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Fine DH, Schreiner H. Oral microbial interactions from an ecological perspective: a narrative review. FRONTIERS IN ORAL HEALTH 2023; 4:1229118. [PMID: 37771470 PMCID: PMC10527376 DOI: 10.3389/froh.2023.1229118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/16/2023] [Indexed: 09/30/2023] Open
Abstract
Landscape ecology is a relatively new field of study within the sub-specialty of ecology that considers time and space in addition to structure and function. Landscape ecology contends that both the configuration (spatial pattern) and the composition (organisms both at the macro and or micro level) of an ecology can change over time. The oral cavity is an ideal place to study landscape ecology because of the variety of landscapes, the dynamic nature of plaque biofilm development, and the easy access to biofilm material. This review is intended to provide some specific clinical examples of how landscape ecology can influence the understanding of oral diseases and act as a supplement to diagnosis and treatment. The purpose of this review is two-fold; (1) to illustrate how landscape ecology can be used to clarify the two most prominent microbiologically induced infections in the oral cavity, and (2) how studies of oral microbiology can be used to enhance the understanding of landscape ecology. The review will distinguish between "habitat" and "niche" in a landscape and extend the concept that a "patch", is the demarcating unit of a habitat within a landscape. The review will describe how; (1) an individual patch, defined by its shape, edges and internal components can have an influence on species within the patch, (2) spatial dynamics over time within a patch can lead to variations or diversities of species within that patch space, and (3) an unwelcoming environment can promote species extinction or departure/dispersion into a more favorable habitat. Understanding this dynamic in relationship to caries and periodontal disease is the focus of this review.
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Affiliation(s)
- Daniel H. Fine
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, United States
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2
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Arbour JH, Stanchak KE. The little fishes that could: smaller fishes demonstrate slow body size evolution but faster speciation in the family Percidae. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Body size affects numerous aspects of organismal biology and many factors have been invoked to explain body size distributions in a macroecological and macroevolutionary context. Body size in the freshwater fish family Percidae is strongly right-skewed (i.e. dominated by small sizes), with small body size potentially being associated with fast water habitats. We constructed a new species-level, multi-locus, time-calibrated phylogeny of Percidae, and used it to test for changes in the rate and pattern of maximum body size evolution. We also tested whether speciation rates varied as a function of body size. We found that Etheostomatinae evolved towards a smaller adaptive optimum in body size compared to the other subfamilies of Percidae, and that this shift was associated with a reduction in the rate of body size evolution. Speciation rates were associated with body size across percids, showing a peak around small to medium body size. Small body size appears to partially, but not fully, explain the diversity of small percids, as many darters fall well below the “optimum” body size. Reinforcement of selection for small body size via selection for novel morphologies or via sexual selection may help to fully explain the remarkable diversity of darter radiation.
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Affiliation(s)
- Jessica H Arbour
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
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MacGuigan DJ, Hoagstrom CW, Domisch S, Hulsey CD, Near TJ. Integrative ichthyological species delimitation in the Greenthroat Darter complex (Percidae: Etheostomatinae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Sami Domisch
- Department of Ecosystem Research Leibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - C. Darrin Hulsey
- Laboratory for Zoology and Evolutionary Biology Department of Biology University of Konstanz Konstanz Germany
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
- Peabody Museum of Natural History Yale University New Haven CT USA
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4
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Corush JB, Fitzpatrick BM, Wolfe EL, Keck BP. Breeding behaviour predicts patterns of natural hybridization in North American minnows (Cyprinidae). J Evol Biol 2020; 34:486-500. [PMID: 33300154 DOI: 10.1111/jeb.13751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 12/01/2022]
Abstract
Premating barriers such as variation in reproductive behaviour can evolve quickly, but because gametic and postzygotic incompatibilities often evolve more slowly, circumstances that bring gametes into contact can breach the boundaries of premating isolation. In aquatic environments, the gametes of organisms with external fertilization are released into a constantly moving environment and may come into contact with heterospecific gametes. In fishes, nest association (spawning in another species' nest) is a behaviour that brings gametes from different species into close spatiotemporal proximity. These interactions might increase chances of hybridization, especially when multiple species associate with a single nest builder. This study addresses these interactions in the largest clade of North American freshwater fishes, the minnows (Cyprinidae). We compiled a list of over 17,000 hybrid specimens in conjunction with species distribution data, breeding behaviours, and an inferred phylogeny to test if breeding behaviour, in addition to evolutionary history, is an important predictor of hybridization. We find that breeding behaviour is a significant predictor of hybridization, even when phylogenetic relatedness and divergence time are accounted for. Specifically, nest associates are more likely to hybridize with other nest associates whereas non-nesting species had relatively low rates of hybridization.
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Affiliation(s)
- Joel B Corush
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA.,Department of Biology, Wayne State University, Detroit, MI, USA
| | - Benjamin M Fitzpatrick
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
| | - Elizabeth L Wolfe
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
| | - Benjamin P Keck
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
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Weyand CA, Piller KR. Assessing phylogeographic variation in the Rosyside Dace (Teleostei, Leuciscidae), a widespread morphologically variable taxon. ZOOL SCR 2020. [DOI: 10.1111/zsc.12439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Courtney A. Weyand
- Department of Biological Sciences; Southeastern Louisiana University; Hammond LA USA
- Department of Biological Sciences; Auburn University; Auburn AL USA
| | - Kyle R. Piller
- Department of Biological Sciences; Southeastern Louisiana University; Hammond LA USA
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Schönhuth S, Gagne RB, Alda F, Neely DA, Mayden RL, Blum MJ. Phylogeography of the widespread creek chub Semotilus atromaculatus (Cypriniformes: Leuciscidae). JOURNAL OF FISH BIOLOGY 2018; 93:778-791. [PMID: 30101564 DOI: 10.1111/jfb.13778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
Abstract
The extent and nature of genetic differentiation in Semotilus atromaculatus, one of the most abundant and widespread leuciscids in North America, were evaluated based on mitochondrial (mt) and nuclear DNA sequence variation. Phylogenetic relationships were first inferred based on a fragment of the cytochrome b (cytb) region and the nuclear intron s7 gene for S. atromaculatus and all other congeners as well as representative species from all other genera in the creek chub-plagopterin clade. The phylogeography of major haplogroups of S. atromaculatus was also assessed according to variation in a fragment of the mitochondrial cytb region from 567 individuals across its range. All analyses identified S. thoreauianus, S. lumbee and S. corporalis as reciprocally monophyletic groups. Analyses of nuclear sequence variation resolved S. atromaculatus as a single clade, where S. thoreauianus and S. lumbee were recovered as the sister group to S. atromaculatus, and S. corporalis was resolved as sister to all other species in the genus. Analyses of mtDNA sequence variation recovered S. atromaculatus as three well supported and differentiated monophyletic groups, with a widespread genetically homogeneous lineage extending across most of the current range of the species; a more geographically restricted and geographically structured lineage in the southern Appalachians, sister group to S. lumbee; and a geographically restricted lineage was identified from two Gulf Slope basins. Evidence of complex mito-nuclear discordance and phylogeographic differentiation within S. atromaculatus illustrates that further analysis of widespread species is warranted to understand North American freshwater fish diversity and distributions.
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Affiliation(s)
- Susana Schönhuth
- Department of Biology, Saint Louis University, St Louis, Missouri
| | - Roderick B Gagne
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana
| | - Fernando Alda
- Louisiana State University, Museum of Natural Science, Baton Rouge, Louisiana
| | - David A Neely
- Tennessee Aquarium Conservation Institute, Chattanooga, Tennessee
| | - Richard L Mayden
- Department of Biology, Saint Louis University, St Louis, Missouri
| | - Michael J Blum
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana
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Borstein SR, O’Meara BC. AnnotationBustR: an R package to extract subsequences from GenBank annotations. PeerJ 2018; 6:e5179. [PMID: 30002984 PMCID: PMC6034590 DOI: 10.7717/peerj.5179] [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: 04/12/2017] [Accepted: 06/18/2018] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND DNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequence records on GenBank contain more than one gene or are portions of genomes. Inconsistencies in the way genes are annotated and the numerous synonyms a single gene may be listed under provide major challenges for extracting large numbers of subsequences for comparative analysis across taxa. At present, there is no easy way to extract portions from many GenBank accessions based on annotations where gene names may vary extensively. RESULTS The R package AnnotationBustR allows users to extract sequences based on GenBank annotations through the ACNUC retrieval system given search terms of gene synonyms and accession numbers. AnnotationBustR extracts subsequences of interest and then writes them to a FASTA file for users to employ in their research endeavors. CONCLUSION FASTA files of extracted subsequences and accession tables generated by AnnotationBustR allow users to quickly find and extract subsequences from GenBank accessions. These sequences can then be incorporated in various analyses, like the construction of phylogenies to test a wide range of ecological and evolutionary hypotheses.
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Affiliation(s)
- Samuel R. Borstein
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
| | - Brian C. O’Meara
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
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Schönhuth S, Vukić J, Šanda R, Yang L, Mayden RL. Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei). Mol Phylogenet Evol 2018; 127:781-799. [PMID: 29913311 DOI: 10.1016/j.ympev.2018.06.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022]
Abstract
The phylogenetic relationships and classification of the freshwater fish order Cypriniformes, like many other species-rich groups of vertebrates, has evolved over time with some consistency and inconsistencies of relationships across various studies. Within Cypriniformes, the Holarctic family Leuciscidae is one of the most widely distributed and highly diverse monophyletic groups of cyprinoids. Despite several studies conducted on this group, alternative hypotheses exist as to the composition and relationships within Leuciscidae. Here we assess the extent, composition, phylogenetic relationships, and taxonomy of this highly diverse group of fishes, using multiple mitochondrial and nuclear loci and a comprehensive and dense taxonomic sampling. Analyses of 418 specimens (410 species) resolve a well-supported Leuciscidae including 362 specimens (358 taxa) in six well-supported subfamilies/major clades: Pseudaspininae/Far East Asian clade (FEA); Laviniinae/North American Western clade (WC); Plagopterinae/North American Creek Chub-Plagopterin clade (CC-P); Leuciscinae/Eurasian Old World clade (OW) (minus Phoxinus) plus North American Notemigonus; Phoxininae/Eurasian Phoxinus clade (PHX); and Pogonichthyinae/North American clade (NA) including all remaining leuciscids. Within Leuciscidae, neither the traditional phoxinins (Phoxinus, FEA, Nearctic genera) nor all Nearctic genera (minus Notemigonus) are resolved as monophyletic; whereas the WC and CC-P form two independent lineages from remaining North American cyprinoids. A close relationship exists between Eurasian Phoxinus, NA, and OW clades, while FEA is the sister group to all remaining Leuciscidae. Major lineages resolved within these six subfamilies are mostly congruent with some previous studies. Our results suggests a complex evolutionary history of this diverse and widespread group of fishes.
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Affiliation(s)
- Susana Schönhuth
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA.
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
| | - Radek Šanda
- Department of Zoology, National Museum, Vaclavske namesti 68, 115 79 Prague, Czech Republic
| | - Lei Yang
- Florida Museum of Natural History, University of Florida, 1659 Museum Rd., Gainesville, FL 32611, USA
| | - Richard L Mayden
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA
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Abstract
The diversity of forms found among animals on Earth is striking. Despite decades of study, it has been difficult to reconcile the patterns of diversity seen between closely related species with those observed when studying single species on ecological timescales. We propose a set of models, called Lévy processes, to attempt to reconcile rapid evolution between species with the relatively stable distributions of phenotypes seen within species. These models, which have been successfully used to model stock market data, allow for long periods of stasis followed by bursts of rapid change. We find that many vertebrate groups are well fitted by Lévy models compared with models for which traits evolve toward a stationary optimum or evolve in an incremental and wandering manner. The relative importance of different modes of evolution in shaping phenotypic diversity remains a hotly debated question. Fossil data suggest that stasis may be a common mode of evolution, while modern data suggest some lineages experience very fast rates of evolution. One way to reconcile these observations is to imagine that evolution proceeds in pulses, rather than in increments, on geological timescales. To test this hypothesis, we developed a maximum-likelihood framework for fitting Lévy processes to comparative morphological data. This class of stochastic processes includes both an incremental and a pulsed component. We found that a plurality of modern vertebrate clades examined are best fitted by pulsed processes over models of incremental change, stationarity, and adaptive radiation. When we compare our results to theoretical expectations of the rate and speed of regime shifts for models that detail fitness landscape dynamics, we find that our quantitative results are broadly compatible with both microevolutionary models and observations from the fossil record.
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Oros M, Choudhury A, Scholz T. A Common Eurasian Fish Tapeworm,Caryophyllaeides fennica(Cestoda), in Western North America: Further Evidence of ‘Amphi-Pacific' Vicariance in Freshwater Fish Parasites. J Parasitol 2017; 103:486-496. [DOI: 10.1645/16-80] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Mikuláš Oros
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovak Republic
| | - Anindo Choudhury
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovak Republic
| | - Tomáš Scholz
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovak Republic
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11
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Near TJ, Simmons JW, Mollish JM, Correa MA, Benavides E, Harrington RC, Keck BP. A New Species of Logperch Endemic to Tennessee (Percidae: Etheostomatinae:Percina). BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2017. [DOI: 10.3374/014.058.0203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Thomas J. Near
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA; Peabody Museum of Natural History, Yale University, New Haven CT 06520-8106 USA
| | - Jeffrey W. Simmons
- Resources and River Management, Tennessee Valley Authority, Chattanooga TN 37402-2881 USA
| | - Jon Michael Mollish
- Resources and River Management, Tennessee Valley Authority, Chattanooga TN 37402-2881 USA
| | - Maria A. Correa
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA
| | - Edgar Benavides
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA
| | - Richard C. Harrington
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA
| | - Benjamin P. Keck
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville TN 37996 USA
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Chira AM, Thomas GH. The impact of rate heterogeneity on inference of phylogenetic models of trait evolution. J Evol Biol 2016; 29:2502-2518. [PMID: 27653965 PMCID: PMC5217074 DOI: 10.1111/jeb.12979] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/14/2016] [Accepted: 09/16/2016] [Indexed: 01/08/2023]
Abstract
Rates of trait evolution are known to vary across phylogenies; however, standard evolutionary models assume a homogeneous process of trait change. These simple methods are widely applied in small‐scale phylogenetic studies, whereas models of rate heterogeneity are not, so the prevalence and patterns of potential rate variation in groups up to hundreds of species remain unclear. The extent to which trait evolution is modelled accurately on a given phylogeny is also largely unknown because studies typically lack absolute model fit tests. We investigated these issues by applying both rate‐static and variable‐rates methods on (i) body mass data for 88 avian clades of 10–318 species, and (ii) data simulated under a range of rate‐heterogeneity scenarios. Our results show that rate heterogeneity is present across small‐scaled avian clades, and consequently applying only standard single‐process models prompts inaccurate inferences about the generating evolutionary process. Specifically, these approaches underestimate rate variation, and systematically mislabel temporal trends in trait evolution. Conversely, variable‐rates approaches have superior relative fit (they are the best model) and absolute fit (they describe the data well). We show that rate changes such as single internal branch variations, rate decreases and early bursts are hard to detect, even by variable‐rates models. We also use recently developed absolute adequacy tests to highlight misleading conclusions based on relative fit alone (e.g. a consistent preference for constrained evolution when isolated terminal branch rate increases are present). This work highlights the potential for robust inferences about trait evolution when fitting flexible models in conjunction with tests for absolute model fit.
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Affiliation(s)
- A M Chira
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - G H Thomas
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Life Sciences, The Natural History Museum, London, UK
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