1
|
Song W, Shi W, Wang H, Zhang Z, Tao R, Liu J, Wang S, Engel MS, Shi C. Comparative analysis of 12 water lily plastid genomes reveals genomic divergence and evolutionary relationships in early flowering plants. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:425-441. [PMID: 39219675 PMCID: PMC11358372 DOI: 10.1007/s42995-024-00242-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 06/25/2024] [Indexed: 09/04/2024]
Abstract
The aquatic plant Nymphaea, a model genus of the early flowering plant lineage Nymphaeales and family Nymphaeaceae, has been extensively studied. However, the availability of chloroplast genome data for this genus is incomplete, and phylogenetic relationships within the order Nymphaeales remain controversial. In this study, 12 chloroplast genomes of Nymphaea were assembled and analyzed for the first time. These genomes were 158,290-160,042 bp in size and contained 113 non-repeat genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. We also report on codon usage, RNA editing sites, microsatellite structures, and new repetitive sequences in this genus. Comparative genomics revealed that expansion and contraction of IR regions can lead to changes in the gene numbers. Additionally, it was observed that the highly variable regions of the chloroplast genome were mainly located in intergenic regions. Furthermore, the phylogenetic tree showed the order Nymphaeales was divided into three families, and the genus Nymphaea can be divided into five (or three) subgenera, with the subgenus Nymphaea being the oldest. The divergence times of nymphaealean taxa were analyzed, with origins of the order Nymphaeales and family Nymphaeaceae being about 194 and 131 million years, respectively. The results of the phylogenetic analysis and estimated divergence times will be useful for future evolutionary studies of basal angiosperm lineages. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-024-00242-0.
Collapse
Affiliation(s)
- Weicai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Wenbo Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Huan Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Zirui Zhang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Ruiqing Tao
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Michael S. Engel
- American Museum of Natural History, New York, NY 10024-5192 USA
- Natural History Museum, and Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS 66045 USA
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650204 China
| |
Collapse
|
2
|
Mutizwa TI, Kadye WT, Bragança PHN, Bere T, Chakona A. Hidden in the riffles: A new suckermouth catfish (Mochokidae, Chiloglanis) from the middle Zambezi River system, Zimbabwe. Zookeys 2024; 1197:57-91. [PMID: 38616924 PMCID: PMC11015093 DOI: 10.3897/zookeys.1197.114679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/22/2024] [Indexed: 04/16/2024] Open
Abstract
The recent surge in the discovery of hidden diversity within rheophilic taxa, particularly in West and East Africa, prompted a closer examination of the extent to which the current taxonomy may obscure the diversity of riffle-dwelling suckermouth catfishes in the genus Chiloglanis in southern Africa. Currently, the region comprises eight valid species within this genus. Seven of them have relatively narrow geographic distribution ranges except for C.neumanni, which is considered to be widely distributed, occurring from the Buzi River system in the south, and its northern limit being the eastward draining river systems in Tanzania. Recent surveys of the middle Zambezi River system revealed Chiloglanis specimens that were distinguishable from the known species of the genus from southern Africa. Integration of molecular and morphological data indicated that these specimens from the Mukwadzi River represent a new species to science, herein described as Chiloglaniscarnatus Mutizwa, Bragança & Chakona, sp. nov. This species is readily distinguished from its southern African congeners by the possession of a distinctive extended dermal tissue covering the base of the dorsal fin and the possession of ten mandibular teeth (vs 8, 12, or 14 in the other taxa). Results from this study add to the growing evidence of a high level of undocumented diversity within riffle-dwelling taxa in southern Africa.
Collapse
Affiliation(s)
- Tadiwa I. Mutizwa
- Department of Ichthyology and Fisheries Science, Faculty of Science, Rhodes University, Prince Alfred Street, PO Box 94, Makhanda, 6140, South AfricaNRF-South African Institute for Aquatic BiodiversityMakhandaSouth Africa
- NRF-South African Institute for Aquatic Biodiversity, Somerset Street, Private Bag 1015, Makhanda, 6140, South AfricaRhodes UniversityMakhandaSouth Africa
| | - Wilbert T. Kadye
- Department of Ichthyology and Fisheries Science, Faculty of Science, Rhodes University, Prince Alfred Street, PO Box 94, Makhanda, 6140, South AfricaNRF-South African Institute for Aquatic BiodiversityMakhandaSouth Africa
- NRF-South African Institute for Aquatic Biodiversity, Somerset Street, Private Bag 1015, Makhanda, 6140, South AfricaRhodes UniversityMakhandaSouth Africa
| | - Pedro H. N. Bragança
- NRF-South African Institute for Aquatic Biodiversity, Somerset Street, Private Bag 1015, Makhanda, 6140, South AfricaRhodes UniversityMakhandaSouth Africa
- Department of Ichthyology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USADepartment of Ichthyology, American Museum of Natural HistoryNew YorkUnited States of America
| | - Taurai Bere
- School of Wildlife, Ecology and Conservation, Chinhoyi University of Technology, Private Bag 7724, Chinhoyi, ZimbabweChinhoyi University of TechnologyChinhoyiZimbabwe
| | - Albert Chakona
- Department of Ichthyology and Fisheries Science, Faculty of Science, Rhodes University, Prince Alfred Street, PO Box 94, Makhanda, 6140, South AfricaNRF-South African Institute for Aquatic BiodiversityMakhandaSouth Africa
- NRF-South African Institute for Aquatic Biodiversity, Somerset Street, Private Bag 1015, Makhanda, 6140, South AfricaRhodes UniversityMakhandaSouth Africa
| |
Collapse
|
3
|
Guimarães Fabreti L, Höhna S. Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors. Syst Biol 2023; 72:1418-1432. [PMID: 37455495 DOI: 10.1093/sysbio/syad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/02/2023] [Accepted: 07/02/2023] [Indexed: 07/18/2023] Open
Abstract
Model selection aims to choose the most adequate model for the statistical analysis at hand. The model must be complex enough to capture the complexity of the data but should be simple enough not to overfit. In phylogenetics, the most common model selection scenario concerns selecting an adequate substitution and partition model for sequence evolution to infer a phylogenetic tree. Previously, several studies showed that substitution model under-parameterization can bias phylogenetic studies. Here, we explored the impact of substitution model over-parameterization in a Bayesian statistical framework. We performed simulations under the simplest substitution model, the Jukes-Cantor model, and compare posterior estimates of phylogenetic tree topologies and tree length under the true model to the most complex model, the $\text{GTR}+\Gamma+\text{I}$ substitution model, including over-splitting the data into additional subsets (i.e., applying partitioned models). We explored 4 choices of prior distributions: the default substitution model priors of MrBayes, BEAST2, and RevBayes and a newly devised prior choice (Tame). Our results show that Bayesian inference of phylogeny is robust to substitution model over-parameterization and over-partitioning but only under our new prior settings. All 3 current default priors introduced biases for the estimated tree length. We conclude that substitution and partition model selection are superfluous steps in Bayesian phylogenetic inference pipelines if well-behaved prior distributions are applied and more effort should focus on more complex and biologically realistic substitution models.
Collapse
Affiliation(s)
- Luiza Guimarães Fabreti
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Sebastian Höhna
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| |
Collapse
|
4
|
AlShamakhi HS, Al-Sadi AM, Cook LG. Phylogenetic Relationships of the Mutualistic Fungi Associated with Macrotermes subhyalinus in Oman. MYCOBIOLOGY 2023; 51:281-287. [PMID: 37929007 PMCID: PMC10621247 DOI: 10.1080/12298093.2023.2258623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 09/11/2023] [Indexed: 11/07/2023]
Abstract
The symbiotic association between fungus-gardening termites Macrotermes and its fungal symbiont has a moderate degree of specificity-although the symbiotic fungi (Termitomyces) form a monophyletic clade, there is not a one-to-one association between termite species and their fungus-garden associates. Here, we aim to determine the origin and phylogenetic relationships of Termitomyces in Oman. We used sequences of the internal transcribed spacer region (ITS) and the nuclear large subunit ribosomal RNA (LSU rRNA, 25S) gene and analyzed these with sequences of Termitomyces from other geographic areas. We find no evidence for more than a single colonization of Oman by Termitomyces. Unexpectedly, we find Termitomyces in Oman is most closely related to the symbiont of M. subhyalinus in West Africa rather than to those of geographically closer populations in East Africa.
Collapse
Affiliation(s)
| | - Abdullah M. Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud, Oman
| | - Lyn G. Cook
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
5
|
Carnegie L, Raghwani J, Fournié G, Hill SC. Phylodynamic approaches to studying avian influenza virus. Avian Pathol 2023; 52:289-308. [PMID: 37565466 DOI: 10.1080/03079457.2023.2236568] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.
Collapse
Affiliation(s)
- L Carnegie
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - J Raghwani
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - G Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - S C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| |
Collapse
|
6
|
A comprehensive phylogeny and revised taxonomy illuminate the origin and diversification of the global radiation of Papilio (Lepidoptera: Papilionidae). Mol Phylogenet Evol 2023; 183:107758. [PMID: 36907224 DOI: 10.1016/j.ympev.2023.107758] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/28/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
The swallowtail genus Papilio (Lepidoptera: Papilionidae) is species rich, distributed worldwide, and has broad morphological habits and ecological niches. Because of its elevated species richness, it has been historically difficult to reconstruct a densely sampled phylogeny for this clade. Here we provide a taxonomic working list for the genus, resulting in 235 Papilio species, and assemble a molecular dataset of seven gene fragments representing ca. 80% of the currently described diversity. Phylogenetic analyses reconstructed a robust tree with highly supported relationships within subgenera, although a few nodes in the early history of the Old World Papilio remain unresolved. Contrasting with previous results, we found that Papilio alexanor is sister to all Old World Papilio and that the subgenus Eleppone is no longer monotypic. The latter includes the recently described Fijian Papilio natewa with the Australian Papilio anactus and is sister to subgenus Araminta (formerly included in subgenus Menelaides) occurring in Southeast Asia. Our phylogeny also includes rarely studied (P. antimachus, P. benguetana) or endangered species (P. buddha, P. chikae). Taxonomic changes resulting from this study are elucidated. Molecular dating and biogeographic analyses indicate that Papilio originated ca. 30 million years ago (Oligocene), in a northern region centered on Beringia. A rapid early Miocene radiation in the Paleotropics is revealed within Old World Papilio, potentially explaining their low early branch support. Most subgenera originated in the early to middle Miocene followed by synchronous southward biogeographic dispersals and repeated local extirpations in northern latitudes. This study provides a comprehensive phylogenetic framework for Papilio with clarification of subgeneric systematics and species taxonomic changes enumerated, which will facilitate further studies to address questions on their ecology and evolutionary biology using this model clade.
Collapse
|
7
|
Abstract
The ongoing global pandemic has sharply increased the amount of data available to researchers in epidemiology and public health. Unfortunately, few existing analysis tools are capable of exploiting all of the information contained in a pandemic-scale data set, resulting in missed opportunities for improved surveillance and contact tracing. In this paper, we develop the variational Bayesian skyline (VBSKY), a method for fitting Bayesian phylodynamic models to very large pathogen genetic data sets. By combining recent advances in phylodynamic modeling, scalable Bayesian inference and differentiable programming, along with a few tailored heuristics, VBSKY is capable of analyzing thousands of genomes in a few minutes, providing accurate estimates of epidemiologically relevant quantities such as the effective reproduction number and overall sampling effort through time. We illustrate the utility of our method by performing a rapid analysis of a large number of SARS-CoV-2 genomes, and demonstrate that the resulting estimates closely track those derived from alternative sources of public health data.
Collapse
Affiliation(s)
- Caleb Ki
- Department of Statistics, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Terhorst
- Department of Statistics, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
8
|
Beck RM, Voss RS, Jansa SA. Craniodental Morphology and Phylogeny of Marsupials. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.457.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Robin M.D. Beck
- School of Science, Engineering and Environment University of Salford, U.K. School of Biological, Earth & Environmental Sciences University of New South Wales, Australia Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Sharon A. Jansa
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota
| |
Collapse
|
9
|
Hallas JM, Parchman TL, Feldman CR. Phylogenomic analyses resolve relationships among garter snakes (Thamnophis: Natricinae: Colubridae) and elucidate biogeographic history and morphological evolution. Mol Phylogenet Evol 2021; 167:107374. [PMID: 34896619 DOI: 10.1016/j.ympev.2021.107374] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022]
Abstract
Garter snakes (Thamnophis) are a successful group of natricines endemic to North America. They have become important natural models for ecological and evolutionary research, yet prior efforts to resolve phylogenetic relationships have resulted in conflicting topologies and weak support for certain relationships. Here, we use genomic data generated with a reduced representation double-digest RADseq approach to reassess evolutionary relationships across Thamnophis. We then use the resulting phylogeny to better understand how biogeography and feeding ecology have influenced lineage diversification and morphological evolution. We recovered highly congruent and strongly supported topologies from maximum likelihood and Bayesian analyses, but some discordance with a multispecies coalescent approach. All phylogenomic estimates split Thamnophis into two clades largely defined by northern and southern North American species. Divergence time estimates and biogeographic analyses indicate a mid-Miocene origin of Thamnophis in Mexico. In addition, historic vicariant events thought to explain biogeographic patterns in other lineages (e.g., Isthmus of Tehuantepec, Rocky Mountain Range, and Trans-Mexican Volcanic Belt) appear to have influenced patterns of diversification in Thamnophis as well. Analyses of morphological traits associated with feeding ecology showed moderate to strong phylogenetic signal. Nevertheless, phylogenetic ANOVA suggested significant differences in certain cranial morphologies between aquatic specialists and garter snakes that are terrestrial-aquatic generalists, independent of evolutionary history. Our new estimate of Thamnophis phylogeny yields an improved understanding of the biogeographic history and morphological evolution of garter snakes, and provides a robust framework for future research on these snakes.
Collapse
Affiliation(s)
- Joshua M Hallas
- Department of Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA; Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA.
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA; Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA
| | - Chris R Feldman
- Department of Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA; Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA
| |
Collapse
|
10
|
Turan D, Küçük F, Güçlü SS, Aksu İ. Turcichondrostoma, a new genus for the Leuciscidae (Teleostei: Cypriniformes) from Southwestern Anatolia. JOURNAL OF FISH BIOLOGY 2021; 99:1968-1977. [PMID: 34478161 DOI: 10.1111/jfb.14903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Turcichondrostoma, a new genus, from the Southwestern Anatolia is distinguished by having fewer gill rakers on first gill arch and morphologies of premaxilla and dentary bones. In addition, as a result of the phylogenetic analyses based on combine data set (mtDNA COI + Cytb) sequences (1706 bp.), Turcichondrostoma genus was recovered with high posterior probability value (BI PP:1.0) and strong-supported bootstrap value (ML BP: 100%) among the former Chondrostoma groups. Also, high K2P mean genetic distance values (more than 7.84%) differentiated genus Turcichondrostoma from the other genera of former Chondrostoma group. The results of both morphological-osteological and molecular analyses are congruent with each other. The results of this study revealed that the genus Turcichondrostoma is easily distinguished from the genera in Chondrostoma group.
Collapse
Affiliation(s)
- Davut Turan
- Fisheries Faculty, Recep Tayyip Erdoğan University, Rize, Turkey
| | - Fahrettin Küçük
- Eğirdir Fisheries Faculty, Isparta University of Applied Sciences, Isparta, Turkey
| | - Salim Serkan Güçlü
- Eğirdir Fisheries Faculty, Isparta University of Applied Sciences, Isparta, Turkey
| | - İsmail Aksu
- Fisheries Faculty, Recep Tayyip Erdoğan University, Rize, Turkey
| |
Collapse
|
11
|
Wertheim JO, Steel M, Sanderson MJ. Accuracy in near-perfect virus phylogenies. Syst Biol 2021; 71:426-438. [PMID: 34398231 PMCID: PMC8385947 DOI: 10.1093/sysbio/syab069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 11/26/2022] Open
Abstract
Phylogenetic trees from real-world data often include short edges with very few substitutions per site, which can lead to partially resolved trees and poor accuracy. Theory indicates that the number of sites needed to accurately reconstruct a fully resolved tree grows at a rate proportional to the inverse square of the length of the shortest edge. However, when inferred trees are partially resolved due to short edges, “accuracy” should be defined as the rate of discovering false splits (clades on a rooted tree) relative to the actual number found. Thus, accuracy can be high even if short edges are common. Specifically, in a “near-perfect” parameter space in which trees are large, the tree length ξ (the sum of all edge lengths) is small, and rate variation is minimal, the expected false positive rate is less than ξ∕3; the exact value depends on tree shape and sequence length. This expected false positive rate is far below the false negative rate for small ξ and often well below 5% even when some assumptions are relaxed. We show this result analytically for maximum parsimony and explore its extension to maximum likelihood using theory and simulations. For hypothesis testing, we show that measures of split “support” that rely on bootstrap resampling consistently imply weaker support than that implied by the false positive rates in near-perfect trees. The near-perfect parameter space closely fits several empirical studies of human virus diversification during outbreaks and epidemics, including Ebolavirus, Zika virus, and SARS-CoV-2, reflecting low substitution rates relative to high transmission/sampling rates in these viruses.
Collapse
Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Mike Steel
- Biomathematics Research Center, School of Mathematics and Statistics, University of Canterbury, Christchurch, 8041, New Zealand
| | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA
| |
Collapse
|
12
|
Tao Q, Barba-Montoya J, Huuki LA, Durnan MK, Kumar S. Relative Efficiencies of Simple and Complex Substitution Models in Estimating Divergence Times in Phylogenomics. Mol Biol Evol 2021; 37:1819-1831. [PMID: 32119075 PMCID: PMC7253201 DOI: 10.1093/molbev/msaa049] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The conventional wisdom in molecular evolution is to apply parameter-rich models of nucleotide and amino acid substitutions for estimating divergence times. However, the actual extent of the difference between time estimates produced by highly complex models compared with those from simple models is yet to be quantified for contemporary data sets that frequently contain sequences from many species and genes. In a reanalysis of many large multispecies alignments from diverse groups of taxa, we found that the use of the simplest models can produce divergence time estimates and credibility intervals similar to those obtained from the complex models applied in the original studies. This result is surprising because the use of simple models underestimates sequence divergence for all the data sets analyzed. We found three fundamental reasons for the observed robustness of time estimates to model complexity in many practical data sets. First, the estimates of branch lengths and node-to-tip distances under the simplest model show an approximately linear relationship with those produced by using the most complex models applied on data sets with many sequences. Second, relaxed clock methods automatically adjust rates on branches that experience considerable underestimation of sequence divergences, resulting in time estimates that are similar to those from complex models. And, third, the inclusion of even a few good calibrations in an analysis can reduce the difference in time estimates from simple and complex models. The robustness of time estimates to model complexity in these empirical data analyses is encouraging, because all phylogenomics studies use statistical models that are oversimplified descriptions of actual evolutionary substitution processes.
Collapse
Affiliation(s)
- Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA
| | - Jose Barba-Montoya
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA
| | - Louise A Huuki
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Mary Kathleen Durnan
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
13
|
Li L, Hu Y, He M, Zhang B, Wu W, Cai P, Huo D, Hong Y. Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia. BMC Genomics 2021; 22:138. [PMID: 33637038 PMCID: PMC7912895 DOI: 10.1186/s12864-021-07427-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/05/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Chloroplast genome resources can provide useful information for the evolution of plant species. Tea plant (Camellia sinensis) is among the most economically valuable member of Camellia. Here, we determined the chloroplast genome of the first natural triploid Chinary type tea ('Wuyi narcissus' cultivar of Camellia sinensis var. sinensis, CWN) and conducted the genome comparison with the diploid Chinary type tea (Camellia sinensis var. sinensis, CSS) and two types of diploid Assamica type teas (Camellia sinensis var. assamica: Chinese Assamica type tea, CSA and Indian Assamica type tea, CIA). Further, the evolutionary mechanism of the chloroplast genome of Camellia sinensis and the relationships of Camellia species based on chloroplast genome were discussed. RESULTS Comparative analysis showed the evolutionary dynamics of chloroplast genome of Camellia sinensis were the repeats and insertion-deletions (indels), and distribution of the repeats, indels and substitutions were significantly correlated. Chinese tea and Indian tea had significant differences in the structural characteristic and the codon usage of the chloroplast genome. Analysis of sequence characterized amplified region (SCAR) using sequences of the intergenic spacers (trnE/trnT) showed none of 292 different Camellia sinensis cultivars had similar sequence characteristic to triploid CWN, but the other four Camellia species did. Estimations of the divergence time showed that CIA diverged from the common ancestor of two Assamica type teas about 6.2 Mya (CI: 4.4-8.1 Mya). CSS and CSA diverged to each other about 0.8 Mya (CI: 0.4-1.5 Mya). Moreover, phylogenetic clustering was not exactly consistent with the current taxonomy of Camellia. CONCLUSIONS The repeat-induced and indel-induced mutations were two important dynamics contributed to the diversification of the chloroplast genome in Camellia sinensis, which were not mutually exclusive. Chinese tea and Indian tea might have undergone different selection pressures. Chloroplast transfer occurred during the polyploid evolution in Camellia sinensis. In addition, our results supported the three different domestication origins of Chinary type tea, Chinese Assamica type tea and Indian Assamica type tea. And, the current classification of some Camellia species might need to be further discussed.
Collapse
Affiliation(s)
- Li Li
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China.
| | - Yunfei Hu
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Min He
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Bo Zhang
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Wei Wu
- College of Mathematics and Computer Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Pumo Cai
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Da Huo
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Yongcong Hong
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China.
| |
Collapse
|
14
|
Nguyen DA, Ngo VL, Nguyen KA, Nguyen CH, Than K. Boosting prior knowledge in streaming variational Bayes. Neurocomputing 2021. [DOI: 10.1016/j.neucom.2020.10.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
15
|
Brito PS, Guimarães EC, Guimarães KLA, Rodrigues LRR, Anjos MR, Katz AM, Carvalho-Costa LF, Ottoni FP. Cryptic speciation in populations of the genus Aphyocharax (Characiformes: Characidae) from eastern Amazon coastal river drainages and surroundings revealed by single locus species delimitation methods. NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2021-0095] [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 Recent studies in eastern Amazon coastal drainages and their surroundings have revealed new fish species that sometimes exhibit little morphological differentiation (cryptic species). Thus, we used a DNA-based species delimitation approach to test if populations showing the morphotype and typical character states of the Aphyocharax avary holotype correspond either to A. avary or A. brevicaudatus, two known species from the region, or if they form independent lineages, indicating cryptic speciation. WP and GMYC analyses recovered five lineages (species) in the ingroup, while a bPTP analysis delimited three lineages. ABGD analyses produced two possible results: one corroborating the WP and GMYC methods and another corroborating the bPTP method. All methods indicate undescribed cryptic species in the region and show variation from at least 1 to 4 species in the ingroup, depending on the approach, corroborating previous studies, and revealing this region as a possible hotspot for discovering undescribed fish species.
Collapse
Affiliation(s)
- Pâmella S. Brito
- Universidade Federal do Maranhão, Brazil; Universidade Federal do Oeste do Pará, Brazil
| | - Erick C. Guimarães
- Universidade Federal do Maranhão, Brazil; Universidade Federal do Oeste do Pará, Brazil
| | | | | | | | | | | | | |
Collapse
|
16
|
Revision of Mediterranean and NE Atlantic Raphitomidae (Gastropoda, Conoidea) 8: The genus Leufroyia Monterosato, 1884. ZOOSYSTEMA 2020. [DOI: 10.5252/zoosystema2020v42a22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
17
|
Ghanimi H, Goddard JHR, Chichvarkhin A, Gosliner TM, Jung DW, Valdés Á. An integrative approach to the systematics of the Berthella californica species complex (Heterobranchia: Pleurobranchidae). THE JOURNAL OF MOLLUSCAN STUDIES 2020; 86:186-200. [PMID: 34024980 PMCID: PMC8116134 DOI: 10.1093/mollus/eyaa001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/22/2019] [Accepted: 12/12/2019] [Indexed: 06/12/2023]
Abstract
Berthella californica (W. H. Dall, 1900) is a widespread species of heterobranch sea slug distributed across the North Pacific Ocean, from Korea and Japan to the Galapagos Islands. Two distinct morphotypes are observed in B. californica, which differ in external coloration, egg-mass morphology and geographic distribution (with the exception of a small range overlap in Southern California). Molecular and morphological data obtained in this study reveals that these two morphotypes constitute distinct species. The name B. californica (type locality: San Pedro, California) is retained for the southern morphotype, whereas the name Berthella chacei (J. Q. Burch, 1944) (type locality: Crescent City, California) is resurrected for the northern morphotype. Moreover, molecular phylogenetic analyses recovered B. californica as sister to Berthellina, in a well-supported clade separate from Berthella, suggesting that the classification of B. californica may need additional revision.
Collapse
Affiliation(s)
- Hessam Ghanimi
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California 91768, USA
| | - Jeffrey H R Goddard
- Marine Science Institute, University of California, Santa Barbara, California 93106-6150, USA
| | - Anton Chichvarkhin
- National Scientific Center of Marine Biology, Russian Academy of Sciences, Palchevskogo 17, 690041 Vladivostok, Russia
| | - Terrence M Gosliner
- Department of Invertebrate Zoology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118, USA
| | - Dae-Wui Jung
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California 91768, USA
| | - Ángel Valdés
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California 91768, USA
| |
Collapse
|
18
|
Morton B, Leung PT, Wei J, Lee GY. Phylogenetic relationships of Asian freshwater Mytiloidea (Bivalvia): a morphological and genetic comparison of Sinomytilus harmandi, Limnoperna fortunei and Septifer bilocularis. MOLLUSCAN RESEARCH 2020. [DOI: 10.1080/13235818.2020.1735984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Brian Morton
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Priscilla T.Y. Leung
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Jiehong Wei
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Gabriel Y. Lee
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, People’s Republic of China
| |
Collapse
|
19
|
Russini V, Giannuzzi-Savelli R, Pusateri F, Prkic J, Fassio G, Modica MV, Oliverio M. Candidate cases of poecilogony in Neogastropoda: implications for the systematics of the genus Raphitoma Bellardi, 1847. INVERTEBR SYST 2020. [DOI: 10.1071/is19039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Poecilogony is the intraspecific variation in developmental mode, with larvae of different types produced by the same individual, population or species. It is very rare among marine invertebrates, and in gastropods has long been described only in a few opisthobranchs. The physiological and regulatory mechanisms underlying larval evolutionary transitions, such as loss of planktotrophy that occurred repeatedly in many caenogastropod lineages, are still largely unknown. We have studied the inter- v. intraspecific variation in larval development in the north-east Atlantic neogastropod genus Raphitoma Bellardi, 1847, starting with an iterative taxonomy approach: 17 morphology-based Preliminary Species Hypotheses were tested against a COI molecular-distance-based method (ABGD), and the retained species hypotheses were eventually inspected for reciprocal monophyly on a multilocus dataset. We subsequently performed an ancestral state reconstruction on an ultrametric tree of the 10 Final Species Hypotheses, time-calibrated by fossils, revealing that the interspecific changes were planktotrophy > lecithotrophy, and all have occurred in the Pleistocene, after 2.5 million years ago. This is suggestive of a major role played by Pleistocene Mediterranean oceanographic conditions – enhanced oligotrophy, unpredictable availability of water column resources – likely to favour loss of planktotrophy. Within this group of species, which has diversified after the Miocene, we identified one pair of sibling species differing in their larval development, Raphitoma cordieri (Payraudeau, 1826) and R. horrida (Monterosato, 1884). However, we also identified two Final Species Hypotheses, each comprising individuals with both larval developmental types. Our working hypothesis is that they correspond to one or two poecilogonous species. If confirmed by other nuclear markers, this would be the first documentation of poecilogony in the Neogastropoda, and the second in the whole Caenogastropoda. Although sibling species with different developmental strategies may offer good models to study some evolutionary aspects, poecilogonous taxa are optimally suited for identifying regulatory and developmental mechanisms underlying evolutionary transitions.
Collapse
|
20
|
de Brito PS, Guimarães EC, Carvalho-Costa LF, Ottoni FP. A new species of Aphyocharax Günther, 1868 (Characiformes, Characidae) from the Maracaçumé river basin, eastern Amazon. ZOOSYST EVOL 2019. [DOI: 10.3897/zse.95.36788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A new species of Aphyocharax is described from the Maracaçumé river basin, eastern Amazon, based on morphological and molecular data. The new species differs from all its congeners, mainly by possessing the upper caudal-fin lobe longer than the lower one in mature males, and other characters related to teeth counts, colour pattern, and body depth at dorsal-fin origin. In addition, the new species is corroborated by a haplotype phylogenetic analyses based on the Cytochrome B (Cytb) mitochondrial gene, where its haplotypes are grouped into an exclusive lineage, supported by maximum posterior probability value, a species delimitation method termed the Wiens and Penkrot analysis (WP).
Collapse
|
21
|
Layton KKS, Middelfart PU, Tatarnic NJ, Wilson NG. Erecting a new family for
Spirostyliferina
, a truncatelloidean microgastropod, and further insights into truncatelloidean phylogeny. ZOOL SCR 2019. [DOI: 10.1111/zsc.12374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kara K. S. Layton
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
- Aquatic and Terrestrial Zoology & Molecular Systematics Unit Western Australian Museum Welshpool Western Australia Australia
| | - Peter U. Middelfart
- Aquatic and Terrestrial Zoology & Molecular Systematics Unit Western Australian Museum Welshpool Western Australia Australia
| | - Nikolai J. Tatarnic
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
- Aquatic and Terrestrial Zoology & Molecular Systematics Unit Western Australian Museum Welshpool Western Australia Australia
| | - Nerida G. Wilson
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
- Aquatic and Terrestrial Zoology & Molecular Systematics Unit Western Australian Museum Welshpool Western Australia Australia
| |
Collapse
|
22
|
Guimarães EC, Silva de Brito P, Feitosa LM, Carvalho Costa L, Ottoni FP. A new cryptic species of Hyphessobrycon Durbin, 1908 (Characiformes, Characidae) from the Eastern Amazon, revealed by integrative taxonomy. ZOOSYST EVOL 2019. [DOI: 10.3897/zse.95.34069] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hyphessobryconcarusp. nov. is described based on five different and independent methods of species delimitation, making the hypothesis of this new species supported by an integrative taxonomy perspective. This new species has a restricted distribution, occurring just in the upper Pindaré river drainage, Mearim river basin, Brazil. It is a member of the rosy tetra clade, which is characterized mainly by the presence of a dark brown or black blotch on dorsal fin and absence of a midlateral stripe on the body. Hyphessobryconcarusp. nov. is distinguished from the members of this clade mainly by the shape of its humeral spot, possessing few irregular inconspicuous vertically arranged chromatophores in the humeral region, or sometimes a very thin and inconspicuous humeral spot, and other characters related to teeth count, and color pattern. The phylogenetic position of the new species within the rosy tetra clade was based on molecular phylogenetic analysis using sequences of the mitochondrial gene cytochrome oxidase subunit 1. In addition, a new clade (here termed Hyphessobryconmicropterus clade) within the rosy tetra clade is proposed based on molecular data, comprising H.carusp. nov., H.micropterus, H.piorskii, and H.simulatus, and with H.carusp. nov. and H.piorskii recovered as sister species. Our results suggest cryptic speciation in the rosy tetra clade and, more specifically, in the H.micropterus clade. We recommend the use of integrative taxonomy for future taxonomic revisions and species descriptions when dealing with species complexes and groups containing possible cryptic species.
Collapse
|
23
|
Wright AM. A Systematist's Guide to Estimating Bayesian Phylogenies From Morphological Data. INSECT SYSTEMATICS AND DIVERSITY 2019; 3:2. [PMID: 31355348 PMCID: PMC6643758 DOI: 10.1093/isd/ixz006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Indexed: 05/07/2023]
Abstract
Phylogenetic trees are crucial to many aspects of taxonomic and comparative biology. Many researchers have adopted Bayesian methods to estimate their phylogenetic trees. In this family of methods, a model of morphological evolution is assumed to have generated the data observed by the researcher. These models make a variety of assumptions about the evolution of morphological characters, and these assumptions are translated into mathematics as parameters. The incorporation of prior distributions further allows researchers to quantify their prior beliefs about the value any one parameter can take. How to translate biological knowledge into mathematical language is difficult, and can be confusing to many biologists. This review aims to help systematics researchers understand the biological meaning of common models and assumptions. Using examples from the insect fossil record, I will demonstrate empirically what assumptions mean in concrete terms, and discuss how researchers can use and understand Bayesian methods for phylogenetic estimation.
Collapse
Affiliation(s)
- April M Wright
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA
| |
Collapse
|
24
|
Brown JW, Parins-Fukuchi C, Stull GW, Vargas OM, Smith SA. Bayesian and likelihood phylogenetic reconstructions of morphological traits are not discordant when taking uncertainty into consideration: a comment on Puttick et al. Proc Biol Sci 2019; 284:rspb.2017.0986. [PMID: 29021179 DOI: 10.1098/rspb.2017.0986] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 05/30/2017] [Indexed: 11/12/2022] Open
Abstract
Puttick et al. (2017 Proc. R. Soc. B284, 20162290 (doi:10.1098/rspb.2016.2290)) performed a simulation study to compare accuracy among methods of inferring phylogeny from discrete morphological characters. They report that a Bayesian implementation of the Mk model (Lewis 2001 Syst. Biol.50, 913-925 (doi:10.1080/106351501753462876)) was most accurate (but with low resolution), while a maximum-likelihood (ML) implementation of the same model was least accurate. They conclude by strongly advocating that Bayesian implementations of the Mk model should be the default method of analysis for such data. While we appreciate the authors' attempt to investigate the accuracy of alternative methods of analysis, their conclusion is based on an inappropriate comparison of the ML point estimate, which does not consider confidence, with the Bayesian consensus, which incorporates estimation credibility into the summary tree. Using simulation, we demonstrate that ML and Bayesian estimates are concordant when confidence and credibility are comparably reflected in summary trees, a result expected from statistical theory. We therefore disagree with the conclusions of Puttick et al. and consider their prescription of any default method to be poorly founded. Instead, we recommend caution and thoughtful consideration of the model or method being applied to a morphological dataset.
Collapse
Affiliation(s)
- Joseph W Brown
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Caroline Parins-Fukuchi
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gregory W Stull
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Oscar M Vargas
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
25
|
Ottoni FP, Mattos JLO, Katz AM, Bragança PH. Phylogeny and species delimitation based on molecular approaches on the species of the Australoheros autrani group (Teleostei, Cichlidae), with biogeographic comments. ZOOSYST EVOL 2019. [DOI: 10.3897/zse.95.31658] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Three distinct and independent molecular-based species delimitation analyses were performed among the species and populations included within theAustraloherosautranigroup, based on sequences of the mitochondrial gene Cytochrome b: a tree-based method proposed by Wiens and Penkrot (WP), a Character-based DNA Barcoding (CBB) and coalescent species delimitation method termed the Bayesian Implementation of the Poisson tree processes (bPTP). The congruence of WP and CBB delimited 11 independent lineages (species), while the bPTP delimited just nine lineages. We did not favour any of the methods, and we considered the possibility of two slightly variant scenarios. A time-calibrated phylogenetic analysis is proposed based on the predominant congruence of the results of these three species delimitation methods herein applied. The monophyly of theA.autranispecies group was highly supported with maximum node support value and diagnosed by 11 nucleotide substitutions. The sister clade of theA.autranispecies group is the clade comprisingA.sp. Timbé do Sul andA.minuano. The phylogenetic analysis supports three main clades within theA.autranispecies group, supported by maximum node support value, with the Southern Mata Atlântica clade as the most basal clade. Divergence time estimates indicate that the diversification of theAustraloherosoriginated during the early Neogene, but only in the late Neogene did the processes of diversification in the southeast and north regions occur. Diversification within theAustraloherosautranispecies group occurred synchronically for the three main clades during the beginning of the Quaternary. It is demonstrated that molecular characters are valuable tools for species recognition, particularly in speciose groups with inconspicuous or difficult to record morphological characters. The resulting phylogeny of theAustraloherosautranigroup is highly compatible with the geological and biogeographic scenarios proposed for the Neogene and Quarternary shaping of the extant river basins of eastern Brazil. Despite the origin of theA.autranigroup being dated to the late Miocene, species level diversification occurred in the Pleistocene and was probably driven by headwater capture events and sea-level fluctuations.
Collapse
|
26
|
Cole ML, Raheem DC, Villet MH. Molecular phylogeny of Chondrocyclus (Gastropoda: Cyclophoridae), a widespread genus of sedentary, restricted-range snails. Mol Phylogenet Evol 2019; 131:193-210. [DOI: 10.1016/j.ympev.2018.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 08/31/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
|
27
|
Mattos JL, Costa WJ. Three new species of the ‘ Geophagus’ brasiliensis species group from the northeast Brazil (Cichlidae, Geophagini). ZOOSYST EVOL 2018. [DOI: 10.3897/zse.94.22685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Morphological characters and phylogenetic trees generated by analyses of segments of two mitochondrial genes cytochrome b and cytochrome c oxidase I support recognition of three new species of the ‘Geophagus’ brasiliensis species group from coastal basins of northeast Brazil. All new species were diagnosed by exclusive morphological characters and exclusive nucleotide transformations. Geophagusrufomarginatus sp. n., from the Rio Buranhém Basin, is distinguished from all other species of the group by dorsal-fin lappets with red edges, the presence of longitudinal series of small light blue spots between the anal-fin spines and rays, and non-denticulated gill-rakers; it is closely related to G.brasiliensis and G.iporangensis. Geophagusmultiocellus sp. n., from the Rio de Contas Basin, is distinguished from all other species of the group by having small pale blue spots with minute bright blue dots at their centres, that are often vertically coalesced to form short bars on the caudal fin. Geophagussantosi sp. n., from the Rio Mariana Basin, is distinguished from all other species of the group by having blue stripes parallel to the dorsal and anal fin rays on their longest portions. Geophagusmultiocellus and G.santosi belong to the same clade of G.itapicuruensis. The clade composed by the Rio Paraguaçu Basin species was recovered as the sister group of the other species of the ‘G.’ brasiliensis species group.
Collapse
|
28
|
Guimarães EC, Brito PSD, Feitosa LM, Carvalho-Costa LF, Ottoni FP. A new species of Hyphessobrycon Durbin from northeastern Brazil: evidence from morphological data and DNA barcoding (Characiformes, Characidae). Zookeys 2018:79-101. [PMID: 29910663 PMCID: PMC6002418 DOI: 10.3897/zookeys.765.23157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 05/07/2018] [Indexed: 11/16/2022] Open
Abstract
A new species of Hyphessobrycon is described for the upper Munim and Preguiças river basins, northeastern Brazil, supported by morphological and molecular species delimitation methods. This new species belongs to the Hyphessobryconsensu stricto group, as it has the three main diagnostic character states of this assemblage: presence of a dark brown or black blotch on the dorsal fin, absence of a black midlateral stripe on its flank and the position of Weberian apparatus upward horizontal through dorsal margin of operculum. Our phylogenetic analysis also supported the allocation of the new species in this group; however, it was not possible to recover the species sister-group. Pristellamaxillaris and Moenkhausiahemigrammoides were recovered as the sister-clade of the Hyphessobryconsensu stricto group.
Collapse
Affiliation(s)
- Erick Cristofore Guimarães
- Universidade Federal do Maranhão, Programa de Pós-Graduação em Biodiversidade e Conservação. Av. dos Portugueses 1966, Cidade Universitária do Bacanga, CEP 65080-805, São Luís, MA, Brazil.,Universidade Federal do Maranhão, Laboratório de Sistemática e Ecologia de Organismos Aquáticos, Centro de Ciências Agrárias e Ambientais, Campus Universitário, CCAA, BR-222, KM 04, S/N, Boa Vista, CEP 65500-000, Chapadinha, MA, Brazil
| | - Pâmella Silva De Brito
- Universidade Federal do Maranhão, Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Amazônia Legal. Av. dos Portugueses 1966, Cidade Universitária do Bacanga, CEP 65080-805, São Luís, MA, Brazil.,Universidade Federal do Maranhão, Laboratório de Sistemática e Ecologia de Organismos Aquáticos, Centro de Ciências Agrárias e Ambientais, Campus Universitário, CCAA, BR-222, KM 04, S/N, Boa Vista, CEP 65500-000, Chapadinha, MA, Brazil
| | - Leonardo Manir Feitosa
- Universidade Federal de Pernambuco, Programa de Pós-Graduação em Biologia Animal. Av. Professor Moraes Rego 1235, Cidade Universitária, CEP: 50670-901, Recife, PE, Brazil
| | - Luís Fernando Carvalho-Costa
- Universidade Federal do Maranhão, Departamento de Biologia, Laboratório de Genética e Biologia Molecular, Av. dos Portugueses 1966, Cidade Universitária do Bacanga, CEP 65080-805, São Luís, MA, Brazil
| | - Felipe Polivanov Ottoni
- Universidade Federal do Maranhão, Programa de Pós-Graduação em Biodiversidade e Conservação. Av. dos Portugueses 1966, Cidade Universitária do Bacanga, CEP 65080-805, São Luís, MA, Brazil.,Universidade Federal do Maranhão, Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Amazônia Legal. Av. dos Portugueses 1966, Cidade Universitária do Bacanga, CEP 65080-805, São Luís, MA, Brazil.,Universidade Federal do Maranhão, Laboratório de Sistemática e Ecologia de Organismos Aquáticos, Centro de Ciências Agrárias e Ambientais, Campus Universitário, CCAA, BR-222, KM 04, S/N, Boa Vista, CEP 65500-000, Chapadinha, MA, Brazil.,Universidade Federal do Maranhão, Programa de Pós-Graduação em Oceanografia. Av. dos Portugueses 1966, Cidade Universitária do Bacanga, CEP 65080-805, São Luís, MA, Brazil
| |
Collapse
|
29
|
Krefeld-Schwalb A, Witte EH, Zenker F. Hypothesis-Testing Demands Trustworthy Data-A Simulation Approach to Inferential Statistics Advocating the Research Program Strategy. Front Psychol 2018; 9:460. [PMID: 29740363 PMCID: PMC5928294 DOI: 10.3389/fpsyg.2018.00460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Abstract
In psychology as elsewhere, the main statistical inference strategy to establish empirical effects is null-hypothesis significance testing (NHST). The recent failure to replicate allegedly well-established NHST-results, however, implies that such results lack sufficient statistical power, and thus feature unacceptably high error-rates. Using data-simulation to estimate the error-rates of NHST-results, we advocate the research program strategy (RPS) as a superior methodology. RPS integrates Frequentist with Bayesian inference elements, and leads from a preliminary discovery against a (random) H0-hypothesis to a statistical H1-verification. Not only do RPS-results feature significantly lower error-rates than NHST-results, RPS also addresses key-deficits of a “pure” Frequentist and a standard Bayesian approach. In particular, RPS aggregates underpowered results safely. RPS therefore provides a tool to regain the trust the discipline had lost during the ongoing replicability-crisis.
Collapse
Affiliation(s)
| | - Erich H Witte
- Institute for Psychology, University of Hamburg, Hamburg, Germany
| | - Frank Zenker
- Department of Philosophy, Lund University, Lund, Sweden
| |
Collapse
|
30
|
Cherlin S, Heaps SE, Nye TMW, Boys RJ, Williams TA, Embley TM. The Effect of Nonreversibility on Inferring Rooted Phylogenies. Mol Biol Evol 2018; 35:984-1002. [PMID: 29149300 PMCID: PMC5889004 DOI: 10.1093/molbev/msx294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Most phylogenetic models assume that the evolutionary process is stationary and reversible. In addition to being biologically improbable, these assumptions also impair inference by generating models under which the likelihood does not depend on the position of the root. Consequently, the root of the tree cannot be inferred as part of the analysis. Yet identifying the root position is a key component of phylogenetic inference because it provides a point of reference for polarizing ancestor-descendant relationships and therefore interpreting the tree. In this paper, we investigate the effect of relaxing the unrealistic reversibility assumption and allowing the position of the root to be another unknown. We propose two hierarchical models that are centered on a reversible model but perturbed to allow nonreversibility. The models differ in the degree of structure imposed on the perturbations. The analysis is performed in the Bayesian framework using Markov chain Monte Carlo methods for which software is provided. We illustrate the performance of the two nonreversible models in analyses of simulated data using two types of topological priors. We then apply the models to a real biological data set, the radiation of polyploid yeasts, for which there is robust biological opinion about the root position. Finally, we apply the models to a second biological alignment for which the rooted tree is controversial: the ribosomal tree of life. We compare the two nonreversible models and conclude that both are useful in inferring the position of the root from real biological data.
Collapse
Affiliation(s)
- Svetlana Cherlin
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sarah E Heaps
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tom M W Nye
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Richard J Boys
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - T Martin Embley
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
31
|
Lamb AM, Gan HM, Greening C, Joseph L, Lee Y, Morán‐Ordóñez A, Sunnucks P, Pavlova A. Climate‐driven mitochondrial selection: A test in Australian songbirds. Mol Ecol 2018; 27:898-918. [DOI: 10.1111/mec.14488] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 11/29/2017] [Accepted: 12/08/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Annika Mae Lamb
- School of Biological Sciences Monash University Melbourne Vic. Australia
| | - Han Ming Gan
- School of Science Monash University Malaysia Bandar Sunway Selangor Malaysia
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds Vic. Australia
| | - Chris Greening
- School of Biological Sciences Monash University Melbourne Vic. Australia
| | - Leo Joseph
- Australian National Wildlife Collection CSIRO National Research Collections Canberra ACT Australia
| | - Yin Peng Lee
- School of Science Monash University Malaysia Bandar Sunway Selangor Malaysia
| | - Alejandra Morán‐Ordóñez
- InForest Joint Research Unit (CTFC‐CREAF) Forest Science Centre of Catalonia Solsona Catalonia Spain
| | - Paul Sunnucks
- School of Biological Sciences Monash University Melbourne Vic. Australia
| | - Alexandra Pavlova
- School of Biological Sciences Monash University Melbourne Vic. Australia
| |
Collapse
|
32
|
Matsen FA, Billey SC, Kas A, Konvalinka M. Tanglegrams: A Reduction Tool for Mathematical Phylogenetics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:343-349. [PMID: 28113515 DOI: 10.1109/tcbb.2016.2613040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees. These relative labelings are naturally formalized as tanglegrams, which have previously been an object of study in coevolutionary analysis. Although there has been considerable work on planar drawings of tanglegrams, they have not been fully explored as combinatorial objects until recently. In this paper, we describe how many discrete mathematical questions on trees "factor" through a problem on tanglegrams, and how understanding that factoring can simplify analysis. Depending on the problem, it may be useful to consider a unordered version of tanglegrams, and/or their unrooted counterparts. For all of these definitions, we show how the isomorphism types of tanglegrams can be understood in terms of double cosets of the symmetric group, and we investigate their automorphisms. Understanding tanglegrams better will isolate the distinct problems on leaf-labeled pairs of trees and reveal natural symmetries of spaces associated with such problems.
Collapse
|
33
|
Zhang M, Shen Z, Meng G, Lu Y, Wang Y. Genome-wide analysis of the Brachypodium distachyon (L.) P. Beauv. Hsp90 gene family reveals molecular evolution and expression profiling under drought and salt stresses. PLoS One 2017; 12:e0189187. [PMID: 29216330 PMCID: PMC5720741 DOI: 10.1371/journal.pone.0189187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/21/2017] [Indexed: 01/31/2023] Open
Abstract
The structure, evolution, and function of heat shock proteins 90 (Hsp90s) have been investigated in great detail in fungi and animals. However, studies on the Hsp90 genes in plants are generally limited. Brachypodium distachyon (L.) P. Beauv., as a model plant for cereal crops, has become a potential biofuel grass. During its long evolution, the Hsp90 gene family in Brachypodium has developed some strategies to cope with adverse environments. How the Hsp90 gene family in Brachypodium evolved in different plant lineages and what its role is in plant responses to drought and salt stresses remains to be elucidated. We used a set of different bioinformatics tools to identify 94 Hsp90 genes from 10 species representing four plant lineages and classified into three subgroups. Eight BdHsp90 genes were detected from B. distachyon. The number of exon-intron structures differed in each subgroup, and the motif analysis revealed that these genes were relatively conservative in each group. The fragments duplication and tandem duplication, which are the prime powers for functional diversity, generally occurred during the duplication of the whole plant genome. Transcriptional analysis of the BdHsp90 genes under salt and drought stress conditions indicated that the expression of these genes was delayed or increased at different stress time points; The expression was more affected in that of Bradi3g39630, Bradi4g06370, and Bradi1g30130. Our findings suggest the involvement of BdHsp90s in plant abiotic stress response, and further consolidate our views on the stress response mechanism of Hsp90 in general.
Collapse
Affiliation(s)
- Ming Zhang
- College of Life Science, Heze University, Shandong, China
| | - Zhiwei Shen
- College of Life Science, Heze University, Shandong, China
| | - Guoqing Meng
- College of Life Science, Heze University, Shandong, China
| | - Yu Lu
- College of Life Science, Heze University, Shandong, China
| | - Yilei Wang
- College of Life Science, Heze University, Shandong, China
- * E-mail:
| |
Collapse
|
34
|
Veera Singham G, Othman AS, Lee CY. Phylogeography of the termite Macrotermes gilvus and insight into ancient dispersal corridors in Pleistocene Southeast Asia. PLoS One 2017; 12:e0186690. [PMID: 29186140 PMCID: PMC5706666 DOI: 10.1371/journal.pone.0186690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 10/05/2017] [Indexed: 11/19/2022] Open
Abstract
Dispersal of soil-dwelling organisms via the repeatedly exposed Sunda shelf through much of the Pleistocene in Southeast Asia has not been studied extensively, especially for invertebrates. Here we investigated the phylogeography of an endemic termite species, Macrotermes gilvus (Hagen), to elucidate the spatiotemporal dynamics of dispersal routes of terrestrial fauna in Pleistocene Southeast Asia. We sampled 213 termite colonies from 66 localities throughout the region. Independently inherited microsatellites and mtDNA markers were used to infer the phylogeographic framework of M. gilvus. Discrete phylogeographic analysis and molecular dating based on fossil calibration were used to infer the dynamics of M. gilvus dispersal in time and space across Southeast Asia. We found that the termite dispersal events were consistently dated within the Pleistocene time frame. The dispersal pattern was multidirectional, radiating eastwards and southwards out of Indochina, which was identified as the origin for dispersal events. We found no direct dispersal events between Sumatra and Borneo despite the presence of a terrestrial connection between them during the Pleistocene. Instead, central Java served as an important link allowing termite colonies to be established in Borneo and Sumatra. Our findings support the hypothesis of a north-south dispersal corridor in Southeast Asia and suggest the presence of alternative dispersal routes across Sundaland during the Pleistocene. For the first time, we also propose that a west-east dispersal through over-water rafting likely occurred across the Pleistocene South China Sea. We found at least two independent entry routes for terrestrial species to infiltrate Sumatra and Borneo at different times.
Collapse
Affiliation(s)
- G. Veera Singham
- Urban Entomology Laboratory, Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
- Population Genetics Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Ahmad Sofiman Othman
- Population Genetics Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Chow-Yang Lee
- Urban Entomology Laboratory, Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| |
Collapse
|
35
|
Campbell MA, Alfaro ME, Belasco M, López JA. Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences. PeerJ 2017; 5:e3548. [PMID: 28929008 PMCID: PMC5592902 DOI: 10.7717/peerj.3548] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/15/2017] [Indexed: 11/20/2022] Open
Abstract
Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.
Collapse
Affiliation(s)
- Matthew A Campbell
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, United States of America.,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States of America
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Max Belasco
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, United States of America
| | - J Andrés López
- School of Fisheries and Ocean Sciencs, University of Alaska Fairbanks, Fairbanks, AK, United States of America.,University of Alaska Museum, Fairbanks, AK, United States of America
| |
Collapse
|
36
|
Vera J, Gutiérrez MH, Palfner G, Pantoja S. Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile. World J Microbiol Biotechnol 2017; 33:157. [PMID: 28726124 DOI: 10.1007/s11274-017-2321-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/14/2017] [Indexed: 11/27/2022]
Abstract
Our study reports the diversity of culturable mycoplankton in the eastern South Pacific Ocean off Chile to contribute with novel knowledge on taxonomy of filamentous fungi isolated from distinct physicochemical and biological marine environments. We characterized spatial distribution of isolates, evaluated their viability and assessed the influence of organic substrate availability on fungal development. Thirty-nine Operational Taxonomic Units were identified from 99 fungal strains isolated from coastal and oceanic waters by using Automatic Barcode Gap Discovery. All Operational Taxonomic Units belonged to phylum Ascomycota and orders Eurotiales, Dothideales, Sordariales and Hypocreales, mainly Penicillium sp. (82%); 11 sequences did not match existing species in GenBank, suggesting occurrence of novel fungal taxa. Our results suggest that fungal communities in the South Pacific Ocean off Chile appear to thrive in a wide range of environmental conditions in the ocean and that substrate availability may be a factor influencing fungal viability in the ocean.
Collapse
Affiliation(s)
- Jeanett Vera
- Graduate Program in Oceanography, Department of Oceanography, University of Concepción, Concepción, Chile
| | - Marcelo H Gutiérrez
- Department of Oceanography and COPAS Sur-Austral, University of Concepción, Concepción, Chile
| | - Götz Palfner
- Department of Botany, University of Concepción, Concepción, Chile
| | - Silvio Pantoja
- Department of Oceanography and COPAS Sur-Austral, University of Concepción, Concepción, Chile.
| |
Collapse
|
37
|
Exploring the shell-based taxonomy of the Sri Lankan land snail Corilla H. and A. Adams, 1855 (Pulmonata: Corillidae) using mitochondrial DNA. Mol Phylogenet Evol 2017; 107:609-618. [DOI: 10.1016/j.ympev.2016.12.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/08/2016] [Accepted: 12/20/2016] [Indexed: 11/22/2022]
|
38
|
Peste des petits ruminants (PPR): A neglected tropical disease in Maghreb region of North Africa and its threat to Europe. PLoS One 2017; 12:e0175461. [PMID: 28426782 PMCID: PMC5398521 DOI: 10.1371/journal.pone.0175461] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/27/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Peste des petits ruminants (PPR) is a contagious disease listed by the World Organisation for Animal health (OIE) as being a specific hazard. It affects sheep, goats, and wild ungulates, and is prevalent throughout the developing world particularly Asia, the Middle East, and Africa. PPR has been targeted for eradication by 2030 by the Food and Agriculture Organization of the United Nations (FAO) and the OIE, after the successful eradication of the related disease, rinderpest in cattle. PPR was first reported in 1942 in the Ivory Coast in Western Africa and has since extended its range in Asia, the Middle East, and Africa posing an immediate threat of incursion into Europe, South East Asia and South Africa. Although robust vaccines are available, the use of these vaccines in a systematic and rational manner is not widespread, resulting in this devastating disease becoming an important neglected tropical disease in the developing world. METHODOLOGY We isolated and characterized the PPR virus from an outbreak in Cheraga, northern Algeria, during October 2015 by analyzing the partial N-gene sequence in comparison with other viruses from the Maghreb region. As well as sequencing the full length viral genome and performing real-time RT-PCR on clinical samples. Maximum-likelihood and Bayesian temporal and phylogeographic analyses were performed to assess the persistence and spread of PPRV circulation from Eastern Africa in the Maghreb region of North Africa. CONCLUSIONS Recent PPR outbreaks in Cheraga, in the northern part of Algiers (October 2015) and North-West Morocco (June, 2015) highlight that PPRV has spread to the northern border of North Africa and may pose a threat of introduction to Europe. Phylogeographic analysis suggests that lineage IV PPRV has spread from Eastern Africa, most likely from the Sudan 2000 outbreak, into Northern Africa resulting in the 2008 Moroccan outbreak. Maximum-likelihood and Bayesian analysis shows that these North African viruses cluster closely together suggesting the existence of continual regional circulation. Considering the same virus is circulating in Algeria, Morocco and Tunisia, implementation of a common Maghreb PPR eradication strategy would be beneficial for the region.
Collapse
|
39
|
Abstract
Molecular evolution can reveal the relationship between sets of homologous sequences and the patterns of change that occur during their evolution. An important aspect of these studies is the inference of a phylogenetic tree, which explicitly describes evolutionary relationships between homologous sequences. This chapter provides an introduction to evolutionary trees and how to infer them from sequence data using some commonly used inferential methodology. It focuses on statistical methods for inferring trees and how to assess the confidence one should have in any resulting tree, with a particular emphasis on the underlying assumptions of the methods and how they might affect the tree estimate. There is also some discussion of the underlying algorithms used to perform tree search and recommendations regarding the performance of different algorithms. Finally, there are a few practical guidelines, including how to combine multiple software packages to improve inference, and a comparison between Bayesian and Maximum likelihood phylogenetics.
Collapse
Affiliation(s)
- Simon Whelan
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| | - David A Morrison
- Department of Organism Biology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
40
|
Klak C, Hanáček P, Bruyns PV. Out of southern Africa: Origin, biogeography and age of the Aizooideae (Aizoaceae). Mol Phylogenet Evol 2016; 109:203-216. [PMID: 27998816 DOI: 10.1016/j.ympev.2016.12.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 12/07/2016] [Accepted: 12/12/2016] [Indexed: 01/28/2023]
Abstract
The Aizooideae is an early-diverging lineage within the Aizoaceae. It is most diverse in southern Africa, but also has endemic species in Australasia, Eurasia and South America. We derived a phylogenetic hypothesis from Bayesian and Maximum Likelihood analyses of plastid DNA-sequences. We find that one of the seven genera, the fynbos-endemic Acrosanthes, does not belong to the Aizooideae, but is an ancient sister-lineage to the subfamilies Mesembryanthemoideae & Ruschioideae. Galenia and Plinthus are embedded inside Aizoon and Aizoanthemum is polyphyletic. The Namibian endemic Tetragonia schenckii is sister to Tribulocarpus of the Sesuvioideae. For the Aizooideae, we explored their possible age by means of relaxed Bayesian dating and used Bayesian Binary MCMC reconstruction of ancestral areas to investigate their area of origin. Early diversification occurred in southern Africa in the Eocene-Oligocene, with a split into a mainly African lineage and an Eurasian-Australasian-African-South American lineage. These subsequently radiated in the early Miocene. For Tetragonia, colonisation of Australasia via long-distance dispersal from Eurasia gave rise to the Australasian lineage from which there were subsequent dispersals to South America and Southern Africa. Despite the relatively old age of the Aizooideae, more than half the species have radiated since the Pleiocene, coinciding with the large and rapid diversification of the Ruschioideae. The lineage made up of Tetragonia schenckii &Tribulocarpus split from the remainder of the Sesuvioideae already in the mid Oligocene and its disjunct distribution between Namibia and north-east Africa may be the result of a previously wider distribution within an early Arid African flora. Our reconstruction of ancestral character-states indicates that the expanding keels giving rise to hygrochastic fruits originated only once, i.e. after the split of the Sesuvioideae from the remainder of the Aizoaceae and that they were subsequently lost many times. Variously winged and spiky fruits, adapted to dispersal by wind and animals, have evolved independently in the Aizooideae and the Sesuvioideae. There is then a greater diversity of dispersal systems in the earlier lineages than in the Mesembryanthemoideae and Ruschioideae, where dispersal is mainly achieved by rain.
Collapse
Affiliation(s)
- Cornelia Klak
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, 7701 Rondebosch, South Africa.
| | - Pavel Hanáček
- Department of Plant Biology, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Peter V Bruyns
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, 7701 Rondebosch, South Africa
| |
Collapse
|
41
|
Stout CC, Tan M, Lemmon AR, Lemmon EM, Armbruster JW. Resolving Cypriniformes relationships using an anchored enrichment approach. BMC Evol Biol 2016; 16:244. [PMID: 27829363 PMCID: PMC5103605 DOI: 10.1186/s12862-016-0819-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp). RESULTS Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae. CONCLUSIONS Most major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited.
Collapse
Affiliation(s)
- Carla C. Stout
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| | - Milton Tan
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306 USA
| | - Emily Moriarty Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306 USA
| | - Jonathan W. Armbruster
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| |
Collapse
|
42
|
McLean BS, Jackson DJ, Cook JA. Rapid divergence and gene flow at high latitudes shape the history of Holarctic ground squirrels (Urocitellus). Mol Phylogenet Evol 2016; 102:174-88. [DOI: 10.1016/j.ympev.2016.05.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022]
|
43
|
Dufort MJ. An augmented supermatrix phylogeny of the avian family Picidae reveals uncertainty deep in the family tree. Mol Phylogenet Evol 2016; 94:313-26. [DOI: 10.1016/j.ympev.2015.08.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 08/22/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
|
44
|
Molecular Phylogenetics: Concepts for a Newcomer. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 160:185-196. [DOI: 10.1007/10_2016_49] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
45
|
Condamine FL, Nagalingum NS, Marshall CR, Morlon H. Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating. BMC Evol Biol 2015; 15:65. [PMID: 25884423 PMCID: PMC4449600 DOI: 10.1186/s12862-015-0347-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/02/2015] [Indexed: 01/21/2023] Open
Abstract
Background Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic estimations for 237 cycad species using three genes and two calibration strategies incorporating up to six fossil constraints to (i) test the impact of two different branching process priors on age estimates, (ii) assess which branching prior better fits the data, (iii) investigate branching prior impacts on diversification analyses, and (iv) provide insights into the diversification history of cycads. Results Using Bayes factors, we compared divergence time estimates and the inferred dynamics of diversification when using Yule versus birth-death priors. Bayes factors were calculated with marginal likelihood estimated with stepping-stone sampling. We found striking differences in age estimates and diversification dynamics depending on prior choice. Dating with the Yule prior suggested that extant cycad genera diversified in the Paleogene and with two diversification rate shifts. In contrast, dating with the birth-death prior yielded Neogene diversifications, and four rate shifts, one for each of the four richest genera. Nonetheless, dating with the two priors provided similar age estimates for the divergence of cycads from Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes factors clearly supported the birth-death prior. Conclusions These results suggest the choice of the branching process prior can have a drastic influence on our understanding of evolutionary radiations. Therefore, all dating analyses must involve a model selection process using Bayes factors to select between a Yule or birth-death prior, in particular on ancient clades with a potential pattern of high extinction. We also provide new insights into the history of cycad diversification because we found (i) periods of extinction along the long branches of the genera consistent with fossil data, and (ii) high diversification rates within the Miocene genus radiations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0347-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Fabien L Condamine
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique), Route de Saclay, 91128, Palaiseau, France. .,Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30, Göteborg, Sweden.
| | - Nathalie S Nagalingum
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, NSW, 2000, Australia.
| | - Charles R Marshall
- Department of Integrative Biology and Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, CA, 94720-4780, USA.
| | - Hélène Morlon
- CNRS, UMR 8197 Institut de Biologie de l'École Normale Supérieure, 46 rue d'Ulm, 75005, Paris, France.
| |
Collapse
|
46
|
Harrison LB, Larsson HCE. Among-Character Rate Variation Distributions in Phylogenetic Analysis of Discrete Morphological Characters. Syst Biol 2014; 64:307-24. [DOI: 10.1093/sysbio/syu098] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Luke B. Harrison
- Redpath Museum, McGill University, 859 Sherbrooke Street West Montreal, Quebec, Canada H3A 0C4 and 2Redpath Museum, McGill University, 859 Sherbrooke ST W, Montreal, Quebec, Canada H3A 0C4
| | - Hans C. E. Larsson
- Redpath Museum, McGill University, 859 Sherbrooke Street West Montreal, Quebec, Canada H3A 0C4 and 2Redpath Museum, McGill University, 859 Sherbrooke ST W, Montreal, Quebec, Canada H3A 0C4
| |
Collapse
|
47
|
Willis CG, Hall JC, Rubio de Casas R, Wang TY, Donohue K. Diversification and the evolution of dispersal ability in the tribe Brassiceae (Brassicaceae). ANNALS OF BOTANY 2014; 114:1675-86. [PMID: 25342656 PMCID: PMC4649692 DOI: 10.1093/aob/mcu196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 08/21/2014] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Dispersal and establishment ability can influence evolutionary processes such as geographic isolation, adaptive divergence and extinction probability. Through these population-level dynamics, dispersal ability may also influence macro-evolutionary processes such as species distributions and diversification. This study examined patterns of evolution of dispersal-related fruit traits, and how the evolution of these traits is correlated with shifts in geographic range size, habitat and diversification rates in the tribe Brassiceae (Brassicaceae). METHODS The phylogenetic analysis included 72 taxa sampled from across the Brassiceae and included both nuclear and chloroplast markers. Dispersal-related fruit characters were scored and climate information for each taxon was retrieved from a database. Correlations between fruit traits, seed characters, habitat, range and climate were determined, together with trait-dependent diversification rates. KEY RESULTS It was found that the evolution of traits associated with limited dispersal evolved only in association with compensatory traits that increase dispersal ability. The evolution of increased dispersal ability occurred in multiple ways through the correlated evolution of different combinations of fruit traits. The evolution of traits that increase dispersal ability was in turn associated with larger seed size, increased geographic range size and higher diversification rates. CONCLUSIONS This study provides evidence that the evolution of increased dispersal ability and larger seed size, which may increase establishment ability, can also influence macro-evolutionary processes, possibly by increasing the propensity for long-distance dispersal. In particular, it may increase speciation and consequent diversification rates by increasing the likelihood of geographic and thereby reproductive isolation.
Collapse
Affiliation(s)
- C G Willis
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - J C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - R Rubio de Casas
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, Granada, 18071, Spain
| | - T Y Wang
- Duke University School of Medicine, Duke University, DUMC 3710, Durham, NC 27710, USA
| | - K Donohue
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| |
Collapse
|
48
|
Padhi A, Ma L. Genetic and epidemiological insights into the emergence of peste des petits ruminants virus (PPRV) across Asia and Africa. Sci Rep 2014; 4:7040. [PMID: 25391314 PMCID: PMC4229660 DOI: 10.1038/srep07040] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 10/27/2014] [Indexed: 11/09/2022] Open
Abstract
Small ruminants are important components in the livelihood of millions of households in many parts of the world. The spread of the highly contagious peste des petits ruminants (PPR) disease, which is caused by an RNA virus, PPRV, across Asia and Africa remains a major concern. The present study explored the evolutionary and epidemiological dynamics of PPRV through the analyses of partial N-gene and F-gene sequences of the virus. All the four previously described PPRV lineages (I-IV) diverged from their common ancestor during the late-19(th) to early-20(th) century. Among the four lineages, PPRV-IV showed pronounced genetic structuring across the region; however, haplotype sharing among the geographic regions, together with the presence of multiple genetic clusters within a country, indicates the possibility of frequent mobility of the diseased individuals across the region. The gradual decline in the effective number of infections suggests a limited genetic variation, which could be attributed to the effective vaccination that has been practiced since 1990s. However, the movement of infected animals across the region likely contributes to the spread of PPRV-IV. No evidence of positive selection was identified from this study.
Collapse
Affiliation(s)
- Abinash Padhi
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD-20742, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD-20742, USA
| |
Collapse
|
49
|
Bentley J, Verboom GA, Bergh NG. Erosive processes after tectonic uplift stimulate vicariant and adaptive speciation: evolution in an Afrotemperate-endemic paper daisy genus. BMC Evol Biol 2014; 14:27. [PMID: 24524661 PMCID: PMC3927823 DOI: 10.1186/1471-2148-14-27] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 02/10/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The role of tectonic uplift in stimulating speciation in South Africa's only alpine zone, the Drakensberg, has not been explicitly examined. Tectonic processes may influence speciation both through the creation of novel habitats and by physically isolating plant populations. We use the Afrotemperate endemic daisy genus Macowania to explore the timing and mode (geographic versus adaptive) of speciation in this region. Between sister species pairs we expect high morphological divergence where speciation has happened in sympatry (adaptive) while with geographic (vicariant) speciation we may expect to find less morphological divergence and a greater degree of allopatry. A dated molecular phylogenetic hypothesis for Macowania elucidates species' relationships and is used to address the potential impact of uplift on diversification. Morphological divergence of a small sample of reproductive and vegetative characters, used as a proxy for adaptive divergence, is measured against species' range distributions to estimate mode of speciation across two subclades in the genus. RESULTS The Macowania crown age is consistent with the hypothesis of post-uplift diversification, and we find evidence for both vicariant and adaptive speciation between the two subclades within Macowania. Both subclades exhibit strong signals of range allopatry, suggesting that geographic isolation was important in speciation. One subclade, associated with dry, rocky environments at high altitudes, shows very little morphological and ecological differentiation but high range allopatry. The other subclade occupies a greater variety of habitats and exhibits far greater morphological differentiation, but contains species with overlapping distribution ranges. CONCLUSIONS Species in Macowania are likely to have diversified in response to tectonic uplift, and we invoke uplift and uplift-mediated erosion as the main drivers of speciation. The greater relative morphological divergence in sympatric species of Macowania indicates that speciation in the non-sympatric taxa may not have required obvious adaptive differences, implying that simple geographic isolation was the driving force for speciation ('neutral speciation').
Collapse
|
50
|
The origin of the early differentiation of Ivies (Hedera L.) and the radiation of the Asian Palmate group (Araliaceae). Mol Phylogenet Evol 2014; 70:492-503. [DOI: 10.1016/j.ympev.2013.10.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 10/18/2013] [Accepted: 10/22/2013] [Indexed: 11/22/2022]
|