High-Throughput Sequencing in Studies of Lichen Population Biology

Werth, Silke; Miao, Vivian; Jónsson, Zophonı́as O.; Andrésson, Ólafur S.

doi:10.1007/978-81-322-2235-4_4

Cited by 6 publications

(4 citation statements)

References 229 publications

(153 reference statements)

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“…Future fieldwork and research must increase the sampling effort in the easternmost distribution range of the target species, and take advantage of high‐throughput sequencing (e.g. genotyping by sequencing and genome‐scale methods, reviewed in Werth, Miao, Jónsson, & Andrésson, ) to produce greater amounts of information. Inferences based on an extended dataset will provide valuable insights into population structure, including questions about how and when the two haplogroups first segregated, the geographical limits of the contact zone, the historical directionality of gene flow, and the levels of among‐population genetic differentiation which are predicted to be high for species inhabiting substrate archipelagos such as gypsum (Moore et al., ).…”

Section: Discussionmentioning

confidence: 99%

How did terricolous fungi originate in the Mediterranean region? A case study with a gypsicolous lichenized species

Chiva

Garrido‐Benavent

Moya

et al. 2019

Journal of Biogeography

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Aim: The historical causes responsible for the wide distribution of terricolous, crustose lichenized fungi across the Mediterranean Basin and the Canary Islands have never been explored. Here, we used the terricolous, circum-Mediterranean/Macaronesian species Buellia zoharyi (Caliciaceae, Ascomycota) to infer the time frame, and the climatic, geological and ecological factors influencing the origin and current spatial distribution of this species. Location: Mediterranean Basin and Canary Islands. Methods: Data from two nuclear markers (nrITS and tef1) obtained from 226 specimens of 23 populations covering the entire distribution range of B. zoharyi were used to calculate genetic diversity indices and haplotype networks and to investigate population size changes and structure. Three secondary calibrations were used to estimate the timing of the divergence of B. zoharyi from its hypothesized sister species, B. elegans, and the diversification of B. zoharyi. Results: We found low nucleotide diversity and two geographically differentiated haplogroups, with a contact zone in the Iberian Peninsula. The three dating approaches established wide temporal windows for the divergence of B. zoharyi from B. elegans (Eocene-Pliocene) and its diversification (Miocene-Pleistocene). These intervals overlap with the origin and diversification ages found in other lichen-forming fungi and vascular plants inhabiting the Mediterranean region. Main conclusions: In the context of lichen biogeography, our results support ecological specialization as well as geological and climatic events as drivers of the evolutionary history of B. zoharyi in the Mediterranean. In particular, the combined effects of the Messinian salinity crisis and the subsequent Zanclean Flood on the availability of gypsum soils in the Mediterranean Basin, as well as the Quaternary climatic oscillations, seem to have collectively shaped the amount and distribution of B. zoharyi population genetic diversity. K E Y W O R D S biogeography, Buellia zoharyi, ecological speciation, gypsum soils, Messinian salinity crisis, Zanclean Flood

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Section: Discussionmentioning

confidence: 99%

How did terricolous fungi originate in the Mediterranean region? A case study with a gypsicolous lichenized species

Chiva

Garrido‐Benavent

Moya

et al. 2019

Journal of Biogeography

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“…Several authors have also uncovered the promiscuity of phycobionts associated with lichen thalli using analyses of conformation polymorphism of the ITS fragments [ 11 , 23 ], microsatellites [ 24 ], and microscopic examinations [ 6 , 25 ]. Because high-throughput sequencing (HTS) allows the detection of a vast number of genotypes, which otherwise remain underestimated with conventional PCR amplifications [ 26 ], meta-community studies represent a potential tool to address questions about lichen phycobiont populations and their interactions with the surrounding environments [ 27 ].…”

Section: Introductionmentioning

confidence: 99%

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses

et al. 2017

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The current literature reveals that the intrathalline coexistence of multiple microalgal taxa in lichens is more common than previously thought, and additional complexity is supported by the coexistence of bacteria and basidiomycete yeasts in lichen thalli. This replaces the old paradigm that lichen symbiosis occurs between a fungus and a single photobiont. The lichen Ramalina farinacea has proven to be a suitable model to study the multiplicity of microalgae in lichen thalli due to the constant coexistence of Trebouxia sp. TR9 and T. jamesii in long-distance populations. To date, studies involving phycobiont diversity within entire thalli are based on Sanger sequencing, but this method seems to underestimate the diversity. Here, we aim to analyze both the microalgal diversity and its community structure in a single thallus of the lichen R. farinacea by applying a 454 pyrosequencing approach coupled with a careful ad hoc-performed protocol for lichen sample processing prior to DNA extraction. To ascertain the reliability of the pyrosequencing results and the applied bioinformatics pipeline results, the thalli were divided into three sections (apical, middle and basal zones), and a mock community sample was used. The developed methodology allowed 40448 filtered algal reads to be obtained from a single lichen thallus, which encompassed 31 OTUs representative of different microalgae genera. In addition to corroborating the coexistence of the two Trebouxia sp. TR9 and T. jamesii taxa in the same thallus, this study showed a much higher microalgal diversity associated with the lichen. Along the thallus ramifications, we also detected variations in phycobiont distribution that might correlate with different microenvironmental conditions. These results highlight R. farinacea as a suitable material for studying microalgal diversity and further strengthen the concept of lichens as multispecies microecosystems. Future analyses will be relevant to ecophysiological and evolutionary studies to understand the roles of the multiple photobionts in lichen symbioses.

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“…The genetic diversity of natural populations results from cumulative effects of historical and present-day processes (Hewitt 2000;Frankman et al 2010); the latter include, for example, changes in the current habitat conditions of the environment, which may influence dispersal, growth and vitality of species. Estimating the genetic variability within and among populations, and revealing genetic patterns of populations, improves out understanding of the population history, genetic differentiation and gene flow among populations (Werth et al 2015). Population genetics also contributes to our knowledge of evolutionary processes, ecology, and conservation biology; for example, knowledge of genetic structure and variation of natural populations could be helpful in predicting the population fate in fluctuating environment (e.g., climate change or forest management) or estimating the effective population size of populations (Scheidegger and Werth 2009;Ouborg 2010).…”

Section: Introductionmentioning

confidence: 99%

Unconstrained gene flow between populations of a widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia

et al. 2018

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Few studies have investigated the genetic diversity of populations of common and widespread lichenized fungi using microsatellite markers, especially the relationships between different measures of genetic diversity and environmental heterogeneity. The main aim of our study was to investigate the population genetics of a widespread and mainly clonally reproducing Usnea subfloridana at the landscape scale, focusing on the comparison of lichen populations within hemiboreal forest stands. Particular attention has been paid to the genetic differentiation of lichen populations in two geographically distinct regions in Estonia and the relationships between forest characteristics and measures of genetic diversity. We genotyped 578 Usnea thalli from eleven lichen populations using seven specific fungal microsatellite markers. Measures of genetic diversity (allelic richness, Shannon's information index, Nei's unbiased genetic diversity, clonal diversity, the number of multilocus genotypes, the number of private alleles, and the minimum number of colonization events) were calculated and compared between Usnea populations. Shared haplotypes, gene flow and AMOVA analyses suggest that unconstrained gene flow and exchange of multilocus genotypes exist between the two geographically remote regions in Estonia. Stand age, mean circumference of the host tree, size of forest site and tree species composition did not show any significant influence on allelic richness, Shannon's information index, Nei's unbiased genetic diversity, clonal diversity, the number of private alleles, and the minimum number of colonization events of U. subfloridana populations. Therefore it was concluded that other factors of habitat heterogeneity could probably have a more significant effect on population genetics of U. subfloridana populations.

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High-Throughput Sequencing in Studies of Lichen Population Biology

Cited by 6 publications

References 229 publications

How did terricolous fungi originate in the Mediterranean region? A case study with a gypsicolous lichenized species

How did terricolous fungi originate in the Mediterranean region? A case study with a gypsicolous lichenized species

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses

Unconstrained gene flow between populations of a widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia

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