1
|
Sirsi S, Rodriguez D, Forstner MRJ. Using genome-wide data to ascertain taxonomic status and assess population genetic structure for Houston toads (Bufo [= Anaxyrus] houstonensis). Sci Rep 2024; 14:3306. [PMID: 38332325 PMCID: PMC10853240 DOI: 10.1038/s41598-024-53705-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 02/04/2024] [Indexed: 02/10/2024] Open
Abstract
The Houston toad (Bufo [= Anaxyrus] houstonensis) is an endangered amphibian with a small geographic range. Land-use changes have primarily driven decline in B. houstonensis with population supplementation predominant among efforts to reduce its current extinction risk. However, there has been historic uncertainty regarding the evolutionary and conservation significance of B. houstonensis. To this end, we used 1170 genome-wide nuclear DNA markers to examine phylogenetic relationships between our focal taxon, representatives of the Nearctic B. americanus group, and B. nebulifer, a sympatric Middle American species. Phylogenetic analyses indicate B. houstonensis is a taxon that is distinct from B. americanus. We corroborated such genetic distinctiveness with an admixture analysis that provided support for recent reproductive isolation between B. americanus and B. houstonensis. However, ABBA-BABA tests for ancient admixture indicated historic gene flow between Nearctic species while no signal of historic gene flow was detected between Nearctic and Middle-American species. We used an admixture analysis to recognize four Management Units (MU) based on observed genetic differentiation within B. houstonensis and recommend captive propagation, population supplementation, and habitat restoration efforts specific to each MU. Our results re-affirm the evolutionary novelty of an endangered relict.
Collapse
Affiliation(s)
- Shashwat Sirsi
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA.
| | - David Rodriguez
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Michael R J Forstner
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| |
Collapse
|
2
|
Pereyra MO, Blotto BL, Baldo D, Chaparro JC, Ron SR, Elias-Costa AJ, Iglesias PP, Venegas PJ, C. Thomé MT, Ospina-Sarria JJ, Maciel NM, Rada M, Kolenc F, Borteiro C, Rivera-Correa M, Rojas-Runjaic FJ, Moravec J, De La Riva I, Wheeler WC, Castroviejo-Fisher S, Grant T, Haddad CF, Faivovich J. Evolution in the Genus Rhinella: A Total Evidence Phylogenetic Analysis of Neotropical True Toads (Anura: Bufonidae). BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2021. [DOI: 10.1206/0003-0090.447.1.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Martín O. Pereyra
- Martín O. Pereyra: División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”–CONICET, Buenos Aires; and Laboratorio de Genética Evolutiva “Claudio J. Bidau,” Instituto de Biología Subtropical (IBS, CONICET), Universidad Naci
| | - Boris L. Blotto
- Boris L. Blotto: División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”–CONICET, Buenos Aires; Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUN
| | - Diego Baldo
- Diego Baldo: Laboratorio de Genética Evolutiva “Claudio J. Bidau,” Instituto de Biología Subtropical (IBS, CONICET), Universidad Nacional de Misiones (UNaM), Posadas, Misiones, Argentina
| | - Juan C. Chaparro
- Juan C. Chaparro: Museo de Biodiversidad del Perú, Cusco, Perú; and Museo de Historia Natural de la Universidad Nacional de San Antonio Abad del Cusco, Paraninfo Universitario, Cusco
| | - Santiago R. Ron
- Santiago R. Ron: Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito
| | - Agustín J. Elias-Costa
- Agustín J. Elias-Costa: División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”–CONICET, Buenos Aires
| | - Patricia P. Iglesias
- Patricia P. Iglesias: Laboratorio de Genética Evolutiva “Claudio J. Bidau”, Instituto de Biología Subtropical (IBS, CONICET), Universidad Nacional de Misiones (UNaM), Posadas, Misiones, Argentina
| | - Pablo J. Venegas
- Pablo J. Venegas: División de Herpetología-Centro de Ornitología y Biodiversidad (CORBIDI), Surco, Lima
| | - Maria Tereza C. Thomé
- Maria Tereza C. Thomé: Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Rio Claro, São Paulo
| | - Jhon Jairo Ospina-Sarria
- Jhon Jairo Ospina-Sarria: Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil; and Calima, Fundación para la Investigación de la Biodiversidad y Conservación en el Trópico, Cali
| | - Natan M. Maciel
- Natan M. Maciel: Laboratório de Herpetologia e Comportamento Animal, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Marco Rada
- Marco Rada: Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo
| | - Francisco Kolenc
- Francisco Kolenc: Sección Herpetología, Museo Nacional de Historia Natural, Montevideo
| | - Claudio Borteiro
- Claudio Borteiro: Sección Herpetología, Museo Nacional de Historia Natural, Montevideo
| | - Mauricio Rivera-Correa
- Mauricio Rivera-Correa: Grupo Herpetológico de Antioquia, Instituto de Biología, Universidad de Antioquia, Medellín
| | - Fernando J.M. Rojas-Runjaic
- Fernando J.M. Rojas-Runjaic: Fundación La Salle de Ciencias Naturales, Museo de Historia Natural La Salle (MHNLS), Venezuela; and Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Jiří Moravec
- Jiří Moravec: Department of Zoology, National Museum, Prague, Czech Republic
| | - Ignacio De La Riva
- Ignacio de la Riva: Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid
| | - Ward C. Wheeler
- Ward C. Wheeler: Division of Invertebrate Zoology, American Museum of Natural History, New York
| | - Santiago Castroviejo-Fisher
- Santiago Castroviejo-Fisher: Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil; and Research Associate, Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, New York
| | - Taran Grant
- Taran Grant: Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo; and Research Associate, Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, New York
| | - Célio F.B. Haddad
- Célio F.B. Haddad: Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Rio Claro, São Paulo
| | - Julián Faivovich
- Julián Faivovich: División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”–CONICET, Buenos Aires; Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires,
| |
Collapse
|
3
|
Hunt JE, Bruno JR, Pratt KG. An Innate Color Preference Displayed by Xenopus Tadpoles Is Persistent and Requires the Tegmentum. Front Behav Neurosci 2020; 14:71. [PMID: 32477078 PMCID: PMC7235192 DOI: 10.3389/fnbeh.2020.00071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/20/2020] [Indexed: 11/26/2022] Open
Abstract
Many animals, especially those that develop externally, are equipped with innate color preferences that promote survival. For example, Xenopus tadpoles are known to phototax most robustly towards mid-spectrum (“green”) wavelengths of light while avoiding shorter (“blue”) wavelengths. The innate preference to phototax towards green likely promotes survival by guiding the tadpoles to green aquatic plants—their source of both food and safety. Here, we characterize the dynamics and circuitry that give rise to this intriguing hard-wired behavior. Using a novel open-field experimental paradigm we found that free-swimming tadpoles indeed spend most of their time in the green portion of the test dish, whether green is pitted against white (brighter than green) or black (darker than green). This preference was modest yet incredibly persistent over time, which, according to the shell game model of predator-prey interactions, minimizes being found by the predator. Furthermore, we found that this innate preference for the color green was experience-independent, and manifested mainly via profoundly slower swimming speeds while in the green region of the test dish. Ablation experiments showed that, at the circuit level, the color-guided swimming behavior requires the tegmentum, but not the optic tectum (OT). Lastly, we determined that exposing tadpoles to the selective serotonin reuptake inhibitor (SSRI) trazodone switched the tadpoles’ preference from color-based to luminance-based, implicating two distinct visual circuits in the tadpole, one that is associated with color-driven behaviors, another associated with luminance-driven behaviors.
Collapse
Affiliation(s)
- Jasper Elan Hunt
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, WY, United States.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - John Rudolph Bruno
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, WY, United States
| | - Kara Geo Pratt
- Department of Zoology and Physiology and Program in Neuroscience, University of Wyoming, Laramie, WY, United States
| |
Collapse
|
4
|
Cai YT, Li Q, Zhang JY, Storey KB, Yu DN. Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses. PeerJ 2020; 8:e8901. [PMID: 32328346 PMCID: PMC7164433 DOI: 10.7717/peerj.8901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 03/12/2020] [Indexed: 12/31/2022] Open
Abstract
Mitogenomes are useful in analyzing phylogenetic relationships and also appear to influence energy metabolism, thermoregulation and osmoregulation. Much evidence has accumulated for positive selection acting on mitochondrial genes associated with environmental adaptation. Hence, the mitogenome is a likely target for environmental selection. The family Bufonidae (true toads) has only nine complete and four partial mitogenomes published compared to the 610 known species of this family. More mitogenomes are needed in order to obtain a clearer understanding of the phylogenetic relationships within Bufonidae that are currently controversial. To date, no mitogenomes have been reported from the genera Anaxyrus and Bufotes. Anaxyrus americanus can live in low temperature environments and Bufotes pewzowi can live in high salinity environments. We sequenced the mitogenomes of these two species to discuss the phylogenetic relationships within Bufonidae and the selection pressures experienced by specimens living in low temperature or saline environments. Like other toads, the circular mitogenomes of both species contained the typical 37 genes. Anaxyrus americanus had the highest A+T content of the complete mitogenome among the Bufonidae. In addition, A. americanus showed a negative AT-skew in the control region, whereas Bufotes pewzowi showed a positive AT-skew. Additionally, both toad species had unique molecular features in common: an ND1 gene that uses TTG as the start codon, an extra unpaired adenine (A) in the anticodon arm of trnS (AGY), and the loss of the DHU loop in trnC. The monophyly of Bufonidae was corroborated by both BI and ML trees. An analysis of selective pressure based on the 13 protein coding genes was conducted using the EasyCodeML program. In the branch model analysis, we found two branches of A. americanus and Bufotes pewzowi that were under negative selection. Additionally, we found two positively selected sites (at positions 115 and 119, BEB value > 0.90) in the ND6 protein in the site model analysis. The residue D (119) was located only in A. americanus and may be related to adaptive evolution in low temperature environments. However, there was no evidence of a positively selected site in Bufotes pewzowi in this study.
Collapse
Affiliation(s)
- Yu-Ting Cai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Qin Li
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Jia-Yong Zhang
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
| | | | - Dan-Na Yu
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
| |
Collapse
|
5
|
Firneno TJ, Townsend JH. Evaluation of species boundaries in sympatric and parapatric populations of Mesoamerican toads. ZOOL SCR 2019. [DOI: 10.1111/zsc.12354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Thomas J. Firneno
- Department of Biology Indiana University of Pennsylvania Indiana Pennsylvania
| | - Josiah H. Townsend
- Department of Biology Indiana University of Pennsylvania Indiana Pennsylvania
| |
Collapse
|
6
|
Ortego J, Gugger PF, Sork VL. Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus). THE NEW PHYTOLOGIST 2018; 218:804-818. [PMID: 29274282 DOI: 10.1111/nph.14951] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/14/2017] [Indexed: 05/15/2023]
Abstract
Here we study hybridization, introgression and lineage diversification in the widely distributed canyon live oak (Quercus chrysolepis) and the relict island oak (Q. tomentella), two Californian golden cup oaks with an intriguing biogeographical history. We employed restriction-site-associated DNA sequencing and integrated phylogenomic and population genomic analyses to study hybridization and reconstruct the evolutionary past of these taxa. Our analyses revealed the presence of two cryptic lineages within Q. chrysolepis. One of these lineages shares its most recent common ancestor with Q. tomentella, supporting the paraphyly of Q. chrysolepis. The split of these lineages was estimated to take place during the late Pliocene or the early Pleistocene, a time corresponding well with the common presence of Q. tomentella in the fossil records of continental California. Analyses also revealed historical hybridization among lineages, high introgression from Q. tomentella into Q. chrysolepis in their current area of sympatry, and widespread admixture between the two lineages of Q. chrysolepis in contact zones. Our results support that the two lineages of Q. chrysolepis behave as a single functional species phenotypically and ecologically well differentiated from Q. tomentella, a situation that can be only accommodated considering hybridization and speciation as a continuum with diffuse limits.
Collapse
Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio 26, Seville, E-41092, Spain
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, 301 Braddock Road, Frostburg, MD, 21532, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA
- Institute of the Environment and Sustainability, University of California, Box 951496, Los Angeles, CA, 90095-1496, USA
| |
Collapse
|
7
|
Salvador de Jesús-Bonilla V, García-París M, Ibarra-Cerdeña CN, Zaldívar-Riverón A. Geographic patterns of phenotypic diversity in incipient species of North American blister beetles (Coleoptera: Meloidae) are not determined by species niches, but driven by demography along the speciation process. INVERTEBR SYST 2018. [DOI: 10.1071/is17072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Epicauta stigmata complex is a group of blister beetles composed of three parapatric or sympatric species that occur in central Mexico to southern USA: E. stigmata, E. uniforma and E. melanochroa. These species are morphologically very similar, and are mainly distinguished by body colour differences. Here we assessed whether phenotypic divergence in coloration patterns define evolutionary units within the complex. We studied the phylogenetic relationships, demographic history and concordances between morphological and ecological traits in the group. The complex apparently had a demographic history of recent population expansion during the last glaciation period 75000 to 9500 years ago. The three species show no reciprocal monophyly, and thus their allospecificity was not confirmed. The current distribution of haplotypes and the genetic divergences in these taxa can be explained by either recent mitochondrial introgression events caused by hybridisation or by incomplete lineage sorting. Colour pattern differences in the complex are not likely a product of local selection acting over a common genetic background. We suggest that phenotypic divergence in colour patterns during an incipient speciation process might be seen as an enhancing factor of cohesion within each of the three evolutionary units.
Collapse
|
8
|
O'Connell KA, Streicher JW, Smith EN, Fujita MK. Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes. Mol Ecol 2017; 26:5729-5751. [PMID: 28802078 DOI: 10.1111/mec.14295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 01/08/2023]
Abstract
Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.
Collapse
Affiliation(s)
- Kyle A O'Connell
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | | | - Eric N Smith
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| |
Collapse
|
9
|
Simeone MC, Grimm GW, Papini A, Vessella F, Cardoni S, Tordoni E, Piredda R, Franc A, Denk T. Plastome data reveal multiple geographic origins of Quercus Group Ilex. PeerJ 2016; 4:e1897. [PMID: 27123376 PMCID: PMC4846808 DOI: 10.7717/peerj.1897] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/15/2016] [Indexed: 01/27/2023] Open
Abstract
Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members of Quercus Group Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.
Collapse
Affiliation(s)
- Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Guido W Grimm
- Department of Palaeontology, University of Wien , Wien , Austria
| | - Alessio Papini
- Dipartimento di Biologia, Università degli studi di Firenze , Firenze , Italy
| | - Federico Vessella
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Enrico Tordoni
- Department of Life Science, Università degli studi di Trieste , Trieste , Italy
| | | | - Alain Franc
- INRA, UMR BIOGECO-1202, Cestas, France; UMR BIOGECO-1202, Université Bordeaux, Talence, France
| | - Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History , Stockholm , Sweden
| |
Collapse
|
10
|
Pereyra MO, Baldo D, Blotto BL, Iglesias PP, Thomé MTC, Haddad CFB, Barrio-Amorós C, Ibáñez R, Faivovich J. Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression. Cladistics 2016; 32:36-53. [PMID: 34732018 DOI: 10.1111/cla.12110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2014] [Indexed: 11/30/2022] Open
Abstract
The Rhinella granulosa group consists of 13 species of toads distributed throughout open areas of South America and Panama. In this paper we perform a phylogenetic analysis considering all but one species of the group, employing five nuclear and four mitochondrial genes, for up to 7910 bp per specimen. Separate phylogenetic analyses under direct optimization (DO) of nuclear and mitochondrial sequences recovered the R. granulosa group as monophyletic and revealed topological incongruence that can be explained mainly by multiple events of hybridization and introgression, both mitochondrial and nuclear. The DO combined analysis, after the exclusion of putatively introgressed or heterozygous genomes, resulted in a phylogenetic hypothesis for the R. granulosa group in which most of the species are recovered as monophyletic, but with interspecific relationships poorly supported. The optimization of morphological (adult and larval), chromosomal, and behavioural characters resulted in 12 putative phenotypic synapomorphies for this species group and some other synapomorphies for internal clades. Our results indicate the need for additional population genetic studies on R. dorbignyi and R. fernandezae to corroborate the taxonomic status of both taxa. Finally, we discuss biological and genetic characteristics of Bufonidae, as possible explanations for the common occurrence of hybridization and introgression observed in some lineages of this family.
Collapse
Affiliation(s)
- Martín O Pereyra
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (CONICET-UNaM), Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones, N3300LQF, Posadas, Misiones, Argentina
| | - Boris L Blotto
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina.,Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, São Paulo, Brazil
| | - Patricia P Iglesias
- Instituto de Ecología, Genética y Evolución de Buenos Aires, IEGEBA-CONICET, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pab. II, C1428EHA, Buenos Aires, Argentina
| | - Maria T C Thomé
- Departamento de Zoologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Av. 24A 1515, CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - Célio F B Haddad
- Departamento de Zoologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Av. 24A 1515, CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - César Barrio-Amorós
- Instituto de Biodiversidad Tropical, Apartado Postal 220-8000, San José, Pérez Zeledón, San Isidro del General, 11901, Costa Rica
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, República de Panamá.,Departamento de Zoología, Universidad de Panamá, Panamá, República de Panamá.,Círculo Herpetológico de Panamá, Estafeta Universitaria, Apartado 10762, Panamá, República de Panamá
| | - Julián Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina.,Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
11
|
Simeone MC, Grimm GW, Papini A, Vessella F, Cardoni S, Tordoni E, Piredda R, Franc A, Denk T. Plastome data reveal multiple geographic origins of Quercus Group Ilex. PeerJ 2016. [PMID: 27123376 DOI: 10.7287/peerj.preprints.1615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members of Quercus Group Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.
Collapse
Affiliation(s)
- Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Guido W Grimm
- Department of Palaeontology, University of Wien , Wien , Austria
| | - Alessio Papini
- Dipartimento di Biologia, Università degli studi di Firenze , Firenze , Italy
| | - Federico Vessella
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE), Università degli Studi della Tuscia , Viterbo , Italy
| | - Enrico Tordoni
- Department of Life Science, Università degli studi di Trieste , Trieste , Italy
| | | | - Alain Franc
- INRA, UMR BIOGECO-1202, Cestas, France; UMR BIOGECO-1202, Université Bordeaux, Talence, France
| | - Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History , Stockholm , Sweden
| |
Collapse
|
12
|
López H, Hernández-Teixidor D, Macías-Hernández N, Juan C, Oromí P. A taxonomic revision and species delimitation of the genus Purpuraria
Enderlein, 1929 (Orthoptera: Pamphagidae) using an integrative approach. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Heriberto López
- Island Ecology and Evolution Research Group (IPNA-CSIC); Tenerife Canary Islands Spain
- Department of Biología Animal; Universidad La Laguna; Tenerife Canary Islands Spain
| | | | | | - Carlos Juan
- Department of Biologia; Universitat Illes Balears; Palma de Mallorca Spain
| | - Pedro Oromí
- Department of Biología Animal; Universidad La Laguna; Tenerife Canary Islands Spain
| |
Collapse
|
13
|
Thomé MTC, Zamudio KR, Haddad CFB, Alexandrino J. Delimiting genetic units in Neotropical toads under incomplete lineage sorting and hybridization. BMC Evol Biol 2012; 12:242. [PMID: 23228224 PMCID: PMC3574056 DOI: 10.1186/1471-2148-12-242] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 12/04/2012] [Indexed: 11/29/2022] Open
Abstract
Background Delimiting genetic units is useful to enhance taxonomic discovery and is often the first step toward understanding evolutionary mechanisms generating diversification. The six species within the Rhinella crucifer group of toads were defined under morphological criteria alone. Previous data suggest limited correspondence of these species to mitochondrial lineages, and morphological intergradation at transitions between forms suggests hybridization. Here we extensively sampled populations throughout the geographic distribution of the group and analyzed mitochondrial and nuclear sequence data to delimit genetic units using tree–based and allele frequency–based approaches. Results These approaches yielded complementary results, with allele frequency-based methods performing unexpectedly well given the limited number of loci examined. Both mitochondrial and nuclear markers supported a genetic structure of five units within the group, with three of the inferred units distributed within its main range, while two other units occur in separate isolates. The inferred units are mostly discordant with currently described forms: unequivocal association exists for only two of the six species in the group. Genetic evidence for hybridization exists for two pairs of units, with clear cyto–nuclear allele mixing observed in one case. Conclusions Our results confirmed that current taxonomy does not represent evolutionary units in the Rhinella crucifer group. Correspondence between genetically distinguishable units and the currently recognized species is only possible for Rhinella henseli and R. inopina. The recognition of other species relies on the reassessment of the geographic range of R. crucifer, the examination of the type series of R. ornata for hybrids, and on the use of additional markers to verify the genetic distinctiveness of R. abei. We state that R. pombali should not remain a valid species since its description appears to be based on hybrids, and that the name R. pombali should be considered a synonym of both R. crucifer and R. ornata. The fifth inferred but undescribed genetic unit may represent a new species. Our results underscore the potential of the R. crucifer species group to contribute to a better understanding of diversification processes and hybridization patterns in the Neotropics, and provide the basis for future evolutionary and taxonomic studies.
Collapse
Affiliation(s)
- Maria Tereza C Thomé
- Departamento de Zoologia, Instituto de Biociências, UNESP - Univ Estadual Paulista, Campus Rio Claro, Caixa Postal 19913506-900, Rio Claro, SP, Brazil.
| | | | | | | |
Collapse
|
14
|
Lee-Yaw JA, Irwin DE. Large geographic range size reflects a patchwork of divergent lineages in the long-toed salamander (Ambystoma macrodactylum). J Evol Biol 2012; 25:2276-87. [DOI: 10.1111/j.1420-9101.2012.02604.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/28/2022]
Affiliation(s)
- J. A. Lee-Yaw
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
| | - D. E. Irwin
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
| |
Collapse
|
15
|
A multilocus perspective on the speciation history of a North American aridland toad (Anaxyrus punctatus). Mol Phylogenet Evol 2012; 64:393-400. [DOI: 10.1016/j.ympev.2012.04.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 04/19/2012] [Accepted: 04/21/2012] [Indexed: 11/21/2022]
|
16
|
Lamb T, Beamer DA. Digits lost or gained? Evidence for pedal evolution in the dwarf salamander complex (Eurycea, Plethodontidae). PLoS One 2012; 7:e37544. [PMID: 22649536 PMCID: PMC3359299 DOI: 10.1371/journal.pone.0037544] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 04/23/2012] [Indexed: 11/19/2022] Open
Abstract
Change in digit number, particularly digit loss, has occurred repeatedly over the evolutionary history of tetrapods. Although digit loss has been documented among distantly related species of salamanders, it is relatively uncommon in this amphibian order. For example, reduction from five to four toes appears to have evolved just three times in the morphologically and ecologically diverse family Plethodontidae. Here we report a molecular phylogenetic analysis for one of these four-toed lineages--the Eurycea quadridigitata complex (dwarf salamanders)--emphasizing relationships to other species in the genus. A multilocus phylogeny reveals that dwarf salamanders are paraphyletic with respect to a complex of five-toed, paedomorphic Eurycea from the Edwards Plateau in Texas. We use this phylogeny to examine evolution of digit number within the dwarf-Edwards Plateau clade, testing contrasting hypotheses of digit loss (parallelism among dwarf salamanders) versus digit gain (re-evolution in the Edwards Plateau complex). Bayes factors analysis provides statistical support for a five-toed common ancestor at the dwarf-Edwards node, favoring, slightly, the parallelism hypothesis for digit loss. More importantly, our phylogenetic results pinpoint a rare event in the pedal evolution of plethodontid salamanders.
Collapse
Affiliation(s)
- Trip Lamb
- Department of Biology, East Carolina University, Greenville, North Carolina, United States of America
| | - David A. Beamer
- Department of Biology, East Carolina University, Greenville, North Carolina, United States of America
- Department of Mathematics and Sciences, Nash Community College, Rocky Mount, North Carolina, United States of America
| |
Collapse
|
17
|
NEWMAN CATHERINEE, RISSLER LESLIEJ. Phylogeographic analyses of the southern leopard frog: the impact of geography and climate on the distribution of genetic lineages vs. subspecies. Mol Ecol 2011; 20:5295-312. [DOI: 10.1111/j.1365-294x.2011.05353.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
18
|
Gene flow and hybridization between numerically imbalanced populations of two duck species in the Falkland Islands. PLoS One 2011; 6:e23173. [PMID: 21887236 PMCID: PMC3162561 DOI: 10.1371/journal.pone.0023173] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 07/11/2011] [Indexed: 11/19/2022] Open
Abstract
Interspecific hybridization is common in plants and animals, particularly in waterfowl (Anatidae). One factor shown to contribute to hybridization is restricted mate choice, which can occur when two species occur in sympatry but one is rare. The Hubbs principle, or “desperation hypothesis,” states that under such circumstances the rarer species is more likely to mate with heterospecifics. Here we report interspecific hybridization between two waterfowl species that coexist in broad sympatry and mixed flocks throughout southern South America. Speckled teal (Anas flavirostris) and yellow-billed pintails (Anas georgica) are abundant in continental South America, but in the Falkland Islands speckled teal outnumber yellow-billed pintails approximately ten to one. Using eight genetic loci (mtDNA and 7 nuclear introns) coupled with Bayesian assignment tests and relatedness analysis, we identified a speckled teal x yellow-billed pintail F1 hybrid female and her duckling sired by a male speckled teal. Although our sample in the Falkland Islands was small, we failed to identify unequivocal evidence of hybridization or introgression in a much larger sample from Argentina using a three-population “isolation with migration” coalescent analysis. While additional data are needed to determine if this event in the Falkland Islands was a rare singular occurrence, our results provide further support for the “desperation hypothesis,” which states that scarcity in one population and abundance of another will often lead to hybridization.
Collapse
|
19
|
Fontenot BE, Makowsky R, Chippindale PT. Nuclear–mitochondrial discordance and gene flow in a recent radiation of toads. Mol Phylogenet Evol 2011; 59:66-80. [DOI: 10.1016/j.ympev.2010.12.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 12/12/2010] [Accepted: 12/23/2010] [Indexed: 12/01/2022]
|
20
|
Nydam ML, Harrison RG. INTROGRESSION DESPITE SUBSTANTIAL DIVERGENCE IN A BROADCAST SPAWNING MARINE INVERTEBRATE. Evolution 2010; 65:429-42. [DOI: 10.1111/j.1558-5646.2010.01153.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
21
|
RISSLER LESLIEJ, SMITH WALTERH. Mapping amphibian contact zones and phylogeographical break hotspots across the United States. Mol Ecol 2010; 19:5404-16. [DOI: 10.1111/j.1365-294x.2010.04879.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
22
|
Maciel NM, Collevatti RG, Colli GR, Schwartz EF. Late Miocene diversification and phylogenetic relationships of the huge toads in the Rhinella marina (Linnaeus, 1758) species group (Anura: Bufonidae). Mol Phylogenet Evol 2010; 57:787-97. [DOI: 10.1016/j.ympev.2010.08.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 08/23/2010] [Accepted: 08/23/2010] [Indexed: 10/19/2022]
|
23
|
Jungels JM, Griffis-Kyle KL, Boeing WJ. Low Genetic Differentiation among Populations of the Great Plains Toad (Bufo cognatus) in Southern New Mexico. COPEIA 2010. [DOI: 10.1643/ch-09-152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
24
|
Garda AA, Pedro VDAS, Lion MB. The Advertisement and Release Calls ofRhinella jimi(Anura, Bufonidae). J HERPETOL 2010. [DOI: 10.2994/057.005.0209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
25
|
Bryson RW, de Oca ANM, Jaeger JR, Riddle BR. Elucidation of cryptic diversity in a widespread nearctic treefrog reveals episodes of mitochondrial gene capture as frogs diversified across a dynamic landscape. Evolution 2010; 64:2315-30. [PMID: 20394664 DOI: 10.1111/j.1558-5646.2010.01014.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We investigate the evolutionary history of the wide-ranging Nearctic treefrog Hyla arenicolor through the integration of extensive range-wide sampling, phylogenetic analyses of multilocus genetic data, and divergence dating. Previous phylogeographic studies of this frog documented a potential signature of introgressive hybridization from an ecologically and morphologically divergent sister species. Based on our Bayesian phylogenetic analyses of mitochondrial DNA, we inferred strong phylogeographic structure in H. arenicolor as indicated by seven well-supported clades, five of which correspond to well-defined biogeographic regions. Clades from the Balsas Basin and southwestern Central Mexican Plateau in Mexico, and the Grand Canyon of Arizona, group with the morphologically, behaviorally, and ecologically divergent mountain treefrogs in the H. eximia group, rendering H. arenicolor as paraphyletic. The phylogenetic position of at least two of these three H. arenicolor clades within the H. eximia group, however, is most likely the result of several episodes of introgressive hybridization and subsequent mitochondrial gene capture separated in time and space, as supported by evidence from the nuclear genes. Hyla arenicolor from the Balsas Basin appear to be deeply divergent from other H. arenicolor and represent a distinctly different species. Results suggests that introgressive hybridization events, both ancient and contemporary, coupled with late Neogene vicariance and Pleistocene climate-driven range shifts, have all played a role in the historical diversification of H. arenicolor.
Collapse
Affiliation(s)
- Robert W Bryson
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada 89154, USA.
| | | | | | | |
Collapse
|
26
|
Vallinoto M, Sequeira F, Sodré D, Bernardi JAR, Sampaio I, Schneider H. Phylogeny and biogeography of theRhinella marinaspecies complex (Amphibia, Bufonidae) revisited: implications for Neotropical diversification hypotheses. ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2009.00415.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
27
|
Goebel AM, Ranker TA, Corn PS, Olmstead RG. Mitochondrial DNA evolution in the Anaxyrus boreas species group. Mol Phylogenet Evol 2009; 50:209-25. [DOI: 10.1016/j.ympev.2008.06.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 06/10/2008] [Accepted: 06/24/2008] [Indexed: 11/27/2022]
|
28
|
Abstract
Understanding the general features of speciation is an important goal in evolutionary biology, and despite significant progress, several unresolved questions remain. We analyzed an extensive comparative dataset consisting of more than 1900 crosses between 92 species of toads to infer patterns of reproductive isolation. This unique dataset provides an opportunity to examine the strength of reproductive isolation, the development and sex ratios of hybrid offspring, patterns of fertility and infertility, and polyploidization in hybrids all in the context of genetic divergence between parental species. We found that the strength of intrinsic postzygotic isolation increases with genetic divergence, but relatively high levels of divergence are necessary before reproductive isolation is complete in toads. Fertilization rates were not correlated to genetic divergence, but hatching success, the number of larvae produced, and the percentage of tadpoles reaching metamorphosis were all inversely related with genetic divergence. Hybrids between species with lower levels of divergence developed to metamorphosis, while hybrids with higher levels of divergence stopped developing in gastrula and larval stages. Sex ratios of hybrid offspring were biased towards males in 70% of crosses and biased towards females in 30% of crosses. Hybrid females from crosses between closely related species were completely fertile, while approximately half (53%) of hybrid males were sterile, with sterility predicted by genetic divergence. The degree of abnormal ploidy in hybrids was positively related to genetic divergence between parental species, but surprisingly, polyploidization had no effect on patterns of asymmetrical inviability. We discuss explanations for these patterns, including the role of Haldane's rule in toads and anurans in general, and suggest mechanisms generating patterns of reproductive isolation in anurans.
Collapse
Affiliation(s)
- John H Malone
- Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America.
| | | |
Collapse
|
29
|
KOSCINSKI DARIA, HANDFORD PAUL, TUBARO PABLOL, SHARP SARAH, LOUGHEED STEPHENC. Pleistocene climatic cycling and diversification of the Andean treefrog,Hypsiboas andinus. Mol Ecol 2008; 17:2012-25. [DOI: 10.1111/j.1365-294x.2008.03733.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
30
|
McGuire JA, Linkem CW, Koo MS, Hutchison DW, Lappin AK, Orange DI, Lemos-Espinal J, Riddle BR, Jaeger JR. MITOCHONDRIAL INTROGRESSION AND INCOMPLETE LINEAGE SORTING THROUGH SPACE AND TIME: PHYLOGENETICS OF CROTAPHYTID LIZARDS. Evolution 2007; 61:2879-97. [DOI: 10.1111/j.1558-5646.2007.00239.x] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
31
|
Moura CJ, Harris DJ, Cunha MR, Rogers AD. DNA barcoding reveals cryptic diversity in marine hydroids (Cnidaria, Hydrozoa) from coastal and deep-sea environments. ZOOL SCR 2007. [DOI: 10.1111/j.1463-6409.2007.00312.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
32
|
Nagata N, Kubota K, Sota T. Phylogeography and introgressive hybridization of the ground beetle Carabus yamato in Japan based on mitochondrial gene sequences. Zoolog Sci 2007; 24:465-74. [PMID: 17867845 DOI: 10.2108/zsj.24.465] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2006] [Accepted: 12/18/2006] [Indexed: 11/17/2022]
Abstract
To study the phylogeography of the ground beetle Carabus yamato in Japan, we compared 1,020-bp sequences of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene from 373 specimens from 37 localities with those of three parapatric species (C. albrechti, C. kimurai, and C. japonicus) that might share mitochondrial lineages with C. yamato through introgressive hybridization. We found 81 haplotypes from C. yamato. Of these, 17 haplotypes were considered to be of an introgressed lineage from C. albrechti, based on the phylogeny and geographic distribution. In addition, one haplotype of C. kimurai was likely an introgressant from C. yamato. Putative introgression events among the four species were restricted to these two directional cases. We analyzed the phylogeography of C. yamato using nested clade phylogeographical analysis and population genetic parameters. The mitochondrial lineages of C. yamato were estimated to have diverged no more than approximately 1.12 million years ago, implying that the estimated historical events occurred after the Early Pleistocene. Carabus yamato was inferred to have experienced a contraction of its distribution range, followed by recent range expansion. Populations in the western and eastern regions, segregated by Ise Bay and the Nobi and Okazaki Plains, diverged in the mitochondrial clades. The northern and most western populations possessed one clade only (except an introgressed lineage), whereas eastern and some southwestern populations possessed several diverged clades, which were considered to be ancestral; these populations may have been associated with refugia during glacial periods.
Collapse
Affiliation(s)
- Nobuaki Nagata
- Department of Zoology, Graudate School of Science, Kyoto University, Kyoto, Japan.
| | | | | |
Collapse
|
33
|
Peters JL, Zhuravlev Y, Fefelov I, Logie A, Omland KE. NUCLEAR LOCI AND COALESCENT METHODS SUPPORT ANCIENT HYBRIDIZATION AS CAUSE OF MITOCHONDRIAL PARAPHYLY BETWEEN GADWALL AND FALCATED DUCK (ANASSPP.). Evolution 2007; 61:1992-2006. [PMID: 17683440 DOI: 10.1111/j.1558-5646.2007.00149.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many species have mitochondrial DNA lineages that are phylogenetically intermixed with other species, but studies have rarely tested the cause of such paraphyly. In this study, we tested two hypotheses that could explain mitochondrial paraphyly of Holarctic gadwalls (Anas strepera) with respect to Asian falcated ducks (A. falcata). First, hybridization could have resulted in falcated duck mitochondrial DNA (mtDNA) introgressing into the gadwall gene pool. Second, gadwalls and falcated ducks could have diverged so recently that mtDNA lineages have not sorted to reciprocal monophyly. We used coalescent analyses of three independent loci to distinguish between these two hypotheses. Two lines of evidence support introgression. First, analyses of the three loci combined show that some introgression is necessary to explain current genetic diversity in gadwalls. Second, we generated alternative predictions regarding time since divergence estimated from mtDNA: falcated ducks and gadwalls would have diverged between 65,000 and 700,000 years before present (ybp) under the introgression hypothesis and between 11,000 and 76,000 ybp under the incomplete lineage sorting hypothesis. The two independent nuclear introns indicated that these species diverged between 210,000 and 5,200,000 ybp, which did not overlap the predicted time for incomplete lineage sorting. These analyses also suggested that ancient introgression ( approximately 14,000 ybp) has resulted in the widespread distribution and high frequency of falcated-like mtDNA (5.5% of haplotypes) in North America. This is the first study to use a rigorous quantitative framework to reject incomplete lineage sorting as the cause of mitochondrial paraphyly.
Collapse
Affiliation(s)
- Jeffrey L Peters
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250, USA.
| | | | | | | | | |
Collapse
|
34
|
Devitt TJ. Phylogeography of the Western Lyresnake (Trimorphodon biscutatus): testing aridland biogeographical hypotheses across the Nearctic-Neotropical transition. Mol Ecol 2007; 15:4387-407. [PMID: 17107472 DOI: 10.1111/j.1365-294x.2006.03015.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Western Lyresnake (Trimorphodon biscutatus) is a widespread, polytypic taxon inhabiting arid regions from the warm deserts of the southwestern United States southward along the Pacific versant of Mexico to the tropical deciduous forests of Mesoamerica. This broadly distributed species provides a unique opportunity to evaluate a priori biogeographical hypotheses spanning two major distinct biogeographical realms (the Nearctic and Neotropical) that are usually treated separately in phylogeographical analyses. I investigated the phylogeography of T. biscutatus using maximum likelihood and Bayesian phylogenetic analysis of mitochondrial DNA (mtDNA) from across this species' range. Phylogenetic analyses recovered five well-supported clades whose boundaries are concordant with existing geographical barriers, a pattern consistent with a model of vicariant allopatric divergence. Assuming a vicariance model, divergence times between mitochondrial lineages were estimated using Bayesian relaxed molecular clock methods calibrated using geological information from putative vicariant events. Divergence time point estimates were bounded by broad confidence intervals, and thus these highly conservative estimates should be considered tentative hypotheses at best. Comparison of mtDNA lineages and taxa traditionally recognized as subspecies based on morphology suggest this taxon is comprised of multiple independent lineages at various stages of divergence, ranging from putative secondary contact and hybridization to sympatry of 'subspecies'.
Collapse
Affiliation(s)
- Thomas J Devitt
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA.
| |
Collapse
|
35
|
PRAMUK JENNIFERB. Phylogeny of South American Bufo (Anura: Bufonidae) inferred from combined evidence. Zool J Linn Soc 2006. [DOI: 10.1111/j.1096-3642.2006.00212.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
36
|
CAMARGO ARLEY, DE SÁ RAFAELO, HEYER WRONALD. Phylogenetic analyses of mtDNA sequences reveal three cryptic lineages in the widespread neotropical frog Leptodactylus fuscus (Schneider, 1799) (Anura, Leptodactylidae). Biol J Linn Soc Lond 2006. [DOI: 10.1111/j.1095-8312.2006.00581.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
37
|
Diegisser T, Seitz A, Johannesen J. Phylogeographic patterns of host-race evolution in Tephritis conura (Diptera: Tephritidae). Mol Ecol 2006; 15:681-94. [PMID: 16499694 DOI: 10.1111/j.1365-294x.2006.02792.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Host-race evolution is a prime candidate for sympatric speciation because host shifts must take place in the presence of both hosts. However, the geographic context in which the shift takes place may have strong allopatric or peripatric components if the primary host within a localized area is scarce or even goes extinct. Inference of the relative importance of the geographic mode of speciation may be gained from phylogeographic imprints. Here, we investigate the phylogeography of host races of the tephritid fly Tephritis conura from sympatric, parapatric and allopatric populations of Cirsium heterophyllum and Cirsium oleraceum (Asteraceae) in Europe, for addressing the age and direction, and the geographic context of host-race formation. Haplotype networks of the host races differed significantly in molecular diversity and topology. However, host-race haplotypes were nested within the same network, with a central haplotype H1 being the most common haplotype in both host races. C. heterophyllum flies were genetically more diverse and substructured than flies from C. oleraceum, suggesting that the latter is the derived race. The phylogeographic imprint indicates either that C. heterophyllum flies colonized C. oleraceum during range expansion or that heterophyllum flies went extinct in an area where oleraceum flies persisted (followed by re-immigration). These imprints are in concordance with peripatric diversification, probably in the European Alps and related to the last ice age, where the host-race diversification was largely completed before the postglacial range expansion on C. oleraceum to current areas of sympatry and parapatry with C. heterophyllum.
Collapse
Affiliation(s)
- Thorsten Diegisser
- Institut für Zoologie, Abteilung für Okologie, Universität Mainz, Germany.
| | | | | |
Collapse
|
38
|
Vences M, Thomas M, Bonett RM, Vieites DR. Deciphering amphibian diversity through DNA barcoding: chances and challenges. Philos Trans R Soc Lond B Biol Sci 2005; 360:1859-68. [PMID: 16221604 PMCID: PMC1609216 DOI: 10.1098/rstb.2005.1717] [Citation(s) in RCA: 288] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Amphibians globally are in decline, yet there is still a tremendous amount of unrecognized diversity, calling for an acceleration of taxonomic exploration. This process will be greatly facilitated by a DNA barcoding system; however, the mitochondrial population structure of many amphibian species presents numerous challenges to such a standardized, single locus, approach. Here we analyse intra- and interspecific patterns of mitochondrial variation in two distantly related groups of amphibians, mantellid frogs and salamanders, to determine the promise of DNA barcoding with cytochrome oxidase subunit I (cox1) sequences in this taxon. High intraspecific cox1 divergences of 7-14% were observed (18% in one case) within the whole set of amphibian sequences analysed. These high values are not caused by particularly high substitution rates of this gene but by generally deep mitochondrial divergences within and among amphibian species. Despite these high divergences, cox1 sequences were able to correctly identify species including disparate geographic variants. The main problems with cox1 barcoding of amphibians are (i) the high variability of priming sites that hinder the application of universal primers to all species and (ii) the observed distinct overlap of intraspecific and interspecific divergence values, which implies difficulties in the definition of threshold values to identify candidate species. Common discordances between geographical signatures of mitochondrial and nuclear markers in amphibians indicate that a single-locus approach can be problematic when high accuracy of DNA barcoding is required. We suggest that a number of mitochondrial and nuclear genes may be used as DNA barcoding markers to complement cox1.
Collapse
Affiliation(s)
- Miguel Vences
- Institute for Biodiversity and Ecosystem Dynamics, Zoological Museum, University of Amsterdam, Mauritskade 61, 1092 AD Amsterdam, The Netherlands.
| | | | | | | |
Collapse
|
39
|
Mead LS, Clayton DR, Nauman RS, Olson DH, Pfrender ME. NEWLY DISCOVERED POPULATIONS OF SALAMANDERS FROM SISKIYOU COUNTY CALIFORNIA REPRESENT A SPECIES DISTINCT FROM PLETHODON STORMI. HERPETOLOGICA 2005. [DOI: 10.1655/03-86] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
40
|
Weisrock DW, Kozak KH, Larson A. Phylogeographic analysis of mitochondrial gene flow and introgression in the salamander, Plethodon shermani. Mol Ecol 2005; 14:1457-72. [PMID: 15813784 DOI: 10.1111/j.1365-294x.2005.02524.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plethodon shermani comprises a series of geographically disjunct populations occupying high-elevation mountain isolates. These populations hybridize at their borders with salamanders of the Plethodon glutinosus species complex, and past range expansions inferred from Pleistocene climatic cycles may have increased the possible genetic interactions between P. shermani and species of the P. glutinosus complex. Because mitochondrial DNA haplotypes often show introgression across species borders, we survey mtDNA variation for evidence of past and ongoing genetic interactions between P. shermani, its close relative Plethodon cheoah, and species of the P. glutinosus complex. Ongoing hybridization with the P. glutinosus-complex species Plethodon teyahalee is accompanied by extensive mitochondrial introgression in some Unicoi populations of P. shermani, but it has little genetic impact on P. shermani populations outside hybrid zones at three other isolates (Tusquitee, Wayah Bald, Standing Indian). Some Unicoi populations of P. shermani exhibit mtDNA evidence of past hybridization with diverse lineages from P. aureolus and P. glutinosus. The Tusquitee isolate of P. shermani is also characterized by mtDNA haplotypes most closely related to Plethodon aureolus and P. glutinosus, presumably introduced by past genetic contact with these species or with introgressed populations of Unicoi P. shermani. The mtDNA variation in sampled populations of the Wayah Bald and Standing Indian isolates of P. shermani appears largely unaffected by ongoing hybridization. Principal components analyses of allozymic data indicate that P. shermani isolates collectively form a genetically homogeneous unit clearly demarcated from species with which they have had current or past genetic interactions. Rapid mtDNA introgression associated with transient contacts between P. shermani and other species permits a fine-level resolution of evolutionary lineages not evident from allozymic data.
Collapse
Affiliation(s)
- D W Weisrock
- Department of Biology, Box 1137, Washington University, Saint Louis, MO 63130, USA.
| | | | | |
Collapse
|
41
|
Pauly GB, Hillis DM, Cannatella DC. The history of a nearctic colonization: molecular phylogenetics and biogeography of the Nearctic toads (Bufo). Evolution 2005; 58:2517-35. [PMID: 15612295 DOI: 10.1111/j.0014-3820.2004.tb00881.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previous hypotheses of phylogenetic relationships among Nearctic toads (Bufonidae) and their congeners suggest contradictory biogeographic histories. These hypotheses argue that the Nearctic Bufo are: (1) a polyphyletic assemblage resulting from multiple colonizations from Africa; (2) a paraphyletic assemblage resulting from a single colonization event from South America with subsequent dispersal into Eurasia; or (3) a monophyletic group derived from the Neotropics. We obtained approximately 2.5 kb of mitochondrial DNA sequence data for the 12S, 16S, and intervening valine tRNA gene from 82 individuals representing 56 species and used parametric bootstrapping to test hypotheses of the biogeographic history of the Nearctic Bufo. We find that the Nearctic species of Bufo are monophyletic and nested within a large clade of New World Bufo to the exclusion of Eurasian and African taxa. This suggests that Nearctic Bufo result from a single colonization from the Neotropics. More generally, we demonstrate the utility of parametric bootstrapping for testing alternative biogeographic hypotheses. Through parametric bootstrapping, we refute several previously published biogeographic hypotheses regarding Bufo. These previous studies may have been influenced by homoplasy in osteological characters. Given the Neotropical origin for Nearctic Bufo, we examine current distributional patterns to assess whether the Nearctic-Neotropical boundary is a broad transition zone or a narrow boundary. We also survey fossil and paleogeographic evidence to examine potential Tertiary and Cretaceous dispersal routes, including the Paleocene Isthmian Link, the Antillean and Aves Ridges, and the current Central American Land Bridge, that may have allowed colonization of the Nearctic.
Collapse
Affiliation(s)
- Gregory B Pauly
- Section of Integrative Biology and Texas Memorial Museum, University of Texas, Austin, Texas 78712, USA.
| | | | | |
Collapse
|
42
|
Abstract
Many of the species that recolonized previously glaciated areas in the Great Lakes basin of North America over the past 10-12,000 years exhibit genetic evidence of multiple invasion routes and present-day secondary contact between deeply divergent lineages. With this in mind, we investigated the phylogeographical structure of genetic variability in Fowler's toads (Bufo fowleri) at the northern edge of its distribution where its range encircles the Lake Erie basin. Because B. fowleri is so closely tied to habitats along the Lake Erie shoreline, we would expect to find clear evidence of the number of invasions leading to the species' colonization of the northern shore. A 540 bp sequence from the mitochondrial control region was amplified and analysed for 158 individuals from 21 populations. Interpopulation sequence variation ranged from 0% to 6%. Phylogenetic analysis of p-distance using the neighbor-joining method revealed two deeply divergent (6% sequence divergence) mtDNA lineages (Phylogroup 1 and 2), possibly arising as a result of secondary contact of populations that entered the region from two separate glacial refugia. However, the phylogeographical pattern was not simple. The populations at Long Point, on the north shore of Lake Erie, clustered with the population from Indiana Dunes on Lake Michigan to form Phylogroup 2 whereas all other B. fowleri populations examined from both sides of Lake Erie constituted Phylogroup 1. Furthermore, mtDNA sequences from the related species Bufo americanus, obtained from populations outside the range of B. fowleri, clustered with mtDNA haplotypes of B. fowleri Phylogroup 1, indicating the possibility of partial introgression of mitochondria from one species to the other.
Collapse
Affiliation(s)
- M A Smith
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada.
| | | |
Collapse
|
43
|
Pauly GB, Hillis DM, Cannatella DC. THE HISTORY OF A NEARCTIC COLONIZATION: MOLECULAR PHYLOGENETICS AND BIOGEOGRAPHY OF THE NEARCTIC TOADS (BUFO). Evolution 2004. [DOI: 10.1554/04-208] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
44
|
Funk DJ, Omland KE. Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2003. [DOI: 10.1146/annurev.ecolsys.34.011802.132421] [Citation(s) in RCA: 1562] [Impact Index Per Article: 74.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel J. Funk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235;
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| | - Kevin E. Omland
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235;
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250;
| |
Collapse
|
45
|
Masta SE, Laurent NM, Routman EJ. Population genetic structure of the toad Bufo woodhousii: an empirical assessment of the effects of haplotype extinction on nested cladistic analysis. Mol Ecol 2003; 12:1541-54. [PMID: 12755882 DOI: 10.1046/j.1365-294x.2003.01829.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nested cladistic analysis (NCA) is increasingly being used to infer historical population-level processes, including population fragmentation, range expansion and long-distance colonization. However, the effects on interpretation of NCA inferences of stochastic extinction of haplotypes due to genetic drift (lineage sorting), or of haplotype loss via localized biotic or climatic influences, have not been thoroughly explored. We provide empirical evidence suggesting that NCA may misinterpret population history when haplotypes or haplotype groups from one clade are replaced by those of another clade. We do so by using NCA to analyse mitochondrial sequences from the toad Bufo woodhousii from 45 locations spanning the Great Plains and southwestern USA. Portions of this region were glaciated and/or desertified in the late Pleistocene and early Holocene, and hence uninhabitable for plains-dwelling organisms. Although NCA inferences of isolation-by-distance and gradual range expansion in B. woodhousii are compatible with expectations based on climatic data and toad biology, NCA also detected several instances of long-distance movement. Such movement seems unlikely, given the low vagility of this species. We conclude that inferences of long-distance colonization likely result from extinction of haplotypes in intervening areas. We suggest using additional methods to look for congruent inferences, and amending the NCA inference key, to help avoid misinterpretations resulting from haplotype extinction.
Collapse
Affiliation(s)
- S E Masta
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132, USA.
| | | | | |
Collapse
|