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Huang JF, Li SQ, Xu R, Peng YQ. East‒West genetic differentiation across the Indo-Burma hotspot: evidence from two closely related dioecious figs. BMC PLANT BIOLOGY 2023; 23:321. [PMID: 37322436 DOI: 10.1186/s12870-023-04324-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Understanding biodiversity patterns and their underlying mechanisms is of interest to ecologists, biogeographers and conservationists and is critically important for conservation efforts. The Indo-Burma hotspot features high species diversity and endemism, yet it also faces significant threats and biodiversity losses; however, few studies have explored the genetic structure and underlying mechanisms of Indo-Burmese species. Here, we conducted a comparative phylogeographic analysis of two closely related dioecious Ficus species, F. hispida and F. heterostyla, based on wide and intensive population sampling across Indo-Burma ranges, using chloroplast (psbA-trnH, trnS-trnG) and nuclear microsatellite (nSSR) markers, as well as ecological niche modeling. RESULTS The results indicated large numbers of population-specific cpDNA haplotypes and nSSR alleles in the two species. F. hispida showed slightly higher chloroplast diversity but lower nuclear diversity than F. heterostyla. Low-altitude mountainous areas of northern Indo-Burma were revealed to have high genetic diversity and high habitat suitability, suggesting potential climate refugia and conservation priority areas. Strong phylogeographic structure and a marked east‒west differentiation pattern were observed in both species, due to the interactions between biotic and abiotic factors. Interspecific dissimilarities at fine-scale genetic structure and asynchronized historical dynamics of east‒west differentiation between species were also detected, which were attributed to different species-specific traits. CONCLUSIONS We confirm hypothesized predictions that interactions between biotic and abiotic factors largely determine the patterns of genetic diversity and phylogeographic structure of Indo-Burmese plants. The east‒west genetic differentiation pattern observed in two targeted figs can be generalized to some other Indo-Burmese plants. The results and findings of this work will contribute to the conservation of Indo-Burmese biodiversity and facilitate targeted conservation efforts for different species.
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Affiliation(s)
- Jian-Feng Huang
- CAS Key Laboratory of Tropical Forest Ecoloy, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
| | - Shu-Qiong Li
- CAS Key Laboratory of Tropical Forest Ecoloy, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui Xu
- Yunnan Academy of Biodiversity/College of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
| | - Yan-Qiong Peng
- CAS Key Laboratory of Tropical Forest Ecoloy, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
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2
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Mao CX, Luo J, Zhang Y, Zhang CQ. Targeted deletion of three CYP51s in Fusarium fujikuroi and their different roles in determining sensitivity to 14α-demethylase inhibitor fungicides. PEST MANAGEMENT SCIENCE 2023; 79:1324-1330. [PMID: 36424479 DOI: 10.1002/ps.7304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 11/01/2022] [Accepted: 11/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Fusarium fujikuroi is the pathogenic agent of rice bakanae disease and has developed serious resistance to prochloraz, a 14α-demethylase inhibitor (DMI). Prochloraz resistance in F. fujikuroi is caused by cooperation between FfCyp51B with Cyp51A and shows cross-resistance only to prothioconazole but not to tebuconazole, difenoconazole, propiconazole, metconazole, hexaconazole, and triadimefon. This study aimed to analyze the functions of the three Cyp51s in F. fujikuroi, especially their role in determining sensitivity to DMIs. RESULTS The respective deletion of FfCyp51A, Cyp51B, and Cyp51C had no obvious effect on morphology, conidium germination, or pathogenicity. The involvement of growth, growth and ergosterol biosynthesis, and conidium production and ergosterol biosynthesis was observed for FfCyp51A, Cyp51B, and Cyp51C, respectively. Compared with the sensitive isolate of F. fujikuroi, the effect on sensitivity to the tested DMIs was divided into four groups: (i) both of Cyp51A and Cyp51B positively regulate the sensitivity to prochloraz and prothioconazole; (ii) Cyp51B positively regulate the sensitivity to tebuconazole and metconazole, but negatively regulate the sensitivity to difenoconazole; (iii) Cyp51A and Cyp51B play opposite roles in the sensitivity to triadimefon. Therefore, deletion of Cyp51A in F. fujikuroi confers a higher sensitivity to triadimefon, while deletion of Cyp51B results in a triadimefon-resistant mutant isolate; (iv) deletion of Cyp51B yielded a mutant isolate that was more resistant to propiconazole and hexaconazole. CONCLUSION Sophisticated interactions exist within the three Cyp51 genes to DMIs fungicides sensitivity in F. fujikuroi, and Cyp51B probably plays a more critical role than Cyp51A and Cyp51C. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Cheng-Xin Mao
- Department of Crop Protection, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Ju Luo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yu Zhang
- Department of Crop Protection, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Chuan-Qing Zhang
- Department of Crop Protection, Zhejiang Agriculture and Forest University, Hangzhou, China
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3
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Iturralde GG, Allgayer H, Valiati VH, Leal-Zanchet AM. A new species of land planarian split off from Luteostriata ernesti (Leal-Zanchet & Froehlich, 2006) based on an integrative approach. STUDIES ON NEOTROPICAL FAUNA AND ENVIRONMENT 2022. [DOI: 10.1080/01650521.2022.2113853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Affiliation(s)
- Giuly G. Iturralde
- Instituto de Pesquisas de Planárias
- Laboratório de Genética e Biologia Molecular
- Programa de Pós-Graduação em Biologia, Universidade do Vale do Rio dos Sinos – UNISINOS, São Leopoldo, Brazil
| | - Heloísa Allgayer
- Laboratório de Genética e Biologia Molecular
- Programa de Pós-Graduação em Biologia, Universidade do Vale do Rio dos Sinos – UNISINOS, São Leopoldo, Brazil
| | - Victor H. Valiati
- Laboratório de Genética e Biologia Molecular
- Programa de Pós-Graduação em Biologia, Universidade do Vale do Rio dos Sinos – UNISINOS, São Leopoldo, Brazil
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4
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Gherbawy YA, Hussein MA, Hassany NA, Shebany YM, Hassan S, El-Dawy EGAE. Phylogeny and pathogenicity of Fusarium solani species complex (FSSC) associated with potato tubers. J Basic Microbiol 2021; 61:1133-1144. [PMID: 34766353 DOI: 10.1002/jobm.202100393] [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: 08/04/2021] [Revised: 10/28/2021] [Accepted: 10/31/2021] [Indexed: 11/10/2022]
Abstract
Potato (Solanum tuberosum L.) is one of the known five crops cultivated throughout the world after corn, barley, cereals, rice, and wheat, due to its content of high carbohydrates. In developing countries, potatoes are especially had valuable contents as a rich source of starch, vitamins C and B6, and essential amino acids. Fusarium solani species complex (FSSC) is one of the prevalent pathogens of potato, causing dry rot in Upper Egypt. In this study, FSSC were isolated and identified from potato tubers based on the morphological and molecular characteristics. F. solani isolates (187) were isolated from infected and noninfected potato tubers collected from various markets in Upper Egypt. Based on the morphology observations, sequence data from amplifying β-tubulin, and specific translation elongation factor (TEF-1α) genes, all of the chosen 88 FSSC isolates were grouped into three major groups (F. keratoplasticum, F. falciforme, and F. solani). All the tested FSSC were able to produce amylases. The selected isolates were examined for their pathogenic ability on healthy potato tubers, which exhibited pathogenic effects; with lesions sizes were quite variable. F. solani SVUFs73 showed a highly virulent effect.
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Affiliation(s)
- Youssuf A Gherbawy
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt.,Applied and Environmental Microbiology Center, Faculty of Science, South Valley University, Qena, Egypt
| | - Mohamed A Hussein
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt.,Applied and Environmental Microbiology Center, Faculty of Science, South Valley University, Qena, Egypt
| | - Nabila A Hassany
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt.,Applied and Environmental Microbiology Center, Faculty of Science, South Valley University, Qena, Egypt
| | - Yassmin M Shebany
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
| | - Sabry Hassan
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
| | - Eman G A E El-Dawy
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt.,Applied and Environmental Microbiology Center, Faculty of Science, South Valley University, Qena, Egypt
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Lago-Barcia D, Silva MS, Carbayo F. Revision and description of six species of Choeradoplana (Platyhelminthes, Tricladida), with an emendation to the genus. Zookeys 2021; 1016:1-48. [PMID: 33628077 PMCID: PMC7892534 DOI: 10.3897/zookeys.1016.59617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/29/2020] [Indexed: 11/12/2022] Open
Abstract
Living representatives of the Neotropical genus Choeradoplana Graff, 1896 (Geoplaninae, Tricladida, Platyhelminthes) are easily recognized by the typical shape of the head which is laterally expanded, rolled-up, and ventrally provided with two glandular cushions. In this study, the morphology and phylogeny (cytochrome C oxidase subunit I gene) of several species of land planarians are taxonomically investigated. Four of the six species studied are new to science, namely: Ch. eudoxiae Silva & Carbayo, sp. nov., Ch. claudioi Lago-Barcia & Carbayo, sp. nov., Ch. onae Lago-Barcia & Carbayo, sp. nov., and Ch. riutortae Lago-Barcia & Carbayo, sp. nov. The species Choeradoplana albonigra and Ch. eudoxiae deviate from the usual body shape pattern in that the head does not present lateral expansions nor glandular cushions, becoming indistinguishable from its sister genus Cephaloflexa. Pseudogeoplana tristriata (Schultze & Müller, 1857) is also redescribed from a newly collected specimen and was discovered to be a member of Choeradoplana. Graff (1899) also studied another specimen that was considered to be conspecific with P. tristriata; however, in this new it is concluded that it is not conspecific but rather a new species. The name Pseudogeoplana aevipandemiae Lago-Barcia & Carbayo, sp. nov. is suggested for Graff's specimen.
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Affiliation(s)
- Domingo Lago-Barcia
- Laboratório de Ecologia e Evolução, Escola de Artes, Ciências e Humanidades (EACH), Universidade de São Paulo (USP), Av. Arlindo Bettio, 1000, São Paulo, SP, 03828-000, Brazil.,Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo (USP), Rua do Matão, Tv. 14, 321, São Paulo, SP, 05508-090, Brazil
| | - Marcos Santos Silva
- Laboratório de Ecologia e Evolução, Escola de Artes, Ciências e Humanidades (EACH), Universidade de São Paulo (USP), Av. Arlindo Bettio, 1000, São Paulo, SP, 03828-000, Brazil
| | - Fernando Carbayo
- Laboratório de Ecologia e Evolução, Escola de Artes, Ciências e Humanidades (EACH), Universidade de São Paulo (USP), Av. Arlindo Bettio, 1000, São Paulo, SP, 03828-000, Brazil.,Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo (USP), Rua do Matão, Tv. 14, 321, São Paulo, SP, 05508-090, Brazil.,Programa de Pós-Graduação em Sistemática, Taxonomia Animal e Biodiversidade, Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, Brazil
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6
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Iturralde GG, Allgayer H, Valiati VH, Leal-Zanchet AM. Seeing the true colours: three new species of Obama (Platyhelminthes:Continenticola) from remnants of Atlantic forest in southern Brazil based on an integrative approach. INVERTEBR SYST 2021. [DOI: 10.1071/is20043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The genus Obama Carbayo, Álvarez-Presas, Olivares, Marques, Froehlich & Riutort, 2013 currently comprises 41 species, most of them from Brazilian rainforests. This study describes three new species, viz. Obama autumna sp. nov., Obama leticiae sp. nov. and Obama aureolineata sp. nov., from remnants of Mixed Ombrophilous Forest in southern Brazil, based on an integrative approach and analyses their relationships within the genus. Obama autumna and O. aureolineata show distinctive colour patterns, contrasting yellow and black, which is unusual in species of the genus. The three species can be easily distinguished from their congeners by their external features and a combination of anatomical characteristics, such as the pharyngeal shape, shape and arrangement of the prostatic vesicle and anatomy of the penis papilla. The morphological hypotheses are corroborated by three species delimitation methods (ABGD, PTP and GMYC) and by phylogenetic analysis of the cytochrome c oxidase subunit I gene using maximum likelihood estimation and Bayesian inference. Furthermore, our phylogenetic analyses point out that Obama may be subdivided into three main clades, containing a variable number of well supported groups, the relationships of which remain unresolved. Obama autumna belongs to a distinct clade in relation to O. aureolineata and O. leticiae. Obama aureolineata belongs to one of the well supported groups, having a close relationship with O. apeva. Obama autumna may be more closely related to O. anthropophila and O. decidualis and O. leticiae to O. braunsi. However, the low nodal support does not allow the phylogenetic relationships of these species to be clearly established. We discuss morphological knowledge gaps in Obama, as well as issues regarding analyses based on molecular markers, which should be addressed to clarify relationships within the genus.
urn:lsid:zoobank.org:pub:9EE7316D-F0BE-49EC-BBFD-5687952D6592
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7
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Guzik MT, Stevens MI, Cooper SJB, Humphreys WF, Austin AD. Extreme genetic diversity among springtails (Collembola) in subterranean calcretes of arid Australia. Genome 2020; 64:181-195. [PMID: 32552081 DOI: 10.1139/gen-2019-0199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The subterranean islands hypothesis for calcretes of the Yilgarn region in Western Australia applies to many stygobitic (subterranean-aquatic) species that are "trapped" evolutionarily within isolated aquifers due to their aquatic lifestyles. In contrast, little is known about the distribution of terrestrial-subterranean invertebrates associated with the calcretes. We used subterranean Collembola from the Yilgarn calcretes to test the hypothesis that troglobitic species, those inhabiting the subterranean unsaturated (non-aquatic) zone of calcretes, are also restricted in their distribution and represent reciprocally monophyletic and endemic lineages. We used the barcoding fragment of the mtDNA cytochrome c oxidase subunit 1 (COI) gene from 183 individuals to reconstruct the phylogenetic history of the genus Pseudosinella Schäffer (Collembola, Lepidocyrtidae) from 10 calcretes in the Yilgarn. These calcretes represent less than 5% of the total possible calcretes in this region, yet we show that their diversity for subterranean Collembola comprises a minimum of 25 new species. Regionally, multiple levels of diversity exist in Pseudosinella, indicative of a complex evolutionary history for this genus in the Yilgarn. These species have probably been impacted by climatic oscillations, facilitating their dispersal across the landscape. The results represent a small proportion of the undiscovered diversity in Australia's arid zone.
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Affiliation(s)
- Michelle T Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, the University of Adelaide, SA 5005, Australia
| | - Mark I Stevens
- Biological and Earth Sciences, South Australian Museum, SA 5000, Australia.,University of South Australia, Clinical and Health Sciences, SA 5000, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, the University of Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - William F Humphreys
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia, Affiliate.,School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, the University of Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
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8
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Hyseni C, Garrick RC. The role of glacial-interglacial climate change in shaping the genetic structure of eastern subterranean termites in the southern Appalachian Mountains, USA. Ecol Evol 2019; 9:4621-4636. [PMID: 31031931 PMCID: PMC6476779 DOI: 10.1002/ece3.5065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/27/2019] [Accepted: 02/25/2019] [Indexed: 11/30/2022] Open
Abstract
The eastern subterranean termite, Reticulitermes flavipes, currently inhabits previously glaciated regions of the northeastern U.S., as well as the unglaciated southern Appalachian Mountains and surrounding areas. We hypothesized that Pleistocene climatic fluctuations have influenced the distribution of R. flavipes, and thus the evolutionary history of the species. We estimated contemporary and historical geographic distributions of R. flavipes by constructing Species Distribution Models (SDM). We also inferred the evolutionary and demographic history of the species using mitochondrial (cytochrome oxidase I and II) and nuclear (endo-beta-1,4-glucanase) DNA sequence data. To do this, genetic populations were delineated using Bayesian spatial-genetic clustering, competing hypotheses about population divergence were assessed using approximate Bayesian computation (ABC), and changes in population size were estimated using Bayesian skyline plots. SDMs identified areas in the north with suitable habitat during the transition from the Last Interglacial to the Last Glacial Maximum, as well as an expanding distribution from the mid-Holocene to the present. Genetic analyses identified three geographically cohesive populations, corresponding with northern, central, and southern portions of the study region. Based on ABC analyses, divergence between the Northern and Southern populations was the oldest, estimated to have occurred 64.80 thousand years ago (kya), which corresponds with the timing of available habitat in the north. The Central and Northern populations diverged in the mid-Holocene, 8.63 kya, after which the Central population continued to expand. Accordingly, phylogeographic patterns of R. flavipes in the southern Appalachians appear to have been strongly influenced by glacial-interglacial climate change. OPEN RESEARCH BADGES This article has been awarded Open Materials, Open Data Badges. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.5061/dryad.5hr7f31.
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Affiliation(s)
- Chaz Hyseni
- Department of BiologyUniversity of MississippiOxfordMississippi
| | - Ryan C. Garrick
- Department of BiologyUniversity of MississippiOxfordMississippi
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9
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Pena GA, Cavaglieri LR, Chulze SN. Fusarium species and moniliformin occurrence in sorghum grains used as ingredient for animal feed in Argentina. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:47-54. [PMID: 29797405 DOI: 10.1002/jsfa.9140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/12/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND A survey on Fusarium species and moniliformin (MON) occurrence in sorghum grains collected from one of the main sorghum-producing areas of Argentina was conducted. Also, growth of F. thapsinum, one of the main sorghum pathogens, and MON production under different water activity (aw ) conditions on a sorghum-based medium were determined. RESULTS Infection of sorghum grains by Fusarium species ranged from 82.5 to 99%; closely related species F. verticillioides, F. thapsinum and F. andiyazi were the most frequently recovered, followed by F. proliferatum and F. subglutinans. By sequencing a portion of the translation elongation factor-1α (TEF-1α) gene and by maximum parsimony analysis, F. verticillioides and closely related species were identified as F. thapsinum, F. andiyazi and F. verticillioides. Species within the F. graminearum species complex (FGSC) were isolated in high frequency. Maximum growth rates of 12 F. thapsinum strains were obtained at 0.995 aw . All evaluated strains were able to produce MON at all aw values tested, but MON production was higher at 0.995-0.982 aw . MON was detected in 41% of the samples at levels ranging from 363.2 to 914.2 µg kg-1 . CONCLUSION This study provides new data on the occurrence of Fusarium species in sorghum grains destined for animal consumption in Argentina. The production of MON at different aw values showed that the toxin can be produced under field conditions. The risk to livestock exposed to daily low levels of MON associated with the toxin occurrence in the sorghum grains analyzed is unknown. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Gabriela A Pena
- Department of Microbiology and Immunology, Faculty of Physical-Chemical and Natural Sciences, National University of Río Cuarto, Río Cuarto, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
| | - Lilia R Cavaglieri
- Department of Microbiology and Immunology, Faculty of Physical-Chemical and Natural Sciences, National University of Río Cuarto, Río Cuarto, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
| | - Sofía N Chulze
- Department of Microbiology and Immunology, Faculty of Physical-Chemical and Natural Sciences, National University of Río Cuarto, Río Cuarto, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
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10
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Álvarez‐Presas M, Mateos E, Riutort M. Hidden diversity in forest soils: Characterization and comparison of terrestrial flatworm's communities in two national parks in Spain. Ecol Evol 2018; 8:7386-7400. [PMID: 30151158 PMCID: PMC6106173 DOI: 10.1002/ece3.4178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/03/2018] [Accepted: 04/20/2018] [Indexed: 11/07/2022] Open
Abstract
Terrestrial flatworms (Platyhelminthes, Tricladida, and Geoplanidae) belong to what is known as cryptic soil fauna of humid forests and are animals not easily found or captured in traps. Nonetheless, they have been demonstrated to be good indicators of the conservation status of their habitat as well as a good model to reconstruct the recent and old events affecting biodiversity. This is mainly due to their delicate constitution, their dependence on the integrity of their habitat, and their very low dispersal capacity. At present, little is known about their communities, except for some studies performed in Brazil. In this work, we analyze for the first time in Europe terrestrial flatworm communities. We have selected two protected areas belonging to the Red Española de Parques Nacionales. Our aims include performing a first study of the species richness and community structure for European terrestrial planarian species at regional and local scale. We evaluate the effect of type of forests in the community composition and flatworms' abundance, but also have into account the phylogenetic framework (never considered in previous studies) analyzed based on molecular data. We find differences in the species composition among parks, with an astonishingly high diversity of endemic species in the Parque Nacional de Picos de Europa and an extremely low diversity of species in the Parque Nacional de Ordesa y Monte Perdido. These divergent patterns cannot be attributed to differences in physical variables, and in addition, the analyses of their phylogenetic relationships and, for a few species, their genetic structure, point to a more probable historical explanation.
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Affiliation(s)
- Marta Álvarez‐Presas
- Departament de Genètica, Microbiologia i EstadísticaInstitut de Recerca de la Biodiversitat (IRBio)Universitat de BarcelonaBarcelonaSpain
| | - Eduardo Mateos
- Departament de Biologia Evolutiva, Ecologia i Ciències AmbientalsUniversitat de BarcelonaBarcelonaSpain
| | - Marta Riutort
- Departament de Genètica, Microbiologia i EstadísticaInstitut de Recerca de la Biodiversitat (IRBio)Universitat de BarcelonaBarcelonaSpain
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11
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‘Endless forms most beautiful’: taxonomic revision of the planarian Geoplana vaginuloides(Darwin, 1844) and discovery of numerous congeners (Platyhelminthes: Tricladida). Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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12
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Riesgo A, Burke EA, Laumer C, Giribet G. Genetic variation and geographic differentiation in the marine triclad Bdelloura candida (Platyhelminthes, Tricladida, Maricola), ectocommensal on the American horseshoe crab Limulus polyphemus. MARINE BIOLOGY 2017; 164:111. [PMID: 28479611 PMCID: PMC5397438 DOI: 10.1007/s00227-017-3132-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 03/30/2017] [Indexed: 06/07/2023]
Abstract
Bdelloura candida (Platyhelminthes, Tricladida, Maricola) is an ectocommensal symbiont on the American horseshoe crab Limulus polyphemus, living on the book gills and appendages, where it spends its entire life. Given its limited dispersal capabilities and its inability to live outside of the host, we hypothesized a genetic structure that parallels that of its host. We obtained 84 planarian individuals from 19 horseshoe crabs collected from 10 sites from Massachusetts to Florida. We amplified the mitochondrial 16S rRNA and the nuclear internal transcribed spacer 2 and conducted phylogeographic and population genetic analyses, which show a clear and strong genetic break between the populations in the Atlantic and the Gulf coasts. Among the Atlantic populations, two additional, weaker barriers located along Cape Hatteras and Cape Cod restrict gene flow. Even though previous studies have suggested that the populations of the host may be in decline, those of B. candida remain stable, and some even shows signatures of expansion. Our results indicate that the phylogeography of these marine ectocommensal triclads closely mirrors that of its Limulus host, and highlight the challenges to both host and symbiont to genetically connect populations across their distribution.
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Affiliation(s)
- Ana Riesgo
- Department of Life Sciences (Invertebrate Division), The Natural History Museum of London, Cromwell Road, London, SW7 5BD UK
| | - Emily A. Burke
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138 USA
| | - Christopher Laumer
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138 USA
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Garrick RC. Genetic insights into family group co-occurrence in Cryptocercus punctulatus, a sub-social woodroach from the southern Appalachian Mountains. PeerJ 2017; 5:e3127. [PMID: 28348934 PMCID: PMC5366060 DOI: 10.7717/peerj.3127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/27/2017] [Indexed: 12/03/2022] Open
Abstract
The wood-feeding cockroach Cryptocercus punctulatus Scudder (Blattodea: Cryptocercidae) is an important member of the dead wood (saproxylic) community in montane forests of the southeastern United States. However, its population biology remains poorly understood. Here, aspects of family group co-occurrence were characterized to provide basic information that can be extended by studies on the evolution and maintenance of sub-sociality. Broad sampling across the species’ range was coupled with molecular data (mitochondrial DNA (mtDNA) sequences). The primary questions were: (1) what proportion of rotting logs contain two or more different mtDNA haplotypes and how often can this be attributed to multiple families inhabiting the same log, (2) are multi-family logs spatially clustered, and (3) what levels of genetic differentiation among haplotypes exist within a log, and how genetically similar are matrilines of co-occurring family groups? Multi-family logs were identified on the premise that three different mtDNA haplotypes, or two different haplotypes among adult females, is inconsistent with a single family group founded by one male–female pair. Results showed that of the 88 rotting logs from which multiple adult C. punctulatus were sampled, 41 logs (47%) contained two or more mtDNA haplotypes, and at least 19 of these logs (22% overall) were inferred to be inhabited by multiple families. There was no strong evidence for spatial clustering of the latter class of logs. The frequency distribution of nucleotide differences between co-occurring haplotypes was strongly right-skewed, such that most haplotypes were only one or two mutations apart, but more substantial divergences (up to 18 mutations, or 1.6% uncorrected sequence divergence) do occasionally occur within logs. This work represents the first explicit investigation of family group co-occurrence in C. punctulatus, providing a valuable baseline for follow-up studies.
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Affiliation(s)
- Ryan C Garrick
- Department of Biology, University of Mississippi , Oxford , MS , United States of America
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14
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Idiosyncratic responses of evergreen broad-leaved forest constituents in China to the late Quaternary climate changes. Sci Rep 2016; 6:31044. [PMID: 27534981 PMCID: PMC4989166 DOI: 10.1038/srep31044] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/06/2016] [Indexed: 11/24/2022] Open
Abstract
Subtropical evergreen broad-leaved forest (EBLF) is one of the most important vegetation types in China. Inferences from palaeo-biome reconstruction (PBR) and phylogeography regarding range shift history of EBLF during the late Quaternary are controversial and should be reconciled. We compared phylogeographic patterns of three EBLF constituents in China, Castanopsis tibetana, Machilus thunbergii and Schima superba. Contrary to a chorus of previous phylogeographic studies and the results of species distribution modelling (SDM) of this study (in situ survival during the LGM), the three species displayed three different phylogeographic patterns that conform to either an in situ survival model or an expansion-contraction model. These results are partially congruent with the inference of PBR that EBLF was absent to the north of 24° N at the LGM. This study suggests that the constituents of EBLF could have responded idiosyncratically to climate changes during the Late Quaternary. The community assemblages of EBLF could have been changing over time, resulting in no palaeo-analogs to modern-day EBLF, which may be the main reason responsible for the failure of PBR to detect the occurrence of EBLF north of 24° N at the LGM.
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15
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Decker P. Phylogenetic analysis of the Australian trans-Bass Strait millipede genus Pogonosternum (Carl, 1912) (Diplopoda, Polydesmida, Paradoxosomatidae) indicates multiple glacial refugia in southeastern Australia. Zookeys 2016:15-31. [PMID: 27110194 PMCID: PMC4829959 DOI: 10.3897/zookeys.578.8052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/10/2016] [Indexed: 11/12/2022] Open
Abstract
This study documents the first detailed phylogenetic analysis of an Australian paradoxosomatid millipede genus. Two mitochondrial genes (partial COI and 16S) as well as partial nuclear 28S rDNA were amplified and sequenced for 41 individuals of the southeastern Australian genus Pogonosternum Jeekel, 1965. The analysis indicates that five species groups of Pogonosternum occur across New South Wales, Victoria and Tasmania: Pogonosternumnigrovirgatum (Carl, 1912), Pogonosternumadrianae Jeekel, 1982, Pogonosternumlaetificum Jeekel, 1982 and two undescribed species. Pogonosternumconiferum (Jeekel, 1965) specimens cluster within Pogonosternumnigrovirgatum. Most of these five species groups exhibit a pattern of high intraspecific genetic variability and highly localized haplotypes, suggesting that they were confined to multiple Pleistocene refugia on the southeastern Australian mainland. The phylogenetic data also show that northwestern Tasmania was colonized by Pogonosternumnigrovirgatum, probably from central Victoria, and northeastern Tasmania by an as yet undescribed species from eastern Victoria.
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16
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Carbayo F, Francoy TM, Giribet G. Non-destructive imaging to describe a new species ofObamaland planarian (Platyhelminthes, Tricladida). ZOOL SCR 2016. [DOI: 10.1111/zsc.12175] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Fernando Carbayo
- Laboratório de Ecologia e Evolução; Escola de Artes; Ciências e Humanidades; Universidade de São Paulo - USP; Av. Arlindo Bettio 1000 CEP 03828-000 São Paulo SP Brazil
- Programa de Pós-Graduação em Zoologia; Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; Rua do Matão Trav. 14 321 Cidade Universitária CEP 05508-900 São Paulo SP Brazil
| | - Tiago M. Francoy
- Laboratório de Ecologia e Evolução; Escola de Artes; Ciências e Humanidades; Universidade de São Paulo - USP; Av. Arlindo Bettio 1000 CEP 03828-000 São Paulo SP Brazil
| | - Gonzalo Giribet
- Museum of Comparative Zoology; Department of Organismic and Evolutionary Biology; Harvard University; 26 Oxford Street Cambridge MA 02139 USA
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17
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Decker P. Integrative taxonomic revision of the polymorphic flat-millipede genera Oncocladosoma and Somethus in South Australia (Diplopoda : Polydesmida : Paradoxosomatidae). INVERTEBR SYST 2016. [DOI: 10.1071/is15047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The South Australian members of the flat-millipede genera Oncocladosoma Jeekel, 1985 and Somethus Chamberlin, 1920 are revised using an integrative approach incorporating sequence data and morphology. The partial mitochondrial cytochrome c oxidase subunit I (COI) barcoding gene and partial nuclear ribosomal 28S rRNA were amplified and sequenced for 15 Oncocladosoma specimens and 10 Somethus specimens and the datasets were used for molecular phylogenetic analysis and genetic distance determination. Both morphology and molecular data indicate that all species of Oncocladosoma fall within Somethus, and therefore, Oncocladosoma is synonymised with Somethus. Within those species supported by molecular data, features of the solenomere tip are relatively stable and useful for species identification. 28S rRNA has proven to provide sufficient nucleotide variation to provisionally discriminate species. Oncocladosoma castaneum ingens Jeekel, 1985, O. clavigerum Jeekel, 1985 and O. conigerum Jeekel, 1985 are junior synonyms of Somethus castaneus, comb. nov., and Somethus modicus Jeekel, 2002 is a synonym of S. scopiferus Jeekel, 2002. New records and electron scanning micrographs of gonopods are provided for S. castaneus, comb. nov., S. inflatus (Jeekel, 2002), comb. nov., S. lancearius Jeekel, 2002, S. scopiferus Jeekel, 2002, and Somethus grossi Jeekel, 1985, together with a key to the South Australian species of Somethus.
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18
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Schmidt SM, Lukasiewicz J, Farrer R, van Dam P, Bertoldo C, Rep M. Comparative genomics of Fusarium oxysporum f. sp. melonis reveals the secreted protein recognized by the Fom-2 resistance gene in melon. THE NEW PHYTOLOGIST 2016; 209:307-18. [PMID: 26305378 PMCID: PMC5769816 DOI: 10.1111/nph.13584] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/29/2015] [Indexed: 05/06/2023]
Abstract
Development of resistant crops is the most effective way to control plant diseases to safeguard food and feed production. Disease resistance is commonly based on resistance genes, which generally mediate the recognition of small proteins secreted by invading pathogens. These proteins secreted by pathogens are called 'avirulence' proteins. Their identification is important for being able to assess the usefulness and durability of resistance genes in agricultural settings. We have used genome sequencing of a set of strains of the melon wilt fungus Fusarium oxysporum f. sp. melonis (Fom), bioinformatics-based genome comparison and genetic transformation of the fungus to identify AVRFOM2, the gene that encodes the avirulence protein recognized by the melon Fom-2 gene. Both an unbiased and a candidate gene approach identified a single candidate for the AVRFOM2 gene. Genetic complementation of AVRFOM2 in three different race 2 isolates resulted in resistance of Fom-2-harbouring melon cultivars. AvrFom2 is a small, secreted protein with two cysteine residues and weak similarity to secreted proteins of other fungi. The identification of AVRFOM2 will not only be helpful to select melon cultivars to avoid melon Fusarium wilt, but also to monitor how quickly a Fom population can adapt to deployment of Fom-2-containing cultivars in the field.
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Affiliation(s)
- Sarah Maria Schmidt
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
| | - Joanna Lukasiewicz
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
| | - Rhys Farrer
- Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter van Dam
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
| | - Chiara Bertoldo
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
| | - Martijn Rep
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
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19
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Rossi I, Amaral SV, Ribeiro GG, Cauduro GP, Fick I, Valiati VH, Leal-Zanchet AM. Two new Geoplaninae species (Platyhelminthes: Continenticola) from Southern Brazil based on an integrative taxonomic approach. J NAT HIST 2015. [DOI: 10.1080/00222933.2015.1084057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Identification of Eastern United States Reticulitermes Termite Species via PCR-RFLP, Assessed Using Training and Test Data. INSECTS 2015; 6:524-37. [PMID: 26463202 PMCID: PMC4553497 DOI: 10.3390/insects6020524] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/30/2015] [Accepted: 06/02/2015] [Indexed: 11/29/2022]
Abstract
Reticulitermes termites play key roles in dead wood decomposition and nutrient cycling in forests. They also damage man-made structures, resulting in considerable economic loss. In the eastern United States, five species (R. flavipes, R. virginicus, R. nelsonae, R. hageni and R. malletei) have overlapping ranges and are difficult to distinguish morphologically. Here we present a molecular tool for species identification. It is based on polymerase chain reaction (PCR) amplification of a section of the mitochondrial cytochrome oxidase subunit II gene, followed by a three-enzyme restriction fragment length polymorphism (RFLP) assay, with banding patterns resolved via agarose gel electrophoresis. The assay was designed using a large set of training data obtained from a public DNA sequence database, then evaluated using an independent test panel of Reticulitermes from the Southern Appalachian Mountains, for which species assignments were determined via phylogenetic comparison to reference sequences. After refining the interpretive framework, the PCR-RFLP assay was shown to provide accurate identification of four co-occurring species (the fifth species, R. hageni, was absent from the test panel, so accuracy cannot yet be extended to training data). The assay is cost- and time-efficient, and will help improve knowledge of Reticulitermes species distributions.
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21
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Alvarez-Presas M, Mateos E, Tudó A, Jones H, Riutort M. Diversity of introduced terrestrial flatworms in the Iberian Peninsula: a cautionary tale. PeerJ 2014; 2:e430. [PMID: 24949245 PMCID: PMC4060057 DOI: 10.7717/peerj.430] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 05/26/2014] [Indexed: 11/23/2022] Open
Abstract
Many tropical terrestrial planarians (Platyhelminthes, Geoplanidae) have been introduced around the globe. One of these species is known to cause significant decline in earthworm populations, resulting in a reduction of ecological functions that earthworms provide. Flatworms, additionally, are a potential risk to other species that have the same dietary needs. Hence, the planarian invasion might cause significant economic losses in agriculture and damage to the ecosystem. In the Iberian Peninsula only Bipalium kewense Moseley, 1878 had been cited till 2007. From that year on, four more species have been cited, and several reports of the presence of these animals in particular gardens have been received. In the present study we have: (1) analyzed the animals sent by non-specialists and also the presence of terrestrial planarians in plant nurseries and garden centers; (2) identified their species through morphological and phylogenetic molecular analyses, including representatives of their areas of origin; (3) revised their dietary sources and (4) used Species Distribution Modeling (SDM) for one species to evaluate the risk of its introduction to natural areas. The results have shown the presence of at least ten species of alien terrestrial planarians, from all its phylogenetic range. International plant trade is the source of these animals, and many garden centers are acting as reservoirs. Also, landscape restoration to reintroduce autochthonous plants has facilitated their introduction close to natural forests and agricultural fields. In conclusion, there is a need to take measures on plant trade and to have special care in the treatment of restored habitats.
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Affiliation(s)
- Marta Alvarez-Presas
- Departament de Genètica, Facultat de Biologia i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain
| | - Eduardo Mateos
- Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona , Barcelona , Spain
| | - Angels Tudó
- Departament de Genètica, Facultat de Biologia i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain
| | - Hugh Jones
- Department of Zoology, The Natural History Museum , London , UK
| | - Marta Riutort
- Departament de Genètica, Facultat de Biologia i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain
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22
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Álvarez-Presas M, Sánchez-Gracia A, Carbayo F, Rozas J, Riutort M. Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism. Heredity (Edinb) 2014; 112:656-65. [PMID: 24549112 PMCID: PMC4023448 DOI: 10.1038/hdy.2014.3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 10/28/2013] [Accepted: 12/10/2013] [Indexed: 11/08/2022] Open
Abstract
The relative importance of the processes that generate and maintain biodiversity is a major and controversial topic in evolutionary biology with large implications for conservation management. The Atlantic Forest of Brazil, one of the world's richest biodiversity hot spots, is severely damaged by human activities. To formulate an efficient conservation policy, a good understanding of spatial and temporal biodiversity patterns and their underlying evolutionary mechanisms is required. With this aim, we performed a comprehensive phylogeographic study using a low-dispersal organism, the land planarian species Cephaloflexa bergi (Platyhelminthes, Tricladida). Analysing multi-locus DNA sequence variation under the Approximate Bayesian Computation framework, we evaluated two scenarios proposed to explain the diversity of Southern Atlantic Forest (SAF) region. We found that most sampled localities harbour high levels of genetic diversity, with lineages sharing common ancestors that predate the Pleistocene. Remarkably, we detected the molecular hallmark of the isolation-by-distance effect and little evidence of a recent colonization of SAF localities; nevertheless, some populations might result from very recent secondary contacts. We conclude that extant SAF biodiversity originated and has been shaped by complex interactions between ancient geological events and more recent evolutionary processes, whereas Pleistocene climate changes had a minor influence in generating present-day diversity. We also demonstrate that land planarians are an advantageous biological model for making phylogeographic and, particularly, fine-scale evolutionary inferences, and propose appropriate conservation policies.
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Affiliation(s)
- M Álvarez-Presas
- Departament de Genètica and Institut
de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona,
Barcelona, Spain
| | - A Sánchez-Gracia
- Departament de Genètica and Institut
de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona,
Barcelona, Spain
| | - F Carbayo
- Laboratório de Ecologia e
Evolução, Escola de Artes, Ciências e Humanidades, Universidade de
São Paulo, São Paulo, Brazil
| | - J Rozas
- Departament de Genètica and Institut
de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona,
Barcelona, Spain
| | - M Riutort
- Departament de Genètica and Institut
de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona,
Barcelona, Spain
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23
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Bull JK, Sunnucks P. Strong genetic structuring without assortative mating or reduced hybrid survival in an onychophoran in the Tallaganda State Forest region, Australia. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- James K. Bull
- School of Biological Sciences; Monash University; Clayton Campus Melbourne Vic. 3800 Australia
| | - Paul Sunnucks
- School of Biological Sciences; Monash University; Clayton Campus Melbourne Vic. 3800 Australia
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24
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Lee TRC, Ho SYW, Wilson GDF, Lo N. Phylogeography and diversity of the terrestrial isopodSpherillo grossus(Oniscidea: Armadillidae) on the Australian East Coast. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Timothy R. C. Lee
- School of Biological Sciences; The University of Sydney; Sydney NSW 2006 Australia
| | - Simon Y. W. Ho
- School of Biological Sciences; The University of Sydney; Sydney NSW 2006 Australia
| | | | - Nathan Lo
- School of Biological Sciences; The University of Sydney; Sydney NSW 2006 Australia
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25
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Bull JK, Sands CJ, Garrick RC, Gardner MG, Tait NN, Briscoe DA, Rowell DM, Sunnucks P. Environmental complexity and biodiversity: the multi-layered evolutionary history of a log-dwelling velvet worm in Montane Temperate Australia. PLoS One 2013; 8:e84559. [PMID: 24358365 PMCID: PMC3866147 DOI: 10.1371/journal.pone.0084559] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/15/2013] [Indexed: 11/19/2022] Open
Abstract
Phylogeographic studies provide a framework for understanding the importance of intrinsic versus extrinsic factors in shaping patterns of biodiversity through identifying past and present microevolutionary processes that contributed to lineage divergence. Here we investigate population structure and diversity of the Onychophoran (velvet worm) Euperipatoides rowelli in southeastern Australian montane forests that were not subject to Pleistocene glaciations, and thus likely retained more forest cover than systems under glaciation. Over a ~100 km transect of structurally-connected forest, we found marked nuclear and mitochondrial (mt) DNA genetic structuring, with spatially-localised groups. Patterns from mtDNA and nuclear data broadly corresponded with previously defined geographic regions, consistent with repeated isolation in refuges during Pleistocene climatic cycling. Nevertheless, some E. rowelli genetic contact zones were displaced relative to hypothesized influential landscape structures, implying more recent processes overlying impacts of past environmental history. Major impacts at different timescales were seen in the phylogenetic relationships among mtDNA sequences, which matched geographic relationships and nuclear data only at recent timescales, indicating historical gene flow and/or incomplete lineage sorting. Five major E. rowelli phylogeographic groups were identified, showing substantial but incomplete reproductive isolation despite continuous habitat. Regional distinctiveness, in the face of lineages abutting within forest habitat, could indicate pre- and/or postzygotic gene flow limitation. A potentially functional phenotypic character, colour pattern variation, reflected the geographic patterns in the molecular data. Spatial-genetic patterns broadly match those in previously-studied, co-occurring low-mobility organisms, despite a variety of life histories. We suggest that for E. rowelli, the complex topography and history of the region has led to interplay among limited dispersal ability, historical responses to environmental change, local adaptation, and some resistance to free admixture at geographic secondary contact, leading to strong genetic structuring at fine spatial scale.
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Affiliation(s)
- James K. Bull
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
- * E-mail:
| | - Chester J. Sands
- Natural Environment Research Council, British Antarctic Survey, Cambridge, United Kingdom
| | - Ryan C. Garrick
- Department of Biology, University of Mississippi, Oxford, Mississippi, United States of America
| | - Michael G. Gardner
- School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - Noel N. Tait
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - David A. Briscoe
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - David M. Rowell
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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26
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Potts AJ, Hedderson TA, Cowling RM. Testing large-scale conservation corridors designed for patterns and processes: comparative phylogeography of three tree species. DIVERS DISTRIB 2013. [DOI: 10.1111/ddi.12113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Alastair J. Potts
- Department of Biological Sciences; Bolus Herbarium; University of Cape Town; Cape Town Western Cape 7700 South Africa
| | - Terry A. Hedderson
- Department of Biological Sciences; Bolus Herbarium; University of Cape Town; Cape Town Western Cape 7700 South Africa
| | - Richard M. Cowling
- Department of Botany; Nelson Mandela Metropolitan University; Port Elizabeth Eastern Cape 6031 South Africa
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27
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Carbayo F, Álvarez-Presas M, Olivares CT, Marques FPL, Froehlich EM, Riutort M. Molecular phylogeny of Geoplaninae (Platyhelminthes) challenges current classification: proposal of taxonomic actions. ZOOL SCR 2013. [DOI: 10.1111/zsc.12019] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Fernando Carbayo
- Laboratório de Ecologia e Evolução; Escola de Artes, Ciências e Humanidades (EACH); Universidade de São Paulo (USP); Av. Arlindo Bettio, 1000; São Paulo; SP; 03828-000; Brazil
| | - Marta Álvarez-Presas
- Departament de Genètica; Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona; Avinguda Diagonal; Barcelona; 643 E-08028; Spain
| | - Cláudia T. Olivares
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo (USP); Rua do Matão; Travessa 14 Cidade Universitária; São Paulo; SP; 05508-900; Brazil
| | - Fernando P. L. Marques
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo (USP); Rua do Matão; Travessa 14 Cidade Universitária; São Paulo; SP; 05508-900; Brazil
| | - Eudóxia M. Froehlich
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo (USP); Rua do Matão; Travessa 14 Cidade Universitária; São Paulo; SP; 05508-900; Brazil
| | - Marta Riutort
- Departament de Genètica; Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona; Avinguda Diagonal; Barcelona; 643 E-08028; Spain
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28
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Pavlova A, Amos JN, Joseph L, Loynes K, Austin JJ, Keogh JS, Stone GN, Nicholls JA, Sunnucks P. PERCHED AT THE MITO-NUCLEAR CROSSROADS: DIVERGENT MITOCHONDRIAL LINEAGES CORRELATE WITH ENVIRONMENT IN THE FACE OF ONGOING NUCLEAR GENE FLOW IN AN AUSTRALIAN BIRD. Evolution 2013; 67:3412-28. [DOI: 10.1111/evo.12107] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 03/04/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Alexandra Pavlova
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
| | - J. Nevil Amos
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
| | - Leo Joseph
- Australian National Wildlife Collection; CSIRO Ecosystem Sciences; GPO Box 1700 Canberra Australian Capital Territory 2601 Australia
| | - Kate Loynes
- Division of Evolution; Ecology and Genetics, Building 116, Daley Road, Research School of Biology, The Australian National University; Canberra Australian Capital Territory 0200 Australia
| | - Jeremy J. Austin
- Australian Centre for Ancient DNA (ACAD); School of Earth & Environmental Sciences, The University of Adelaide; Darling Building North Terrace Campus South Australia 5005 Australia
- Sciences Department; Museum Victoria; Carlton Gardens Melbourne Victoria 3001 Australia
| | - J. Scott Keogh
- Division of Evolution; Ecology and Genetics, Building 116, Daley Road, Research School of Biology, The Australian National University; Canberra Australian Capital Territory 0200 Australia
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road Edinburgh EH9 3JT Scotland
| | - James A. Nicholls
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road Edinburgh EH9 3JT Scotland
| | - Paul Sunnucks
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
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Álvarez-Presas M, Mateos E, Vila-Farré M, Sluys R, Riutort M. Evidence for the persistence of the land planarian species Microplana terrestris (Müller, 1774) (Platyhelminthes, Tricladida) in microrefugia during the Last Glacial Maximum in the northern section of the Iberian Peninsula. Mol Phylogenet Evol 2012; 64:491-9. [DOI: 10.1016/j.ympev.2012.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 04/26/2012] [Accepted: 05/02/2012] [Indexed: 11/29/2022]
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Phylogeography of Saproxylic and Forest Floor Invertebrates from Tallaganda, South-eastern Australia. INSECTS 2012; 3:270-94. [PMID: 26467960 PMCID: PMC4553628 DOI: 10.3390/insects3010270] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/21/2012] [Accepted: 02/22/2012] [Indexed: 12/02/2022]
Abstract
The interaction between physiogeographic landscape context and certain life history characteristics, particularly dispersal ability, can generate predictable outcomes for how species responded to Pleistocene (and earlier) climatic changes. Furthermore, the extent to which impacts of past landscape-level changes ‘scale-up’ to whole communities has begun to be addressed via comparative phylogeographic analyses of co-distributed species. Here we present an overview of a body of research on flightless low-mobility forest invertebrates, focusing on two springtails and two terrestrial flatworms, from Tallaganda on the Great Dividing Range of south-eastern Australia. These species are distantly-related, and represent contrasting trophic levels (i.e., slime-mold-grazers vs. higher-level predators). However, they share an association with the dead wood (saproxylic) habitat. Spatial patterns of intraspecific genetic diversity partly conform to topography-based divisions that circumscribe five ‘microgeographic regions’ at Tallaganda. In synthesizing population processes and past events that generated contemporary spatial patterns of genetic diversity in these forest floor invertebrates, we highlight cases of phylogeographic congruence, pseudo-congruence, and incongruence. Finally, we propose conservation-oriented recommendations for the prioritisation of areas for protection.
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BEAVIS AMBERS, SUNNUCKS PAUL, ROWELL DAVIDM. Microhabitat preferences drive phylogeographic disparities in two Australian funnel web spiders. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01753.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Smith CI, Tank S, Godsoe W, Levenick J, Strand E, Esque T, Pellmyr O. Comparative phylogeography of a coevolved community: concerted population expansions in Joshua trees and four yucca moths. PLoS One 2011; 6:e25628. [PMID: 22028785 PMCID: PMC3196504 DOI: 10.1371/journal.pone.0025628] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 09/08/2011] [Indexed: 01/26/2023] Open
Abstract
Comparative phylogeographic studies have had mixed success in identifying common phylogeographic patterns among co-distributed organisms. Whereas some have found broadly similar patterns across a diverse array of taxa, others have found that the histories of different species are more idiosyncratic than congruent. The variation in the results of comparative phylogeographic studies could indicate that the extent to which sympatrically-distributed organisms share common biogeographic histories varies depending on the strength and specificity of ecological interactions between them. To test this hypothesis, we examined demographic and phylogeographic patterns in a highly specialized, coevolved community--Joshua trees (Yucca brevifolia) and their associated yucca moths. This tightly-integrated, mutually interdependent community is known to have experienced significant range changes at the end of the last glacial period, so there is a strong a priori expectation that these organisms will show common signatures of demographic and distributional changes over time. Using a database of >5000 GPS records for Joshua trees, and multi-locus DNA sequence data from the Joshua tree and four species of yucca moth, we combined paleaodistribution modeling with coalescent-based analyses of demographic and phylgeographic history. We extensively evaluated the power of our methods to infer past population size and distributional changes by evaluating the effect of different inference procedures on our results, comparing our palaeodistribution models to Pleistocene-aged packrat midden records, and simulating DNA sequence data under a variety of alternative demographic histories. Together the results indicate that these organisms have shared a common history of population expansion, and that these expansions were broadly coincident in time. However, contrary to our expectations, none of our analyses indicated significant range or population size reductions at the end of the last glacial period, and the inferred demographic changes substantially predate Holocene climate changes.
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MACQUEEN PEGGY, SEDDON JENNIFERM, GOLDIZEN ANNEW. Effects of historical forest contraction on the phylogeographic structure of Australo-Papuan populations of the red-legged pademelon (Macropodidae: Thylogale stigmatica). AUSTRAL ECOL 2011. [DOI: 10.1111/j.1442-9993.2011.02309.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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COOPER STEVENJB, HARVEY MARKS, SAINT KATHLEENM, MAIN BARBARAY. Deep phylogeographic structuring of populations of the trapdoor spider Moggridgea tingle (Migidae) from southwestern Australia: evidence for long-term refugia within refugia. Mol Ecol 2011; 20:3219-36. [DOI: 10.1111/j.1365-294x.2011.05160.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Marske KA, Leschen RA, Buckley TR. Reconciling phylogeography and ecological niche models for New Zealand beetles: Looking beyond glacial refugia. Mol Phylogenet Evol 2011; 59:89-102. [DOI: 10.1016/j.ympev.2011.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 11/12/2010] [Accepted: 01/13/2011] [Indexed: 02/07/2023]
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Griffiths KE, Trueman JW, Brown GR, Peakall R. Molecular genetic analysis and ecological evidence reveals multiple cryptic species among thynnine wasp pollinators of sexually deceptive orchids. Mol Phylogenet Evol 2011; 59:195-205. [PMID: 21310250 DOI: 10.1016/j.ympev.2011.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 01/18/2011] [Accepted: 02/02/2011] [Indexed: 10/18/2022]
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Evidence for population fragmentation within a subterranean aquatic habitat in the Western Australian desert. Heredity (Edinb) 2011; 107:215-30. [PMID: 21343944 DOI: 10.1038/hdy.2011.6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The evolution of subterranean animals following multiple colonisation events from the surface has been well documented, but few studies have investigated the potential for species diversification within cavernicolous habitats. Isolated calcrete (carbonate) aquifers in central Western Australia have been shown to contain diverse assemblages of aquatic subterranean invertebrate species (stygofauna) and to offer a unique model system for exploring the mechanisms of speciation in subterranean ecosystems. In this paper, we investigated the hypothesis that microallopatric speciation processes (fragmentation and isolation by distance (IBD)) occur within calcretes using a comparative phylogeographic study of three stygobiontic diving beetle species, one amphipod species and a lineage of isopods. Specimens were sequenced for the mitochondrial cytochrome c oxidase 1 gene from three main sites: Quandong Well, Shady Well (SW) and Mt. Windarra (MW), spanning a 15 km region of the Laverton Downs Calcrete. Phylogenetic and haplotype network analyses revealed that each species possessed a single divergent clade of haplotypes that were present only at the southern MW site, despite the existence of other haplotypes at MW that were shared with SW. IBD between MW and SW was evident, but the common phylogeographic pattern most likely resulted from fragmentation, possibly by a salt lake adjacent to MW. These findings suggest that microallopatric speciation within calcretes may be a significant diversifying force, although the proportion of stygofauna species that may have resulted from in situ speciation in this system remains to be determined.
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ÁLVAREZ-PRESAS M, CARBAYO F, ROZAS J, RIUTORT M. Land planarians (Platyhelminthes) as a model organism for fine-scale phylogeographic studies: understanding patterns of biodiversity in the Brazilian Atlantic Forest hotspot. J Evol Biol 2011; 24:887-96. [DOI: 10.1111/j.1420-9101.2010.02220.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lemmon AR, Lemmon EM. A likelihood framework for estimating phylogeographic history on a continuous landscape. Syst Biol 2010; 57:544-61. [PMID: 18686193 DOI: 10.1080/10635150802304761] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Due to lack of an adequate statistical framework, biologists studying phylogeography are abandoning traditional methods of estimating phylogeographic history in favor of statistical methods designed to test a priori hypotheses. These new methods may, however, have limited descriptive utility. Here, we develop a new statistical framework that can be used to both test a priori hypotheses and estimate phylogeographic history of a gene (and the statistical confidence in that history) in the absence of such hypotheses. The statistical approach concentrates on estimation of geographic locations of the ancestors of a set of sampled organisms. Now we use (2) to derive the likelihood of the ancestral geographic coordinates and the value of the scaled dispersal parameter, given the observed geographic coordinates (assuming known topology and branch lengths). Using a maximum likelihood approach, which is implemented in the new program PhyloMapper, we apply this statistical framework to a 246-taxon mitochondrial genealogy of North American chorus frogs, focusing in detail on one of these species. We demonstrate three lines of evidence for recent northward expansion of the mitochondrion of the coastal clade of Pseudacris feriarum: higher per-generation dispersal distance in the recently colonized region, a noncentral ancestral location, and directional migration. After illustrating one method of accommodating phylogenetic uncertainty, we conclude by discussing how extensions of this framework could function to incorporate a priori ecological and geological information into phylogeographic analyses.
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Affiliation(s)
- Alan R Lemmon
- Section of Integrative Biology, University of Texas-Austin, Austin, Texas 78712, USA.
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Garrick RC, Sunnucks P, Dyer RJ. Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation. BMC Evol Biol 2010; 10:118. [PMID: 20429950 PMCID: PMC2880299 DOI: 10.1186/1471-2148-10-118] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 04/30/2010] [Indexed: 01/25/2023] Open
Abstract
Background A widely-used approach for screening nuclear DNA markers is to obtain sequence data and use bioinformatic algorithms to estimate which two alleles are present in heterozygous individuals. It is common practice to omit unresolved genotypes from downstream analyses, but the implications of this have not been investigated. We evaluated the haplotype reconstruction method implemented by PHASE in the context of phylogeographic applications. Empirical sequence datasets from five non-coding nuclear loci with gametic phase ascribed by molecular approaches were coupled with simulated datasets to investigate three key issues: (1) haplotype reconstruction error rates and the nature of inference errors, (2) dataset features and genotypic configurations that drive haplotype reconstruction uncertainty, and (3) impacts of omitting unresolved genotypes on levels of observed phylogenetic diversity and the accuracy of downstream phylogeographic analyses. Results We found that PHASE usually had very low false-positives (i.e., a low rate of confidently inferring haplotype pairs that were incorrect). The majority of genotypes that could not be resolved with high confidence included an allele occurring only once in a dataset, and genotypic configurations involving two low-frequency alleles were disproportionately represented in the pool of unresolved genotypes. The standard practice of omitting unresolved genotypes from downstream analyses can lead to considerable reductions in overall phylogenetic diversity that is skewed towards the loss of alleles with larger-than-average pairwise sequence divergences, and in turn, this causes systematic bias in estimates of important population genetic parameters. Conclusions A combination of experimental and computational approaches for resolving phase of segregating sites in phylogeographic applications is essential. We outline practical approaches to mitigating potential impacts of computational haplotype reconstruction on phylogeographic inferences. With targeted application of laboratory procedures that enable unambiguous phase determination via physical isolation of alleles from diploid PCR products, relatively little investment of time and effort is needed to overcome the observed biases.
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Affiliation(s)
- Ryan C Garrick
- Department of Biology, Virginia Commonwealth University, Richmond, 23284, USA.
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Inference of population history by coupling exploratory and model-driven phylogeographic analyses. Int J Mol Sci 2010; 11:1190-227. [PMID: 20480016 PMCID: PMC2871112 DOI: 10.3390/ijms11041190] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/18/2010] [Accepted: 03/19/2010] [Indexed: 11/16/2022] Open
Abstract
Understanding the nature, timing and geographic context of historical events and population processes that shaped the spatial distribution of genetic diversity is critical for addressing questions relating to speciation, selection, and applied conservation management. Cladistic analysis of gene trees has been central to phylogeography, but when coupled with approaches that make use of different components of the information carried by DNA sequences and their frequencies, the strength and resolution of these inferences can be improved. However, assessing concordance of inferences drawn using different analytical methods or genetic datasets, and integrating their outcomes, can be challenging. Here we overview the strengths and limitations of different types of genetic data, analysis methods, and approaches to historical inference. We then turn our attention to the potentially synergistic interactions among widely-used and emerging phylogeographic analyses, and discuss some of the ways that spatial and temporal concordance among inferences can be assessed. We close this review with a brief summary and outlook on future research directions.
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Malekian M, Cooper SJB, Carthew SM. Phylogeography of the Australian sugar glider (Petaurus breviceps): evidence for a new divergent lineage in eastern Australia. AUST J ZOOL 2010. [DOI: 10.1071/zo10016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The sugar glider (Petaurus breviceps) shows considerable variation in external morphology and mitochondrial DNA (mtDNA) diversity across its distribution in New Guinea and Australia. Here we investigate the phylogeography of P. breviceps in Australia using data from two mitochondrial genes (ND2 and ND4) and a nuclear gene (ω-globin). Phylogenetic analyses revealed the existence of two divergent mtDNA clades that are distributed over distinct geographical regions, one from coastal New South Wales and south-eastern Queensland and a second over the remaining distributional range of the species in Australia. The two groups generally had distinct ω-globin haplotypes that differed by one or two mutational steps. Analyses of Molecular Variation further supported the presence of at least two populations, accounting for 84.8% of the total mtDNA variation and 44% of the ω-globin variation. The general concordance of phylogeographic and population analyses suggests that population subdivision, possibly resulting from the combined influences of aridification after the Pliocene and uplift of the Great Dividing Range has impacted the evolution of P. breviceps. Our results also show that the geographical distribution of the two evolutionary lineages does not correspond with the distribution of the current morphological subspecies and we further propose that they be considered as separate Evolutionarily Significant Units for the purposes of conservation management.
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Mateos E, Cabrera C, Carranza S, Riutort M. Molecular analysis of the diversity of terrestrial planarians (Platyhelminthes, Tricladida, Continenticola) in the Iberian Peninsula. ZOOL SCR 2009. [DOI: 10.1111/j.1463-6409.2009.00398.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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MACQUEEN PEGGY, GOLDIZEN ANNEW, SEDDON JENNIFERM. Response of a southern temperate marsupial, the Tasmanian pademelon (Thylogale billardierii), to historical and contemporary forest fragmentation. Mol Ecol 2009; 18:3291-306. [DOI: 10.1111/j.1365-294x.2009.04262.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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HANSEN BIRGITAD, HARLEY DANIELKP, LINDENMAYER DAVIDB, TAYLOR ANDREAC. Population genetic analysis reveals a long-term decline of a threatened endemic Australian marsupial. Mol Ecol 2009; 18:3346-62. [DOI: 10.1111/j.1365-294x.2009.04269.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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46
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Kearney M, Blacket MJ. The evolution of sexual and parthenogenetic Warramaba: a window onto Plio-Pleistocene diversification processes in an arid biome. Mol Ecol 2009; 17:5257-75. [PMID: 19120998 DOI: 10.1111/j.1365-294x.2008.03991.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Environmental changes over the Plio-Pleistocene have been key drivers of speciation patterns and genetic diversification in high-latitude and mesic environments, yet comparatively little is known about the evolutionary history of species in arid environments. We applied phylogenetic and phylogeographic analyses to understand the evolutionary history of Warramaba grasshoppers from the Australian arid zone, a group including sexual and parthenogenetic lineages. Sequence data (mitochondrial COI) showed that the four major sexual lineages within Warramaba most likely diverged in the Pliocene, around 2-7 million years ago. All sexual lineages exhibited considerable phylogenetic structure. Detailed analyses of the hybrid parthenogenetic species W. virgo and its sexual progenitors showed a pattern of high phylogenetic diversity and phylogeographic structure in northern lineages, and low diversity and evidence for recent expansion in southern lineages. Northern sexual lineages persisted in localized refugia over the Pleistocene, with sustained barriers promoting divergence over this period. Southern parts of the present range became periodically unsuitable during the Pleistocene, and it is into this region that parthenogenetic lineages have expanded. Our results strongly parallel those for sexual and parthenogenetic lineages of the gecko Heteronotia from the same region, indicating a highly general effect of Plio-Pleistocene environmental change on diversification processes in arid Australia.
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Affiliation(s)
- Michael Kearney
- Department of Zoology, University of Melbourne, Parkville, Vic. 3010, Australia.
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Maciá-Vicente JG, Jansson HB, Talbot NJ, Lopez-Llorca LV. Real-time PCR quantification and live-cell imaging of endophytic colonization of barley (Hordeum vulgare) roots by Fusarium equiseti and Pochonia chlamydosporia. THE NEW PHYTOLOGIST 2009; 182:213-228. [PMID: 19170898 DOI: 10.1111/j.1469-8137.2008.02743.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
*New tools were developed for the study of the endophytic development of the fungal species Fusarium equiseti and Pochonia chlamydosporia in barley (Hordeum vulgare) roots. These were applied to monitor the host colonization patterns of these potential candidates for biocontrol of root pathogens. * Molecular beacons specific for either F. equiseti or P. chlamydosporia were designed and used in real-time polymerase chain reaction (PCR) quantification of fungal populations in roots. Genetic transformation of isolates with the green fluorescent protein (GFP) gene was carried out using an Agrobacterium tumefaciens-mediated transformation protocol, and spatial patterns of root colonization were investigated by laser confocal microscopy. * Quantification of endophytes by real-time PCR in roots of barley gave similar results for all fungi, and was more accurate than culturing methods. Conversely, monitoring of root colonization by GFP-expressing transformants showed differences in the endophytic behaviours of the two species, and provided evidence of a plant response against endophyte colonization. * Both F. equiseti and P. chlamydosporia colonized barley roots endophytically, escaping attempts by the host to prevent fungal growth within root tissues. This strongly supports a balanced antagonism between the virulence of the colonizing endophyte and the plant defence response. Development of real-time PCR techniques and GFP transformants of these fungal species will facilitate future work to determine their biocontrol capacity.
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Affiliation(s)
- Jose G Maciá-Vicente
- Laboratory of Plant Pathology, Department of Marine Sciences and Applied Biology, Multidisciplinary Institute for Environmental Studies (MIES) Ramón Margalef, University of Alicante, Apto 99, 03080 Alicante, Spain
| | - Hans-Börje Jansson
- Laboratory of Plant Pathology, Department of Marine Sciences and Applied Biology, Multidisciplinary Institute for Environmental Studies (MIES) Ramón Margalef, University of Alicante, Apto 99, 03080 Alicante, Spain
| | - Nicholas J Talbot
- School of Biosciences, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK
| | - Luis V Lopez-Llorca
- Laboratory of Plant Pathology, Department of Marine Sciences and Applied Biology, Multidisciplinary Institute for Environmental Studies (MIES) Ramón Margalef, University of Alicante, Apto 99, 03080 Alicante, Spain
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Beheregaray LB. Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere. Mol Ecol 2008; 17:3754-74. [PMID: 18627447 DOI: 10.1111/j.1365-294x.2008.03857.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phylogeography is a young, vigorous and integrative field of study that uses genetic data to understand the history of populations. This field has recently expanded into many areas of biology and also into several historical disciplines of Earth sciences. In this review, I present a numerical synthesis of the phylogeography literature based on an examination of over 3000 articles published during the first 20 years of the field (i.e. from 1987 to 2006). Information from several topics needed to evaluate the progress, tendencies and deficiencies of the field is summarized for 10 major groups of organisms and at a global scale. The topics include the geography of phylogeographic surveys, comparative nature of studies, temporal scales and major environments investigated, and genetic markers used. I also identify disparities in research productivity between the developing and the developed world, and propose ways to reduce some of the challenges faced by phylogeographers from less affluent countries. Phylogeography has experienced explosive growth in recent years fuelled by developments in DNA technology, theory and statistical analysis. I argue that the intellectual maturation of the field will eventually depend not only on these recent developments, but also on syntheses of comparative information across different regions of the globe. For this to become a reality, many empirical phylogeographic surveys in regions of the Southern Hemisphere (and in developing countries of the Northern Hemisphere) are needed. I expect the information and views presented here will assist in promoting international collaborative work in phylogeography and in guiding research efforts at both regional and global levels.
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Affiliation(s)
- Luciano B Beheregaray
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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Byrne M, Yeates DK, Joseph L, Kearney M, Bowler J, Williams MAJ, Cooper S, Donnellan SC, Keogh JS, Leys R, Melville J, Murphy DJ, Porch N, Wyrwoll KH. Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota. Mol Ecol 2008; 17:4398-417. [PMID: 18761619 DOI: 10.1111/j.1365-294x.2008.03899.x] [Citation(s) in RCA: 321] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The integration of phylogenetics, phylogeography and palaeoenvironmental studies is providing major insights into the historical forces that have shaped the Earth's biomes. Yet our present view is biased towards arctic and temperate/tropical forest regions, with very little focus on the extensive arid regions of the planet. The Australian arid zone is one of the largest desert landform systems in the world, with a unique, diverse and relatively well-studied biota. With foci on palaeoenvironmental and molecular data, we here review what is known about the assembly and maintenance of this biome in the context of its physical history, and in comparison with other mesic biomes. Aridification of Australia began in the Mid-Miocene, around 15 million years, but fully arid landforms in central Australia appeared much later, around 1-4 million years. Dated molecular phylogenies of diverse taxa show the deepest divergences of arid-adapted taxa from the Mid-Miocene, consistent with the onset of desiccation. There is evidence of arid-adapted taxa evolving from mesic-adapted ancestors, and also of speciation within the arid zone. There is no evidence for an increase in speciation rate during the Pleistocene, and most arid-zone species lineages date to the Pliocene or earlier. The last 0.8 million years have seen major fluctuations of the arid zone, with large areas covered by mobile sand dunes during glacial maxima. Some large, vagile taxa show patterns of recent expansion and migration throughout the arid zone, in parallel with the ice sheet-imposed range shifts in Northern Hemisphere taxa. Yet other taxa show high lineage diversity and strong phylogeographical structure, indicating persistence in multiple localised refugia over several glacial maxima. Similar to the Northern Hemisphere, Pleistocene range shifts have produced suture zones, creating the opportunity for diversification and speciation through hybridisation, polyploidy and parthenogenesis. This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes. There is a clear need for more detailed and targeted phylogeographical studies of Australia's arid biota and we suggest a framework and a set of a priori hypotheses by which to proceed.
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Affiliation(s)
- M Byrne
- Science Division, Department of Environment and Conservation, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia.
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