1
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Vélez A, Sandoval SM. Size matters: individual variation in auditory sensitivity may influence sexual selection in Pacific treefrogs (Pseudacris regilla). J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2024:10.1007/s00359-024-01690-w. [PMID: 38367051 DOI: 10.1007/s00359-024-01690-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 02/19/2024]
Abstract
The matched filter hypothesis proposes a close match between senders and receivers and is supported by several studies on variation in signal properties and sensory-processing mechanisms among species and populations. Importantly, within populations, individual variation in sensory processing may affect how receivers perceive signals. Our main goals were to characterize hearing sensitivity of Pacific treefrogs (Pseudacris regilla), assess patterns of individual variation in hearing sensitivity, and evaluate how among-individual variation in hearing sensitivity and call frequency content affect auditory processing of communication signals. Overall, males and females are most sensitive to frequencies between 2.0 and 2.5 kHz, which matches the dominant frequency of the call, and have a second region of high sensitivity between 400 and 800 Hz that does not match the fundamental frequency of the call. We found high levels of among-individual variation in hearing sensitivity, primarily driven by subject size. Importantly, patterns of among-individual variation in hearing differ between males and females. Cross-correlation analyses reveal that among-individual variation in hearing sensitivity may lead to differences on how receivers, particularly females, perceive male calls. Our results suggest that individual variation in sensory processing may affect signal perception and influence the evolution of sexually selected traits.
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Affiliation(s)
- Alejandro Vélez
- Department of Psychology, University of Tennessee, Knoxville, TN, USA.
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA.
| | - Sam Moreno Sandoval
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
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2
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Pérez-Rodríguez R, Domínguez-Domínguez O, Pedraza-Lara C, Rosas-Valdez R, Pérez-Ponce de León G, García-Andrade AB, Doadrio I. Multi-locus phylogeny of the catfish genus Ictalurus Rafinesque, 1820 (Actinopterygii, Siluriformes) and its systematic and evolutionary implications. BMC Ecol Evol 2023; 23:27. [PMID: 37370016 PMCID: PMC10304232 DOI: 10.1186/s12862-023-02134-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: 04/29/2022] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Ictalurus is one of the most representative groups of North American freshwater fishes. Although this group has a well-studied fossil record and has been the subject of several morphological and molecular phylogenetic studies, incomplete taxonomic sampling and insufficient taxonomic studies have produced a rather complex classification, along with intricate patterns of evolutionary history in the genus that are considered unresolved and remain under debate. RESULTS Based on four loci and the most comprehensive taxonomic sampling analyzed to date, including currently recognized species, previously synonymized species, undescribed taxa, and poorly studied populations, this study produced a resolved phylogenetic framework that provided plausible species delimitation and an evolutionary time framework for the genus Ictalurus. CONCLUSIONS Our phylogenetic hypothesis revealed that Ictalurus comprises at least 13 evolutionary units, partially corroborating the current classification and identifying populations that emerge as putative undescribed taxa. The divergence times of the species indicate that the diversification of Ictalurus dates to the early Oligocene, confirming its status as one of the oldest genera within the family Ictaluridae.
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Affiliation(s)
- Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, 58000, Michoacán, México
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, 58000, Michoacán, México
| | - Carlos Pedraza-Lara
- Forensic Science, Medicine School, National Autonomous University of Mexico, Circuito de la investigación científica s/n, Ciudad Universitaria, Coyoacan, 04510, CdMx, Mexico
| | - Rogelio Rosas-Valdez
- Laboratorio de Colecciones Biológicas y Sistemática Molecular, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Av. Preparatoria S/N, Campus Universitario II, Col. Agronómica, Zacatecas, C. P. 98066, México
| | - Gerardo Pérez-Ponce de León
- Instituto de Biología, UNAM, Circuito exterior s/n, Ciudad Universitaria, Coyoacán, C.P. 04510, D.F, México
- Escuela Nacional de Estudios Superiores Unidad Mérida, Universidad Nacional Autónoma de México, Km 4.5 Carretera Mérida-Tetiz, Ucú, Yucatán, México
| | - Ana Berenice García-Andrade
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, 58000, Michoacán, México
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, Xalapa, 91070, Veracruz, México
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, c/José Gutiérrez Abascal 2, Madrid, E-28006, España.
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3
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Espeland M, Chazot N, Condamine FL, Lemmon AR, Lemmon EM, Pringle E, Heath A, Collins S, Tiren W, Mutiso M, Lees DC, Fisher S, Murphy R, Woodhall S, Tropek R, Ahlborn SS, Cockburn K, Dobson J, Bouyer T, Kaliszewska ZA, Baker CCM, Talavera G, Vila R, Gardiner AJ, Williams M, Martins DJ, Sáfián S, Edge DA, Pierce NE. Rapid radiation of ant parasitic butterflies during the Miocene aridification of Africa. Ecol Evol 2023; 13:e10046. [PMID: 37193112 PMCID: PMC10182571 DOI: 10.1002/ece3.10046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/14/2023] [Indexed: 05/18/2023] Open
Abstract
Africa has undergone a progressive aridification during the last 20 My that presumably impacted organisms and fostered the evolution of life history adaptations. We test the hypothesis that shift to living in ant nests and feeding on ant brood by larvae of phyto-predaceous Lepidochrysops butterflies was an adaptive response to the aridification of Africa that facilitated the subsequent radiation of butterflies in this genus. Using anchored hybrid enrichment we constructed a time-calibrated phylogeny for Lepidochrysops and its closest, non-parasitic relatives in the Euchrysops section (Poloyommatini). We estimated ancestral areas across the phylogeny with process-based biogeographical models and diversification rates relying on time-variable and clade-heterogeneous birth-death models. The Euchrysops section originated with the emerging Miombo woodlands about 22 million years ago (Mya) and spread to drier biomes as they became available in the late Miocene. The diversification of the non-parasitic lineages decreased as aridification intensified around 10 Mya, culminating in diversity decline. In contrast, the diversification of the phyto-predaceous Lepidochrysops lineage proceeded rapidly from about 6.5 Mya when this unusual life history likely first evolved. The Miombo woodlands were the cradle for diversification of the Euchrysops section, and our findings are consistent with the hypothesis that aridification during the Miocene selected for a phyto-predaceous life history in species of Lepidochrysops, with ant nests likely providing caterpillars a safe refuge from fire and a source of food when vegetation was scarce.
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Affiliation(s)
- Marianne Espeland
- Centre for Taxonomy and MorphologyLeibniz Institute for the Analysis of Evolutionary Change – Museum KoenigBonnGermany
- Department of Organismic and Evolutionary Biology and Museum of Comparative ZoologyHarvard UniversityCambridgeMassachusettsUSA
| | - Nicolas Chazot
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Fabien L. Condamine
- CNRSUMR 5554 Institut des Sciences de l'Evolution de MontpellierMontpellierFrance
| | - Alan R. Lemmon
- Department of Scientific ComputingFlorida State UniversityTallahasseeFloridaUSA
| | | | | | - Alan Heath
- Lepidopterists' Society of AfricaKnysnaSouth Africa
| | | | | | | | - David C. Lees
- Department of Life SciencesNatural History MuseumLondonUK
| | | | | | | | - Robert Tropek
- Department of Ecology, Faculty of ScienceCharles UniversityPragueCzechia
- Institute of Entomology, Biology CentreCzech Academy of SciencesCeske BudejoviceCzechia
| | - Svenja S. Ahlborn
- Centre for Taxonomy and MorphologyLeibniz Institute for the Analysis of Evolutionary Change – Museum KoenigBonnGermany
| | | | | | | | - Zofia A. Kaliszewska
- Department of Organismic and Evolutionary Biology and Museum of Comparative ZoologyHarvard UniversityCambridgeMassachusettsUSA
| | - Christopher C. M. Baker
- Department of Organismic and Evolutionary Biology and Museum of Comparative ZoologyHarvard UniversityCambridgeMassachusettsUSA
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)BarcelonaSpain
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC‐UPF)BarcelonaSpain
| | | | | | - Dino J. Martins
- Turkana Basin InstituteStony Brook UniversityStony BrookNew YorkUSA
| | - Szabolcs Sáfián
- Institute of Silviculture and Forest ProtectionUniversity of SopronSopronHungary
| | | | - Naomi E. Pierce
- Department of Organismic and Evolutionary Biology and Museum of Comparative ZoologyHarvard UniversityCambridgeMassachusettsUSA
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4
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Romeiro-Brito M, Khan G, Perez MF, Zappi DC, Taylor NP, Olsthoorn G, Franco FF, Moraes EM. Revisiting phylogeny, systematics, and biogeography of a Pleistocene radiation. AMERICAN JOURNAL OF BOTANY 2023; 110:1-17. [PMID: 36708517 DOI: 10.1002/ajb2.16134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Pilosocereus (Cactaceae) is an important dry forest element in all subregions and transitional zones of the neotropics, with the highest diversity in eastern Brazil. The genus is subdivided into informal taxonomic groups; however, most of these are not supported by recent molecular phylogenetic inferences. This lack of confidence is probably due to the use of an insufficient number of loci and the complexity of cactus diversification. Here, we explored the species relationships in Pilosocereus in more detail, integrating multilocus phylogenetic approaches with the assessment of the ancestral range and the effect of geography on diversification shifts. METHODS We used 28 nuclear, plastid, and mitochondrial loci from 54 plant samples of 31 Pilosocereus species for phylogenetic analyses. We used concatenated and coalescent phylogenetic trees and Bayesian models to estimate the most likely ancestral range and diversification shifts. RESULTS All Pilosocereus species were clustered in the same branch, except P. bohlei. The phylogenetic relationships were more associated with the geographic distribution than taxonomic affinities among taxa. The genus began diversifying during the Plio-Pleistocene transition in the Caatinga domain and experienced an increased diversification rate during the Calabrian age. CONCLUSIONS We recovered a well-supported multispecies coalescent phylogeny. Our results refine the pattern of rapid diversification of Pilosocereus species across neotropical drylands during the Pleistocene and highlight the need for taxonomic rearrangements in the genus. We recovered a pulse of diversification during the Pleistocene that was likely driven by multiple dispersal and vicariance events within and among the Caatinga, Cerrado, and Atlantic Forest domains.
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Affiliation(s)
- Monique Romeiro-Brito
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky-University Oldenburg, Carl von Ossietzky-Str. 9-11, 26111, Oldenburg, Germany
| | - Manolo F Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Daniela C Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília (UNB), PO Box 04457, Brasília, DF, 70910-970, Brazil
| | - Nigel P Taylor
- University of Gibraltar, Gibraltar Botanic Gardens Campus, The Alameda, PO Box 843, GX11 1AA, Gibraltar
| | | | - Fernando F Franco
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
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5
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Makunin A, Korlević P, Park N, Goodwin S, Waterhouse RM, von Wyschetzki K, Jacob CG, Davies R, Kwiatkowski D, St Laurent B, Ayala D, Lawniczak MKN. A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus. Mol Ecol Resour 2022; 22:28-44. [PMID: 34053186 PMCID: PMC7612955 DOI: 10.1111/1755-0998.13436] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 05/19/2021] [Indexed: 01/04/2023]
Abstract
Anopheles is a diverse genus of mosquitoes comprising over 500 described species, including all known human malaria vectors. While a limited number of key vector species have been studied in detail, the goal of malaria elimination calls for surveillance of all potential vector species. Here, we develop a multilocus amplicon sequencing approach that targets 62 highly variable loci in the Anopheles genome and two conserved loci in the Plasmodium mitochondrion, simultaneously revealing both the mosquito species and whether that mosquito carries malaria parasites. We also develop a cheap, nondestructive, and high-throughput DNA extraction workflow that provides template DNA from single mosquitoes for the multiplex PCR, which means specimens producing unexpected results can be returned to for morphological examination. Over 1000 individual mosquitoes can be sequenced in a single MiSeq run, and we demonstrate the panel's power to assign species identity using sequencing data for 40 species from Africa, Southeast Asia, and South America. We also show that the approach can be used to resolve geographic population structure within An. gambiae and An. coluzzii populations, as the population structure determined based on these 62 loci from over 1000 mosquitoes closely mirrors that revealed through whole genome sequencing. The end-to-end approach is quick, inexpensive, robust, and accurate, which makes it a promising technique for very large-scale mosquito genetic surveillance and vector control.
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Affiliation(s)
- Alex Makunin
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Petra Korlević
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Naomi Park
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | | | | | | | - Diego Ayala
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
- CIRMF, Franceville, Gabon
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6
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Douglas J, Jiménez-Silva CL, Bouckaert R. OUP accepted manuscript. Syst Biol 2022; 71:901-916. [PMID: 35176772 PMCID: PMC9248896 DOI: 10.1093/sysbio/syac010] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 11/16/2022] Open
Abstract
As genomic sequence data become increasingly available, inferring the phylogeny of the
species as that of concatenated genomic data can be enticing. However, this approach makes
for a biased estimator of branch lengths and substitution rates and an inconsistent
estimator of tree topology. Bayesian multispecies coalescent (MSC) methods address these
issues. This is achieved by constraining a set of gene trees within a species tree and
jointly inferring both under a Bayesian framework. However, this approach comes at the
cost of increased computational demand. Here, we introduce StarBeast3—a software package
for efficient Bayesian inference under the MSC model via Markov chain Monte Carlo. We gain
efficiency by introducing cutting-edge proposal kernels and adaptive operators, and
StarBeast3 is particularly efficient when a relaxed clock model is applied. Furthermore,
gene-tree inference is parallelized, allowing the software to scale with the size of the
problem. We validated our software and benchmarked its performance using three real and
two synthetic data sets. Our results indicate that StarBeast3 is up to one-and-a-half
orders of magnitude faster than StarBeast2, and therefore more than two orders faster than
*BEAST, depending on the data set and on the parameter, and can achieve convergence on
large data sets with hundreds of genes. StarBeast3 is open-source and is easy to set up
with a friendly graphical user interface. [Adaptive; Bayesian inference; BEAST 2;
effective population sizes; high performance; multispecies coalescent; parallelization;
phylogenetics.]
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Affiliation(s)
- Jordan Douglas
- School of Computer Science, University of Auckland, 9 Symonds
Street Level 1 Student Commons, Auckland 1010, New Zealand
- Correspondence to be sent to: School of Computer Science,
University of Auckland, 9 Symonds Street Level 1 Student Commons, Auckland 1010, New
Zealand; E-mail:
| | - Cinthy L Jiménez-Silva
- School of Computer Science, University of Auckland, 9 Symonds
Street Level 1 Student Commons, Auckland 1010, New Zealand
| | - Remco Bouckaert
- School of Computer Science, University of Auckland, 9 Symonds
Street Level 1 Student Commons, Auckland 1010, New Zealand
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Ethier JP, Fayard A, Soroye P, Choi D, Mazerolle MJ, Trudeau VL. Life history traits and reproductive ecology of North American chorus frogs of the genus Pseudacris (Hylidae). Front Zool 2021; 18:40. [PMID: 34452622 PMCID: PMC8394169 DOI: 10.1186/s12983-021-00425-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/16/2021] [Indexed: 11/10/2022] Open
Abstract
Amphibian biodiversity is declining globally, with over 40% of species being considered threatened to become extinct. Crucial to the success of conservation initiatives are a comprehensive understanding of life history and reproductive ecology of target species. Here we provide an overview of the Pseudacris genus, including breeding behaviour, reproduction, development, survival and longevity. We present an updated distribution map of the 18 species found throughout North America. We also summarize the conservation status at the national and subnational (state, provincial, and territorial) levels, in Canada, USA, and Mexico, to evaluate the relationship between life history traits and extinction risk. Results show a high degree of consistency in the life history traits of Pseudacris species considering their relative diversity and wide distribution in North America. However, data are lacking for several species, particularly in the Fat Frog and West Coast clades, causing some uncertainties and discrepancies in the literature. We also found that the most threatened populations of chorus frog were located in the east coast of the USA, potentially as a result of increased levels of anthropogenic disturbance. We suggest that the similarities in life history traits among chorus frog species provides an opportunity for collaboration and united efforts for the conservation of the genus.
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Affiliation(s)
- Jeffrey P Ethier
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | - Aurore Fayard
- Centre d'etude de la Foret, Département des Sciences du Bois et de la Forêt, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Peter Soroye
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Daeun Choi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Marc J Mazerolle
- Centre d'etude de la Foret, Département des Sciences du Bois et de la Forêt, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Vance L Trudeau
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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Jadin RC, Orlofske SA, Jezkova T, Blair C. Single-locus species delimitation and ecological niche modelling provide insights into the evolution, historical distribution and taxonomy of the Pacific chorus frogs. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
The Pacific chorus frogs are a complex of three wide-ranging species (i.e. Hyliola hypochondriaca, Hyliola regilla, Hyliola sierra) whose current taxonomy remains unresolved. We conducted species delimitation analyses of these taxa using fragments of the cytochrome b and 12S–16S mtDNA genes to assess the species diversity. Importantly, we included samples from new locations throughout the range to better understand species distributions and identify potential contact zones among clades. Our analyses revealed three slightly parapatric but distinct species-level clades. Molecular dating revealed that these species began diverging in the Pleistocene c. 1.4 Mya with H. hypochondriaca and H. sierra diverging more recently c. 0.8 Mya. We found that populations from western Montana and Idaho originated recently from populations to the southwest that belong to H. sierra, rather than from H. regilla populations directly to the west. Population sizes of each species expanded c. 130–80 Kya with H. hypochondriaca exhibiting a more pronounced expansion beginning c. 100 Kya than the more gradual expansion of the other two species. The climatic niche models suggest that distributions of the three species were similar during the last interglacial (LIG) as they are today. During the Last Glacial Maximum (LGM), H. hypochondriaca and H. sierra occupied a larger range than they do today whereas H. regilla occupied a smaller refugium, shifted south from the current distribution. This study highlights the continued effectiveness of utilizing single-locus data sets for species delimitation and biogeographic analyses.
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Affiliation(s)
- Robert C Jadin
- Department of Biology and Museum of Natural History, University of Wisconsin, Stevens Point, WI, USA
- Department of Biology, University of Wisconsin, Eau Claire, WI, USA
| | - Sarah A Orlofske
- Department of Biology and Museum of Natural History, University of Wisconsin, Stevens Point, WI, USA
| | - Tereza Jezkova
- Department of Biology, Miami University, Oxford, Ohio, USA
| | - Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, Brooklyn, NY, USA
- Biology PhD Program, CUNY Graduate Center, New York, NY, USA
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9
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Banker SE, Lemmon AR, Hassinger AB, Dye M, Holland SD, Kortyna ML, Ospina OE, Ralicki H, Lemmon EM. Hierarchical Hybrid Enrichment: Multitiered Genomic Data Collection Across Evolutionary Scales, With Application to Chorus Frogs (Pseudacris). Syst Biol 2021; 69:756-773. [PMID: 31886503 PMCID: PMC7302053 DOI: 10.1093/sysbio/syz074] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/26/2019] [Accepted: 11/04/2019] [Indexed: 01/25/2023] Open
Abstract
Determining the optimal targets of genomic subsampling for phylogenomics, phylogeography, and population genomics remains a challenge for evolutionary biologists. Of the available methods for subsampling the genome, hybrid enrichment (sequence capture) has become one of the primary means of data collection for systematics, due to the flexibility and cost efficiency of this approach. Despite the utility of this method, information is lacking as to what genomic targets are most appropriate for addressing questions at different evolutionary scales. In this study, first, we compare the benefits of target loci developed for deep- and shallow scales by comparing these loci at each of three taxonomic levels: within a genus (phylogenetics), within a species (phylogeography), and within a hybrid zone (population genomics). Specifically, we target evolutionarily conserved loci that are appropriate for deeper phylogenetic scales and more rapidly evolving loci that are informative for phylogeographic and population genomic scales. Second, we assess the efficacy of targeting multiple-locus sets for different taxonomic levels in the same hybrid enrichment reaction, an approach we term hierarchical hybrid enrichment. Third, we apply this approach to the North American chorus frog genus Pseudacris to answer key evolutionary questions across taxonomic and temporal scales. We demonstrate that in this system the type of genomic target that produces the most resolved gene trees differs depending on the taxonomic level, although the potential for error is substantially lower for the deep-scale loci at all levels. We successfully recover data for the two different locus sets with high efficiency. Using hierarchical data targeting deep and shallow levels: we 1) resolve the phylogeny of the genus Pseudacris and introduce a novel visual and hypothesis testing method that uses nodal heat maps to examine the robustness of branch support values to the removal of sites and loci; 2) estimate the phylogeographic history of Pseudacris feriarum, which reveals up to five independent invasions leading to sympatry with congener Pseudacris nigrita to form replicated reinforcement contact zones with ongoing gene flow into sympatry; and 3) quantify with high confidence the frequency of hybridization in one of these zones between P. feriarum and P. nigrita, which is lower than microsatellite-based estimates. We find that the hierarchical hybrid enrichment approach offers an efficient, multitiered data collection method for simultaneously addressing questions spanning multiple evolutionary scales. [Anchored hybrid enrichment; heat map; hybridization; phylogenetics; phylogeography; population genomics; reinforcement; reproductive character displacement.].
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Affiliation(s)
- Sarah E Banker
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Integrative Biology, University of California, Berkeley, #3160 Berkeley, CA 94720-3160, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Alyssa Bigelow Hassinger
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12th Avenue, 300 Aronoff Laboratory, Columbus, OH 43210, USA
| | - Mysia Dye
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Sean D Holland
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Oscar E Ospina
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Hannah Ralicki
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Biological Science, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06268, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
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10
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Ospina OE, Tieu L, Apodaca JJ, Lemmon EM. Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States. COPEIA 2020. [DOI: 10.1643/ch2020009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Oscar E. Ospina
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
| | - Lynee Tieu
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
| | - Joseph J. Apodaca
- Tangled Bank Conservation, 128 Bingham Road, Suite 1150, Asheville, North Carolina 28806;
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
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11
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Vélez A, Guajardo AS. Individual variation in two types of advertisement calls of Pacific tree frogs, Hyliola (=Pseudacris) regilla, and the implications for sexual selection and species recognition. BIOACOUSTICS 2020; 30:437-457. [PMID: 34239226 PMCID: PMC8259394 DOI: 10.1080/09524622.2020.1803133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/03/2020] [Indexed: 10/23/2022]
Abstract
Anuran advertisement calls play a fundamental role in social interactions related to reproduction, like territory defense and mate attraction. As such, advertisement calls are often shaped by natural and sexual selection. Therefore, to understand the evolution, function, and mechanisms of signal production and perception, it is important to characterize sources and patterns of variation in call properties. We recorded and analyzed the two types of advertisement calls produced by Pacific tree frogs, Hyliola regilla: diphasic and monophasic calls. Specifically, we examined (i) the relationship between call properties and both body size and physical condition, (ii) patterns of within- and among-individual variation in call properties, and (iii) acoustic differences between diphasic and monophasic calls. While only one property of diphasic calls correlates with physical condition, spectral properties of both types of calls correlate with body size. Patterns of within- and among-individual variation were similar between call types and, overall, consistent with patterns reported for closely related species. Monophasic calls have lower frequencies, are delivered faster, and have higher call effort and duty cycle than diphasic calls. We discuss our results in relation to sexual selection and formulate hypotheses about the evolution, function, and mechanisms of acoustic communication in Pacific tree frogs.
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Affiliation(s)
- Alejandro Vélez
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132, USA
| | - Adriana S. Guajardo
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132, USA
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12
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Faivovich J, Pereyra MO, Luna MC, Hertz A, Blotto BL, Vásquez-Almazán CR, McCranie JR, Sánchez DA, Baêta D, Araujo-Vieira K, Köhler G, Kubicki B, Campbell JA, Frost DR, Wheeler WC, Haddad CF. On the Monophyly and Relationships of Several Genera of Hylini (Anura: Hylidae: Hylinae), with Comments on Recent Taxonomic Changes in Hylids. SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2018. [DOI: 10.2994/sajh-d-17-00115.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Julián Faivovich
- Division Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” —Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Martín O. Pereyra
- Division Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” —Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - María Celeste Luna
- Division Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” —Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Andreas Hertz
- Senckenberg Forschungsinstitut und Naturmuseum, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Boris L. Blotto
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, CEP 05508-090 São Paulo, São Paulo, Brazil
| | - Carlos R. Vásquez-Almazán
- Museo de Historia Natural, Escuela de Biología, Universidad de San Carlos de Guatemala, Calle Mariscal Cruz 1-56 zona 10, Ciudad de Guatemala, Guatemala
| | | | - David A. Sánchez
- Department of Biology, The University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Délio Baêta
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de Zoologia and Centro de Aquicultura, Av. 24A 1515, CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - Katyuscia Araujo-Vieira
- Division Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” —Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Gunther Köhler
- Senckenberg Forschungsinstitut und Naturmuseum, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Brian Kubicki
- Costa Rican Amphibian Research Center, Guayacán, Provincia de Limón, Costa Rica
| | - Jonathan A. Campbell
- Department of Biology, The University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Darrel R. Frost
- Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79 Street, New York, NY 10024, USA
| | - Ward C. Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79 Street, New York, NY 10024, USA
| | - Célio F.B. Haddad
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de Zoologia and Centro de Aquicultura, Av. 24A 1515, CEP 13506-900, Rio Claro, São Paulo, Brazil
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13
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Dupuis JR, Bremer FT, Kauwe A, San Jose M, Leblanc L, Rubinoff D, Geib SM. HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing. Mol Ecol Resour 2018. [PMID: 29633537 DOI: 10.1101/213454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.
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Affiliation(s)
- Julian R Dupuis
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Forest T Bremer
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Angela Kauwe
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
| | - Michael San Jose
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Luc Leblanc
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho
| | - Daniel Rubinoff
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Scott M Geib
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
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14
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Dupuis JR, Bremer FT, Kauwe A, San Jose M, Leblanc L, Rubinoff D, Geib SM. HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing. Mol Ecol Resour 2018; 18:1000-1019. [PMID: 29633537 DOI: 10.1111/1755-0998.12783] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/07/2018] [Accepted: 03/19/2018] [Indexed: 01/22/2023]
Abstract
High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.
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Affiliation(s)
- Julian R Dupuis
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Forest T Bremer
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Angela Kauwe
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
| | - Michael San Jose
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Luc Leblanc
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho
| | - Daniel Rubinoff
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Scott M Geib
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
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15
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Ogilvie HA, Bouckaert RR, Drummond AJ. StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates. Mol Biol Evol 2018; 34:2101-2114. [PMID: 28431121 PMCID: PMC5850801 DOI: 10.1093/molbev/msx126] [Citation(s) in RCA: 248] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be sequenced for a given study, but using that many genes with *BEAST is intractably slow. An alternative is to use heuristic methods which compromise accuracy or completeness in return for speed. A common heuristic is concatenation, which assumes that the evolutionary history of each gene tree is identical to the species tree. This is an inconsistent estimator of species tree topology, a worse estimator of divergence times, and induces spurious substitution rate variation when incomplete lineage sorting is present. Another class of heuristics directly motivated by the MSC avoids many of the pitfalls of concatenation but cannot be used to estimate divergence times. To enable fuller use of available data and more accurate inference of species tree topologies, divergence times, and substitution rates, we have developed a new version of *BEAST called StarBEAST2. To improve convergence rates we add analytical integration of population sizes, novel MCMC operators and other optimizations. Computational performance improved by 13.5× and 13.8× respectively when analyzing two empirical data sets, and an average of 33.1× across 30 simulated data sets. To enable accurate estimates of per-species substitution rates, we introduce species tree relaxed clocks, and show that StarBEAST2 is a more powerful and robust estimator of rate variation than concatenation. StarBEAST2 is available through the BEAUTi package manager in BEAST 2.4 and above.
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Affiliation(s)
- Huw A Ogilvie
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia.,Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
| | - Remco R Bouckaert
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.,Department of Computer Science, University of Auckland, Auckland, New Zealand
| | - Alexei J Drummond
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.,Department of Computer Science, University of Auckland, Auckland, New Zealand
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16
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Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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17
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Rothfels CJ, Pryer KM, Li FW. Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. THE NEW PHYTOLOGIST 2017; 213:413-429. [PMID: 27463214 DOI: 10.1111/nph.14111] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 06/14/2016] [Indexed: 05/27/2023]
Abstract
Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate Complexes (Purc)) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multi-labeled species tree for a subset of our accessions. We amplified four c. 1-kb-long nuclear loci and sequenced them in a parallel-tagged amplicon sequencing approach using the PacBio platform. Purc infers the final sequences from the raw reads via an iterative approach that corrects PCR and sequencing errors and removes PCR-mediated recombinant sequences (chimeras). We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads, Purc was able to accurately infer the underlying sequences. This approach makes it easy and economical to study the phylogenetics of polyploids, and, in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.
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Affiliation(s)
- Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | | | - Fay-Wei Li
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- Department of Biology, Duke University, Durham, NC, 27705, USA
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18
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Newman CE, Austin CC. Sequence capture and next‐generation sequencing of ultraconserved elements in a large‐genome salamander. Mol Ecol 2016; 25:6162-6174. [DOI: 10.1111/mec.13909] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/26/2016] [Accepted: 11/01/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Catherine E. Newman
- Museum of Natural Science Louisiana State University 119 Foster Hall Baton Rouge LA 70803 USA
- Department of Biological Sciences Louisiana State University 202 Life Sciences Building Baton Rouge LA 70803 USA
| | - Christopher C. Austin
- Museum of Natural Science Louisiana State University 119 Foster Hall Baton Rouge LA 70803 USA
- Department of Biological Sciences Louisiana State University 202 Life Sciences Building Baton Rouge LA 70803 USA
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19
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Li Y, Kocot KM, Whelan NV, Santos SR, Waits DS, Thornhill DJ, Halanych KM. Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods. ZOOL SCR 2016. [DOI: 10.1111/zsc.12201] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Yuanning Li
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University 36830 Auburn AL USA
| | - Kevin M. Kocot
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University 36830 Auburn AL USA
- Department of Biological Sciences & Alabama Museum of Natural History The University of Alabama 35847 Tuscaloosa AL USA
| | - Nathan V. Whelan
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University 36830 Auburn AL USA
| | - Scott R. Santos
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University 36830 Auburn AL USA
| | - Damien S. Waits
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University 36830 Auburn AL USA
| | - Daniel J. Thornhill
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University 36830 Auburn AL USA
| | - Kenneth M. Halanych
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University 36830 Auburn AL USA
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20
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Barrow LN, Bigelow AT, Phillips CA, Lemmon EM. Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex. Mol Ecol 2015; 24:4739-58. [DOI: 10.1111/mec.13343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 07/24/2015] [Accepted: 08/08/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Lisa N. Barrow
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
| | - Alyssa T. Bigelow
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
| | - Christopher A. Phillips
- Illinois Natural History Survey Prairie Research Institute University of Illinois 185 Natural Resources Bldg, 607 E. Peabody Drive Champaign IL 61820 USA
| | - Emily Moriarty Lemmon
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
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21
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Zepeda Mendoza ML, Sicheritz-Pontén T, Gilbert MTP. Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. Brief Bioinform 2015; 16:745-58. [PMID: 25673291 PMCID: PMC4570204 DOI: 10.1093/bib/bbv001] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/16/2014] [Indexed: 01/19/2023] Open
Abstract
DNA-based taxonomic and functional profiling is widely used for the characterization of organismal communities across a rapidly increasing array of research areas that include the role of microbiomes in health and disease, biomonitoring, and estimation of both microbial and metazoan species richness. Two principal approaches are currently used to assign taxonomy to DNA sequences: DNA metabarcoding and metagenomics. When initially developed, each of these approaches mandated their own particular methods for data analysis; however, with the development of high-throughput sequencing (HTS) techniques they have begun to share many aspects in data set generation and processing. In this review we aim to define the current characteristics, goals and boundaries of each field, and describe the different software used for their analysis. We argue that an appreciation of the potential and limitations of each method can help underscore the improvements required by each field so as to better exploit the richness of current HTS-based data sets.
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22
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Warwick AR, Travis J, Lemmon EM. Geographic variation in the Pine Barrens Treefrog (Hyla andersonii): concordance of genetic, morphometric and acoustic signal data. Mol Ecol 2015; 24:3281-98. [DOI: 10.1111/mec.13242] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Alexa R. Warwick
- Department of Biological Science; Florida State University; 319 Stadium Drive Tallahassee FL 32306 USA
| | - Joseph Travis
- Department of Biological Science; Florida State University; 319 Stadium Drive Tallahassee FL 32306 USA
| | - Emily Moriarty Lemmon
- Department of Biological Science; Florida State University; 319 Stadium Drive Tallahassee FL 32306 USA
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23
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Feng YJ, Liu QF, Chen MY, Liang D, Zhang P. Parallel tagged amplicon sequencing of relatively long PCR products using the Illumina HiSeq platform and transcriptome assembly. Mol Ecol Resour 2015; 16:91-102. [PMID: 25959587 DOI: 10.1111/1755-0998.12429] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 11/30/2022]
Abstract
In phylogenetics and population genetics, a large number of loci are often needed to accurately resolve species relationships. Normally, loci are enriched by PCR and sequenced by Sanger sequencing, which is expensive when the number of amplicons is large. Next-generation sequencing (NGS) techniques are increasingly used for parallel amplicon sequencing, which reduces sequencing costs tremendously, but has not reduced preparation costs very much. Moreover, for most current NGS methods, amplicons need to be purified and quantified before sequencing and their lengths are also restricted (normally <700 bp). Here, we describe an approach to sequence pooled amplicons of any length using the Illumina platform. Using this method, amplicons are pooled at equal volume rather than at equal concentration, thus eliminating the laborious purification and quantification steps. We then shear the pooled amplicons, repair the ends, add sample identifying linkers and pool multiple samples prior to Illumina library preparation. Data are then assembled using the transcriptome assembly program trinity, which is optimized to deal with templates of highly varying quantities. We demonstrated the utility of our approach by recovering 93.5% of the target amplicons (size up to 1650 bp) in full length for a 16 taxa × 101 loci project, using ~2.0 GB of Illumina HiSeq paired-end 90-bp data. Overall, we validate a rapid, cost-effective and scalable approach to sequence a large number of targeted loci from a large number of samples that is particularly suitable for both phylogenetics and population genetics studies that require a modest scale of data.
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Affiliation(s)
- Yan-Jie Feng
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qing-Feng Liu
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Meng-Yun Chen
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
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24
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Brandley MC, Bragg JG, Singhal S, Chapple DG, Jennings CK, Lemmon AR, Lemmon EM, Thompson MB, Moritz C. Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards. BMC Evol Biol 2015; 15:62. [PMID: 25880916 PMCID: PMC4434831 DOI: 10.1186/s12862-015-0318-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/24/2015] [Indexed: 01/31/2023] Open
Abstract
Background High-throughput sequencing using targeted enrichment and transcriptomic methods enables rapid construction of phylogenomic data sets incorporating hundreds to thousands of loci. These advances have enabled access to an unprecedented amount of nucleotide sequence data, but they also pose new questions. Given that the loci targeted for enrichment are often highly conserved, how informative are they at different taxonomic scales, especially at the intraspecific/phylogeographic scale? We investigate this question using Australian scincid lizards in the Eugongylus group (Squamata: Scincidae). We sequenced 415 anchored hybrid enriched (AHE) loci for 43 individuals and mined 1650 exons (1648 loci) from transcriptomes (transcriptome mining) from 11 individuals, including multiple phylogeographic lineages within several species of Carlia, Lampropholis, and Saproscincus skinks. We assessed the phylogenetic information content of these loci at the intergeneric, interspecific, and phylogeographic scales. As a further test of the utility at the phylogeographic scale, we used the anchor hybrid enriched loci to infer lineage divergence parameters using coalescent models of isolation with migration. Results Phylogenetic analyses of both data sets inferred very strongly supported trees at all taxonomic levels. Further, AHE loci yielded estimates of divergence times between closely related lineages that were broadly consistent with previous population-level analyses. Conclusions Anchored-enriched loci are useful at the deep phylogeny and phylogeographic scales. Although overall phylogenetic support was high throughout the Australian Eugongylus group phylogeny, there were nonetheless some conflicting or unresolved relationships, especially regarding the placement of Pseudemoia, Cryptoblepharus, and the relationships amongst closely-related species of Tasmanian Niveoscincus skinks. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0318-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew C Brandley
- School of Biological Sciences, Heydon-Laurence Building A08, University of Sydney, Sydney, NSW, 2006, Australia. .,New York University - Sydney, The Rocks, NSW, 2000, Australia.
| | - Jason G Bragg
- Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Canberra, ACT 0200, Australia.
| | - Sonal Singhal
- Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720, USA. .,Department of Integrative Biology, University of California, 3060 Valley Life Sciences Building, Berkeley, CA, 94720, USA.
| | - David G Chapple
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC, 3800, Australia.
| | - Charlotte K Jennings
- Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720, USA. .,Department of Integrative Biology, University of California, 3060 Valley Life Sciences Building, Berkeley, CA, 94720, USA.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306, USA.
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL, 32306, USA.
| | - Michael B Thompson
- School of Biological Sciences, Heydon-Laurence Building A08, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Craig Moritz
- Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Canberra, ACT 0200, Australia. .,The Commonwealth Scientific and Industrial Research Organization Ecosystem Sciences Division, GPO Box 1700, Canberra, ACT, 2601, Australia.
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Díaz-Rodríguez J, Gonçalves H, Sequeira F, Sousa-Neves T, Tejedo M, Ferrand N, Martínez-Solano I. Molecular evidence for cryptic candidate species in Iberian Pelodytes (Anura, Pelodytidae). Mol Phylogenet Evol 2015; 83:224-41. [DOI: 10.1016/j.ympev.2014.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/03/2014] [Accepted: 12/14/2014] [Indexed: 11/16/2022]
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