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Liu C, Wang CY, Wu ZX, Yang HX, Guan JY. Diversity-induced resonance in a globally coupled bistable system with diversely distributed heterogeneity. CHAOS (WOODBURY, N.Y.) 2022; 32:083112. [PMID: 36049925 DOI: 10.1063/5.0094685] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
A moderate degree of diversity, in form of quenched noise or intrinsic heterogeneity, can significantly strengthen the collective response of coupled extended systems. As yet, related discoveries on diversity-induced resonance are mainly concentrated on symmetrically distributed heterogeneity, e.g., the Gaussian or uniform distributions with zero-mean. The necessary conditions that guarantee the arise of resonance phenomenon in heterogeneous oscillators remain largely unknown. In this work, we show that the standard deviation and the ratio of negative entities of a given distribution jointly modulate diversity-induced resonance and the concomitance of negative and positive entities is the prerequisite for this resonant behavior emerging in diverse symmetrical and asymmetrical distributions. Particularly, for a proper degree of diversity of a given distribution, the collective signal response behaves like a bell-shaped curve as the ratio of negative oscillator increases, which can be termed negative-oscillator-ratio induced resonance. Furthermore, we analytically reveal that the ratio of negative oscillators plays a gating role in the resonance phenomenon on the basis of a reduced equation. Finally, we examine the robustness of these results in globally coupled bistable elements with asymmetrical potential functions. Our results suggest that the phenomenon of diversity-induced resonance can arise in arbitrarily distributed heterogeneous bistable oscillators by regulating the ratio of negative entities appropriately.
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Affiliation(s)
- Cong Liu
- Lanzhou Center for Theoretical Physics and Key Laboratory of Theoretical Physics of Gansu Province, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Chong-Yang Wang
- Institute of Computational Physics and Complex Systems, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Zhi-Xi Wu
- Lanzhou Center for Theoretical Physics and Key Laboratory of Theoretical Physics of Gansu Province, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Han-Xin Yang
- Department of Physics, Fuzhou University, Fuzhou 350116, People's Republic of China
| | - Jian-Yue Guan
- Lanzhou Center for Theoretical Physics and Key Laboratory of Theoretical Physics of Gansu Province, Lanzhou University, Lanzhou, Gansu 730000, China
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2
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Freund F, Siri-Jégousse A. The minimal observable clade size of exchangeable coalescents. BRAZ J PROBAB STAT 2021. [DOI: 10.1214/20-bjps480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Fabian Freund
- Crop Plant Biodiversity and Breeding Informatics Group (350b), Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, 70599 Stuttgart, Germany
| | - Arno Siri-Jégousse
- Departamento de Probabilidad y Estadística, IIMAS, Universidad Nacional Autónoma de México, Mexico City, Mexico
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3
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Castilla AR, Méndez-Vigo B, Marcer A, Martínez-Minaya J, Conesa D, Picó FX, Alonso-Blanco C. Ecological, genetic and evolutionary drivers of regional genetic differentiation in Arabidopsis thaliana. BMC Evol Biol 2020; 20:71. [PMID: 32571210 PMCID: PMC7310121 DOI: 10.1186/s12862-020-01635-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Disentangling the drivers of genetic differentiation is one of the cornerstones in evolution. This is because genetic diversity, and the way in which it is partitioned within and among populations across space, is an important asset for the ability of populations to adapt and persist in changing environments. We tested three major hypotheses accounting for genetic differentiation-isolation-by-distance (IBD), isolation-by-environment (IBE) and isolation-by-resistance (IBR)-in the annual plant Arabidopsis thaliana across the Iberian Peninsula, the region with the largest genomic diversity. To that end, we sampled, genotyped with genome-wide SNPs, and analyzed 1772 individuals from 278 populations distributed across the Iberian Peninsula. RESULTS IBD, and to a lesser extent IBE, were the most important drivers of genetic differentiation in A. thaliana. In other words, dispersal limitation, genetic drift, and to a lesser extent local adaptation to environmental gradients, accounted for the within- and among-population distribution of genetic diversity. Analyses applied to the four Iberian genetic clusters, which represent the joint outcome of the long demographic and adaptive history of the species in the region, showed similar results except for one cluster, in which IBR (a function of landscape heterogeneity) was the most important driver of genetic differentiation. Using spatial hierarchical Bayesian models, we found that precipitation seasonality and topsoil pH chiefly accounted for the geographic distribution of genetic diversity in Iberian A. thaliana. CONCLUSIONS Overall, the interplay between the influence of precipitation seasonality on genetic diversity and the effect of restricted dispersal and genetic drift on genetic differentiation emerges as the major forces underlying the evolutionary trajectory of Iberian A. thaliana.
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Affiliation(s)
- Antonio R Castilla
- Centre for Applied Ecology "Prof. Baeta Neves", InBIO, School of Agriculture, University of Lisbon, Lisbon, Portugal
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Arnald Marcer
- CREAF, Centre de Recerca Ecològica i Aplicacions Forestals, Bellaterra, E08193, Cerdanyola de Vallès, Catalonia, Spain
- Universitat Autònoma de Barcelona, Bellaterra, E08193, Cerdanyola de Vallès, Catalonia, Spain
| | | | - David Conesa
- Departament d'Estadística i Investigació Operativa, Universitat de València, Valencia, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain.
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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4
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Disanto F, Wiehe T. Measuring the external branches of a Kingman tree: A discrete approach. Theor Popul Biol 2020; 134:92-105. [PMID: 32485202 DOI: 10.1016/j.tpb.2020.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 04/02/2020] [Accepted: 05/21/2020] [Indexed: 10/24/2022]
Abstract
The Kingman coalescent process is a classical model of gene genealogies in population genetics. It generates Yule-distributed, binary ranked tree topologies - also called histories - with a finite number of n leaves, together with n-1 exponentially distributed time lengths: one for each layer of the history. Using a discrete approach, we study the lengths of the external branches of Yule distributed histories, where the length of an external branch is defined as the rank of its parent node. We study the multiplicity of external branches of given length in a random history of n leaves. A correspondence between the external branches of the ordered histories of size n and the non-peak entries of the permutations of size n-1 provides easy access to the length distributions of the first and second longest external branches in a random Yule history and coalescent tree of size n. The length of the longest external branch is also studied in dependence of root balance of a random tree. As a practical application, we compare the observed and expected number of mutations on the longest external branches in samples from natural populations.
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Affiliation(s)
| | - Thomas Wiehe
- Institut für Genetik, Universität zu Köln, Germany.
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5
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del Valle JC, Herman JA, Whittall JB. Genome skimming and microsatellite analysis reveal contrasting patterns of genetic diversity in a rare sandhill endemic (Erysimum teretifolium, Brassicaceae). PLoS One 2020; 15:e0227523. [PMID: 32459825 PMCID: PMC7252598 DOI: 10.1371/journal.pone.0227523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/28/2020] [Indexed: 11/19/2022] Open
Abstract
Barriers between islands often inhibit gene flow creating patterns of isolation by distance. In island species, the majority of genetic diversity should be distributed among isolated populations. However, a self-incompatible mating system leads to higher genetic variation within populations and very little between-population subdivision. We examine these two contrasting predictions in Erysimum teretifolium, a rare self-incompatible plant endemic to island-like sandhill habitats in Santa Cruz County, California. We used genome skimming and nuclear microsatellites to assess the distribution of genetic diversity within and among eight of the 13 remaining populations. Phylogenetic analyses of the chloroplast genomes revealed a deep separation of three of the eight populations. The nuclear ribosomal DNA cistron showed no genetic subdivision. Nuclear microsatellites suggest 83% of genetic variation resides within populations. Despite this, 18 of 28 between-population comparisons exhibited significant population structure (mean FST = 0.153). No isolation by distance existed among all populations, however when one outlier population was removed from the analysis due to uncertain provenance, significant isolation by distance emerged (r2 = 0.5611, p = 0.005). Population census size did not correlate with allelic richness as predicted on islands. Bayesian population assignment detected six genetic groupings with substantial admixture. Unique genetic clusters were concentrated at the periphery of the species’ range. Since the overall distribution of nuclear genetic diversity reflects E. tereifolium’s self-incompatible mating system, the vast majority of genetic variation could be sampled within any individual population. Yet, the chloroplast genome results suggest a deep split and some of the nuclear microsatellite analyses indicate some island-like patterns of genetic diversity. Restoration efforts intending to maximize genetic variation should include representatives from both lineages of the chloroplast genome and, for maximum nuclear genetic diversity, should include representatives of the smaller, peripheral populations.
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Affiliation(s)
- José Carlos del Valle
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain
| | - Julie A. Herman
- Department of Biology, Santa Clara University, Santa Clara, CA, United States of America
| | - Justen B. Whittall
- Department of Biology, Santa Clara University, Santa Clara, CA, United States of America
- * E-mail:
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6
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Xiao S, Ji Y, Liu J, Gong X. Genetic characterization of the entire range of Cycas panzhihuaensis (Cycadaceae). PLANT DIVERSITY 2020; 42:7-18. [PMID: 32140633 PMCID: PMC7046506 DOI: 10.1016/j.pld.2019.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
Cycas panzhihuaensis L. Zhou & S. Y. Yang (Cycadaceae) is an endangered gymnosperm species endemic to the dry-hot valley of the Jinsha River basin in southwest China. Although the wild C. panzhihuaensis population from Panzhihua Cycad Natural Reserve is well protected and its genetic diversity has been well assessed, the genetic characteristics of populations outside the nature reserve, which face larger risks of extinction, remain unknown. Furthermore, the population genetics and historical dynamics of this endemic and endangered species have not been examined across its entire range. In this study, to analyze the genetic diversity, phylogeographical structure and demographic history of C. panzhihuaensis from all its seven known locations, we sequenced and compared molecular data from chloroplastic DNA (psbA-trnH, psbM-trnD, and trnS-trnG), single-copy nuclear genes (PHYP, AC5, HSP70, and AAT) from 61 individuals, as well as 11 nuclear microsatellite loci (SSR) from 102 individuals. We found relatively high genetic diversity within populations and high genetic differentiation among populations of C. panzhihuaensis, which is consistent with the patterns of other Asian inland cycads. Although no significant phylogeographical structure was detected, we found that small and unprotected populations possess higher genetic diversity and more unique haplotypes, which revises our understanding of diversity within this species and deserves due attention. Analysis of demographic dynamics suggest that human activity might be the key threat to C. panzhihuaensis. Based on the genetic characterization of C. panzhihuaensis, we propose several practical guidelines for the conservation of this species, especially for the populations with small sizes.
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Affiliation(s)
- Siyue Xiao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei RD, Panlong District, Kunming, Yunnan province, 650201, China
- University of Chinese Academy of Sciences, No. 19A, Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Yunheng Ji
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei RD, Panlong District, Kunming, Yunnan province, 650201, China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei RD, Panlong District, Kunming, Yunnan province, 650201, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei RD, Panlong District, Kunming, Yunnan province, 650201, China
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7
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Lecocq T, Michez D, Gérard M, Vereecken NJ, Delangre J, Rasmont P, Vray S, Dufrêne M, Mardulyn P, Dellicour S. Divergent geographic patterns of genetic diversity among wild bees: Conservation implications. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Thomas Lecocq
- Université de Lorraine; INRA; URAFPA; Nancy France
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
| | - Denis Michez
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
| | - Maxence Gérard
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
| | - Nicolas J. Vereecken
- Agroecology & Pollination; Landscape Ecology & Plant Production Systems; Université libre de Bruxelles (ULB); Brussels Belgium
| | - Jessica Delangre
- Biodiversity & Landscape; Gembloux Agro-Bio Tech; University of Liège; Gembloux Belgium
| | - Pierre Rasmont
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
| | - Sarah Vray
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
- Department of Geography; University of Namur; Namur Belgium
| | - Marc Dufrêne
- Biodiversity & Landscape; Gembloux Agro-Bio Tech; University of Liège; Gembloux Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology; Université libre de Bruxelles (ULB); Bruxelles Belgium
| | - Simon Dellicour
- KU Leuven Department of Microbiology and Immunology; Rega Institute; Laboratory for Clinical and Epidemiological Virology; Leuven Belgium
- Spatial Epidemiology Lab (SpELL); Université Libre de Bruxelles; CP160/12 50, av. FD Roosevelt; 1050 Bruxelles Belgium
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8
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Werfel J, Ingber DE, Bar-Yam Y. Theory and associated phenomenology for intrinsic mortality arising from natural selection. PLoS One 2017; 12:e0173677. [PMID: 28355288 PMCID: PMC5371302 DOI: 10.1371/journal.pone.0173677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 02/25/2017] [Indexed: 11/30/2022] Open
Abstract
Standard evolutionary theories of aging and mortality, implicitly based on assumptions of spatial averaging, hold that natural selection cannot favor shorter lifespan without direct compensating benefit to individual reproductive success. However, a number of empirical observations appear as exceptions to or are difficult to reconcile with this view, suggesting explicit lifespan control or programmed death mechanisms inconsistent with the classic understanding. Moreover, evolutionary models that take into account the spatial distributions of populations have been shown to exhibit a variety of self-limiting behaviors, maintained through environmental feedback. Here we extend recent work on spatial modeling of lifespan evolution, showing that both theory and phenomenology are consistent with programmed death. Spatial models show that self-limited lifespan robustly results in long-term benefit to a lineage; longer-lived variants may have a reproductive advantage for many generations, but shorter lifespan ultimately confers long-term reproductive advantage through environmental feedback acting on much longer time scales. Numerous model variations produce the same qualitative result, demonstrating insensitivity to detailed assumptions; the key conditions under which self-limited lifespan is favored are spatial extent and locally exhaustible resources. Factors including lower resource availability, higher consumption, and lower dispersal range are associated with evolution of shorter lifespan. A variety of empirical observations can parsimoniously be explained in terms of long-term selective advantage for intrinsic mortality. Classically anomalous empirical data on natural lifespans and intrinsic mortality, including observations of longer lifespan associated with increased predation, and evidence of programmed death in both unicellular and multicellular organisms, are consistent with specific model predictions. The generic nature of the spatial model conditions under which intrinsic mortality is favored suggests a firm theoretical basis for the idea that evolution can quite generally select for shorter lifespan directly.
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Affiliation(s)
- Justin Werfel
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, United States of America
- New England Complex Systems Institute, Cambridge, Massachusetts, United States of America
- Harvard Medical School and Children’s Hospital, Boston, Massachusetts, United States of America
| | - Donald E. Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, United States of America
- Harvard Medical School and Children’s Hospital, Boston, Massachusetts, United States of America
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
| | - Yaneer Bar-Yam
- New England Complex Systems Institute, Cambridge, Massachusetts, United States of America
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9
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Salvi D, Pinho C, Harris DJ. Digging up the roots of an insular hotspot of genetic diversity: decoupled mito-nuclear histories in the evolution of the Corsican-Sardinian endemic lizard Podarcis tiliguerta. BMC Evol Biol 2017; 17:63. [PMID: 28253846 PMCID: PMC5335832 DOI: 10.1186/s12862-017-0899-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 01/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mediterranean islands host a disproportionately high level of biodiversity and endemisms. Growing phylogeographic evidence on island endemics has unveiled unexpectedly complex patterns of intra-island diversification, which originated at diverse spatial and temporal scales. We investigated multilocus genetic variation of the Corsican-Sardinian endemic lizard Podarcis tiliguerta with the aim of shedding more light on the evolutionary processes underlying the origin of Mediterranean island biodiversity. RESULTS We analysed DNA sequences of mitochondrial (12S and nd4) and nuclear (acm4 and mc1r) gene fragments in 174 individuals of P. tiliguerta from 81 localities across the full range of the species in a geographic and genealogical framework. We found surprisingly high genetic diversity both at mitochondrial and nuclear loci. Seventeen reciprocally monophyletic allopatric mitochondrial haplogroups were sharply divided into four main mitochondrial lineages (two in Corsica and two in Sardinia) of Miocene origin. In contrast, shallow divergence and shared diversity within and between islands was observed at the nuclear loci. We evaluated alternative biogeographic and evolutionary scenarios to explain such profound discordance in spatial and phylogenetic patterning between mitochondrial and nuclear genomes. While neutral models provided unparsimonious explanations for the observed pattern, the hypothesis of environmental selection driving mitochondrial divergence in the presence of nuclear gene flow is favoured. CONCLUSIONS Our study on the genetic variation of P. tiliguerta reveals surprising levels of diversity underlining a complex phylogeographic pattern with a striking example of mito-nuclear discordance. These findings have profound implications, not only for the taxonomy and conservation of P. tiliguerta. Growing evidence on deep mitochondrial breaks in absence of geographic barriers and of climatic factors associated to genetic variation of Corsican-Sardinian endemics warrants additional investigation on the potential role of environmental selection driving the evolution of diversity hotspots within Mediterranean islands.
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Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100 Coppito, L'Aquila, Italy. .,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
| | - Catarina Pinho
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
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10
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Mimura M, Yahara T, Faith DP, Vázquez‐Domínguez E, Colautti RI, Araki H, Javadi F, Núñez‐Farfán J, Mori AS, Zhou S, Hollingsworth PM, Neaves LE, Fukano Y, Smith GF, Sato Y, Tachida H, Hendry AP. Understanding and monitoring the consequences of human impacts on intraspecific variation. Evol Appl 2017; 10:121-139. [PMID: 28127389 PMCID: PMC5253428 DOI: 10.1111/eva.12436] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/20/2016] [Indexed: 12/15/2022] Open
Abstract
Intraspecific variation is a major component of biodiversity, yet it has received relatively little attention from governmental and nongovernmental organizations, especially with regard to conservation plans and the management of wild species. This omission is ill-advised because phenotypic and genetic variations within and among populations can have dramatic effects on ecological and evolutionary processes, including responses to environmental change, the maintenance of species diversity, and ecological stability and resilience. At the same time, environmental changes associated with many human activities, such as land use and climate change, have dramatic and often negative impacts on intraspecific variation. We argue for the need for local, regional, and global programs to monitor intraspecific genetic variation. We suggest that such monitoring should include two main strategies: (i) intensive monitoring of multiple types of genetic variation in selected species and (ii) broad-brush modeling for representative species for predicting changes in variation as a function of changes in population size and range extent. Overall, we call for collaborative efforts to initiate the urgently needed monitoring of intraspecific variation.
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Affiliation(s)
- Makiko Mimura
- Department of Bioenvironmental SystemsTamagawa UniversityTokyoJapan
| | - Tetsukazu Yahara
- Department of Biology and Institute of Decision Science for a Sustainable SocietyKyushu UniversityFukuokaJapan
| | - Daniel P. Faith
- The Australian Museum Research InstituteThe Australian MuseumSydneyNSWAustralia
| | | | | | - Hitoshi Araki
- Research Faculty of AgricultureHokkaido UniversitySapporoHokkaidoJapan
| | - Firouzeh Javadi
- Department of Biology and Institute of Decision Science for a Sustainable SocietyKyushu UniversityFukuokaJapan
| | - Juan Núñez‐Farfán
- Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoMéxicoMéxico
| | - Akira S. Mori
- Graduate School of Environment and Information SciencesYokohama National UniversityYokohamaJapan
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijingChina
| | | | - Linda E. Neaves
- Royal Botanic Garden EdinburghEdinburghUK
- Australian Centre for Wildlife Genomics, Australian Museum Research InstituteAustralian MuseumSydneyNSWAustralia
| | - Yuya Fukano
- Department of Biology and Institute of Decision Science for a Sustainable SocietyKyushu UniversityFukuokaJapan
| | - Gideon F. Smith
- Department of BotanyNelson Mandela Metropolitan UniversityPort ElizabethSouth Africa
- Departamento de Ciências da VidaCentre for Functional EcologyUniversidade de CoimbraCoimbraPortugal
| | | | - Hidenori Tachida
- Department of Biology and Institute of Decision Science for a Sustainable SocietyKyushu UniversityFukuokaJapan
| | - Andrew P. Hendry
- Redpath Museum and Department of BiologyMcGill UniversityMontrealQuebecCanada
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11
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Scriber JM. Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes. INSECTS 2013; 5:1-61. [PMID: 26462579 PMCID: PMC4592632 DOI: 10.3390/insects5010001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/04/2013] [Accepted: 12/06/2013] [Indexed: 01/11/2023]
Abstract
Comprising 50%-75% of the world's fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience) may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including "invasive species" in various ecosystems as they may become disrupted in different ways by rapid climate change. "Invasive genes" (into new species and populations) need to be recognized for their positive creative potential and addressed in conservation programs. "Genetic rescue" via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae) with their long-term historical data base (phylogeographical diversity changes) and recent (3-decade) climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced "reshuffling" (recombinations) of species composition, genotypes, and genomes may become increasingly ecologically and evolutionarily predictable, but future conservation management programs are more likely to remain constrained by human behavior than by lack of academic knowledge.
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Affiliation(s)
- Jon Mark Scriber
- Department of Entomology, Michigan State University, East Lansing, Michigan, MI 48824, USA.
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
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12
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Leather SR. Institutional vertebratism hampers insect conservation generally; not just saproxylic beetle conservation. Anim Conserv 2013. [DOI: 10.1111/acv.12068] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S. R. Leather
- Department of Crop & Environment Science; Harper Adams University; Newport; UK
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13
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Abstract
Neutral models, in which genetic change arises through random variation without fitness differences, have proven remarkably successful in describing observed patterns of biodiversity, despite the manifest role of selection in evolution. Here we investigate the effect of barriers on biodiversity by simulating the expansion of a population around a barrier to form a ring species, in which the two ends of the population are reproductively isolated despite ongoing gene flow around the ring. We compare the spatial and genetic properties of a neutral agent-based population model to the greenish warblers' complex, a well-documented example of an actual ring species in nature. Our results match the distribution of subspecies, the principal components of genetic diversity, and the linear spatial-genetic correlation of the observed data, even though selection is expected to be important for traits of this species. We find that ring species are often unstable to speciation or mixing but can persist for extended times depending on species and landscape features. For the greenish warblers, our analysis implies that the expanded area near the point of secondary contact is important for extending the duration of the ring, and thus, for the opportunity to observe this ring species. Nevertheless it also suggests the ring will break up into multiple species in 10,000 to 50,000 y. These results imply that simulations can be used to accurately describe empirical data for complex spatial-genetic traits of an individual species.
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14
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Lee-Yaw JA, Irwin DE. Large geographic range size reflects a patchwork of divergent lineages in the long-toed salamander (Ambystoma macrodactylum). J Evol Biol 2012; 25:2276-87. [DOI: 10.1111/j.1420-9101.2012.02604.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/28/2022]
Affiliation(s)
- J. A. Lee-Yaw
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
| | - D. E. Irwin
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
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15
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Correlation of intracellular trehalose concentration with desiccation resistance of soil Escherichia coli populations. Appl Environ Microbiol 2012; 78:7407-13. [PMID: 22885754 DOI: 10.1128/aem.01904-12] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Naturalized soil Escherichia coli populations need to resist common soil desiccation stress in order to inhabit soil environments. In this study, four representative soil E. coli strains and one lab strain, MG1655, were tested for desiccation resistance via die-off experiments in sterile quartz sand under a potassium acetate-induced desiccation condition. The desiccation stress caused significantly lower die-off rates of the four soil strains (0.17 to 0.40 day(-1)) than that of MG1655 (0.85 day(-1)). Cellular responses, including extracellular polymeric substance (EPS) production, exogenous glycine betaine (GB) uptake, and intracellular compatible organic solute synthesis, were quantified and compared under the desiccation and hydrated control conditions. GB uptake appeared not to be a specific desiccation response, while EPS production showed considerable variability among the E. coli strains. All E. coli strains produced more intracellular trehalose, proline, and glutamine under the desiccation condition than the hydrated control, and only the trehalose concentration exhibited a significant correlation with the desiccation-contributed die-off coefficients (Spearman's ρ = -1.0; P = 0.02). De novo trehalose synthesis was further determined for 15 E. coli strains from both soil and nonsoil sources to determine its prevalence as a specific desiccation response. Most E. coli strains (14/15) synthesized significantly more trehalose under the desiccation condition, and the soil E. coli strains produced more trehalose (106.5 ± 44.9 μmol/mg of protein [mean ± standard deviation]) than the nonsoil reference strains (32.5 ± 10.5 μmol/mg of protein).
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16
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Irwin DE. Local Adaptation along Smooth Ecological Gradients Causes Phylogeographic Breaks and Phenotypic Clustering. Am Nat 2012; 180:35-49. [DOI: 10.1086/666002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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17
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Allen B, Traulsen A, Tarnita CE, Nowak MA. How mutation affects evolutionary games on graphs. J Theor Biol 2012; 299:97-105. [PMID: 21473871 PMCID: PMC3150603 DOI: 10.1016/j.jtbi.2011.03.034] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 03/27/2011] [Accepted: 03/29/2011] [Indexed: 11/16/2022]
Abstract
Evolutionary dynamics are affected by population structure, mutation rates and update rules. Spatial or network structure facilitates the clustering of strategies, which represents a mechanism for the evolution of cooperation. Mutation dilutes this effect. Here we analyze how mutation influences evolutionary clustering on graphs. We introduce new mathematical methods to evolutionary game theory, specifically the analysis of coalescing random walks via generating functions. These techniques allow us to derive exact identity-by-descent (IBD) probabilities, which characterize spatial assortment on lattices and Cayley trees. From these IBD probabilities we obtain exact conditions for the evolution of cooperation and other game strategies, showing the dual effects of graph topology and mutation rate. High mutation rates diminish the clustering of cooperators, hindering their evolutionary success. Our model can represent either genetic evolution with mutation, or social imitation processes with random strategy exploration.
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Affiliation(s)
- Benjamin Allen
- Program for Evolutionary Dynamics, Department of Mathematics, Harvard University, One Brattle Square, Cambridge, MA 02138, United States.
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18
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Pickles RSA, Groombridge JJ, Zambrana Rojas VD, Van Damme P, Gottelli D, Kundu S, Bodmer R, Ariani CV, Iyengar A, Jordan WC. Evolutionary history and identification of conservation units in the giant otter, Pteronura brasiliensis. Mol Phylogenet Evol 2011; 61:616-27. [PMID: 21925282 DOI: 10.1016/j.ympev.2011.08.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 08/01/2011] [Accepted: 08/17/2011] [Indexed: 11/29/2022]
Abstract
The giant otter, Pteronura brasiliensis, occupies a range including the major drainage basins of South America, yet the degree of structure that exists within and among populations inhabiting these drainages is unknown. We sequenced portions of the mitochondrial DNA (mtDNA) cytochrome b (612bp) and control region (383 bp) genes in order to determine patterns of genetic variation within the species. We found high levels of mtDNA haplotype diversity (h = 0.93 overall) and support for subdivision into four distinct groups of populations, representing important centers of genetic diversity and useful units for prioritizing conservation within the giant otter. We tested these results against the predictions of three hypotheses of Amazonian diversification (Pleistocene Refugia, Paleogeography, and Hydrogeology). While the phylogeographic pattern conformed to the predictions of the Refugia Hypothesis, molecular dating using a relaxed clock revealed the phylogroups diverged from one another between 1.69 and 0.84 Ma, ruling out the influence of Late Pleistocene glacial refugia. However, the role of Plio-Pleistocene climate change could not be rejected. While the molecular dating also makes the influence of geological arches according to the Paleogeography Hypothesis extremely unlikely, the recent Pliocene formation of the Fitzcarrald Arch and its effect of subsequently altering drainage pattern could not be rejected. The data presented here support the interactions of both climatic and hydrological changes resulting from geological activity in the Plio-Pleistocene, in shaping the phylogeographic structure of the giant otter.
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Affiliation(s)
- R S A Pickles
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, United Kingdom.
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Norris V, Zemirline A, Amar P, Audinot JN, Ballet P, Ben-Jacob E, Bernot G, Beslon G, Cabin A, Fanchon E, Giavitto JL, Glade N, Greussay P, Grondin Y, Foster JA, Hutzler G, Jost J, Kepes F, Michel O, Molina F, Signorini J, Stano P, Thierry AR. Computing with bacterial constituents, cells and populations: from bioputing to bactoputing. Theory Biosci 2011; 130:211-28. [PMID: 21384168 PMCID: PMC3163788 DOI: 10.1007/s12064-010-0118-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Accepted: 12/15/2010] [Indexed: 10/29/2022]
Abstract
The relevance of biological materials and processes to computing-alias bioputing-has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating.
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Affiliation(s)
- Vic Norris
- Epigenomics Project, Genopole Campus 1, Bât. Genavenir 6, 5 rue Henri Desbruères, 91030, Évry Cedex, France.
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20
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Genotypic diversity of Escherichia coli in the water and soil of tropical watersheds in Hawaii. Appl Environ Microbiol 2011; 77:3988-97. [PMID: 21515724 DOI: 10.1128/aem.02140-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High levels of Escherichia coli were frequently detected in tropical soils in Hawaii, which present important environmental sources of E. coli to water bodies. This study systematically examined E. coli isolates from water and soil of several watersheds in Hawaii and observed high overall genotypic diversity (35.5% unique genotypes). In the Manoa watershed, fewer than 9.3% of the observed E. coli genotypes in water and 6.6% in soil were shared between different sampling sites, suggesting the lack of dominant fecal sources in the watershed. High temporal variability of E. coli genotypes in soil was also observed, which suggests a dynamic E. coli population corresponding with the frequently observed high concentrations in tropical soils. When E. coli genotypes detected from the same sampling events were compared, limited sharing between the soil and water samples was observed in the majority of comparisons (73.5%). However, several comparisons reported up to 33.3% overlap of E. coli genotypes between soil and water, illustrating the potential for soil-water interactions under favorable environmental conditions. In addition, genotype accumulation curves for E. coli from water and soil indicated that the sampling efforts in the Manoa watershed could not exhaust the overall genotypic diversity. Comparisons of E. coli genotypes from other watersheds on Oahu, Hawaii, identified no apparent grouping according to sampling locations. The results of the present study demonstrate the complexity of using E. coli as a fecal indicator bacterium in tropical watersheds and highlight the need to differentiate environmental sources of E. coli from fecal sources in water quality monitoring.
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21
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de Thoisy B, da Silva AG, Ruiz-García M, Tapia A, Ramirez O, Arana M, Quse V, Paz-y-Miño C, Tobler M, Pedraza C, Lavergne A. Population history, phylogeography, and conservation genetics of the last Neotropical mega-herbivore, the lowland tapir (Tapirus terrestris). BMC Evol Biol 2010; 10:278. [PMID: 20840756 PMCID: PMC2949869 DOI: 10.1186/1471-2148-10-278] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 09/14/2010] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Understanding the forces that shaped Neotropical diversity is central issue to explain tropical biodiversity and inform conservation action; yet few studies have examined large, widespread species. Lowland tapir (Tapirus terrrestris, Perissodactyla, Tapiridae) is the largest Neotropical herbivore whose ancestors arrived in South America during the Great American Biotic Interchange. A Pleistocene diversification is inferred for the genus Tapirus from the fossil record, but only two species survived the Pleistocene megafauna extinction. Here, we investigate the history of lowland tapir as revealed by variation at the mitochondrial gene Cytochrome b, compare it to the fossil data, and explore mechanisms that could have shaped the observed structure of current populations. RESULTS Separate methodological approaches found mutually exclusive divergence times for lowland tapir, either in the late or in the early Pleistocene, although a late Pleistocene divergence is more in tune with the fossil record. Bayesian analysis favored mountain tapir (T. pinchaque) paraphyly in relation to lowland tapir over reciprocal monophyly, corroborating the inferences from the fossil data these species are sister taxa. A coalescent-based analysis rejected a null hypothesis of allopatric divergence, suggesting a complex history. Based on the geographic distribution of haplotypes we propose (i) a central role for western Amazonia in tapir diversification, with a key role of the ecological gradient along the transition between Andean subcloud forests and Amazon lowland forest, and (ii) that the Amazon river acted as an barrier to gene flow. Finally, the branching patterns and estimates based on nucleotide diversity indicate a population expansion after the Last Glacial Maximum. CONCLUSIONS This study is the first examining lowland tapir phylogeography. Climatic events at the end of the Pleistocene, parapatric speciation, divergence along the Andean foothill, and role of the Amazon river, have similarly shaped the history of other taxa. Nevertheless further work with additional samples and loci is needed to improve our initial assessment. From a conservation perspective, we did not find a correspondence between genetic structure in lowland tapir and ecogeographic regions proposed to define conservation priorities in the Neotropics. This discrepancy sheds doubt into this scheme's ability to generate effective conservation planning for vagile species.
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22
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23
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Suwannakul S, Stafford GP, Whawell SA, Douglas CWI. Identification of bistable populations of Porphyromonas gingivalis that differ in epithelial cell invasion. MICROBIOLOGY-SGM 2010; 156:3052-3064. [PMID: 20576685 DOI: 10.1099/mic.0.038075-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bistable populations of bacteria give rise to two or more subtypes that exhibit different phenotypes. We have explored whether the periodontal pathogen Porphyromonas gingivalis exhibits bistable invasive phenotypes. Using a modified cell invasion assay, we show for the first time that there are two distinct subtypes within a population of P. gingivalis strains NCTC 11834 and W50 that display differences in their ability to invade oral epithelial cells. The highly invasive subtype invades cells at 10-30-fold higher levels than the poorly invasive subtype and remains highly invasive for approximately 12-16 generations. Analysis of the gingipain activity of these subtypes revealed that the highly invasive type had reduced cell-associated arginine-specific protease activity. The role of Arg-gingipain activity in invasion was verified by enhancement of invasion by rgpAB mutations and by inclusion of an Arg-gingipain inhibitor in invasion assays using wild-type bacteria. In addition, a population of ΔrgpAB bacteria did not contain a hyperinvasive subtype. Screening of the protease activity of wild-type populations of both strains identified high and low protease subtypes which also showed a corresponding reduction or enhancement, respectively, of invasive capabilities. Microarray analysis of these bistable populations revealed a putative signature set of genes that includes oxidative stress resistance and iron transport genes, and which might be critical to invasion of or survival within epithelial cells.
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Affiliation(s)
- S Suwannakul
- Oral and Maxillofacial Pathology, School of Clinical Dentistry, The University of Sheffield, Sheffield S10 2TA, UK
| | - G P Stafford
- Oral and Maxillofacial Pathology, School of Clinical Dentistry, The University of Sheffield, Sheffield S10 2TA, UK
| | - S A Whawell
- Oral and Maxillofacial Pathology, School of Clinical Dentistry, The University of Sheffield, Sheffield S10 2TA, UK
| | - C W I Douglas
- Oral and Maxillofacial Pathology, School of Clinical Dentistry, The University of Sheffield, Sheffield S10 2TA, UK
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24
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Nguyen B, Spillner A, Emerson BC, Moulton V. Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity. Algorithms Mol Biol 2010; 5:19. [PMID: 20302665 PMCID: PMC2853546 DOI: 10.1186/1748-7188-5-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 03/20/2010] [Indexed: 12/29/2022] Open
Abstract
We introduce a method to help identify how the genetic diversity of a species within a geographic region might have arisen. This problem appears, for example, in the context of identifying refugia in phylogeography, and in the conservation of biodiversity where it is a factor in nature reserve selection. Complementing current methods for measuring genetic diversity, we analyze pairwise distances between the haplotypes of a species found in a geographic region and derive a quantity, called haplotype connectivity, that aims to capture how divergent the haplotypes are relative to one another. We propose using haplotype connectivity to indicate whether, for geographic regions that harbor a highly diverse collection of haplotypes, diversity evolved inside a region over a long period of time (a "hot-spot") or is the result of a more recent mixture (a "melting-pot"). We describe how the haplotype connectivity for a collection of haplotypes can be computed efficiently and briefly discuss some related optimization problems that arise in this context. We illustrate the applicability of our method using two previously published data sets of a species of beetle from the genus Brachyderes and a species of tree from the genus Pinus.
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Affiliation(s)
- Binh Nguyen
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andreas Spillner
- Department of Mathematics and Computer Science, University of Greifswald, 17489 Greifswald, Germany
| | - Brent C Emerson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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25
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Sun GQ, Liu QX, Jin Z, Chakraborty A, Li BL. Influence of infection rate and migration on extinction of disease in spatial epidemics. J Theor Biol 2010; 264:95-103. [PMID: 20085769 DOI: 10.1016/j.jtbi.2010.01.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 12/23/2009] [Accepted: 01/07/2010] [Indexed: 11/29/2022]
Abstract
Extinction of disease can be explained by the patterns of epidemic spreading, yet the underlying causes of extinction are far from being well understood. To reveal a mechanism of disease extinction, a cellular automata model with both birth, death rate and migration is presented. We find that, in single patch, when the infection rate is small or large enough, the disease will disappear for a long time. When the invasion form is in the coexistence of stable spiral and turbulent wave state, the disease will persist. Also, we find that the migration has dual effects on the epidemic spreading. On one hand, in the extinction region of single patch, if the migration rate is large enough, there is a phase transition from the disease free to endemic state in two patches. On the other hand, migration will induce extinction in the regime, which can ensure the persistence of the disease in single patch, due to emergence of anti-phase synchrony. The results obtained well reveal the effect of infection rate and migration on the extinction of the disease, which enriches the finding in the filed of epidemiology and may provide some new ideas to control the disease in the real world.
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Affiliation(s)
- Gui-Quan Sun
- Department of Mathematics, North University of China, Taiyuan, Shan'xi 030051, People's Republic of China.
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26
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Abstract
Environmental changes have caused episodes of habitat expansions in the evolutionary history of many species. These range changes affect the dynamics of biological evolution in multiple ways. Recent microbial experiments as well as simulations suggest that enhanced genetic drift at the frontier of a two-dimensional range expansion can cause genetic sectoring patterns with fractal domain boundaries. Here, we propose and analyze a simple model of asexual biological evolution at expanding frontiers that explains these neutral patterns and predicts the effect of natural selection. We find that beneficial mutations give rise to sectors with an opening angle that depends sensitively on the selective advantage of the mutants. Deleterious mutations, on the other hand, are not able to establish a sector permanently. They can, however, temporarily "surf" on the population front, and thereby reach unusually high frequencies. As a consequence, expanding frontiers are loaded with a high fraction of mutants at mutation-selection balance. Numerically, we also determine the condition at which the wild type is lost in favor of deleterious mutants (genetic meltdown) at a growing front. Our prediction for this error threshold differs qualitatively from existing well-mixed theories, and sets tight constraints on sustainable mutation rates for populations that undergo frequent range expansions.
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Affiliation(s)
- Oskar Hallatschek
- Max Planck Research Group for Biological Physics and Evolutionary Dynamics, Max Planck Institute for Dynamics and Self-Organization, 37073 Göttingen, Germany.
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27
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The biogeographical distribution of closely related freshwater sediment bacteria is determined by environmental selection. ISME JOURNAL 2007; 1:596-605. [PMID: 18043667 DOI: 10.1038/ismej.2007.74] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The role of environmental selection in governing the structure of communities of freshwater sulfur bacteria (Achromatium spp) was experimentally tested by mixing sediments from two geographically separated lakes (Rydal Water (RY) and Hell Kettles (HK)) that harboured Achromatium spp. Community profiles of Achromatium spp in sediment microcosms at day 0 and after 60 days were compared to determine whether initial Achromatium community composition or subsequent selection by the sediment environment had greater influence in dictating the final Achromatium community structure. It was found that Achromatium spp from the HK community became established in mixed sediments at the expense of members of the RY community. This selection for the HK Achromatium community was more pronounced when sediment composition was manipulated to resemble HK sediments. Our findings definitively demonstrate that environmental selection is the primary determinant of Achromatium community structure in these sediments.
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28
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Caliebe A, Neininger R, Krawczak M, Rösler U. On the length distribution of external branches in coalescence trees: Genetic diversity within species. Theor Popul Biol 2007; 72:245-52. [PMID: 17643459 DOI: 10.1016/j.tpb.2007.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Revised: 04/30/2007] [Accepted: 05/04/2007] [Indexed: 11/23/2022]
Abstract
Let Z(n) denote the length of an external branch, chosen at random from a Kingman n-coalescent. Based on a recursion for the distribution of Z(n), we show that nZ(n) converges in distribution, as n tends to infinity, to a non-negative random variable Z with density x--> 8/(2+x)(3), x>or=0. This result facilitates the study of the time to the most recent common ancestor of a randomly chosen individual and its closest relative in a given population. This time span also reflects the maximum relatedness between a single individual and the rest of the population. Therefore, it measures the uniqueness of a random individual, a central characteristic of the genetic diversity of a population.
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Affiliation(s)
- Amke Caliebe
- Institut für Medizinische Informatik und Statistik, Christian-Albrechts-Universität Kiel, 24105 Kiel, Germany.
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29
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Ramette A, Tiedje JM. Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. MICROBIAL ECOLOGY 2007; 53:197-207. [PMID: 17106806 DOI: 10.1007/s00248-005-5010-2] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Accepted: 05/25/2005] [Indexed: 05/07/2023]
Abstract
New questions about microbial ecology and diversity combined with significant improvement in the resolving power of molecular tools have helped the reemergence of the field of prokaryotic biogeography. Here, we show that biogeography may constitute a cornerstone approach to study diversity patterns at different taxonomic levels in the prokaryotic world. Fundamental processes leading to the formation of biogeographic patterns are examined in an evolutionary and ecological context. Based on different evolutionary scenarios, biogeographic patterns are thus posited to consist of dramatic range expansion or regression events that would be the results of evolutionary and ecological forces at play at the genotype level. The deterministic or random nature of those underlying processes is, however, questioned in light of recent surveys. Such scenarios led us to predict the existence of particular genes whose presence or polymorphism would be associated with cosmopolitan taxa. Furthermore, several conceptual and methodological pitfalls that could hamper future developments of the field are identified, and future approaches and new lines of investigation are suggested.
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Affiliation(s)
- Alban Ramette
- Center for Microbial Ecology, Michigan State University, 540 Plant and Soil Sciences Building, East Lansing, MI 48824-1325, USA.
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30
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Pfaffelhuber P, Wakolbinger A. The process of most recent common ancestors in an evolving coalescent. Stoch Process Their Appl 2006. [DOI: 10.1016/j.spa.2006.04.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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de Aguiar MAM, Epstein IR, Bar-Yam Y. Analytically solvable model of probabilistic network dynamics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 72:067102. [PMID: 16486098 DOI: 10.1103/physreve.72.067102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Revised: 08/29/2005] [Indexed: 05/06/2023]
Abstract
We present a simple model of network dynamics that can be solved analytically for fully connected networks. We obtain the dynamics of response of the system to perturbations. The analytical solution is an excellent approximation for random networks. A comparison with the scale-free network, though qualitatively similar, shows the effect of distinct topology.
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Affiliation(s)
- M A M de Aguiar
- New England Complex Systems Institute, Cambridge, Massachusetts 02138, USA
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32
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Goldstone RL, Janssen MA. Computational models of collective behavior. Trends Cogn Sci 2005; 9:424-30. [PMID: 16085450 DOI: 10.1016/j.tics.2005.07.009] [Citation(s) in RCA: 195] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Revised: 06/28/2005] [Accepted: 07/22/2005] [Indexed: 11/20/2022]
Abstract
Computational models of human collective behavior offer promise in providing quantitative and empirically verifiable accounts of how individual decisions lead to the emergence of group-level organizations. Agent-based models (ABMs) describe interactions among individual agents and their environment, and provide a process-oriented alternative to descriptive mathematical models. Recent ABMs provide compelling accounts of group pattern formation, contagion and cooperation, and can be used to predict, manipulate and improve upon collective behavior. ABMs overcome an assumption that underlies much of cognitive science--that the individual is the crucial unit of cognition. The alternative advocated here is that individuals participate in collective organizations that they might not understand or even perceive, and that these organizations affect and are affected by individual behavior.
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33
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Naganuma T, Hua PN, Okamoto T, Ban S, Imura S, Kanda H. Depth distribution of euryhaline halophilic bacteria in Suribati Ike, a meromictic lake in East Antarctica. Polar Biol 2005. [DOI: 10.1007/s00300-005-0026-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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34
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Rauch EM, Bar-Yam Y. Estimating the total genetic diversity of a spatial field population from a sample and implications of its dependence on habitat area. Proc Natl Acad Sci U S A 2005; 102:9826-9. [PMID: 15998741 PMCID: PMC1174974 DOI: 10.1073/pnas.0408471102] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The total genetic diversity of a species is a key factor in its persistence and conservation. Because realistic sample sizes are far smaller than the total population, it is impractical to exhaustively characterize diversity of most populations. Here, we demonstrate the possibility of calculating the genetic diversity of a spatial population from a sample using genealogical models. We trace the history of a population by simulating the locations of the ancestors of a particular sample of the population backwards in time. We use this method to estimate the genetic diversity of the global population of Pseudomonas bacteria. The same results are obtained whether using a global sample or a subsample restricted to a particular geographic region (California). The results are also validated by comparing additional predictions of the model to the data. Furthermore, we use these results to show that the level of genetic diversity in a population depends strongly on the size of its habitat, much more strongly than does biodiversity as measured by the number of species. The strong dependence of diversity on habitat area has significant implications for conservation strategies.
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Affiliation(s)
- Erik M Rauch
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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