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Pezzini FF, Ferrari G, Forrest LL, Hart ML, Nishii K, Kidner CA. Target capture and genome skimming for plant diversity studies. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11537. [PMID: 37601316 PMCID: PMC10439825 DOI: 10.1002/aps3.11537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 06/16/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high-molecular-weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast-freeze newly collected living samples to conserve high-quality DNA can be complicated when plants are only found in remote areas. Therefore, short-read reduced-genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non-model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best-informed choice regarding reduced genome representation for evolutionary studies of non-model plants in cases where whole-genome sequencing remains impractical.
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Affiliation(s)
| | - Giada Ferrari
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
| | | | | | - Kanae Nishii
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
| | - Catherine A Kidner
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
- School of Biological Sciences University of Edinburgh Edinburgh United Kingdom
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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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Costa GJ, Nunes VL, Marabuto E, Mendes R, Silva DN, Pons P, Bas JM, Hertach T, Paulo OS, Simões PC. The effect of the Messinian salinity crisis on the early diversification of the
Tettigettalna
cicadas. ZOOL SCR 2022. [DOI: 10.1111/zsc.12571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gonçalo J. Costa
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Vera L. Nunes
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Eduardo Marabuto
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Raquel Mendes
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Diogo N. Silva
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Pere Pons
- Departament de Ciències Ambientals Universitat de Girona Girona Catalonia Spain
| | - Josep M. Bas
- Departament de Ciències Ambientals Universitat de Girona Girona Catalonia Spain
| | - Thomas Hertach
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
- Natural History Museum of Bern Bern Switzerland
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Paula C. Simões
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
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4
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Wu L, Tong Y, Ayivi SPG, Storey KB, Zhang JY, Yu DN. The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless Isopachys gyldenstolpei. Animals (Basel) 2022; 12:ani12162015. [PMID: 36009607 PMCID: PMC9404441 DOI: 10.3390/ani12162015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/27/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
In order to adapt to diverse habitats, organisms often evolve corresponding adaptive mechanisms to cope with their survival needs. The species-rich family of Scincidae contains both limbed and limbless species, which differ fundamentally in their locomotor demands, such as relying on the movement of limbs or only body swing to move. Locomotion requires energy, and different types of locomotion have their own energy requirements. Mitochondria are the energy factories of living things, which provide a lot of energy for various physiological activities of organisms. Therefore, mitochondrial genomes could be tools to explore whether the limb loss of skinks are selected by adaptive evolution. Isopachys gyldenstolpei is a typical limbless skink. Here, we report the complete mitochondrial genomes of I. gyldenstolpei, Sphenomorphus indicus, and Tropidophorus hainanus. The latter two species were included as limbed comparator species to the limbless I. gyldenstolpei. The results showed that the full lengths of the mitochondrial genomes of I. gyldenstolpei, S. indicus, and T. hainanus were 17,210, 16,944, and 17,001 bp, respectively. Three mitochondrial genomes have typical circular double-stranded structures similar to other reptiles, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and the control region. Three mitochondrial genomes obtained in this study were combined with fifteen mitochondrially complete genomes of Scincidae in the NCBI database; the phylogenetic relationship between limbless I. gyldenstolpei and limbed skinks (S. indicus and T. hainanus) is discussed. Through BI and ML trees, Sphenomorphinae and Mabuyinae were monophyletic, while the paraphyly of Scincinae was also recovered. The limbless skink I. gyldenstolpei is closer to the species of Tropidophorus, which has formed a sister group with (T. hainanus + T. hangman). In the mitochondrial genome adaptations between limbless I. gyldenstolpei and limbed skinks, one positively selected site was found in the branch-site model analysis, which was located in ND2 (at position 28, BEB value = 0.907). Through analyzing the protein structure and function of the selected site, we found it was distributed in mitochondrial protein complex I. Positive selection of some mitochondrial genes in limbless skinks may be related to the requirement of energy to fit in their locomotion. Further research is still needed to confirm this conclusion though.
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Affiliation(s)
- Lian Wu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China or
| | - Yao Tong
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China or
| | | | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China or
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China or
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
- Correspondence:
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5
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Slavenko A, Dror L, Camaiti M, Farquhar JE, Shea GM, Chapple DG, Meiri S. Evolution of diel activity patterns in skinks (Squamata: Scincidae), the world's second-largest family of terrestrial vertebrates. Evolution 2022; 76:1195-1208. [PMID: 35355258 PMCID: PMC9322454 DOI: 10.1111/evo.14482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 01/21/2023]
Abstract
Many animals have strict diel activity patterns, with unique adaptations for either diurnal or nocturnal activity. Diel activity is phylogenetically conserved, yet evolutionary shifts in diel activity occur and lead to important changes in an organism's morphology, physiology, and behavior. We use phylogenetic comparative methods to examine the evolutionary history of diel activity in skinks, one of the largest families of terrestrial vertebrates. We examine how diel patterns are associated with microhabitat, ambient temperatures, and morphology. We found support for a nondiurnal ancestral skink. Strict diurnality in crown group skinks only evolved during the Paleogene. Nocturnal habits are associated with fossorial activity, limb reduction and loss, and warm temperatures. Our results shed light on the evolution of diel activity patterns in a large radiation of terrestrial ectotherms and reveal how both intrinsic biotic and extrinsic abiotic factors can shape the evolution of animal activity patterns.
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Affiliation(s)
- Alex Slavenko
- School of BiosciencesUniversity of SheffieldSheffieldSouth YorkshireUnited Kingdom
| | - Liat Dror
- School of ZoologyTel Aviv UniversityTel AvivIsrael
| | - Marco Camaiti
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
| | - Jules E. Farquhar
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
| | - Glenn M. Shea
- Sydney School of Veterinary Science B01University of SydneyNew South WalesAustralia,Australian Museum Research InstituteThe Australian MuseumSydneyNew South WalesAustralia
| | - David G. Chapple
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
| | - Shai Meiri
- School of ZoologyTel Aviv UniversityTel AvivIsrael,The Steinhardt Museum of Natural HistoryTel AvivIsrael
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6
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Onditi KO, Demos TC, Kerbis Peterhans J, Chen ZZ, Bryja J, Lavrenchenko LA, Musila S, Verheyen E, Van de Perre F, Akaibe BD, de la Sancha NU, Jiang XL. Historical biogeography, systematics, and integrative taxonomy of the non-Ethiopian speckled pelage brush-furred rats (Lophuromys flavopunctatus group). BMC Ecol Evol 2021; 21:89. [PMID: 34011264 PMCID: PMC8132446 DOI: 10.1186/s12862-021-01813-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/19/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity and evolution. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys. RESULTS The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agree with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene. CONCLUSION The phylogenetic associations and divergence times of the L. flavopunctatus group support the hypothesis that paleoclimatic impacts and ecosystem refugia during the Pleistocene impacted the evolutionary radiation of these rodents. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.
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Affiliation(s)
- Kenneth Otieno Onditi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- Mammal Section, Zoology Department, National Museums of Kenya, Nairobi, Kenya
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Nairobi, Kenya
| | - Terrence C Demos
- Science & Education, Field Museum of Natural History, Chicago, USA
| | - Julian Kerbis Peterhans
- Science & Education, Field Museum of Natural History, Chicago, USA
- College of Arts and Sciences, Roosevelt University, Chicago, USA
| | - Zhong-Zheng Chen
- Collaborative Innovation Centre of Recovery and Reconstruction of Degraded Ecosystems in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Anhui, China
| | - Josef Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Leonid A Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Science, Moscow, Russia
| | - Simon Musila
- Mammal Section, Zoology Department, National Museums of Kenya, Nairobi, Kenya
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Nairobi, Kenya
| | - Erik Verheyen
- Operational Direction Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, Brussels, Belgium
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Frederik Van de Perre
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Benjamin Dudu Akaibe
- Department of Ecology and Animal Resource Management, Faculty of Science, Biodiversity Monitoring Centre, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Noé U de la Sancha
- Science & Education, Field Museum of Natural History, Chicago, USA
- Department of Biological Sciences, Chicago State University, Chicago, USA
| | - Xue-Long Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Nairobi, Kenya.
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7
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Freitas FV, Branstetter MG, Griswold T, Almeida EAB. Partitioned Gene-Tree Analyses and Gene-Based Topology Testing Help Resolve Incongruence in a Phylogenomic Study of Host-Specialist Bees (Apidae: Eucerinae). Mol Biol Evol 2021; 38:1090-1100. [PMID: 33179746 PMCID: PMC7947843 DOI: 10.1093/molbev/msaa277] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Incongruence among phylogenetic results has become a common occurrence in analyses of genome-scale data sets. Incongruence originates from uncertainty in underlying evolutionary processes (e.g., incomplete lineage sorting) and from difficulties in determining the best analytical approaches for each situation. To overcome these difficulties, more studies are needed that identify incongruences and demonstrate practical ways to confidently resolve them. Here, we present results of a phylogenomic study based on the analysis 197 taxa and 2,526 ultraconserved element (UCE) loci. We investigate evolutionary relationships of Eucerinae, a diverse subfamily of apid bees (relatives of honey bees and bumble bees) with >1,200 species. We sampled representatives of all tribes within the group and >80% of genera, including two mysterious South American genera, Chilimalopsis and Teratognatha. Initial analysis of the UCE data revealed two conflicting hypotheses for relationships among tribes. To resolve the incongruence, we tested concatenation and species tree approaches and used a variety of additional strategies including locus filtering, partitioned gene-trees searches, and gene-based topological tests. We show that within-locus partitioning improves gene tree and subsequent species-tree estimation, and that this approach, confidently resolves the incongruence observed in our data set. After exploring our proposed analytical strategy on eucerine bees, we validated its efficacy to resolve hard phylogenetic problems by implementing it on a published UCE data set of Adephaga (Insecta: Coleoptera). Our results provide a robust phylogenetic hypothesis for Eucerinae and demonstrate a practical strategy for resolving incongruence in other phylogenomic data sets.
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Affiliation(s)
- Felipe V Freitas
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT
| | - Terry Griswold
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT
| | - Eduardo A B Almeida
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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8
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Thorn KM, Hutchinson MN, Lee MSY, Brown NJ, Camens AB, Worthy TH. A new species of Proegernia from the Namba Formation in South Australia and the early evolution and environment of Australian egerniine skinks. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201686. [PMID: 33972861 PMCID: PMC8074667 DOI: 10.1098/rsos.201686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
The diverse living Australian lizard fauna contrasts greatly with their limited Oligo-Miocene fossil record. New Oligo-Miocene fossil vertebrates from the Namba Formation (south of Lake Frome, South Australia) were uncovered from multiple expeditions from 2007 to 2018. Abundant disarticulated material of small vertebrates was concentrated in shallow lenses along the palaeolake edges, now exposed on the western of Lake Pinpa also known from Billeroo Creek 2 km northeast. The fossiliferous lens within the Namba Formation hosting the abundant aquatic (such as fish, platypus Obdurodon and waterfowl) and diverse terrestrial (such as possums, dasyuromorphs and scincids) vertebrates and is hereafter recognized as the Fish Lens. The stratigraphic provenance of these deposits in relation to prior finds in the area is also established. A new egerniine scincid taxon Proegernia mikebulli sp. nov. described herein, is based on a near-complete reconstructed mandible, maxilla, premaxilla and pterygoid. Postcranial scincid elements were also recovered with this material, but could not yet be confidently associated with P. mikebulli. This new taxon is recovered as the sister species to P. palankarinnensis, in a tip-dated total-evidence phylogenetic analysis, where both are recovered as stem Australian egerniines. These taxa also help pinpoint the timing of the arrival of scincids to Australia, with egerniines the first radiation to reach the continent.
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Affiliation(s)
- K. M. Thorn
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia
- South Australian Museum, North Terrace, Adelaide 5000, South Australia
| | - M. N. Hutchinson
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia
- South Australian Museum, North Terrace, Adelaide 5000, South Australia
| | - M. S. Y. Lee
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia
- South Australian Museum, North Terrace, Adelaide 5000, South Australia
| | - N. J. Brown
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia
| | - A. B. Camens
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia
| | - T. H. Worthy
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia
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9
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Figueiredo PICC, Malabarba LR, Fagundes NJR. Hydrography rather than lip morphology better explains the evolutionary relationship between Gymnogeophagus labiatus and G. lacustris in Southern Brazil (Cichlidae: Geophagini). NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2020-0154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT Gymnogeophagus labiatus and G. lacustris have been long recognized as sister species exhibiting different ecological requirements. Gymnogeophagus labiatus occurs in rock bottom rivers in the hydrographic basins of Patos Lagoon (HBP) and Tramandaí River (HBT), while G. lacustris is exclusive from sand bottom coastal lagoons of the HBT. In this study, we used molecular markers, morphological measurements and data from nuptial male coloration to investigate the evolutionary relationship between these species in each hydrographic basin. We found, for all data sets, a closer relationship between G. labiatus and G. lacustris from the HBT than between G. labiatus populations from HBT and HBP. In particular, lip area had a large intraspecific plasticity, being uninformative to diagnose G. lacustris from G. labiatus. Molecular clock-based estimates suggest a recent divergence between species in the HBT (17,000 years ago), but not between G. labiatus from HBP and HBT (3.6 millions of years ago). Finally, we also found a divergent G. labiatus genetic lineage from the Camaquã River, in the HBP. These results show that the current taxonomy of G. labiatus and G. lacustris does not properly represent evolutionary lineages in these species.
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Affiliation(s)
| | - Luiz R. Malabarba
- Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
| | - Nelson J. R. Fagundes
- Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
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10
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Machado L, Salvi D, James Harris D, Brito JC, Crochet PA, Geniez P, Ahmadzadeh F, Carranza S. Systematics, biogeography and evolution of the Saharo-Arabian naked-toed geckos genus Tropiocolotes. Mol Phylogenet Evol 2020; 155:106969. [PMID: 33031930 DOI: 10.1016/j.ympev.2020.106969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/02/2020] [Accepted: 09/28/2020] [Indexed: 11/18/2022]
Abstract
Plate tectonics constitute one of the main mechanisms of biological diversification on Earth, often being associated with cladogenetic events at different phylogenetic levels, as well as with exchange of faunas and floras across previously isolated biogeographic regions. North Africa and Arabia share a complex geological history that dates back to the break-up of the Arabian plate from the African plate ~30-25 Mya, followed by various geological events, such as the formation of the Red Sea or the connection between the African, Arabian and Eurasian plates. Species with Saharo-Arabian distributions have shown a close association between their evolutionary history and these geological events. In this study, we investigate the systematics, biogeography and evolution of the genus Tropiocolotes, a group of small ground-dwelling geckos, comprised by 12 species distributed from the Atlantic coast of North Africa to southwestern Iran. Species delimitation analyses uncovered the existence of high levels of undescribed diversity, with forms here considered at the species level including Tropiocolotes tripolitanus (Mauritania and southern Morocco), T. nattereri (southern Israel) and T. scorteccii (Yemen and Oman). Phylogenetic and biogeographic analyses recovered two main clades, an exclusively African clade and a Saharo-Arabian clade, that split ~25 Mya following the vicariant event mediated by the separation of the Arabian and African plates. The complex geological activity around the Red Sea is associated with the diversification within the Saharo-Arabian clade, including the colonization of North Africa from a second Tropiocolotes group. Results also provide new insights into the geographic distribution of Tropiocolotes nubicus, previously considered as exclusively associated to the Nile River valley, extending its known distribution further west, up to the Central Mountains of the Sahara. Accordingly, the Nile River seems to act as a major biogeographic barrier, separating Tropiocolotes nubicus and T. steudneri in their western and eastern margins, respectively.
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Affiliation(s)
- Luís Machado
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBio Laboratório Associado, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal; Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
| | - Daniele Salvi
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBio Laboratório Associado, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Department of Health, Life and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - D James Harris
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBio Laboratório Associado, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - José C Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBio Laboratório Associado, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Pierre-André Crochet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Philippe Geniez
- CEFE, Univ Montpellier, CNRS, PSL-EPHE, IRD, Univ Paul Valéry Montpellier 3, Biogéographie et Ecologie des Vertébrés, Montpellier, France
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran 1983963113, Iran
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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11
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Perea S, Sousa‐Santos C, Robalo J, Doadrio I. Multilocus phylogeny and systematics of Iberian endemicSqualius(Actinopterygii, Leuciscidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Silvia Perea
- Department of Biodiversity and Evolutionary Biology Museo Nacional de Ciencias Naturales - CSIC Madrid Spain
| | - Carla Sousa‐Santos
- MARE – Marine and Environmental Sciences Centre ISPA‐Instituto Universitário Lisbon Portugal
| | - Joana Robalo
- MARE – Marine and Environmental Sciences Centre ISPA‐Instituto Universitário Lisbon Portugal
| | - Ignacio Doadrio
- Department of Biodiversity and Evolutionary Biology Museo Nacional de Ciencias Naturales - CSIC Madrid Spain
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12
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Mao Y, Hou S, Shi J, Economo EP. TREEasy: An automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data. Mol Ecol Resour 2020; 20. [PMID: 32073732 DOI: 10.1111/1755-0998.13149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/27/2020] [Accepted: 02/10/2020] [Indexed: 11/30/2022]
Abstract
Multilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user-friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python-TREEasy-that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ-Tree), species inference from concatenated data (with IQ-Tree and RaxML-NG), species tree inference from gene trees (with ASTRAL, MP-EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the "WGD clade" of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology (https://github.com/MaoYafei/TREEasy).
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Affiliation(s)
- Yafei Mao
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Siqing Hou
- Cognitive Neurorobotics Research Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Junfeng Shi
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
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13
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Santibáñez-López CE, Ojanguren-Affilastro AA, Sharma PP. Another one bites the dust: taxonomic sampling of a key genus in phylogenomic datasets reveals more non-monophyletic groups in traditional scorpion classification. INVERTEBR SYST 2020. [DOI: 10.1071/is19033] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Historically, morphological characters have been used to support the monophyly, composition, and phylogenetic relationships of scorpion families. Although recent phylogenomic analyses have recovered most of these traditional higher-level relationships as non-monophyletic, certain key taxa have yet to be sampled using a phylogenomic approach. Salient among these is the monotypic genus Caraboctonus Pocock,1893, the type species of the family Caraboctonidae Kraepelin, 1905. Here, we examined the putative monophyly and phylogenetic placement of this family, sampling the library of C. keyserlingi Pocock, 1893 using high throughput transcriptomic sequencing. Our phylogenomic analyses recovered Caraboctonidae as polyphyletic due to the distant placement of the genera Caraboctonus and Hadrurus Thorell, 1876. Caraboctonus was stably recovered as the sister-group of the monotypic family Superstitioniidae Stahnke, 1940, whereas Hadrurus formed an unstable relationship with Uroctonus Thorell, 1876and Belisarius Simon, 1879. Four-cluster likelihood mapping revealed that the instability inherent to the placement of Hadrurus, Uroctonus and Belisarius was attributable to significant gene tree conflict in the internodes corresponding to their divergences. To redress the polyphyly of Caraboctonidae, the following systematic actions have been taken: (1) the family Caraboctonidae has been delimited to consist of 23 species in the genera Caraboctonus and Hadruroides Pocock, 1893; (2) Caraboctonidae, previously included in the superfamily Iuroidea Thorell, 1876 or as incertae sedis, is transferred to the superfamily Caraboctonoidea (new rank); (3) the superfamily Hadruroidea (new rank) is established and the status of Hadrurinae Stahnke, 1973 is elevated to family (Hadruridae new status) including 9 species in the genera Hadrurus and Hoffmannihadrurus Fet & Soleglad, 2004 and (4) we treat Uroctonus and Belisarius as insertae sedis with respect to superfamilial placement. Our systematic actions engender the monophyly of both Iuroidea and Caraboctonidae. Future phylogenomic investigations should target similar taxon-poor and understudied lineages of potential phylogenetic significance, which are anticipated to reveal additional non-monophyletic groups.
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14
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Sánchez-Martínez PM, Ramírez-Pinilla MP, Meneses-Pelayo E, Nunes PMS. Hemipenial morphology of nine South American species of Mabuya (Scincidae: Lygosominae) with comments on the morphology of the family. Anat Rec (Hoboken) 2019; 303:2917-2930. [PMID: 31815369 DOI: 10.1002/ar.24329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 09/09/2019] [Accepted: 10/25/2019] [Indexed: 11/08/2022]
Abstract
Species of the genus Mabuya are barely recognizable because of their highly conservative external morphology, resulting in unstable systematic and taxonomic status. Considering that hemipenial morphology has been extensively used as a source of systematic information for several groups of Squamata, we described the hemipenial morphology of nine species of Mabuya, searching for diagnostic features useful to taxonomic and systematic studies. To have comparative parameters within the family, we also presented the description of the hemipenes of two other Scincidae species (i.e., Trachylepis atlantica and Tiliqua rugosa). This information, together with the available literature, was analyzed in a comparative framework, allowing us to define some variation for the genus and family. The hemipenial morphology of the species of Mabuya studied is very conservative; features that show subtle variation were the shape of the protuberances present on the asulcate face of the hemipenial body and the presence and type of a lateral fold, on the body. Also, within the family, some variation was found in the shape and length of lobes, length of branches of the sulcus spermaticus, and in the kind of folds and protuberances in both faces of the lobes and hemipenial body. Although these features were not tested in a systematic context, this information suggested variations in hemipenial morphology that could contribute to taxonomic diagnostics and phylogenetic characters. The importance of obtaining proper preparations for gathering accurate information is emphasized, and the use of fresh-killed specimens that shows fewer difficulties for the procedures of preparation is highly recommended.
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Affiliation(s)
- Paola María Sánchez-Martínez
- Grupo de Morfología y Ecología Evolutiva, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Sede Bogotá, Colombia
| | | | - Elson Meneses-Pelayo
- Grupo de estudios en anfibios y reptiles de Santander (GEARS), Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - Pedro M Sales Nunes
- Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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15
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Bribiesca-Contreras G, Pineda-Enríquez T, Márquez-Borrás F, Solís-Marín FA, Verbruggen H, Hugall AF, O'Hara TD. Dark offshoot: Phylogenomic data sheds light on the evolutionary history of a new species of cave brittle star. Mol Phylogenet Evol 2019; 136:151-163. [PMID: 30981811 DOI: 10.1016/j.ympev.2019.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/28/2019] [Accepted: 04/10/2019] [Indexed: 11/28/2022]
Abstract
Caves are a useful system for testing evolutionary and biogeographic hypotheses, as they are isolated, and their environmental conditions have resulted in adaptive selection across different taxa. Although in recent years many more cave species have been discovered, cave-dwelling members of the class Ophiuroidea (brittle stars) remain scarce. Out of the more than two thousand species of brittle stars described to date, only three are regarded as true cave-dwellers. These occurrences represent rare colonising events, compared to other groups that are known to have successfully diversified in these systems. A third species from an anchihaline cave system in the Yucatan Peninsula, Mexico, has been previously identified from cytochrome oxidase I (COI) barcodes. In this study, we reassess the species boundaries of this putative cave species using a phylogenomic dataset (20 specimens in 13 species, 100 exons, 18.7 kbp). We perform species delimitation analyses using robust full-coalescent methods for discovery and validation of hypotheses on species boundaries, as well as infer its phylogenetic relationships with species distributed in adjacent marine regions, in order to investigate the origin of this cave-adapted species. We assess which hypotheses on the origin of subterranean taxa can be applied to this species by taking into account its placement within the genus Ophionereis and its demographic history. We provide a detailed description of Ophionereis commutabilis n. sp., and evaluate its morphological characters in the light of its successful adaptation to life in caves.
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Affiliation(s)
- Guadalupe Bribiesca-Contreras
- Museum Victoria, GPO Box 666, Melbourne 3001, Australia; School of Biosciences, University of Melbourne, Victoria 3010, Australia.
| | - Tania Pineda-Enríquez
- Department of Biology, Division of Invertebrate Zoology, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA; Natural History Museum of Los Angeles County, 900 Exposition Blvd, Los Angeles, CA 90007, USA
| | - Francisco Márquez-Borrás
- Laboratorio de Sistemática y Ecología de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito Universitario s/n, Ciudad de México CP 04510, Mexico; Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito Universitario s/n, Ciudad de México CP 04510, Mexico
| | - Francisco A Solís-Marín
- Laboratorio de Sistemática y Ecología de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito Universitario s/n, Ciudad de México CP 04510, Mexico
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Victoria 3010, Australia
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16
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Freitas ES, Datta-Roy A, Karanth P, Grismer LL, Siler CD. Multilocus phylogeny and a new classification for African, Asian and Indian supple and writhing skinks (Scincidae: Lygosominae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe genera Lepidothyris, Lygosoma and Mochlus comprise the writhing or supple skinks, a group of semi-fossorial, elongate-bodied skinks distributed across the Old World Tropics. Due to their generalized morphology and lack of diagnostic characters, species- and clade-level relationships have long been debated. Recent molecular phylogenetic studies of the group have provided some clarification of species-level relationships, but a number of issues regarding higher level relationships among genera still remain. Here we present a phylogenetic estimate of relationships among species in Lygosoma, Mochlus and Lepidothyris generated by concatenated and species tree analyses of multilocus data using the most extensive taxonomic sampling of the group to date. We also use multivariate statistics to examine species and clade distributions in morpho space. Our results reject the monophyly of Lygosoma s.l., Lygosoma s.s. and Mochlus, which highlights the instability of the current taxonomic classification of the group. We, therefore, revise the taxonomy of the writhing skinks to better reflect the evolutionary history of Lygosoma s.l. by restricting Lygosoma for Southeast Asia, resurrecting the genus Riopa for a clade of Indian and Southeast Asian species, expanding the genus Mochlus to include all African species of writhing skinks and describing a new genus in Southeast Asia.
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Affiliation(s)
- Elyse S Freitas
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Aniruddha Datta-Roy
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | - Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - L Lee Grismer
- Department of Biology, La Sierra University, Riverside, California, USA
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
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17
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Parks MB, Wickett NJ, Alverson AJ. Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta). Mol Biol Evol 2019; 35:80-93. [PMID: 29040712 PMCID: PMC5850769 DOI: 10.1093/molbev/msx268] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support for critical nodes. We applied phylogenetic paralog pruning techniques to a data set of 94 diatom genomes and transcriptomes to infer perennially difficult species relationships, using concatenation and summary-coalescent methods to reconstruct species trees from data sets spanning a wide range of thresholds for taxon and column occupancy in gene alignments. Conflicts between gene and species trees decreased with both increasing taxon occupancy and bootstrap cutoffs applied to gene trees. Concordance between gene and species trees was lowest for short internodes and increased logarithmically with increasing edge length, suggesting that incomplete lineage sorting disproportionately affects species tree inference at short internodes, which are a common feature of the diatom phylogeny. Although species tree topologies were largely consistent across many data treatments, concatenation methods appeared to outperform summary-coalescent methods for sparse alignments. Our results underscore that approaches to species-tree inference based on few loci are likely to be misled by unrepresentative sampling of gene histories, particularly in lineages that may have diversified rapidly. In addition, phylogenomic studies of diatoms, and potentially other hyperdiverse groups, should maximize the number of gene trees with high taxon occupancy, though there is clearly a limit to how many of these genes will be available.
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Affiliation(s)
- Matthew B Parks
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL
| | - Norman J Wickett
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR
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18
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Simmons MP, Sloan DB, Springer MS, Gatesy J. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Mol Phylogenet Evol 2019; 131:80-92. [DOI: 10.1016/j.ympev.2018.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023]
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19
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Labisko J, Griffiths RA, Chong-Seng L, Bunbury N, Maddock ST, Bradfield KS, Taylor ML, Groombridge JJ. Endemic, endangered and evolutionarily significant: cryptic lineages in Seychelles’ frogs (Anura: Sooglossidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jim Labisko
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
- Island Biodiversity and Conservation, Anse Royale, Mahé, Seychelles
| | - Richard A Griffiths
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | | | - Nancy Bunbury
- Seychelles Islands Foundation, Victoria, Mahé, Seychelles
- Centre for Ecology and Conservation, University of Exeter, UK
| | - Simon T Maddock
- Island Biodiversity and Conservation, Anse Royale, Mahé, Seychelles
- School of Biology, Chemistry and Forensic Science, Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, UK
- Department of Life Sciences, The Natural History Museum, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Michelle L Taylor
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Jim J Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
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20
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Machado L, Šmíd J, Mazuch T, Sindaco R, Al Shukaili AS, Carranza S. Systematics of the Saharo‐Arabian clade of the Palearctic naked‐toed geckos with the description of a new species of
Tropiocolotes
endemic to Oman. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Luis Machado
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBio Laboratório Associado Universidade do Porto Vairão Portugal
- Departamento de Biologia Faculdade de Ciencias da Universidade do Porto Porto Portugal
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Jiří Šmíd
- Department of Zoology National Museum Prague Czech Republic
- Department of Zoology Faculty of Science Charles University in Prague Prague Czech Republic
| | | | | | | | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
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21
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Worldwide phylogeny of three-spined sticklebacks. Mol Phylogenet Evol 2018; 127:613-625. [DOI: 10.1016/j.ympev.2018.06.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/16/2018] [Accepted: 06/04/2018] [Indexed: 11/23/2022]
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22
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Freitas L, Mello B, Schrago CG. Multispecies coalescent analysis confirms standing phylogenetic instability in Hexapoda. J Evol Biol 2018; 31:1623-1631. [PMID: 30058265 DOI: 10.1111/jeb.13355] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 06/28/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
The multispecies coalescent (MSC) has been increasingly used in phylogenomic analyses due to the accommodation of gene tree topological heterogeneity by taking into account population-level processes, such as incomplete lineage sorting. In this sense, the phylogeny of insect species, which are characterized by their large effective population sizes, is suitable for a coalescent-based analysis. Furthermore, studies so far recovered short internal branches at early divergences of the insect tree of life, indicating fast evolutionary radiations that increase the probability of incomplete lineage sorting in deep time. Here, we investigated the performance of the MSC for a phylogenomic data set of hexapods compiled by Misof et al. (2014, Science 346:763). Our analysis recovered the monophyly of most insect orders, and major phylogenetic relationships were in agreement with current insect systematics. We identified, however, some evolutionary associations that were consistently problematic. Most noticeable, Hexapod monophyly was disrupted by the sister group relationship between the remiped crustacean and Insecta. Additionally, the interordinal relationships within Polyneoptera and Neuropteroidea were found to be phylogenetically unstable. We show that these controversial phylogenetic arrangements were also poorly supported by previous analyses, and therefore, we evaluated their robustness to stochastic errors from sampling sites and terminals, confirming standing problems in hexapod phylogeny in the genomics age.
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Affiliation(s)
- Lucas Freitas
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Beatriz Mello
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carlos G Schrago
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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23
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Species limits in the Morelet’s Alligator lizard (Anguidae: Gerrhonotinae). Mol Phylogenet Evol 2018; 120:16-27. [DOI: 10.1016/j.ympev.2017.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 09/21/2017] [Accepted: 11/27/2017] [Indexed: 11/22/2022]
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24
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Streicher JW, Miller EC, Guerrero PC, Correa C, Ortiz JC, Crawford AJ, Pie MR, Wiens JJ. Evaluating methods for phylogenomic analyses, and a new phylogeny for a major frog clade (Hyloidea) based on 2214 loci. Mol Phylogenet Evol 2018; 119:128-143. [DOI: 10.1016/j.ympev.2017.10.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/21/2017] [Accepted: 10/22/2017] [Indexed: 01/28/2023]
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25
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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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Tripp EA, Tsai YE, Zhuang Y, Dexter KG. RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia. Ecol Evol 2017; 7:7920-7936. [PMID: 29043045 PMCID: PMC5632676 DOI: 10.1002/ece3.3274] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/16/2017] [Accepted: 06/20/2017] [Indexed: 01/04/2023] Open
Abstract
Deserts, even those at tropical latitudes, often have strikingly low levels of plant diversity, particularly within genera. One remarkable exception to this pattern is the genus Petalidium (Acanthaceae), in which 37 of 40 named species occupy one of the driest environments on Earth, the Namib Desert of Namibia and neighboring Angola. To contribute to understanding this enigmatic diversity, we generated RADseq data for 47 accessions of Petalidium representing 22 species. We explored the impacts of 18 different combinations of assembly parameters in de novo assembly of the data across nine levels of missing data plus a best practice assembly using a reference Acanthaceae genome for a total of 171 sequence datasets assembled. RADseq data assembled at several thresholds of missing data, including 90% missing data, yielded phylogenetic hypotheses of Petalidium that were confidently and nearly fully resolved, which is notable given that divergence time analyses suggest a crown age for African species of 3.6-1.4 Ma. De novo assembly of our data yielded the most strongly supported and well-resolved topologies; in contrast, reference-based assembly performed poorly, perhaps due in part to moderate phylogenetic divergence between the reference genome, Ruellia speciosa, and the ingroup. Overall, we found that Petalidium, despite the harshness of the environment in which species occur, shows a net diversification rate (0.8-2.1 species per my) on par with those of diverse genera in tropical, Mediterranean, and alpine environments.
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Affiliation(s)
- Erin A. Tripp
- Department of Ecology & Evolutionary BiologyUCB 334University of ColoradoBoulderCOUSA
- Museum of Natural HistoryUCB 350University of ColoradoBoulderCOUSA
| | - Yi‐Hsin Erica Tsai
- Department of Ecology & Evolutionary BiologyUCB 334University of ColoradoBoulderCOUSA
- Museum of Natural HistoryUCB 350University of ColoradoBoulderCOUSA
| | - Yongbin Zhuang
- Department of Ecology & Evolutionary BiologyUCB 334University of ColoradoBoulderCOUSA
- Museum of Natural HistoryUCB 350University of ColoradoBoulderCOUSA
| | - Kyle G. Dexter
- School of GeoSciencesUniversity of EdinburghEdinburghUK
- Royal Botanic Garden EdinburghEdinburghUK
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Paluh DJ, Bauer AM. Comparative skull anatomy of terrestrial and crevice-dwelling Trachylepis skinks (Squamata: Scincidae) with a survey of resources in scincid cranial osteology. PLoS One 2017; 12:e0184414. [PMID: 28902864 PMCID: PMC5597209 DOI: 10.1371/journal.pone.0184414] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 08/23/2017] [Indexed: 11/20/2022] Open
Abstract
Skinks account for more than 25% of all lizard species; however, representatives of fewer than a quarter of all species have been characterized osteologically. All but a few of the available cranial descriptions concentrate solely on characters that can be seen externally on the intact skull. Mabuyid skinks of the genus Trachylepis are the dominant, fully limbed skinks in Sub-Saharan Africa, and nearly all species have the same generalized body plan. Although a few rock crevice-dwelling species possess slight body depression, extreme dorsoventral depression is observed only in Trachylepis laevis. We investigated the detailed skull anatomy of three Trachylepis skinks (T. laevis, T. sulcata, and T. gonwouoi, a recently described species allied to T. affinis) using high-resolution X-ray micro-computed tomography. Our goals were to review the scincid cranial osteology literature in a phylogenetic context, provide a detailed anatomical atlas for the mabuyid lineage, and investigate the morphological adaptations of the highly modified T. laevis. Our results demonstrate that there is significant morphological variation between these three taxa, including the loss and fusion of structures, as well as changes in the shape, scale, and relationship between individual elements. Trachylepis laevis possesses several osteological modifications that have produced a reducton in head depth that are likely functional consequences of extreme rupicolous habits, including a flat skull roof, many strongly recumbent elements, and a depressed neurocranium.We hypothesize these modifications may correspond to descreased bite force and increased capabilities of cranial kinesis. Our study is the first element-by-element description of a skink using computed tomography technology.
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Affiliation(s)
- Daniel J. Paluh
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
- * E-mail: (DJP); (AMB)
| | - Aaron M. Bauer
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
- * E-mail: (DJP); (AMB)
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Bahmani Z, Rastegar-Pouyani E, Rastegar-Pouyani N. The phylogenetic relationships and molecular systematics of scincid lizards of the genus Heremites (Sauria, Scincidae) in the Middle East based on mtDNA sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:846-855. [PMID: 28885068 DOI: 10.1080/24701394.2017.1373107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The taxonomic status of species included in the genus Heremites in Iran and Iraq is uncertain. Three of these species have been assigned to the genus based on morphology: Heremites auratus transcaucasica, H. vittatus, and H. septemtaeniatus. We examined the phylogenetic relationships and taxonomic status of the Iranian and Iraqi species of Heremites by performing phylogenetic analyses using mitochondrial DNA sequences (cytochrome b and 16S rRNA). Phylogenetic relationships and estimated genetic distances indicated that the Heremites populations of the area (Iran and Iraq) form five distinct clades. Three of these clades are found only in Iran, specifically in: (1) Fars and Hormozgan provinces; (2) Northeastern Khuzestan; and (3) Khorasan and Isfahan provinces. The fourth clade (H. septemtaeniatus) is found in west and Mahshahr in Iran as well as in eastern and northern parts of Iraq. The fifth clade, Heremites vittatus, is found in Iran and Iraq. We also confirm the absence of H. auratus in Iran and Iraq. It also indicated that H. vittatus is sister taxon to the other groups that our analyses estimate the divergence of this clade in the Middle Miocene (15.9 Mya). The clade containing the Fars-Hormozgan and Khuzestan populations diverged at the end of the Miocene (8.5 Mya). The Isfahan and Khorasan populations separated at the Pliocene (4.2 Mya) from the western Iranian group, the group in Mahshahr, Iran and the groups in northern and eastern Iraq.
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Affiliation(s)
- Zahed Bahmani
- a Department of Biology, Faculty of Science , Razi University , Kermanshah , Iran.,b Iranian Plateau Herpetology Research Group (IPHRG), Faculty of Science , Razi University , Kermanshah , Iran
| | | | - Nasrullah Rastegar-Pouyani
- a Department of Biology, Faculty of Science , Razi University , Kermanshah , Iran.,b Iranian Plateau Herpetology Research Group (IPHRG), Faculty of Science , Razi University , Kermanshah , Iran
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Liu Y, Fend SV, Martinsson S, Luo X, Ohtaka A, Erséus C. Multi-locus phylogenetic analysis of the genus Limnodrilus (Annelida: Clitellata: Naididae). Mol Phylogenet Evol 2017; 112:244-257. [DOI: 10.1016/j.ympev.2017.04.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/24/2017] [Accepted: 04/20/2017] [Indexed: 12/14/2022]
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30
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Feijoo M, Parada A. Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage. Mol Phylogenet Evol 2017; 113:76-83. [PMID: 28487261 DOI: 10.1016/j.ympev.2017.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 05/04/2017] [Accepted: 05/04/2017] [Indexed: 02/04/2023]
Abstract
In the last few years high-throughput sequencing technologies have permitted significant advances in mammalian phylogenetic studies from a genomic perspective. However, these studies have been restricted to a sparse number of species with available reference genomes. Thus, several issues inside the eutherian mammals phylogeny remain unresolved. This may be due in part to limited taxon sampling, as taxonomic density is known to affect phylogenetic resolution. In this context, we present a protocol to increase taxon coverage using high-throughput sequencing data (RNA or DNA) generated for other biological studies and available in public databases. Following this procedure we addressed pending or controversial issues concerning the phylogenetic position of Dermoptera, Pholidota and Chiroptera, considering multiple and independent loci. Also for Chiroptera and Arctoidea we evaluated the relationships of the lineages that compose it. Although the maximum number of genes used is moderate (95), in some cases taxon coverage doubles that of previous related studies. Globally, all coalescent-based (STAR, MP-EST and ASTRAL) and concatenated (IQ-TREE and BEAST2) methods used for species tree reconstruction were consistent to each other and most of interrogated nodes received high statistical support.
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Affiliation(s)
- M Feijoo
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo CP 11400, Uruguay.
| | - A Parada
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia CP 5090000, Chile.
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31
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Wang N, Hosner PA, Liang B, Braun EL, Kimball RT. Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data. Mol Phylogenet Evol 2017; 109:217-225. [DOI: 10.1016/j.ympev.2017.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 12/24/2016] [Accepted: 01/07/2017] [Indexed: 12/09/2022]
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32
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Zhao L, Li X, Zhang N, Zhang SD, Yi TS, Ma H, Guo ZH, Li DZ. Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids. Mol Phylogenet Evol 2016; 105:166-176. [DOI: 10.1016/j.ympev.2016.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 06/06/2016] [Accepted: 06/27/2016] [Indexed: 12/28/2022]
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33
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Hidden diversity before our eyes: Delimiting and describing cryptic lichen-forming fungal species in camouflage lichens (Parmeliaceae, Ascomycota). Fungal Biol 2016; 120:1374-1391. [DOI: 10.1016/j.funbio.2016.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/24/2016] [Accepted: 06/01/2016] [Indexed: 12/19/2022]
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34
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Figueroa A, McKelvy AD, Grismer LL, Bell CD, Lailvaux SP. A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus. PLoS One 2016; 11:e0161070. [PMID: 27603205 PMCID: PMC5014348 DOI: 10.1371/journal.pone.0161070] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/28/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). RESULTS Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. CONCLUSION Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.
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Affiliation(s)
- Alex Figueroa
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America
| | - Alexander D. McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, NY, United States of America
- Department of Biology, 6S-143, College of Staten Island, 2800 Victory Boulevard, Staten Island, NY, United States of America
| | - L. Lee Grismer
- Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA, United States of America
| | - Charles D. Bell
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America
| | - Simon P. Lailvaux
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America
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35
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Karin BR, Metallinou M, Weinell JL, Jackman TR, Bauer AM. Resolving the higher-order phylogenetic relationships of the circumtropical Mabuya group (Squamata: Scincidae): An out-of-Asia diversification. Mol Phylogenet Evol 2016; 102:220-32. [DOI: 10.1016/j.ympev.2016.05.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/28/2016] [Accepted: 05/26/2016] [Indexed: 01/25/2023]
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36
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Šmíd J, Shobrak M, Wilms T, Joger U, Carranza S. Endemic diversification in the mountains: genetic, morphological, and geographical differentiation of the Hemidactylus geckos in southwestern Arabia. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0293-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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Linkem CW, Minin VN, Leaché AD. Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae). Syst Biol 2016; 65:465-77. [PMID: 26738927 PMCID: PMC6383586 DOI: 10.1093/sysbio/syw001] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/29/2015] [Indexed: 01/28/2023] Open
Abstract
The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of Life. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data via loci concatenation will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often employ coalescent-based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve place the species tree within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent-based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scincidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for investigating and overcoming this challenge.
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Affiliation(s)
| | - Vladimir N Minin
- Department of Biology, University of Washington, Seattle WA; Department of Statistics, University of Washington, Seattle WA
| | - Adam D Leaché
- Department of Biology, University of Washington, Seattle WA; Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195, USA
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38
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Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree. Syst Biol 2016; 65:772-91. [DOI: 10.1093/sysbio/syw035] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 03/30/2016] [Indexed: 01/14/2023] Open
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Molecular phylogeny of Panaspis and Afroablepharus skinks (Squamata: Scincidae) in the savannas of sub-Saharan Africa. Mol Phylogenet Evol 2016; 100:409-423. [PMID: 27118179 DOI: 10.1016/j.ympev.2016.04.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 03/13/2016] [Accepted: 04/20/2016] [Indexed: 11/20/2022]
Abstract
African snake-eyed skinks are relatively small lizards of the genera Panaspis and Afroablepharus. Species allocation of these genera frequently changed during the 20th century based on morphology, ecology, and biogeography. Members of these genera occur primarily in savanna habitats throughout sub-Saharan Africa and include species whose highly conserved morphology poses challenges for taxonomic studies. We sequenced two mitochondrial (16S and cyt b) and two nuclear genes (PDC and RAG1) from 76 Panaspis and Afroablepharus samples from across eastern, central, and southern Africa. Concatenated gene-tree and divergence-dating analyses were conducted to infer phylogenies and biogeographic patterns. Molecular data sets revealed several cryptic lineages, with most radiations occurring during the mid-Miocene to Pliocene. We infer that rifting processes (including the formation of the East African Rift System) and climatic oscillations contributed to the expansion and contraction of savannas, and caused cladogenesis in snake-eyed skinks. Species in Panaspis and Afroablepharus used in this study, including type species for both genera, formed a monophyletic group. As a result, the latter genus should be synonymized with the former, which has priority. Conservatively, we continue to include the West African species P. breviceps and P. togoensis within an expanded Panaspis, but note that they occur in relatively divergent clades, and their taxonomic status may change with improved taxon sampling. Divergence estimates and cryptic speciation patterns of snake-eyed skinks were consistent with previous studies of other savanna vertebrate lineages from the same areas examined in this study.
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40
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Streicher JW, Wiens JJ. Phylogenomic analyses reveal novel relationships among snake families. Mol Phylogenet Evol 2016; 100:160-169. [PMID: 27083862 DOI: 10.1016/j.ympev.2016.04.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 03/25/2016] [Accepted: 04/11/2016] [Indexed: 02/01/2023]
Abstract
Snakes are a diverse and important group of vertebrates. However, relationships among the major groups of snakes have remained highly uncertain, with recent studies hypothesizing very different (and typically weakly supported) relationships. Here, we address family-level snake relationships with new phylogenomic data from 3776 nuclear loci from ultraconserved elements (1.40million aligned base pairs, 52% missing data overall) sampled from 29 snake species that together represent almost all families, a dataset ∼100 times larger than used in previous studies. We found relatively strong support from species-tree analyses (NJst) for most relationships, including three largely novel clades: (1) a clade uniting the boas, pythons and their relatives, (2) a clade placing cylindrophiids and uropeltids with this clade, and (3) a clade uniting bolyeriids (Round Island boas) with pythonids and their relatives (xenopeltids and loxocemids). Relationships among families of advanced snakes (caenophidians) were also strongly supported. The results show the potential for phylogenomic analyses to resolve difficult groups, but also show a surprising sensitivity of the analyses to the inclusion or exclusion of outgroups.
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Affiliation(s)
- Jeffrey W Streicher
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK.
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA.
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Improved resolution and a novel phylogeny for the Neotropical triplefin blennies (Teleostei: Tripterygiidae). Mol Phylogenet Evol 2016; 96:70-78. [DOI: 10.1016/j.ympev.2015.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/24/2015] [Accepted: 12/01/2015] [Indexed: 11/22/2022]
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42
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Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches. Sci Rep 2016; 6:22262. [PMID: 26915968 PMCID: PMC4768097 DOI: 10.1038/srep22262] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/10/2016] [Indexed: 11/10/2022] Open
Abstract
Evolutionary histories are now being inferred from unprecedented, genome-scale datasets for a broad range of organismal groups. While phylogenomic data has helped in resolving a number of difficult, long-standing questions, constructing appropriate datasets from genomes is not straightforward, particularly in non-model groups. Here we explore the utility of phylogenomic data to infer robust phylogenies for a lineage of closely related lichen-forming fungal species. We assembled multiple, distinct nuclear phylogenomic datasets, ranging from ca. 25 Kb to 16.8 Mb and inferred topologies using both concatenated gene tree approaches and species tree methods based on the multispecies coalescent model. In spite of evidence for rampant incongruence among individual loci, these genome-scale datasets provide a consistent, well-supported phylogenetic hypothesis using both concatenation and multispecies coalescent approaches (ASTRAL-II and SVDquartets). However, the popular full hierarchical coalescent approach implemented in *BEAST provided inconsistent inferences, both in terms of nodal support and topology, with smaller subsets of the phylogenomic data. While comparable, well-supported topologies can be accurately inferred with only a small fraction of the overall genome, consistent results across a variety of datasets and methodological approaches provide reassurance that phylogenomic data can effectively be used to provide robust phylogenies for closely related lichen-forming fungal lineages.
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43
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Zheng Y, Wiens JJ. Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Mol Phylogenet Evol 2016; 94:537-547. [DOI: 10.1016/j.ympev.2015.10.009] [Citation(s) in RCA: 383] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/30/2015] [Accepted: 10/08/2015] [Indexed: 11/24/2022]
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Richart CH, Hayashi CY, Hedin M. Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies. Mol Phylogenet Evol 2015; 95:171-82. [PMID: 26691642 DOI: 10.1016/j.ympev.2015.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 09/16/2015] [Accepted: 11/13/2015] [Indexed: 11/19/2022]
Abstract
Phylogenetic resolution of ancient rapid radiations has remained problematic despite major advances in statistical approaches and DNA sequencing technologies. Here we report on a combined phylogenetic approach utilizing transcriptome data in conjunction with Sanger sequence data to investigate a tandem of ancient divergences in the harvestmen superfamily Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi). We rely on Sanger sequences to resolve nodes within and between closely related genera, and use RNA-seq data from a subset of taxa to resolve a short and ancient internal branch. We use several analytical approaches to explore this succession of ancient diversification events, including concatenated and coalescent-based analyses and maximum likelihood gene trees for each locus. We evaluate the robustness of phylogenetic inferences using a randomized locus sub-sampling approach, and find congruence across these methods despite considerable incongruence across gene trees. Incongruent gene trees are not recovered in frequencies expected from a simple multispecies coalescent model, and we reject incomplete lineage sorting as the sole contributor to gene tree conflict. Using these approaches we attain robust support for higher-level phylogenetic relationships within Ischyropsalidoidea.
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Affiliation(s)
- Casey H Richart
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA; Department of Biology, University of California, Riverside, CA 92521, USA.
| | - Cheryl Y Hayashi
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
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Molecular phylogenetics and biogeography of the Neotropical skink genus Mabuya Fitzinger (Squamata: Scincidae) with emphasis on Colombian populations. Mol Phylogenet Evol 2015; 93:188-211. [DOI: 10.1016/j.ympev.2015.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/23/2015] [Accepted: 07/24/2015] [Indexed: 01/05/2023]
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Ruane S, Raxworthy CJ, Lemmon AR, Lemmon EM, Burbrink FT. Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes. BMC Evol Biol 2015; 15:221. [PMID: 26459325 PMCID: PMC4603904 DOI: 10.1186/s12862-015-0503-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/01/2015] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS. Here, we determine how a 5-locus Sanger dataset compares with a 377-locus anchored genomics dataset for understanding the evolutionary history of the pseudoxyrhophiine snake radiation centered in Madagascar. The Pseudoxyrhophiinae comprise ~86 % of Madagascar's serpent diversity, yet they are poorly known with respect to ecology, behavior, and systematics. Using the 377-locus NGS dataset and the summary statistics species-tree methods STAR and MP-EST, we estimated a well-supported species tree that provides new insights concerning intergeneric relationships for the pseudoxyrhophiines. We also compared how these and other methods performed with respect to estimating tree topology using datasets with varying numbers of loci. METHODS Using Sanger sequencing and an anchored phylogenomics approach, we sequenced datasets comprised of 5 and 377 loci, respectively, for 23 pseudoxyrhophiine taxa. For each dataset, we estimated phylogenies using both gene-tree (concatenation) and species-tree (STAR, MP-EST) approaches. We determined the similarity of resulting tree topologies from the different datasets using Robinson-Foulds distances. In addition, we examined how subsets of these data performed compared to the complete Sanger and anchored datasets for phylogenetic accuracy using the same tree inference methodologies, as well as the program *BEAST to determine if a full coalescent model for species tree estimation could generate robust results with fewer loci compared to the summary statistics species tree approaches. We also examined the individual gene trees in comparison to the 377-locus species tree using the program MetaTree. RESULTS Using the full anchored dataset under a variety of methods gave us the same, well-supported phylogeny for pseudoxyrhophiines. The African pseudoxyrhophiine Duberria is the sister taxon to the Malagasy pseudoxyrhophiines genera, providing evidence for a monophyletic radiation in Madagascar. In addition, within Madagascar, the two major clades inferred correspond largely to the aglyphous and opisthoglyphous genera, suggesting that feeding specializations associated with tooth venom delivery may have played a major role in the early diversification of this radiation. The comparison of tree topologies from the concatenated and species-tree methods using different datasets indicated the 5-locus dataset cannot beused to infer a correct phylogeny for the pseudoxyrhophiines under any method tested here and that summary statistics methods require 50 or more loci to consistently recover the species-tree inferred using the complete anchored dataset. However, as few as 15 loci may infer the correct topology when using the full coalescent species tree method *BEAST. MetaTree analyses of each gene tree from the Sanger and anchored datasets found that none of the individual gene trees matched the 377-locus species tree, and that no gene trees were identical with respect to topology. CONCLUSIONS Our results suggest that ≥50 loci may be necessary to confidently infer phylogenies when using summaryspecies-tree methods, but that the coalescent-based method *BEAST consistently recovers the same topology using only 15 loci. These results reinforce that datasets with small numbers of markers may result in misleading topologies, and further, that the method of inference used to generate a phylogeny also has a major influence on the number of loci necessary to infer robust species trees.
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Affiliation(s)
- Sara Ruane
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
| | - Christopher J Raxworthy
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
| | - Alan R Lemmon
- Department of Biology, Florida State University, 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA.
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University, 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA.
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
- Biology Department, College of Staten Island/CUNY, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.
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Hestetun JT, Vacelet J, Boury-Esnault N, Borchiellini C, Kelly M, Ríos P, Cristobo J, Rapp HT. The systematics of carnivorous sponges. Mol Phylogenet Evol 2015; 94:327-45. [PMID: 26416707 DOI: 10.1016/j.ympev.2015.08.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 11/19/2022]
Abstract
Carnivorous sponges are characterized by their unique method of capturing mesoplanktonic prey coupled with the complete or partial reduction of the aquiferous system characteristic of the phylum Porifera. Current systematics place the vast majority of carnivorous sponges within Cladorhizidae, with certain species assigned to Guitarridae and Esperiopsidae. Morphological characters have not been able to show whether this classification is evolutionary accurate, and whether carnivory has evolved once or in several lineages. In the present paper we present the first comprehensive molecular phylogeny of the carnivorous sponges, interpret these results in conjunction with morphological characters, and propose a revised classification of the group. Molecular phylogenies were inferred using 18S rDNA and a combined dataset of partial 28S rDNA, COI and ALG11 sequences. The results recovered carnivorous sponges as a clade closely related to the families Mycalidae and Guitarridae, showing family Cladorhizidae to be monophyletic and also including carnivorous species currently placed in other families. The genus Lycopodina is resurrected for species currently placed in the paraphyletic subgenus Asbestopluma (Asbestopluma) featuring forceps spicules and lacking sigmas or sigmancistras. The genera Chondrocladia and Cladorhiza are found to be monophyletic. However, results indicate that the subgenus Chondrocladia is polyphyletic with respect to the subgenera Meliiderma and Symmetrocladia. Euchelipluma, formerly Guitarridae, is retained, but transferred to Cladorhizidae. The four known carnivorous species currently in Esperiopsis are transferred to Abyssocladia. Neocladia is a junior homonym and is here renamed Koltunicladia. Our results provide strong evidence in support of the hypothesis that carnivory in sponges has evolved only once. While spicule characters mostly reflect monophyletic groups at the generic level, differences between genera represent evolution within family Cladorhizidae rather than evolution of carnivory in separate lineages. Conflicting spicule characters can be reinterpreted to support the inclusion of all carnivorous sponges within Cladorhizidae, and a carnivorous habit should thus be considered the main diagnostic character in systematic classification.
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Affiliation(s)
- Jon Thomassen Hestetun
- Department of Biology and Centre for Geobiology, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway.
| | - Jean Vacelet
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13397 Marseille, France.
| | - Nicole Boury-Esnault
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13397 Marseille, France.
| | - Carole Borchiellini
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13397 Marseille, France.
| | - Michelle Kelly
- National Centre for Aquatic Biodiversity and Biosecurity, National Institute of Water and Atmospheric Research, P.O. Box 109-695, Newmarket, Auckland, New Zealand.
| | - Pilar Ríos
- Instituto Español de Oceanografía, Centro Oceanográfico de Gijón, Av./Príncipe de Asturias 70 bis, 33212 Gijón, Asturias, Spain.
| | - Javier Cristobo
- Instituto Español de Oceanografía, Centro Oceanográfico de Gijón, Av./Príncipe de Asturias 70 bis, 33212 Gijón, Asturias, Spain; Departamento de Zoología y Antropología Física, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain.
| | - Hans Tore Rapp
- Department of Biology and Centre for Geobiology, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway; Uni Environment, P.O. Box 7810, N-5020 Bergen, Norway.
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Streicher JW, Schulte JA, Wiens JJ. How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards. Syst Biol 2015; 65:128-45. [PMID: 26330450 DOI: 10.1093/sysbio/syv058] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 08/04/2015] [Indexed: 11/12/2022] Open
Abstract
Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolved) question is whether sampling should be designed to maximize sampling of taxa or genes, or to minimize the inclusion of missing data cells. Here, we explore this question for an ancient, rapid radiation of lizards, the pleurodont iguanians. Pleurodonts include many well-known clades (e.g., anoles, basilisks, iguanas, and spiny lizards) but relationships among families have proven difficult to resolve strongly and consistently using traditional sequencing approaches. We generated up to 4921 ultraconserved elements with sampling strategies including 16, 29, and 44 taxa, from 1179 to approximately 2.4 million characters per matrix and approximately 30% to 60% total missing data. We then compared mean branch support for interfamilial relationships under these 15 different sampling strategies for both concatenated (maximum likelihood) and species tree (NJst) approaches (after showing that mean branch support appears to be related to accuracy). We found that both approaches had the highest support when including loci with up to 50% missing taxa (matrices with ~40-55% missing data overall). Thus, our results show that simply excluding all missing data may be highly problematic as the primary guiding principle for the inclusion or exclusion of taxa and genes. The optimal strategy was somewhat different for each approach, a pattern that has not been shown previously. For concatenated analyses, branch support was maximized when including many taxa (44) but fewer characters (1.1 million). For species-tree analyses, branch support was maximized with minimal taxon sampling (16) but many loci (4789 of 4921). We also show that the choice of these sampling strategies can be critically important for phylogenomic analyses, since some strategies lead to demonstrably incorrect inferences (using the same method) that have strong statistical support. Our preferred estimate provides strong support for most interfamilial relationships in this important but phylogenetically challenging group.
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Affiliation(s)
- Jeffrey W Streicher
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK and
| | - James A Schulte
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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Multi-locus fossil-calibrated phylogeny of Atheriniformes (Teleostei, Ovalentaria). Mol Phylogenet Evol 2015; 86:8-23. [PMID: 25769409 DOI: 10.1016/j.ympev.2015.03.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/21/2015] [Accepted: 03/02/2015] [Indexed: 11/21/2022]
Abstract
Phylogenetic relationships among families within the order Atheriniformes have been difficult to resolve on the basis of morphological evidence. Molecular studies so far have been fragmentary and based on a small number taxa and loci. In this study, we provide a new phylogenetic hypothesis based on sequence data collected for eight molecular markers for a representative sample of 103 atheriniform species, covering 2/3 of the genera in this order. The phylogeny is calibrated with six carefully chosen fossil taxa to provide an explicit timeframe for the diversification of this group. Our results support the subdivision of Atheriniformes into two suborders (Atherinopsoidei and Atherinoidei), the nesting of Notocheirinae within Atherinopsidae, and the monophyly of tribe Menidiini, among others. We propose taxonomic changes for Atherinopsoidei, but a few weakly supported nodes in our phylogeny suggests that further study is necessary to support a revised taxonomy of Atherinoidei. The time-calibrated phylogeny was used to infer ancestral habitat reconstructions to explain the current distribution of marine and freshwater taxa. Based on these results, the current distribution of Atheriniformes is likely due to widespread marine dispersal along the margins of continents, infrequent trans-oceanic dispersal, and repeated invasion of freshwater habitats. This conclusion is supported by post-Gondwanan divergence times among families within the order, and a high probability of a marine ancestral habitat.
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