Abstract: We utilized ITS and mtSSU sequence data to study the phylogenetic relationships of Lepraria samples collected in the Southern Hemisphere, including Australia, Chile, New Zealand and Antarctica. Morphological characters and the secondary chemistry of the specimens were also examined. Using a combination of morphological, chemical and molecular data, we identified nine lineages in our material. The lineages are: Lepraria toilenae, L. eburnea, L. nothofagi, L. straminea, L. caerulescens, L. finkii, and three previously undescribed clades that are here described as L. chileana, L. neozelandica and L. ulrikii. The first is described from Chile. The second occurs in New Zealand, and the third has an Australasian distribution, occurring in New Zealand, mainland Australia, and Tasmania. In addition, L. straminea is identified as an usnic acid-producing species of the genus Lepraria. Moreover, L. caerulescens is confirmed as a distinct species.
Countries/Continents: Australia/Australasia/Chile/South America/New Zealand/Antarctica
Notes: New: Lepraria chileana Grewe, Barcenas-Peña, Diaz & Lumbsch (from Chile), L. neozelandica Barcenas-Peña, Grewe & Lumbsch (from New Zealand), L. ulrikii Grewe, Barcenas-Peña, Diaz & Lumbsch (from Australia & New Zealand).
URL: https://doi.org/10.1639/0007-2745-124.4.494
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Keywords: PARMOTREMA/ SOUTHEAST UNITED STATES/ new taxa
Abstract: 4 fig. [New: Parmotrema subrigidum Egan sp. nov. (Florida and southeastern U.S. from Texas to Delaware).]
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Abstract: Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.
URL: https://imafungus.biomedcentral.com/articles/10.1186/s43008-020-00051-x
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Keywords: FUNGAL PRIMERS/ DNA REPLICATION LICENSING FACTOR/ EVOLUTION/ MCM7/ MS277/ PHYLOGENY/ PRE-RRNA PROCESSING PROTEIN/ TSR1
Abstract: ["Here we report degenerate primers that amplify the single-copy genes Mcm7 (MS456) and Tsr1 (MS277) across a wide range of Pezizomycotina (Ascomycota). Authors present a phylogenetic analysis of 59 taxa.]
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Abstract: Evolutionary histories are now being inferred from unprecedented, genome-scale datasets for a broad range of organismal groups. While phylogenomic data has helped in resolving a number of difficult, long-standing questions, constructing appropriate datasets from genomes is not straightforward, particularly in non-model groups. Here we explore the utility of phylogenomic data to infer robust phylogenies for a lineage of closely related lichen-forming fungal species. We assembled multiple, distinct nuclear phylogenomic datasets, ranging from ca. 25 Kb to 16.8 Mb and inferred topologies using both concatenated gene tree approaches and species tree methods based on the multispecies coalescent model. In spite of evidence for rampant incongruence among individual loci, these genome-scale datasets provide a consistent, well-supported phylogenetic hypothesis using both concatenation and multispecies coalescent approaches (ASTRAL-II and SVDquartets). However, the popular full hierarchical coalescent approach implemented in *BEAST provided inconsistent inferences, both in terms of nodal support and topology, with smaller subsets of the phylogenomic data. While comparable, well-supported topologies can be accurately inferred with only a small fraction of the overall genome, consistent results across a variety of datasets and methodological approaches provide reassurance that phylogenomic data can effectively be used to provide robust phylogenies for closely related lichen-forming fungal lineages.
URL: http://www.nature.com/articles/srep22262
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Abstract: Species in the fungal genus Sticta form symbiotic associations primarily with either green algae or cyanobacteria, but tripartite associations or photosymbiodemes involving both types of photobionts occur in some species. Sticta is known to associate with green algae in the genus Symbiochloris. However, previous studies have shown that algae from other genera, such as Heveochlorella, may also be suitable partners for Sticta. We examined the diversity of green algal partners in the genus Sticta and assessed the patterns of association between the host fungus and its algal symbiont. We used multi-locus sequence data from multiple individuals collected in Australia, Cuba, Madagascar, Mauritius, New Zealand, Reunion and South America to infer phylogenies for fungal and algal partners and performed tests of congruence to assess coevolution between the partners. In addition, event-based methods were implemented to examine which cophylogenetic processes have led to the observed association patterns in Sticta and its green algal symbionts. Our results show that in addition to Symbiochloris, Sticta associates with green algae from the genera Chloroidium, Coccomyxa, Elliptochloris and Heveochlorella, the latter being the most common algal symbiont associated with Sticta in this study. Geography plays a strong role in shaping fungal-algal association patterns in Sticta as mycobionts associate with different algal lineages in different geographic locations. While fungal and algal phylogenies were mostly congruent, event-based methods did not find any evidence for cospeciation between the partners. Instead, the association patterns observed in Sticta and associated algae, were largely explained by other cophylogenetic events such as host-switches, losses of symbiont and failure of the symbiont to diverge with its host. Our results also show that tripartite associations with green algae evolved multiple times in Sticta.
URL: https://www.sciencedirect.com/science/article/abs/pii/S1055790320301329?via%3Dihub
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Abstract: Traditional taxonomic studies provide only a limited understanding of species richness within a group. Their usefulness for assessing species diversity could also be limited as many lack sufficient sampling and/or fail to integrate different data types for assessing species boundaries. To explore the challenges and limitations of estimating species richness in lichens, we employed an integrative taxonomic approach to elucidate diversification patterns of the genus Sticta (Peltigeraceae) in Puerto Rico. Specimens were collected throughout the island, and a six‐locus dataset was generated to infer phylogenetic relationships among Puerto Rican Sticta and their continental counterparts. Phylogenetic analysis was combined with species delimitation methods and analysis of morpho‐anatomical characters to assess diversity patterns and clarify species‐level taxonomy. We found that Sticta is represented by 16 species in Puerto Rico and that at least 11 (69%) of them are potentially endemic to the island. We describe eight of these in this work: S. borinquensis sp. nov., S. corymbosa sp. nov., S. densiphyllidiata sp. nov., S. guilartensis sp. nov., S. harrisii sp. nov., S. parvilobata sp. nov., S. riparia sp. nov., and S. tainorum sp. nov. These species do not cluster in a monophyletic assemblage but are scattered over the broader Sticta phylogeny, indicating at least eight separate dispersal events. Putative endemic species were found to have close allies occurring in South America. Careful re‐examination of material revealed phenotypical characters that separate most species, suggesting low levels of cryptic diversity. We highlight that integrating molecular methods and other sources of information in species discovery along with comprehensive sampling efforts can greatly enhance our knowledge about diversity patterns in poorly studied groups and regions. Furthermore, species and ecosystems in the Caribbean are being threatened by substantial human‐driven changes (e.g., deforestation, climate change). Consequences of these impacts include reduction in already restricted habitats and potential extinction. We argue that studies analyzing species diversity within a phylogenetic framework could better inform conservation efforts aimed at addressing these challenges.
Countries/Continents: Caribbean/Puerto Rico
Notes: New (all from Puerto Rico): Sticta borinquensis Merc.-Díaz & Lücking, S. corymbosa Merc.-Díaz & Moncada, S. densiphyllidiata Merc.-Díaz & Lücking, S. guilartensis Merc.-Díaz, S. harrisii Merc.-Díaz, Moncada & Lücking, S. parvilobata Merc.-Díaz, S. riparia Merc.-Díaz, S. tainorum Merc.-Díaz.
URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/tax.12320
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Abstract: The past few decades has seen a surge in molecular data used to understand the evolution of lichenized fungi. Studies have been conducted to understand the taxonomic placement of lichenized fungi in the fungal kingdom, the diversification of higherlevel taxonomic groups, the delimitation of species, and the genetic structure of populations. As in many other groups, the taxonomic value of morphological and chemical phenotypic characters for lichenized fungi are difficult to assess without other independent sources of data. Therefore, molecular data have provided a new line of evidence to critically evaluate the usefulness of phenotypic characters. Today lichenologists are using molecular data to test traditional hypotheses of homology based on phenotypic data. Generally, the findings are that many traditional systematic concepts are incongruent with molecular concepts, but a deeper understanding of the evolutionary history is gained. The first chapter in this dissertation introduces the evolution, taxonomy, and biogeography of lichenized fungi. The remaining chapters all use molecular data to understand the evolutionary relationships of lichenized fungi at different levels of taxonomy. Two chapters focus on the diversification of taxonomic groups above the species level, the next chapter focuses on population genetics, and the final chapter focuses on the delimitation of species boundaries. Three chapters in this dissertation focus on the lobarioid clade in the family Peltigeraceae which until the past 10 years was not well studied. The lobarioid clade was once the family Lobariaceae, but it was recently synonymized with Peltigeraceae using a temporal banding approach. Temporalbanding is becoming a trend in higherlevel classification of lichenized fungi and uses timecalibrated phylogenies to identify and define temporal bands for comparable ranks above the species level and aims for a more consistent taxonomic ranking system. Chapter two, “Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group” is the first study in lichenized fungi to use targetcapturing. Nearly 400 singlecopy nuclear loci were sequenced to reconstruct the first timecalibrated phylogeny of the lobarioid clade of Peltigeraceae. The first molecular phylogeny reconstructed for this clade used three genetic loci, but could not resolve the nodes along the backbone, leaving the relationships of genera unresolved. Using two orders of magnitude more loci, this study aimed to resolve these relationships. The stem age of the lobariod clade was like other families found in previous research and the generic relationships became clearer, but the backbone was still resistant to resolution. Further investigation found evidence that this was can be explained by historic processes, including ancient hybridizations and rapid diversification that occurred near the CretaceousPaleogene boundary. Hundreds of individual gene trees had massive genetree discordance and evidence for ancient reticulate evolution. Due to these evolutionary processes, even with 400 loci, the generic relationships remain somewhat unresolved, but a clearer understanding of the processes influencing the evolution of the group was gained. Chapter three, “Oligocene origin and drivers of diversification in the genus Sticta” used a fivelocus timecalibrated phylogeny to understand the timing of diversification of the genus. This study was the first to reconstruct a timecalibrated, multilocus phylogeny for the genus Sticta. Other genuslevel studies in lichenized fungi that estimated divergence times among species at worldwide to regional scales found that most lichenized genera diversified within the last 40 Mya and in Sticta, the timing of diversification was similar. This dissertation chapter also used ancestral state reconstructions to understand the how photobiont association and Andean uplift influenced the diversification of the genus. An ancestral range reconstruction was also conducted to estimate where Sticta could have originated. Chapter four is the final chapter on lobarioid species, “Using RADseq to understand the circumAntarctic distribution of the lichenized fungus Pseudocyphellaria glabra” uses restrictionsiteassociated DNA sequencing (RADseq) to understand the biogeography and population genetics of a single species with a disjunct range, separated by oceans and seas, occurring in Australia, Chile, and New Zealand. The use of RADseq is challenging in lichenized fungi because isolation of DNA from a lichen thallus results in a metagenome composed mostly of the mycobiont DNA, but it also contains DNA of the photobiont and the microbiome. In this chapter, a reference genome was generated so P. glabra mycobiont RAD loci could be used to estimate patterns of genetic differentiation among populations collected in Australia, Chile, and New Zealand and to infer how major physical barriers such as the Pacific Ocean limit genetic exchange among populations. Chapter five, “Picking holes in traditional species delimitations: an integrative taxonomic reassessment of the Parmotrema perforatum group” focuses on a species complex in another family, Parmeliaceae. This species delimitation study required the collection of population samples from eastern Texas and western Louisiana, where all six species live in sympatry. The aim was to use a sevenlocus dataset and the integration of a variety of analytical methods determine if the genetic lineages inferred correlated with the traditional species circumscriptions based on secondary chemistry and mode of reproduction. Integrative taxonomy is increasingly used in lichenized fungi to assess species boundaries that were established using phenotypic characters and most studies find that traditional phenotypebased species delimitation vastly underestimated the number of species observed with the “general lineage concept“ (GLC) of species. The GLC encourages the use of multiple sources of data to serve as independent lines of evidence in order to generate a robust hypothesis of species boundaries. In this final dissertation chapter, multiple lines of evidence were used including concatenated maximum likelihood phylogeny reconstruction, Bayesian STRUCTURE analysis, multispecies coalescent species tree estimations, and the morphology conidia to determine species boundaries. The main result was that genetic lineages did not correspond directly with the traditional sixspecies delimitation based solely on secondary chemistry and reproductive mode. The genetic data discovered three lineages with a more complicated evolutionary history than traditionally assumed. This dissertation outlines the work that was a training program on the latest research techniques in the field of lichenology. The research conducted encompassed most aspects that a professional systematist will encounter in a career. This includes planning field collection trips in the USA and foreign countries, which required obtaining grants and collection permits, preparation of logistical aspects, such as rental cars and accommodations, finding appropriate habitats, collecting and identifying specimens in the field, and finally, getting the specimens back safely so the research could be conducted. Once back in Chicago, the specimens were processed for deposition in the herbarium of the Field Museum, prepared for DNA isolation and sequencing, and analyzed on high performance servers. But the most challenging aspect was interpreting the results of the analyses, finding what was learned, and then framing the ideas in the context of what is already known, not just in the field of lichenology, but in the broader disciplines of systematics and evolutionary biology. The Biological Sciences PhD program at UIC and the collections and laboratories at the Field Museum provided excellent training for me to transform myself from an amateur lichen enthusiast, to a scientist that understands lichens in a much broader perspective.
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Abstract: Accurate species delimitation is important since species are a fundamental unit in biological research. In lichenized-fungi, species delimitation has been difficult due to a lack in taxonomically important characters and due to the limits of traditional, morphology-based species concepts. We apply an integrative approach to reassess the taxonomy of the Parmotrema perforatum group; six closely related species divided into three species pairs, each pair comprising one apotheciate (sexual) and one sorediate (asexual) species. Each pair is further characterized by a distinct combination of secondary metabolites. Species boundaries were reexamined using an integrative approach incorporating morphological, chemical, and molecular sequence data to delimit species boundaries. Phylogenies were inferred from a seven-locus DNA sequence dataset using both concatenated gene tree and coalescent-based species tree inference methods. We employed multispecies coalescent method implemented in the program BP&P to validate candidate species. Micromorphological measurements of conidia were found to be congruent with clusters found in the phylogenetic analyses, uncovering unknown evolutionary relationships. Each approach that we applied to the P. perforatum group consistently recovered four of the currently circumscribed species P. perforatum, P. hypotropum, P. subrigidum, and P. louisianae, while P. preperforatum and P. hypoleucinum were consistently interpreted as conspecific.
URL: http://ial8.luomus.fi/wp-content/uploads/2014/09/IAL8_abstracts3007.pdf
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Abstract: In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.
URL: https://www.nature.com/articles/s41598-019-45455-x
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Abstract: A major challenge to evolutionary biologists is to understand how biodiversity is distributed through space and time and across the tree of life. Diversification of organisms is influenced by many factors that act at different times and geographic locations but it is still not clear which have a significant impact and how drivers interact. To study diversification, we chose the lichen genus Sticta, by sampling through most of the global range and producing a time tree. We estimate that Sticta originated about 30 million years ago, but biogoegraphic analysis was unclear in estimating the origin of the genus. Furthermore, we investigated the effect of dispersal ability finding that Sticta has a high dispersal rate, as collections from Hawaii showed that divergent lineages colonized the islands at least four times. Symbiont interactions were investigated using BiSSE to understand if green-algal or cyanobacterial symbiont interactions influenced diversification, only to find that the positive results were driven almost completely by Type I error. On the other hand, another BiSSE analysis found that an association with Andean tectonic activity increases the speciation rate of species.
URL: https://www.sciencedirect.com/science/article/pii/S1055790317305584
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Abstract: Accurate species delimitation is important as species are a fundamental unit in ecological, evolutionary and conservation biology research. In lichenized fungi, species delimitation has been difficult due to a lack of taxonomically important characteristics and due to the limits of traditional, morphology-based species concepts. In this study we reassess the current taxonomy of the Parmotrema perforatum group, which recognizes six closely related species divided into three species pairs, each pair comprising one apotheciate (sexual) and one sorediate (asexual) species. Each pair is further characterized by a distinct combination of secondary metabolites. It was hypothesized that the three apotheciate species are reproductively isolated sibling species and that each sorediate species evolved once from the chemically identical apotheciate species. In this study, species boundaries were re-examined using an integrative approach incorporating morphological, chemical and molecular sequence data to delimit species boundaries. Phylogenetic trees were inferred from a seven-locus DNA sequence dataset using concatenated gene tree and coalescent-based species-tree inference methods. Furthermore, we employed a multi-species coalescent method to validate candidate species. Micromorphological measurements of conidia were found to be congruent with phylogenetic clusters. Each approach that we applied to the P. perforatum group consistently recovered four of the currently circumscribed species (P. perforatum, P. hypotropum, P. subrigidum and P. louisianae), whereas P. preperforatum and P. hypoleucinum were consistently combined and are thus interpreted as conspecific.
Notes: Further evidence that molecular data do not support the species as currently circumscribed in this group.
URL: http://onlinelibrary.wiley.com.proxy.library.cornell.edu/doi/10.1111/boj.12483/full
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Abstract: Rapid radiations in Fungi are only beginning to be studied with phylogenomic data. The evolutionary history of the lichenized fungal order Peltigerales has not been well resolved, particularly for the Collematineae. Here, we used concatenation and coalescent-based species tree methods to reconstruct the phylogeny of the Peltigerales based on sequences of 125 nuclear single-copy exon sequences among 60 samples, representing 58 species. Despite uneven, lineage-specific missing data and significant topological incongruence of individual exon trees, the resulting phylogenies were concordant and successfully resolved the phylogenetic relationships of the Peltigerales. Relationships in the Collematineae were defined by short branches and lower nodal support than in other parts of the tree, due in part to conflicting signal in exon trees, suggesting rapid diversification events in the early evolution of the suborder. Using tree distance measures, we were able to identify a minimum subset of exons that could reconstruct phylogenetic relationships in Peltigerales with higher support than the 125-exon dataset. Comparisons between the minimum and complete datasets in species tree inferences, bipartition analyses, and divergence time estimations displayed similar results, although the minimum dataset was characterized by higher levels of error in estimations of divergence times. Contrasting our inferences from the complete and minimum datasets to those derived from few nuclear and mitochondrial loci reveal that our topology is concordant with topologies reconstructed using the nuclear large subunit and mitochondrial small subunit ribosomal DNA markers, but the target capture datasets had much higher support values. We demonstrated how target capture approaches can effectively decipher ancient rapid radiations in cases where well resolved individual exon trees are sufficiently sampled and how to identify subsets of loci that are appropriate for fungal order-level phylogenetics.
URL: https://link.springer.com/article/10.1007/s13225-021-00476-8
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Abstract: Aim: The Southern Ocean landmasses have intrigued biologists for centuries because they share many taxonomic groups. Such disjunct taxa can provide insight into evolutionary processes that connect populations or drive divergence. The lichenized fungus Pseudocyphellaria glabra, for example, has a disjunct distribution—separated by the Tasman Sea and the Pacific Ocean—yet whether these locations should be genetically distinct is unclear. The large distances between continents may be expected to prohibit gene flow, but strong and sustained winds in the Southern Hemisphere and the small size of P. glabra propagules may facilitate migration. We compared support for these two hypotheses. Location: Southeastern Australia, Tasmania, New Zealand and Southern Chile. Taxon: Pseudocyphellaria glabra (Hook. f. & Taylor) C.W. Dodge, 1948 (Ascomycota, Peltigeraceae) Methods: We collected 371 samples across the disjunct range of P. glabra. We generated genomic data using restriction site‐associated DNA sequencing and reconstructed a Maximum Likelihood phylogeny using 29,098 unlinked SNPs. We then conducted population genomic analyses using 3,756 SNPs including a minimum‐spanning network, principal components analysis, discriminate analysis of principal components, and k‐means clustering. Results: Maximum likelihood analysis recovered multiple well‐supported clades that roughly corresponded to geography. Population genomic analyses identified genetic structuring that generally corresponded with geographic distance; however, some individuals from Chile and Australia were assigned to genetic clusters found in New Zealand, suggesting that recent dispersal events from New Zealand have successfully colonized Chile and Australia. Main conclusion: Populations of P. glabra from Australia, Chile and New Zealand are genetically distinct, but frequent long‐distance dispersal during the Quaternary probably prevented speciation. This study demonstrates the power of restriction‐site associated DNA sequencing for discernment between divergent and connective evolutionary forces that simultaneously influence the population structure of species with disjunct ranges in the Southern Ocean landmasses.
URL: https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbi.13983
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Number of records in database: 53317.
Current date: 2023.12.07.OK