jackson DA. Abiotic factors influence species co-occurrence patterns of lake fishes. J Anim Ecol 2021; 90:2859-2874. [PMID: 34498261 DOI: 10.1111/1365-2656.13587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 08/17/2021] [Indexed: 11/30/2022]
Abstract
Abiotic factors are recognized for their strong influence on community structure. Habitat diversity is related to resource availability that influences species richness and abundance. In lakes, surface area and depth have been used as measures of the size and diversity of habitat, and have strong effects on the structure of entire communities. We tested whether abiotic variables, related to habitat size, influence co-occurrence patterns of species pairs of fishes by analysing groups of lakes within a specific area and depth categories in two regions in Ontario, Canada. We used null models to obtain co-occurrence patterns and standard effect sizes for each species pair within each area and depth category. We estimated standard effect sizes relative to lake area or depth and determined whether species co-occurrence patterns change systematically as these measures of habitat increase. We evaluated groups of species where factors such as predation and habitat filtering have been shown to structure those assemblages, and we tested whether area and depth alter the species associations and our interpretation of these relationships. We found significant differences between the observed and expected distributions of regression slopes relating co-occurrences to area and depth in both regions across all species, which indicated the strong influence of both variables on the overall co-occurrence patterns. We observed a significant negative trend of the co-occurrence patterns across lake area categories for the predator-prey species, indicating that the effect of predation was stronger in smaller lakes, but it was reduced in larger lakes, possibly due to increased habitat and resource availability. We show that pooling results as done in standard community null models can lead to Type II errors due to the 'cancellation' of opposing ecological signals. Our results demonstrate the effect of environmental variables on species co-occurrence patterns, but the divergent results obtained between geographical regions suggest that such patterns are context-dependent. This study emphasizes the importance of considering abiotic factors in null models of species co-occurrence to obtain reliable and detailed information about the association patterns between species.
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Affiliation(s)
- Ruben D Cordero
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Donald A Jackson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Diversification and Evolutionary Histories of Patagonian Steppe Lizards. NATURAL AND SOCIAL SCIENCES OF PATAGONIA 2020. [DOI: 10.1007/978-3-030-42752-8_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Ruiz Barlett T, Martin GM, Laguna MF, Abramson G, Monjeau A. Climatic constraints and the distribution of Patagonian mice. J Mammal 2019. [DOI: 10.1093/jmammal/gyz149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Abstract
We generated potential distribution models for 14 sigmodontine rodent species that inhabit the Andean–Patagonian forest region and adjacent areas, and retrieved the main climatic variables responsible for these models. Our main objective was to compare these climatic variables and the distribution patterns generated for each species, and explore the effects of the physical environment in shaping the composition of rodent communities in the area. We retrieved a total of 1,215 records of species presence from 580 sites. Maxent was used to generate potential distribution models for the 14 rodent species studied. We used a total of 20 variables obtained from the WorldClim database, including elevation and 19 bioclimatic variables, in addition to normalized difference vegetation index (NDVI) and enhanced vegetation index (EVI). Our results showed a clear discrimination between two groups of rodents, one concentrated in the western part of our study area, with more humid climate and a rugged mountainous and discontinuous habitat, and another inhabiting the eastern, drier part of our study area, which appears to be more uniform in habitat characteristics. These groups showed a mosaic of phylogenetically non-related species from different tribes, that probably arrived or expanded into Patagonia during the last millennia. The overlap of all models showed the forest-steppe ecotone east of Nahuel Huapi Lake and south to −43° latitude as the area with the highest species richness (8–11 species). All species showed a high correspondence with temperature and precipitation that define patterns at a landscape scale, with little to very little information contained in the typical vegetation variables that would define local conditions.
En este trabajo generamos modelos de distribución potencial para cada especie de roedor sigmodontino que habita la región de los bosques andino-patagónicos y áreas adyacentes, identificando las principales variables climáticas que influyen en dichas distribuciones. Nuestro principal objetivo fue comparar las variables climáticas y los patrones de distribución generados para cada especie, y explorar los efectos del entorno físico en la composición de los ensambles de especies. Recopilamos un total de 1215 registros de presencia de especies de 580 sitios. Se utilizó MaxEnt para generar los modelos de distribución potencial de las 14 especies de roedores estudiadas, con 20 variables obtenidas de la base de datos WorldClim, incluida la elevación, 19 variables bioclimáticas, además del NDVI y EVI. Nuestros resultados muestran una clara discriminación entre dos grupos de roedores, uno concentrado en el área occidental, con un clima más húmedo y montañoso, y otro que habita en el área más seca del este. Curiosamente, estos grupos muestran un mosaico de especies, filogenéticamente no relacionadas y de diferentes tribus, que probablemente llegaron o se expandieron en la Patagonia durante los últimos milenios. La superposición de todos los modelos muestra el ecotono bosque-estepa, al este del lago Nahuel Huapi y hacia el sur hasta los -43°, como la zona más rica en especies (8 a 11 especies). Todas las especies muestran una alta correspondencia con las variables ambientales (temperatura y precipitación) que definen patrones a escala del paisaje, con muy poca información contenida en las variables típicas de la vegetación que definirían las condiciones locales.
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Affiliation(s)
| | - Gabriel M Martin
- Centro de Investigación Esquel de Montaña y Estepa Patagónica (CIEMEP), CONICET – Universidad Nacional de la Patagonia, Roca 780 CP 9200, Esquel, Chubut, Argentina
- Laboratorio de Investigaciones en Evolución y Biodiversidad (LIEB), Facultad de Ciencias Naturales y Ciencias de la Salud, CP9200, Esquel, Chubut, Argentina
| | - María Fabiana Laguna
- Centro Atómico Bariloche and CONICET, R8402AGP San Carlos de Bariloche, Argentina
| | - Guillermo Abramson
- Centro Atómico Bariloche and CONICET, R8402AGP San Carlos de Bariloche, Argentina
- Instituto Balseiro, R8402AGP San Carlos de Bariloche, Argentina
| | - Adrián Monjeau
- Fundacion Bariloche and CONICET, R8402AGP, San Carlos de Bariloche, Argentina
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Sunny A, Gandarilla-Aizpuro FJ, Monroy-Vilchis O, Zarco-Gonzalez MM. Potential distribution and habitat connectivity of Crotalus triseriatus in Central Mexico. HERPETOZOA 2019. [DOI: 10.3897/herpetozoa.32.e36361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The dusky rattlesnake, Crotalustriseriatus, used to be very abundant in many parts of the highlands of central Mexico, but with the increasing human population and associated activities, the rattlesnake habitats and populations have suffered drastic reductions and fragmentation. At the moment, the most important habitat features, associated with the presence of C.triseriatus, the current potential distribution and the landscape connectivity amongst the populations of the State of Mexico and Mexico City, are unknown. Therefore, we used the maximum entropy modelling software (MAXENT) to analyse the current potential distribution and most important habitat features, associated with the presence of the species. The variables with the highest contribution to the model were: proportion of Abies forest, minimum temperature of coldest month, maximum temperature of the warmest month, proportion of Pinus forest and annual precipitation. Furthermore, we found connectivity corridors only within mountain chains. Our results highlight the necessity for conserving the patches of Abies forest and preserving the populations of C.triseriatus and the connectivity of the landscape.
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Kelt DA, Heske EJ, Lambin X, Oli MK, Orrock JL, Ozgul A, Pauli JN, Prugh LR, Sollmann R, Sommer S. Advances in population ecology and species interactions in mammals. J Mammal 2019. [DOI: 10.1093/jmammal/gyz017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
AbstractThe study of mammals has promoted the development and testing of many ideas in contemporary ecology. Here we address recent developments in foraging and habitat selection, source–sink dynamics, competition (both within and between species), population cycles, predation (including apparent competition), mutualism, and biological invasions. Because mammals are appealing to the public, ecological insight gleaned from the study of mammals has disproportionate potential in educating the public about ecological principles and their application to wise management. Mammals have been central to many computational and statistical developments in recent years, including refinements to traditional approaches and metrics (e.g., capture-recapture) as well as advancements of novel and developing fields (e.g., spatial capture-recapture, occupancy modeling, integrated population models). The study of mammals also poses challenges in terms of fully characterizing dynamics in natural conditions. Ongoing climate change threatens to affect global ecosystems, and mammals provide visible and charismatic subjects for research on local and regional effects of such change as well as predictive modeling of the long-term effects on ecosystem function and stability. Although much remains to be done, the population ecology of mammals continues to be a vibrant and rapidly developing field. We anticipate that the next quarter century will prove as exciting and productive for the study of mammals as has the recent one.
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Affiliation(s)
- Douglas A Kelt
- Department of Wildlife, Fish, & Conservation Biology, University of California, Davis, CA, USA
| | - Edward J Heske
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Xavier Lambin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Madan K Oli
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - John L Orrock
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA
| | - Arpat Ozgul
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Jonathan N Pauli
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, WI, USA
| | - Laura R Prugh
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, USA
| | - Rahel Sollmann
- Department of Wildlife, Fish, & Conservation Biology, University of California, Davis, CA, USA
| | - Stefan Sommer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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Nicola MV, Johnson LA, Pozner R. Unraveling patterns and processes of diversification in the South Andean-Patagonian Nassauvia subgenus Strongyloma (Asteraceae, Nassauvieae). Mol Phylogenet Evol 2019; 136:164-182. [PMID: 30858079 DOI: 10.1016/j.ympev.2019.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 02/11/2019] [Accepted: 03/07/2019] [Indexed: 12/26/2022]
Abstract
Congruence among different sources of data is highly desirable in phylogenetic analyses. However, plastid and nuclear DNA may record different evolutionary processes such that incongruence among results from these sources can help unravel complex evolutionary histories. That is the case of Nassauvia subgenus Strongyloma (Asteraceae), a taxon with five putative species distributed in the southern Andes and Patagonian steppe. Morphometric and phylogeographic information cast doubt on the integrity of its species, and previous molecular data even questioned the monophyly of the subgenus. We tested those questions using plastid and nuclear DNA sequences by the application of different methods such as phylogenetic trees, networks, a test of genealogical sorting, an analysis of population structure, calibration of the trees, and hybridization test, assembling non-synchronous incongruent results at subgenus and species levels in a single reconstruction. The integration of our molecular analyses and previous taxonomic, morphological, and molecular studies support subgenus Strongyloma as a monophyletic group. However, the topology of the nuclear trees and the evidence of polyploids within subgenus Nassauvia, suggest a hypothetical origin and initial radiation of Nassauvia related to an ancient hybridization event that occurred around 17-6.3 Myr ago near the Andes in west-central Patagonia. Plastid data suggest a recent diversification within subgenus Strongyloma, at most 9.8 Myr ago, towards the Patagonian steppe east of the Andes. These processes cause phylogenies to deviate from the species tree since each putative species lack exclusive ancestry. The non-monophyly of its species using both plastid and nuclear data is caused mainly by incomplete lineage sorting occurred since the Miocene. The final uplift of the Andes and Pliocene-Pleistocene glacial-interglacial and its consequences on the landscape and climate structured the genetic composition of this group of plants in the Patagonian steppe. The molecular data presented here agree with previous morphological studies, in that the five putative species typically accepted in this subgenus are not independent taxa. This study emphasizes that adding more than one sequence per species, not combining data with dissimilar inheritance patterns without first performed incongruence tests, exploring data through different methodologies, considering the timing of events, and searching for the causes of poorly resolved and/or incongruent phylogenies help to reveal complex biological underlying processes, which might otherwise remain hidden.
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Affiliation(s)
- Marcela V Nicola
- Instituto de Botánica Darwinion (CONICET-ANCEFN), Labardén 200, C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina.
| | - Leigh A Johnson
- Department of Biology and Bean Life Science Museum, 4102 LSB, Brigham Young University, Provo, UT 84602, USA
| | - Raúl Pozner
- Instituto de Botánica Darwinion (CONICET-ANCEFN), Labardén 200, C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina
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Sunny A, Monroy-Vilchis O, Zarco-González MM. Genetic diversity and structure of Crotalus triseriatus, a rattlesnake of central Mexico. J Genet 2018. [DOI: 10.1007/s12041-018-1004-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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10
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Heredia-Bobadilla RL, Monroy-Vilchis O, Zarco-González MM, Martínez-Gómez D, Mendoza-Martínez GD, Sunny A. Genetic variability and structure of an isolated population of Ambystoma altamirani, a mole salamander that lives in the mountains of one of the largest urban areas in the world. J Genet 2018; 96:873-883. [PMID: 29321345 DOI: 10.1007/s12041-017-0823-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Amphibians are globally threatened by habitat loss and fragmentation; species within the order Ambystoma are not the exception, as there are 18 species of mole salamanders in México, of which 16 are endemic and all species are under some national or international status of protection. The mole salamander, Ambystoma altamirani is a microendemic species, which is distributed in central México, within the trans-Mexican volcanic belt, and is one of the most threatened species due to habitat destruction and the introduction of exotic species. Nine microsatellite markers were used to determine the genetic structure, genetic variability, effective population size, presence of bottlenecks and inbreeding coefficient of one population of A. altamirani to generate information which might help to protect and conserve this threatened species. We found two genetic subpopulations with significant level of genetic structure (FST = 0.005) and high levels of genetic variability (Ho = 0.883; He = 0.621); we also found a small population size (Ne = 8.8), the presence of historical (M = 0.486) and recent bottlenecks under IAM and TPM models, with a low, but significant coefficient of inbreeding (FIS = -0.451). This information will help us to raise conservation strategies of this microendemic mole salamander species.
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Affiliation(s)
- Rosa-Laura Heredia-Bobadilla
- Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México, Instituto literario # 100, Colonia Centro, CP 50000 Toluca, Estado de México, México.
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Labaroni CA, Malleret MM, Novillo A, Ojeda A, Rodriguez D, Cuello P, Ojeda R, Dardo Martí, Lanzone C. Karyotypic variation in the Andean rodent Phyllotisxanthopygus (Waterhouse, 1837) (Rodentia, Cricetidae, Sigmodontinae). COMPARATIVE CYTOGENETICS 2014; 8:369-381. [PMID: 25610549 PMCID: PMC4296722 DOI: 10.3897/compcytogen.v8i4.8115] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 10/01/2014] [Indexed: 10/26/2023]
Abstract
Phyllotisxanthopygus (Waterhouse, 1837) is an Andean rodent endemic to South America. Despite its wide geographical distribution in Argentina, few individuals have been studied on the cytogenetic level and only through conventional staining. In this work, chromosome characterization of Argentine samples of this species was performed using solid staining, C-banding and base-specific fluorochromes. Twenty two specimens were analyzed, collected in the provinces of Jujuy, Catamarca, and the north and south of Mendoza. All studied specimens showed 2n=38, having mostly the bi-armed autosomes, metacentric or submetacentric. Fundamental Number varied between 70 and 72. These changes were due to the presence of chromosome heteromorphisms in individuals from southern Mendoza and Jujuy. C-banding revealed pericentromeric blocks of constitutive heterochromatin in most chromosomes. Acrocentric chromosomes involved in heteromorphisms showed high variation in the amount of heterochromatin within and among populations. Additionally, banding with fluorochromes (DAPI and chromomycin A3) revealed homologous localization of AT and GC rich regions among chromosomes of the different populations analyzed. Comparisons among heteromorphic pairs suggested, however, that the variation might be the result of complex chromosome rearrangements, involving possibly amplifications and/or deletions of heterochromatic segments. These results are in accordance with molecular studies that indicate genetic variability within and among the populations of this taxon.
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Affiliation(s)
- Carolina Alicia Labaroni
- Laboratorio de Genética Evolutiva, IBS (CONICET-UNaM), Félix de Azara 1552, CP3300 Posadas, Misiones, Argentina
| | - Matías Maximiliano Malleret
- Laboratorio de Genética Evolutiva, IBS (CONICET-UNaM), Félix de Azara 1552, CP3300 Posadas, Misiones, Argentina
| | - Agustina Novillo
- Grupo de Investigaciones de la Biodiversidad (GiB), IADIZA, CONICET, CCT-Mendoza, CC 507, CP5500 Mendoza, Argentina, Instituto Argentino de Zonas Áridas
| | - Agustina Ojeda
- Grupo de Investigaciones de la Biodiversidad (GiB), IADIZA, CONICET, CCT-Mendoza, CC 507, CP5500 Mendoza, Argentina, Instituto Argentino de Zonas Áridas
| | - Daniela Rodriguez
- Grupo de Investigaciones de la Biodiversidad (GiB), IADIZA, CONICET, CCT-Mendoza, CC 507, CP5500 Mendoza, Argentina, Instituto Argentino de Zonas Áridas
| | - Pablo Cuello
- Grupo de Investigaciones de la Biodiversidad (GiB), IADIZA, CONICET, CCT-Mendoza, CC 507, CP5500 Mendoza, Argentina, Instituto Argentino de Zonas Áridas
| | - Ricardo Ojeda
- Grupo de Investigaciones de la Biodiversidad (GiB), IADIZA, CONICET, CCT-Mendoza, CC 507, CP5500 Mendoza, Argentina, Instituto Argentino de Zonas Áridas
| | - Dardo Martí
- Laboratorio de Genética Evolutiva, IBS (CONICET-UNaM), Félix de Azara 1552, CP3300 Posadas, Misiones, Argentina
| | - Cecilia Lanzone
- Laboratorio de Genética Evolutiva, IBS (CONICET-UNaM), Félix de Azara 1552, CP3300 Posadas, Misiones, Argentina
- Grupo de Investigaciones de la Biodiversidad (GiB), IADIZA, CONICET, CCT-Mendoza, CC 507, CP5500 Mendoza, Argentina, Instituto Argentino de Zonas Áridas
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Nicola MV, Sede SM, Pozner R, Johnson LA. Phylogeography and palaeodistribution modelling of Nassauvia subgenus Strongyloma (Asteraceae): exploring phylogeographical scenarios in the Patagonian steppe. Ecol Evol 2014; 4:4270-86. [PMID: 25540689 PMCID: PMC4267866 DOI: 10.1002/ece3.1268] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/04/2014] [Indexed: 11/22/2022] Open
Abstract
The Patagonian steppe is an immense, cold, arid region, yet phylogeographically understudied. Nassauvia subgen. Strongyloma is a characteristic element of the steppe, exhibiting a continuum of morphological variation. This taxon provides a relevant phylogeographical model not only to understand how past environmental changes shaped the genetic structure of its populations, but also to explore phylogeographical scenarios at the large geographical scale of the Patagonian steppe. Here, we (1) assess demographic processes and historical events that shaped current geographic patterns of haplotypic diversity; (2) analyze hypotheses of isolation in refugia, fragmentation of populations, and/or colonization of available areas during Pleistocene glaciations; and (3) model extant and palaeoclimatic distributions to support inferred phylogeographical patterns. Chloroplast intergenic spacers, rpl32–trnL and trnQ–5′rps16, were sequenced for 372 individuals from 63 populations. Nested clade analysis, analyses of molecular variance, and neutrality tests were performed to assess genetic structure and range expansion. The present potential distribution was modelled and projected onto a last glacial maximum (LGM) model. Of 41 haplotypes observed, ten were shared among populations associated with different morphological variants. Populations with highest haplotype diversity and private haplotypes were found in central-western and south-eastern Patagonia, consistent with long-term persistence in refugia during Pleistocene. Palaeomodelling suggested a shift toward the palaeoseashore during LGM; new available areas over the exposed Atlantic submarine platform were colonized during glaciations with postglacial retraction of populations. A scenario of fragmentation and posterior range expansion may explain the observed patterns in the center of the steppe, which is supported by palaeomodelling. Northern Patagonian populations were isolated from southern populations by the Chubut and the Deseado river basins during glaciations. Pleistocene glaciations indirectly impacted the distribution, demography, and diversification of subgen. Strongyloma through decreased winter temperatures and water availability in different areas of its range.
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Affiliation(s)
- Marcela V Nicola
- Instituto de Botánica Darwinion C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina
| | - Silvana M Sede
- Instituto de Botánica Darwinion C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina
| | - Raúl Pozner
- Instituto de Botánica Darwinion C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina
| | - Leigh A Johnson
- Department of Biology and Bean Life Science Museum, Brigham Young University 4102 LSB, Provo, Utah, 84602, USA
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Genetic diversity and structure of an endemic and critically endangered stream river salamander (Caudata: Ambystoma leorae) in Mexico. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0520-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Morando M, Avila LJ, Perez CH, Hawkins MA, Sites JW. A molecular phylogeny of the lizard genus Phymaturus (Squamata, Liolaemini): Implications for species diversity and historical biogeography of southern South America. Mol Phylogenet Evol 2013; 66:694-714. [DOI: 10.1016/j.ympev.2012.10.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 10/09/2012] [Accepted: 10/22/2012] [Indexed: 10/27/2022]
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15
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Schmidt AM, Jacklyn P, Korb J. Isolated in an ocean of grass: low levels of gene flow between termite subpopulations. Mol Ecol 2013; 22:2096-105. [PMID: 23419176 DOI: 10.1111/mec.12233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 12/16/2012] [Accepted: 12/18/2012] [Indexed: 11/30/2022]
Abstract
Habitat fragmentation is one of the most important causes of biodiversity loss, but many species are distributed in naturally patchy habitats. Such species are often organized in highly dynamic metapopulations or in patchy populations with high gene flow between subpopulations. Yet, there are also species that exist in stable patchy habitats with small subpopulations and presumably low dispersal rates. Here, we present population genetic data for the 'magnetic' termite Amitermes meridionalis, which show that short distances between subpopulations do not hinder exceptionally strong genetic differentiation (FST : 0.339; RST : 0.636). Despite the strong genetic differentiation between subpopulations, we did not find evidence for genetic impoverishment. We propose that loss of genetic diversity might be counteracted by a long colony life with low colony turnover. Indeed, we found evidence for the inheritance of colonies by so-called 'replacement reproductives'. Inhabiting a mound for several generations might result in loss of gene diversity within a colony but maintenance of gene diversity at the subpopulation level.
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Affiliation(s)
- Anna M Schmidt
- Department of Behavioral Biology, University of Osnabrueck, Osnabrueck, Germany.
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16
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Turchetto-Zolet AC, Pinheiro F, Salgueiro F, Palma-Silva C. Phylogeographical patterns shed light on evolutionary process in South America. Mol Ecol 2012; 22:1193-213. [PMID: 23279129 DOI: 10.1111/mec.12164] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 10/31/2012] [Accepted: 11/06/2012] [Indexed: 11/28/2022]
Abstract
The South American continent is composed of several biogeographical regions harbouring the highest biodiversity on the globe, encompassing five of the world's biodiversity 'hot spots'. Nonetheless, the patterns and processes responsible for shaping its astonishing species diversity are largely unknown. Here, we present a review of current South American phylogeographical knowledge based on published articles on this topic. An appraisal of the literature reveals emerging phylogeographical patterns in the biota of South America. The striking phylogeographical divergence observed among organism lineages in South American studies is suggestive of high levels of undocumented species diversity. The interplay between Pleistocene climatic oscillations and Pliocene/Miocene orogenic events has contributed to shaping the current diversity and distribution of modern lineages in both the tropical and temperate regions of South America. Although older divergence times were observed for a range of species, most herpetofauna underwent an intraspecific lineage split much earlier than other organisms. The geographical ranges of species associated with forest habitats were reduced mainly during glacial cycles, whereas species associated with open vegetation domains have shown variable responses to climatic oscillations. The results suggest a highly complex mosaic of phylogeographical patterns in South America. We suggest future research directions to promote a better understanding of the origin and maintenance of the South American biota.
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Affiliation(s)
- A C Turchetto-Zolet
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, IB/UFRGS, Porto Alegre, RS, Brazil
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Gallardo MH, Suárez-Villota EY, Nuñez JJ, Vargas RA, Haro R, Köhler N. Phylogenetic analysis and phylogeography of the tetraploid rodentTympanoctomys barrerae(Octodontidae): insights on its origin and the impact of Quaternary climate changes on population dynamics. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.02016.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Milton H. Gallardo
- Institute of Marine and Limnological Sciences; Universidad Austral de Chile; Casilla 567; Valdivia; Chile
| | | | - José J. Nuñez
- Institute of Marine and Limnological Sciences; Universidad Austral de Chile; Casilla 567; Valdivia; Chile
| | - Rodrigo A. Vargas
- Institute of Marine and Limnological Sciences; Universidad Austral de Chile; Casilla 567; Valdivia; Chile
| | - Ronie Haro
- Institute of Marine and Limnological Sciences; Universidad Austral de Chile; Casilla 567; Valdivia; Chile
| | - Nélida Köhler
- Institute of Environmental and Evolutionary Sciences; Universidad Austral de Chile; Valdivia; Chile
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González-Wevar CA, Hüne M, Cañete JI, Mansilla A, Nakano T, Poulin E. Towards a model of postglacial biogeography in shallow marine species along the Patagonian Province: lessons from the limpet Nacella magellanica (Gmelin, 1791). BMC Evol Biol 2012; 12:139. [PMID: 22871029 PMCID: PMC3582430 DOI: 10.1186/1471-2148-12-139] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/25/2012] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Patagonia extends for more than 84,000 km of irregular coasts is an area especially apt to evaluate how historic and contemporary processes influence the distribution and connectivity of shallow marine benthic organisms. The true limpet Nacella magellanica has a wide distribution in this province and represents a suitable model to infer the Quaternary glacial legacy on marine benthic organisms. This species inhabits ice-free rocky ecosystems, has a narrow bathymetric range and consequently should have been severely affected by recurrent glacial cycles during the Quaternary. We performed phylogeographic and demographic analyses of N. magellanica from 14 localities along its distribution in Pacific Patagonia, Atlantic Patagonia, and the Falkland/Malvinas Islands. RESULTS Mitochondrial (COI) DNA analyses of 357 individuals of N. magellanica revealed an absence of genetic differentiation in the species with a single genetic unit along Pacific Patagonia. However, we detected significant genetic differences among three main groups named Pacific Patagonia, Atlantic Patagonia and Falkland/Malvinas Islands. Migration rate estimations indicated asymmetrical gene flow, primarily from Pacific Patagonia to Atlantic Patagonia (Nem=2.21) and the Falkland/Malvinas Islands (Nem=16.6). Demographic reconstruction in Pacific Patagonia suggests a recent recolonization process (< 10 ka) supported by neutrality tests, mismatch distribution and the median-joining haplotype genealogy. CONCLUSIONS Absence of genetic structure, a single dominant haplotype, lack of correlation between geographic and genetic distance, high estimated migration rates and the signal of recent demographic growth represent a large body of evidence supporting the hypothesis of rapid postglacial expansion in this species in Pacific Patagonia. This expansion could have been sustained by larval dispersal following the main current system in this area. Lower levels of genetic diversity in inland sea areas suggest that fjords and channels represent the areas most recently colonized by the species. Hence recolonization seems to follow a west to east direction to areas that were progressively deglaciated. Significant genetic differences among Pacific, Atlantic and Falkland/Malvinas Islands populations may be also explained through disparities in their respective glaciological and geological histories. The Falkland/Malvinas Islands, more than representing a glacial refugium for the species, seems to constitute a sink area considering the strong asymmetric gene flow detected from Pacific to Atlantic sectors. These results suggest that historical and contemporary processes represent the main factors shaping the modern biogeography of most shallow marine benthic invertebrates inhabiting the Patagonian Province.
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Affiliation(s)
- Claudio A González-Wevar
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras # 3425, Ñuñoa, Santiago, Chile
| | - Mathias Hüne
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras # 3425, Ñuñoa, Santiago, Chile
- Departamento de Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile
| | - Juan I Cañete
- Departamento de Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile
| | - Andrés Mansilla
- Departamento de Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile
| | - Tomoyuki Nakano
- Seto Marine Biological Laboratory, Field Science Education and Research Centre, Kyoto Univeristy, 459 Shirahama, Nishimuro, Wakayama, 649-2211, Japan
| | - Elie Poulin
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras # 3425, Ñuñoa, Santiago, Chile
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Palma RE, Boric-Bargetto D, Torres-Pérez F, Hernández CE, Yates TL. Glaciation effects on the phylogeographic structure of Oligoryzomys longicaudatus (Rodentia: Sigmodontinae) in the southern Andes. PLoS One 2012; 7:e32206. [PMID: 22396751 PMCID: PMC3291571 DOI: 10.1371/journal.pone.0032206] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 01/24/2012] [Indexed: 12/04/2022] Open
Abstract
The long-tailed pygmy rice rat Oligoryzomys longicaudatus (Sigmodontinae), the major reservoir of Hantavirus in Chile and Patagonian Argentina, is widely distributed in the Mediterranean, Temperate and Patagonian Forests of Chile, as well as in adjacent areas in southern Argentina. We used molecular data to evaluate the effects of the last glacial event on the phylogeographic structure of this species. We examined if historical Pleistocene events had affected genetic variation and spatial distribution of this species along its distributional range. We sampled 223 individuals representing 47 localities along the species range, and sequenced the hypervariable domain I of the mtDNA control region. Aligned sequences were analyzed using haplotype network, bayesian population structure and demographic analyses. Analysis of population structure and the haplotype network inferred three genetic clusters along the distribution of O. longicaudatus that mostly agreed with the three major ecogeographic regions in Chile: Mediterranean, Temperate Forests and Patagonian Forests. Bayesian Skyline Plots showed constant population sizes through time in all three clusters followed by an increase after and during the Last Glacial Maximum (LGM; between 26,000-13,000 years ago). Neutrality tests and the "g" parameter also suggest that populations of O. longicaudatus experienced demographic expansion across the species entire range. Past climate shifts have influenced population structure and lineage variation of O. longicaudatus. This species remained in refugia areas during Pleistocene times in southern Temperate Forests (and adjacent areas in Patagonia). From these refugia, O. longicaudatus experienced demographic expansions into Patagonian Forests and central Mediterranean Chile using glacial retreats.
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Affiliation(s)
- R Eduardo Palma
- Centro de Estudios Avanzados en Ecología y Biodiversidad, CASEB, and Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
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20
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Castañeda-Rico S, León-Paniagua L, Ruedas LA, Vázquez-Domínguez E. High genetic diversity and extreme differentiation in the two remaining populations of Habromys simulatus. J Mammal 2011. [DOI: 10.1644/10-mamm-a-171.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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21
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Estimating habitat suitability for potential hantavirus reservoirs in north-western Patagonia using satellite imagery: Searching for the best predictive tools. Mamm Biol 2011. [DOI: 10.1016/j.mambio.2011.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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22
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Masello JF, Quillfeldt P, Munimanda GK, Klauke N, Segelbacher G, Schaefer HM, Failla M, Cortés M, Moodley Y. The high Andes, gene flow and a stable hybrid zone shape the genetic structure of a wide-ranging South American parrot. Front Zool 2011; 8:16. [PMID: 21672266 PMCID: PMC3142489 DOI: 10.1186/1742-9994-8-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 06/15/2011] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND While the gene flow in some organisms is strongly affected by physical barriers and geographical distance, other highly mobile species are able to overcome such constraints. In southern South America, the Andes (here up to 6,900 m) may constitute a formidable barrier to dispersal. In addition, this region was affected by cycles of intercalating arid/moist periods during the Upper/Late Pleistocene and Holocene. These factors may have been crucial in driving the phylogeographic structure of the vertebrate fauna of the region. Here we test these hypotheses in the burrowing parrot Cyanoliseus patagonus (Aves, Psittaciformes) across its wide distributional range in Chile and Argentina. RESULTS Our data show a Chilean origin for this species, with a single migration event across the Andes during the Upper/Late Pleistocene, which gave rise to all extant Argentinean mitochondrial lineages. Analyses suggest a complex population structure for burrowing parrots in Argentina, which includes a hybrid zone that has remained stable for several thousand years. Within this zone, introgression by expanding haplotypes has resulted in the evolution of an intermediate phenotype. Multivariate regressions show that present day climatic variables have a strong influence on the distribution of genetic heterogeneity, accounting for almost half of the variation in the data. CONCLUSIONS Here we show how huge barriers like the Andes and the regional environmental conditions imposed constraints on the ability of a parrot species to colonise new habitats, affecting the way in which populations diverged and thus, genetic structure. When contact between divergent populations was re-established, a stable hybrid zone was formed, functioning as a channel for genetic exchange between populations.
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Affiliation(s)
- Juan F Masello
- Max Planck Institute for Ornithology, Vogelwarte Radolfzell, Radolfzell, Germany
| | - Petra Quillfeldt
- Max Planck Institute for Ornithology, Vogelwarte Radolfzell, Radolfzell, Germany
| | - Gopi K Munimanda
- Konrad Lorenz Institute for Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Austria
| | - Nadine Klauke
- Department of Evolutionary Biology and Animal Ecology, University of Freiburg, Germany
| | - Gernot Segelbacher
- Department of Wildlife Ecology and Management, University of Freiburg, Germany
| | - H Martin Schaefer
- Department of Evolutionary Biology and Animal Ecology, University of Freiburg, Germany
| | | | - Maritza Cortés
- Laboratorio de Ecología y Diversidad de Aves Marinas, Universidad Católica del Norte, Coquimbo, Chile
| | - Yoshan Moodley
- Konrad Lorenz Institute for Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Austria
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Xu J, Pérez-Losada M, Jara CG, Crandall KA. Pleistocene glaciation leaves deep signature on the freshwater crab Aegla alacalufi in Chilean Patagonia. Mol Ecol 2011; 18:904-18. [PMID: 19207249 DOI: 10.1111/j.1365-294x.2008.04070.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Quaternary glacial cycles have played an important role in shaping the biodiversity in temperate regions. This is well documented in Northern Hemisphere, but much less understood for Southern Hemisphere. We used mitochondrial DNA and nuclear elongation factor 1α intron sequences to examine the Pleistocene glacial impacts on the phylogeographical pattern of the freshwater crab Aegla alacalufi in Chilean Patagonia. Phylogenetic analyses, which separated the glaciated populations on eastern continent into a north group (seven populations) and a south group (one population), revealed a shallow phylogenetic structure in the north group but a deep one in the non-glaciated populations on western islands, indicating the significant influence of glaciation on these populations. Phylogenies also identified the Yaldad population on Chiloé Island as a potentially unrecognized new species. The non-glaciated populations showed higher among population genetic divergence than the glaciated ones, but lower population genetic diversity was not detected in the latter. The two glaciated groups, which diverged from the non-glaciated populations at ~96,800-29,500 years ago and ~104,200-73,800 years ago, respectively, seem to have different glacial refugia. Unexpectedly, the non-glaciated islands did not serve as refugia for them. Demographic expansion was detected in the glaciated north group, with a constant population increase after the last glacial maximum. Nested clade analyses suggest a possible colonization from western islands to eastern continent. After arriving on the continent and surviving the last glacial period there, populations likely have expanded from high to low altitude, following the flood of melting ice. Aegla alacalufi genetic diversity has been primarily affected by Pleistocene glaciation and minimally by drainage isolation.
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Affiliation(s)
- Jiawu Xu
- Department of Biology & Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA.
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SÉRSIC ALICIAN, COSACOV ANDREA, COCUCCI ANDREAA, JOHNSON LEIGHA, POZNER RAÚL, AVILA LUCIANOJ, SITES Jr. JACKW, MORANDO MARIANA. Emerging phylogeographical patterns of plants and terrestrial vertebrates from Patagonia. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01656.x] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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PARDIÑAS ULYSESFJ, TETA PABLO, D'ELÍA GUILLERMO, LESSA ENRIQUEP. The evolutionary history of sigmodontine rodents in Patagonia and Tierra del Fuego. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01679.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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González-Wevar CA, Nakano T, Cañete JI, Poulin E. Concerted genetic, morphological and ecological diversification in Nacella limpets in the Magellanic Province. Mol Ecol 2011; 20:1936-51. [PMID: 21418364 DOI: 10.1111/j.1365-294x.2011.05065.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Common inhabitants of Antarctic and Subantarctic rocky shores, the limpet genus Nacella, includes 15 nominal species distributed in different provinces of the Southern Ocean. The Magellanic Province represents the area with the highest diversity of the genus. Phylogenetic reconstructions showed an absence of reciprocal monophyly and high levels of genetic identity among nominal species in this Province and therefore imply a recent diversification in southern South America. Because most of these taxa coexist along their distribution range with clear differences in their habitat preferences, Nacella is a suitable model to explore diversification mechanisms in an area highly affected by recurrent Pleistocene continental ice cap advances and retreats. Here, we present genetic and morphological comparisons among sympatric Magellanic nominal species of Nacella. We amplified a fragment of the COI gene for 208 individuals belonging to seven sympatric nominal species and performed geometric morphometric analyses of their shells. We detected a complete congruence between genetic and morphological results, leading us to suggest four groups of Nacella among seven analysed nominal species. Congruently, each of these groups was related to different habitat preferences such as bathymetric range and substrate type. A plausible explanation for these results includes an ecologically based allopatric speciation process in Nacella. Major climatic changes during the Plio-Pleistocene glacial cycles may have enhanced differentiation processes. Finally, our results indicate that the systematics of the group requires a deep revision to re-evaluate the taxonomy of Nacella and to further understand the Pleistocene legacy of the glacial cycles in the southern tip of South America.
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Affiliation(s)
- C A González-Wevar
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras # 3425, Ñuñoa, Santiago, Chile.
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Phylogeography of the Patagonian otter Lontra provocax: adaptive divergence to marine habitat or signature of southern glacial refugia? BMC Evol Biol 2011; 11:53. [PMID: 21356052 PMCID: PMC3056781 DOI: 10.1186/1471-2148-11-53] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 02/28/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A number of studies have described the extension of ice cover in western Patagonia during the Last Glacial Maximum, providing evidence of a complete cover of terrestrial habitat from 41°S to 56°S and two main refugia, one in south-eastern Tierra del Fuego and the other north of the Chiloé Island. However, recent evidence of high genetic diversity in Patagonian river species suggests the existence of aquatic refugia in this region. Here, we further test this hypothesis based on phylogeographic inferences from a semi-aquatic species that is a top predator of river and marine fauna, the huillín or Southern river otter (Lontra provocax). RESULTS We examined mtDNA sequences of the control region, ND5 and Cytochrome-b (2151 bp in total) in 75 samples of L. provocax from 21 locations in river and marine habitats. Phylogenetic analysis illustrates two main divergent clades for L. provocax in continental freshwater habitat. A highly diverse clade was represented by haplotypes from the marine habitat of the Southern Fjords and Channels (SFC) region (43°38' to 53°08'S), whereas only one of these haplotypes was paraphyletic and associated with northern river haplotypes. CONCLUSIONS Our data support the hypothesis of the persistence of L. provocax in western Patagonia, south of the ice sheet limit, during last glacial maximum (41°S latitude). This limit also corresponds to a strong environmental change, which might have spurred L. provocax differentiation between the two environments.
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Túnez JI, Cappozzo HL, Nardelli M, Cassini MH. Population genetic structure and historical population dynamics of the South American sea lion, Otaria flavescens, in north-central Patagonia. Genetica 2010; 138:831-41. [DOI: 10.1007/s10709-010-9466-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 05/24/2010] [Indexed: 11/25/2022]
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Zemlak TS, Habit EM, Walde SJ, Carrea C, Ruzzante DE. Surviving historical Patagonian landscapes and climate: molecular insights from Galaxias maculatus. BMC Evol Biol 2010. [PMID: 20211014 DOI: 10.1186/1471–2148–10–67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The dynamic geological and climatic histories of temperate South America have played important roles in shaping the contemporary distributions and genetic diversity of endemic freshwater species. We use mitochondria and nuclear sequence variation to investigate the consequences of mountain barriers and Quaternary glacial cycles for patterns of genetic diversity in the diadromous fish Galaxias maculatus in Patagonia (approximately 300 individuals from 36 locations). RESULTS Contemporary populations of G. maculatus, east and west of the Andes in Patagonia, represent a single monophyletic lineage comprising several well supported groups. Mantel tests using control region data revealed a strong positive relationship when geographic distance was modeled according to a scenario of marine dispersal. (r = 0.69, P = 0.055). By contrast, direct distance between regions was poorly correlated with genetic distance (r = -0.05, P = 0.463). Hierarchical AMOVAs using mtDNA revealed that pooling samples according to historical (pre-LGM) oceanic drainage (Pacific vs. Atlantic) explained approximately four times more variance than pooling them into present-day drainage (15.6% vs. 3.7%). Further post-hoc AMOVA tests revealed additional genetic structure between populations east and west of the Chilean Coastal Cordillera (coastal vs. interior). Overall female effective population size appears to have remained relatively constant until roughly 0.5 Ma when population size rapidly increased several orders of magnitude [100x (60x-190x)] to reach contemporary levels. Maximum likelihood analysis of nuclear alleles revealed a poorly supported gene tree which was paraphyletic with respect to mitochondrial-defined haplogroups. CONCLUSIONS First diversifying in the central/north-west region of Patagonia, G. maculatus extended its range into Argentina via the southern coastal regions that join the Pacific and Atlantic oceans. More recent gene flow between northern populations involved the most ancient and most derived lineages, and was likely facilitated by drainage reversal(s) during one or more cooling events of the late Pleistocene. Overall female effective population size represents the end result of a widespread and several hundred-fold increase over approximately 0.5 Ma, spanning several climatic fluctuations of the Pleistocene. The minor influence of glacial cycles on the genetic structure and diversity of G. maculatus likely reflects the access to marine refugia during repeated bouts of global cooling. Evidence of genetic structure that was detected on a finer scale between lakes/rivers is most likely the result of both biological attributes (i.e., resident non-migratory behavior and/or landlocking and natal homing in diadromous populations), and the Coastal Cordillera as a dispersal barrier.
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Affiliation(s)
- Tyler S Zemlak
- Department of Biology, Dalhousie University, Halifax Nova Scotia, Canada.
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Zemlak TS, Habit EM, Walde SJ, Carrea C, Ruzzante DE. Surviving historical Patagonian landscapes and climate: molecular insights from Galaxias maculatus. BMC Evol Biol 2010; 10:67. [PMID: 20211014 PMCID: PMC2838892 DOI: 10.1186/1471-2148-10-67] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Accepted: 03/08/2010] [Indexed: 11/24/2022] Open
Abstract
Background The dynamic geological and climatic histories of temperate South America have played important roles in shaping the contemporary distributions and genetic diversity of endemic freshwater species. We use mitochondria and nuclear sequence variation to investigate the consequences of mountain barriers and Quaternary glacial cycles for patterns of genetic diversity in the diadromous fish Galaxias maculatus in Patagonia (~300 individuals from 36 locations). Results Contemporary populations of G. maculatus, east and west of the Andes in Patagonia, represent a single monophyletic lineage comprising several well supported groups. Mantel tests using control region data revealed a strong positive relationship when geographic distance was modeled according to a scenario of marine dispersal. (r = 0.69, P = 0.055). By contrast, direct distance between regions was poorly correlated with genetic distance (r = -0.05, P = 0.463). Hierarchical AMOVAs using mtDNA revealed that pooling samples according to historical (pre-LGM) oceanic drainage (Pacific vs. Atlantic) explained approximately four times more variance than pooling them into present-day drainage (15.6% vs. 3.7%). Further post-hoc AMOVA tests revealed additional genetic structure between populations east and west of the Chilean Coastal Cordillera (coastal vs. interior). Overall female effective population size appears to have remained relatively constant until roughly 0.5 Ma when population size rapidly increased several orders of magnitude [100× (60×-190×)] to reach contemporary levels. Maximum likelihood analysis of nuclear alleles revealed a poorly supported gene tree which was paraphyletic with respect to mitochondrial-defined haplogroups. Conclusions First diversifying in the central/north-west region of Patagonia, G. maculatus extended its range into Argentina via the southern coastal regions that join the Pacific and Atlantic oceans. More recent gene flow between northern populations involved the most ancient and most derived lineages, and was likely facilitated by drainage reversal(s) during one or more cooling events of the late Pleistocene. Overall female effective population size represents the end result of a widespread and several hundred-fold increase over approximately 0.5 Ma, spanning several climatic fluctuations of the Pleistocene. The minor influence of glacial cycles on the genetic structure and diversity of G. maculatus likely reflects the access to marine refugia during repeated bouts of global cooling. Evidence of genetic structure that was detected on a finer scale between lakes/rivers is most likely the result of both biological attributes (i.e., resident non-migratory behavior and/or landlocking and natal homing in diadromous populations), and the Coastal Cordillera as a dispersal barrier.
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Affiliation(s)
- Tyler S Zemlak
- Department of Biology, Dalhousie University, Halifax Nova Scotia, Canada.
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Hu XL, Cao GL, Xue RY, Zheng XJ, Zhang X, Duan HR, Gong CL. The complete mitogenome and phylogenetic analysis of Bombyx mandarina strain Qingzhou. Mol Biol Rep 2009; 37:2599-608. [DOI: 10.1007/s11033-009-9781-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Accepted: 08/19/2009] [Indexed: 11/27/2022]
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Jeong HC, Kim JA, Im HH, Jeong HU, Hong MY, Lee JE, Han YS, Kim I. Mitochondrial DNA sequence variation of the swallowtail butterfly, Papilio xuthus, and the cabbage butterfly, Pieris rapae. Biochem Genet 2009; 47:165-78. [PMID: 19184408 DOI: 10.1007/s10528-008-9214-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Accepted: 10/03/2008] [Indexed: 10/21/2022]
Abstract
We analyzed a portion of mitochondrial COI gene sequences (658 bp) to investigate the genetic diversity and geographic variation of the swallowtail butterfly, Papilio xuthus L. (Lepidoptera: Papilionidae), and the cabbage butterfly, Pieris rapae L. (Lepidoptera: Pieridae). Papilio xuthus showed a moderate level of sequence divergence (0.91% at maximum) in 15 haplotypes, whereas Pi. rapae showed a moderate to high level of sequence divergence (1.67% at maximum) in 30 haplotypes, compared with other relevant studies. Analyses of population genetic structure showed that most populations are not genetically differentiated in both species. The distribution pattern of both species appears to be consistent with category IV of the phylogeographic pattern sensu Avise: a phylogenetic continuity, an absence of regional isolation of mtDNA clones, and extensive distribution of close clones. The observed pattern of genetic diversity and geographic variation of the two butterfly species seem to reflect the abundant habitats, abundant host plants, and flying abilities in connection with the lack of historical biogeographic barriers.
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Affiliation(s)
- Heon Cheon Jeong
- Department of Biological Science, Andong National University, Andong, Republic of Korea
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Zemlak TS, Habit EM, Walde SJ, Battini MA, Adams EDM, Ruzzante DE. Across the southern Andes on fin: glacial refugia, drainage reversals and a secondary contact zone revealed by the phylogeographical signal of Galaxias platei in Patagonia. Mol Ecol 2008; 17:5049-61. [PMID: 19017262 DOI: 10.1111/j.1365-294x.2008.03987.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We employed DNA sequence variation at two mitochondrial (control region, COI) regions from 212 individuals of Galaxias platei (Pisces, Galaxiidae) collected throughout Patagonia (25 lakes/rivers) to examine how Andean orogeny and the climatic cycles throughout the Quaternary affected the genetic diversity and phylogeography of this species. Phylogenetic analyses revealed four deep genealogical lineages which likely represent the initial division of G. platei into eastern and western lineages by Andean uplift, followed by further subdivision of each lineage into separate glacial refugia by repeated Pleistocene glacial cycles. West of the Andes, refugia were likely restricted to the northern region of Patagonia with small relicts in the south, whereas eastern refugia appear to have been much larger and widespread, consisting of separate northern and southern regions that collectively spanned most of Argentinean Patagonia. The retreat of glacial ice following the last glacial maximum allowed re-colonization of central Chile from nonlocal refugia from the north and east, representing a region of secondary contact between all four glacial lineages. Northwestern glacial relicts likely followed pro-glacial lakes into central Chilean Patagonia, whereas catastrophic changes in drainage direction (Atlantic --> Pacific) for several eastern palaeolakes were the likely avenues for invasions from the east. These mechanisms, combined with evidence for recent, rapid and widespread population growth could explain the extensive contemporary distribution of G. platei throughout Patagonia.
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Affiliation(s)
- Tyler S Zemlak
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4J1.
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Morando M, Avila LJ, Turner CR, Sites JW. Molecular evidence for a species complex in the patagonian lizard Liolaemus bibronii and phylogeography of the closely related Liolaemus gracilis (Squamata: Liolaemini). Mol Phylogenet Evol 2007; 43:952-73. [PMID: 17116410 DOI: 10.1016/j.ympev.2006.09.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Revised: 09/14/2006] [Accepted: 09/18/2006] [Indexed: 11/25/2022]
Abstract
The lizard genus Liolaemus is endemic to temperate South America and includes 190 species. Liolaemus bibronii has a large geographic distribution and inhabits a great diversity of habitats, including the Monte, Steppe, and high Andean grassland environments. Liolaemus gracilis has a similar body size and shape to L. bibronii; the two are parapatrically distributed, and L. gracilis is also widely distributed. Here we use the mtDNA cytb sequence data of these two species to investigate lizard phylogeographic patterns in southern South America. L. bibronii is paraphyletic with respect to L. gracilis, Liolaemus ramirezae, Liolaemus robertmertensi and Liolaemus saxatilis; it is composed of many genetically different allopatric haploclades, some of which are reciprocally monophyletic. We also found evidence for introgression between L. bibronii and L. gracilis in the same area that introgression was hypothesized in the Liolaemus darwinii complex. We discuss the distribution of the major haploclades with inferences of their population histories, the concordance of these clades' distributions and histories with other lizard complexes studied with the same markers and methods, and taxonomic implications of these results.
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Affiliation(s)
- Mariana Morando
- CONICET-CENPAT, Boulevard Almirante Brown s/n, 9120, Puerto Madryn, Chubut, Argentina.
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González-Ittig RE, Patton JL, Gardenal CN. Analysis of Cytochrome-bNucleotide Diversity Confirms a Recent Range Expansion in Calomys musculinus (Rodentia, Muridae). J Mammal 2007. [DOI: 10.1644/06-mamm-a-091r1.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Ascunce MS, Hasson E, Mulligan CJ, Mudry MD. Mitochondrial sequence diversity of the southernmost extant New World monkey, Alouatta caraya. Mol Phylogenet Evol 2006; 43:202-15. [PMID: 17126568 DOI: 10.1016/j.ympev.2006.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 09/06/2006] [Accepted: 10/02/2006] [Indexed: 11/30/2022]
Abstract
Variability in mitochondrial DNA sequences was analyzed in the howler monkey, Alouatta caraya, in order to delineate evolutionary relationships among populations in the most southerly distributed New World monkey. Based on new and previously published sequence data, fourteen cytochrome b haplotypes were observed among 33 howlers sampled in Argentina, Paraguay and Brazil, and grouped in two main haplogroups. In northeastern Argentina and southern Paraguay, new sequence data on 73 specimens sampled from six localities gave 34 control region haplotypes that also clustered in two main haplogroups. At this southern distribution, both mitochondrial markers revealed the presence of two sympatric and differentiated clades that we interpret to be the consequence of a secondary contact between previously allopatric populations. Given evidence for a demographic expansion at the beginning of the Holocene 15,500-7000 years ago (Fu's test, F(S)=-12.137; P<0.001), we suggest that atleast two populations of A. caraya have colonized the southernmost range since the Holocene employing forested corridors on the Paraná and Paraguay Rivers.
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Affiliation(s)
- M S Ascunce
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab: 2, 4to.Piso, Buenos Aires, C1428EHA, Argentina.
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Ruzzante DE, Walde SJ, Cussac VE, Dalebout ML, Seibert J, Ortubay S, Habit E. Phylogeography of the Percichthyidae (Pisces) in Patagonia: roles of orogeny, glaciation, and volcanism. Mol Ecol 2006; 15:2949-68. [PMID: 16911213 DOI: 10.1111/j.1365-294x.2006.03010.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We used molecular evidence to examine the roles that vicariance mechanisms (mountain-building and drainage changes during the Pleistocene) have played in producing phylogeographical structure within and among South American fish species of the temperate perch family Percichthyidae. The percichthyids include two South American genera, Percichthys and Percilia, each containing several species, all of which are endemic to southern Argentina and Chile (Patagonia). Maximum-likelihood phylogenies constructed using mitochondrial DNA (mtDNA) control region haplotypes and nuclear GnRH3-2 intron allele sequences support the current taxonomy at the genus level (both Percichthys and Percilia form strongly supported, monophyletic clades) but indicate that species-level designations need revision. Phylogeographical patterns at the mtDNA support the hypothesis that the Andes have been a major barrier to gene flow. Most species diversity occurs in watersheds to the west of the Andes, together with some ancient divergences among conspecific populations. In contrast, only one species (Percichthys trucha) is found east of the Andes, and little to no phylogeographical structure occurs among populations in this region. Mismatch analyses of mtDNA sequences suggest that eastern populations last went through a major bottleneck c. 188 000 bp, a date consistent with the onset of the penultimate and largest Pleistocene glaciation in Patagonia. We suggest that eastern populations have undergone repeated founder-flush events as a consequence of glacial cycles, and that the shallow phylogeny is due to mixing during recolonization periods. The area of greater diversity west of the Andes lies outside the northern limit of the glaciers. mtDNA mismatch analysis of the genus Percilia which is restricted to this area suggests a long-established population at equilibrium. We conclude that patterns of genetic diversity in these South American genera have been primarily influenced by barriers to gene flow (Andean orogeny, and to a lesser extent, isolation in river drainages), and by glacial cycles, which have resulted in population contraction, re-arrangement of some watersheds, and the temporary breakdown of dispersal barriers among eastern river systems.
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Affiliation(s)
- Daniel E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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Piggott MP, Banks SC, Taylor AC. Population structure of brush-tailed rock-wallaby (Petrogale penicillata) colonies inferred from analysis of faecal DNA. Mol Ecol 2006; 15:93-105. [PMID: 16367833 DOI: 10.1111/j.1365-294x.2005.02784.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic data obtained using faecal DNA were used to elucidate the population structure of four brush-tailed rock-wallaby (Petrogale penicillata) colonies located in Wollemi National Park, New South Wales. The results suggested that the four sampled colonies are genetically differentiated and do not form a panmictic unit. Based on assignment tests, approximately 5% of sampled individuals were inferred to be dispersers and both male and female migrants were detected. Multilocus spatial autocorrelation analyses provided evidence for increased philopatry among females compared to males within the largest colony in the valley. Females in close spatial proximity were more genetically similar than expected under a random distribution of females, and females separated by more than 400 m were less genetically similar than expected. In contrast, there was no evidence of a significant clustering of related males. This suggests that within-colony dispersal is male biased. We also investigated the best strategies for conserving genetic diversity in this population. All of the four sampled colonies were found to contain distinct components of the genetic diversity of the Wolgan Valley P. penicillata population and loss of any colony is likely to result in the loss of unique alleles. Conservation and management plans should take into account that these colonies represent genetically differentiated discrete subpopulations. This approach is also the best strategy for maintaining the genetic diversity of the populations in this valley.
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Affiliation(s)
- M P Piggott
- Australian Centre for Biodiversity, Analysis, Policy and Management, School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia.
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Russo IRM, Chimimba CT, Bloomer P. MITOCHONDRIAL DNA DIFFERENTIATION BETWEEN TWO SPECIES OF AETHOMYS (RODENTIA: MURIDAE) FROM SOUTHERN AFRICA. J Mammal 2006. [DOI: 10.1644/05-mamm-a-222r3.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Roberts TE. History, ocean channels, and distance determine phylogeographic patterns in three widespread Philippine fruit bats (Pteropodidae). Mol Ecol 2006; 15:2183-99. [PMID: 16780434 DOI: 10.1111/j.1365-294x.2006.02928.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The comparative phylogeography of widespread, codistributed species provides unique insights into regional biodiversity and diversification patterns. I used partial DNA sequences of the mitochondrial genes ND2 and cyt b to investigate phylogeographic structure in three widespread Philippine fruit bats. Ptenochirus jagori is endemic to the oceanic region of the Philippines and is most abundant in lowland primary forest. Macroglossus minimus and Cynopterus brachyotis are most common in disturbed and open habitats and are not endemic. In all three, genetic differentiation is present at multiple spatial scales and is associated to some degree with Pleistocene landbridge island groups. In P. jagori and C. brachyotis, genetic distance is correlated with geographic distance; in C. brachyotis and M. minimus, it is correlated with the sea-crossing distance between islands. P. jagori has the least overall genetic structure of these three species, whereas C. brachyotis and M. minimus have more geographic association among haplotypes, suggesting that phylogeographic patterns are linked to ecology and habitat preference. However, contrary to expectation, the two widespread, disturbed habitat species have more structure than the endemic species. Mismatch distributions suggest rapid changes in effective population size in C. brachyotis and P. jagori, whereas M. minimus appears to be demographically more stable. Geologic and geographic history are important in structuring variation, and phylogeographic patterns are the result of dynamic long-term processes rather than simply reflecting current conditions.
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Affiliation(s)
- Trina E Roberts
- University of Chicago, Committee on Evolutionary Biology, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA.
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41
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Does Breeding Site Fidelity Drive Phenotypic and Genetic Sub-Structuring of a Population of Arctic Charr? Evol Ecol 2006. [DOI: 10.1007/s10682-005-2489-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Li A, Zhao Q, Tang S, Zhang Z, Pan S, Shen G. Molecular phylogeny of the domesticated silkworm,Bombyx mori, based on the sequences of mitochondrialcytochrome b genes. J Genet 2005; 84:137-42. [PMID: 16131713 DOI: 10.1007/bf02715839] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Pupae from the Chinese wild mulberry silkworm, Bombyx mandarina, and 11 representative strains of the domesticated silkworm, Bombyx mori were selected for preparation of mitochondrial DNA. The 5'-end fragments of cytochrome b genes (Cytb) were generated by polymerase chain reaction products and sequenced directly. The homologous sequences of the Japanese B. mandarina and three strains of B. mori were from the GenBank database. The sequences of the 16 silkworm strains were analysed with DNASTAR software and a phylogenic tree was constructed using PHYLIP software. The result showed that: (i) The sequence divergence between the strains of B. mori and the Japanese B. mandarina was larger (5.4%-5.8%) compared with that between strains of B. mori and the Chinese B. mandarina (0.8% -1.9%). Analysis of clustering also showed that the sequences of B. mori strains and Chinese B. mandarina clustered into group (B group), while that of Japanese B. mandarina (A group) was outside this cluster. This may be evidence for the hypothesis that B. mori originated from Chinese B. mandarina. (ii) Among 14 strains of B. mori, sequence divergence was small and the most divergence was seen between strains Yanhe-1 and Chuxiong, whose sequences branched off from those of the other B. mori strains on the phylogenetic tree. From this and from historical records, we infer that the strains Yanhe-1 and Chuxiong originated independently from southwest China.
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Affiliation(s)
- Ailing Li
- The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212 018, Jiangsu Province, China
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Hulva P, Horácek I, Strelkov PP, Benda P. Molecular architecture of Pipistrellus pipistrellus/Pipistrellus pygmaeus complex (Chiroptera: Vespertilionidae): further cryptic species and Mediterranean origin of the divergence. Mol Phylogenet Evol 2004; 32:1023-35. [PMID: 15288073 DOI: 10.1016/j.ympev.2004.04.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Revised: 04/06/2004] [Indexed: 11/26/2022]
Abstract
Previous genetic analyses have demonstrated that two phonic types of one of the most common European bats, the Common pipistrelle, belong to distinct species, although they are almost identical morphologically (45 kHz Pipistrellus pipistrellus and 55 kHz Pipistrellus pygmaeus). To reconstruct the history of the species complex and explain the codistribution of both forms in Europe and the Mediterranean, we performed phylogenetic analysis based on a 402-bp portion of the cytochrome b gene. Particular attention was paid to the eastern and southern parts of the range where no data were available. We found further distinctive allopatric haplotypes from Libya and Morocco. The difference of about 6-7% described in the Libyan population suggests the occurrence of a new species in the southern Mediterranean. The species status of Moroccan population is also discussed. The phylogeographic patterns obtained and analysis of fossil records support the hypothesis of expansion of both species into Europe from the Mediterranean region during the Holocene. The allopatric speciation model fits our data best. The paleobiographic scenario envisaged is corroborated also by molecular clock estimations and correlations with Late Neogene environmental changes in the Mediterranean region which ended with the Messinian salinity crisis.
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Affiliation(s)
- Pavel Hulva
- Department of Zoology, Charles University, Vinicná 7, 128 44 Prague 2, Czech Republic.
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Johnson JA, Toepfer JE, Dunn PO. Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie-chickens. Mol Ecol 2004; 12:3335-47. [PMID: 14629350 DOI: 10.1046/j.1365-294x.2003.02013.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Greater prairie-chickens (Tympanuchus cupido pinnatus) were once found throughout the tallgrass prairie of midwestern North America but over the last century these prairies have been lost or fragmented by human land use. As a consequence, many current populations of prairie-chickens have become isolated and small. This fragmentation of populations is expected to lead to reductions in genetic variation as a result of random genetic drift and a decrease in gene flow. As expected, we found that genetic variation at both microsatellite DNA and mitochondrial DNA (mtDNA) markers was reduced in smaller populations, particularly in Wisconsin. There was relatively little range-wide geographical structure (FST) when we examined mtDNA haplotypes but there was a significant positive relationship between genetic (FST) and geographical distance (isolation by distance). In contrast, microsatellite DNA loci revealed significant geographical structure (FST) and a weak effect of isolation by distance throughout the range. These patterns were much stronger when populations with reduced levels of genetic variability (Wisconsin) were removed from the analyses. This suggests that the effects of genetic drift were stronger than gene flow at microsatellite loci, whereas these forces were in range-wide equilibrium at mtDNA markers. These differences between the two molecular markers may be explained by a larger effective population size (Ne) for mtDNA, which is expected in species such as prairie-chickens that have female-biased dispersal and high levels of polygyny. Our results suggest that historic populations of prairie-chickens were once interconnected by gene flow but current populations are now isolated. Thus, maintaining gene flow may be important for the long-term persistence of prairie-chicken populations.
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Affiliation(s)
- Jeff A Johnson
- Department of Biological Sciences, University of Wisconsin-Milwaukee, PO Box 413, Milwaukee, WI 53201, USA
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Planes S, Fauvelot C. Isolation by distance and vicariance drive genetic structure of a coral reef fish in the Pacific Ocean. Evolution 2002; 56:378-99. [PMID: 11926506 DOI: 10.1111/j.0014-3820.2002.tb01348.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We studied the genetic diversity of a coral reef fish species to investigate the origin of the differentiation. A total of 727 Acanthurus triostegus collected from 15 locations throughout the Pacific were analyzed for 20 polymorphic loci. The genetic structure showed limited internal disequilibrium within each population; 3.7% of the loci showed significant Hardy-Weinberg disequilibrium, mostly associated with Adh*, and we subsequently removed this locus from further analysis of geographic pattern. The genetic structure of A. triostegus throughout the tropical Pacific Ocean revealed a strong geographic pattern. Overall, there was significant population differentiation (multilocus F(ST) = 0.199), which was geographically structured according to bootstraps of neighbor-joining analysis on Nei's unbiased genetic distances and AMOVA analysis. The genetic structure revealed five geographic groups in the Pacific Ocean: western Pacific (Guam, Philippines, Palau, and Great Barrier Reef); central Pacific (Solomons, New Caledonia, and Fiji); and three groups made up of the eastern populations, namely Hawaiian Archipelago (north), Marquesas (equatorial), and southern French Polynesia (south) that incorporates Clipperton Island located in the northeastern Pacific. In addition, heterozygosity values were found to be geographically structured with higher values grouped within Polynesian and Clipperton populations, which exhibited lower population size. Finally, the genetic differentiation (F(ST)) was significantly correlated with geographic distance when populations from the Hawaiian and Marquesas archipelagos were separated from all the other locations. These results show that patterns of differentiation vary within the same species according to the spatial scale, with one group probably issued from vicariance, whereas the other followed a pattern of isolation by distance. The geographic pattern for A. triostegus emphasizes the diversity of the evolutionary processes that lead to the present genetic structure with some being more influential in certain areas or according to a particular spatial scale.
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Affiliation(s)
- S Planes
- Ecole Pratique des Hautes Etudes-ESA CNRS 8046, Université de Perpignan, France.
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Planes S, Fauvelot C. ISOLATION BY DISTANCE AND VICARIANCE DRIVE GENETIC STRUCTURE OF A CORAL REEF FISH IN THE PACIFIC OCEAN. Evolution 2002. [DOI: 10.1554/0014-3820(2002)056[0378:ibdavd]2.0.co;2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Vallianatos M, Lougheed SC, Boag PT. Phylogeography and genetic characteristics of a putative secondary-contact zone of the loggerhead shrike in central and eastern North America. CAN J ZOOL 2001. [DOI: 10.1139/z01-157] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The loggerhead shrike (Lanius ludovicianus) is found throughout North America in grassland and open scrub habitats. We previously described four loggerhead shrike management units found in central and eastern North America within the geographic ranges of three subspecies, L. l. migrans, L. l. ludovicianus, and L. l. excubitorides. A contact zone has been suggested to occur between L. l. migrans and L. l. excubitorides. The present study uses mitochondrial DNA sequence data to explore historical, ecological, and geographical factors that may have played a role in the genetic differentiation of these four management units, and examines the evidence for and characteristics of the migransexcubitorides contact zone. Geographically discrete, monophyletic clades were not evident, but the distribution of haplotypes (especially those exceeding 10% overall frequency) indicated some phylogeographic structure that perhaps reflects an intermediate stage of differentiation between paraphyly and reciprocal monophyly. The contact zone between L. l. migrans and L. l. excubitorides is supported by the mixing of haplotypes unique to each of the hybridizing populations and intermediate frequencies of common haplotypes. We interpret these patterns as possibly reflecting the impact of both glacial refugial dynamics and anthropogenic changes to habitat in eastern North America.
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Schulte-Hostedde AI, Gibbs HL, Millar JS. Microgeographic genetic structure in the yellow-pine chipmunk (Tamias amoenus). Mol Ecol 2001; 10:1625-31. [PMID: 11472531 DOI: 10.1046/j.1365-294x.2001.01298.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
While there is evidence for broad-scale genetic structure in small mammals, few studies have used variable DNA-based genetic markers to examine genetic differentiation at microgeographic (tens of kilometres) scales. Yellow-pine chipmunks (Tamias amoenus) live in the heterogeneous landscape of the Rockies in southwest Alberta and are generally restricted to areas of low elevation. We used seven microsatellite loci to determine whether chipmunks show evidence of population genetic structure among three closely situated sites (< 15 km) in the Kananaskis Valley, Alberta. We found evidence for genetic structure in the form of significant differences in allele frequencies among populations and significantly nonzero values of FST for both overall and pairwise population comparisons. However, FIS values for each population were not significantly different from zero, suggesting little evidence for inbreeding within populations. Genetic differentiation probably occurs as a result of the strong effect of drift in very small (N(e) approximately 25) populations of these animals even in the face of substantial immigration rates.
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Affiliation(s)
- A I Schulte-Hostedde
- Ecology and Evolution Group, Department of Zoology, University of Western Ontario, London, Ontario, Canada, N6A 5B7.
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Kramer KM, Birney EC. EFFECT OF LIGHT INTENSITY ON ACTIVITY PATTERNS OF PATAGONIAN LEAF-EARED MICE,PHYLLOTIS XANTHOPYGUS. J Mammal 2001. [DOI: 10.1644/1545-1542(2001)082<0535:eolioa>2.0.co;2] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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50
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Pogson GH, Taggart CT, Mesa KA, Boutilier RG. ISOLATION BY DISTANCE IN THE ATLANTIC COD, GADUS MORHUA, AT LARGE AND SMALL GEOGRAPHIC SCALES. Evolution 2001. [DOI: 10.1554/0014-3820(2001)055[0131:ibdita]2.0.co;2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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