Diversidad de especies de Xanthoparmelia (Parmeliaceae) en la vegetación de matorrales xerofíticos mexicanos, evidenciada por datos moleculares, morfológicos y químicos

The genus Xanthoparmelia is the largest genus of lichen- forming fungi with about 800 species worldwide. Xanthoparmelia is also common in the deserts of central Mexico, but only a few molecular studies exist on its species’ diversity in this region. In this study, we sampled 38 Xanthoparmelia species from around the world including species from the xerophytic scrubs of central Mexico to assess the diversity using an integrative approach. Molecular phylogenetic analyses were performed using a combination of the ITS, mtSSU and nuLSU genetic markers. We evaluated our phylogenetic results in a context of traditional morphological and chemical characters. The combined evidence of molecular, morphological, and chemical data identified a total of 18 Xanthoparmelia species-level lineages occurring in central Mexico. However, numerous traditionally circumscribed species did not form monophyletic groups in the molecular phylogenetic reconstructions. This conflict indicates that taxonomy and species delimitation in the genus Xanthoparmelia requires revision and emphasizes the importance of molecular evidence for more robust species delimitations in this genus.Xanthoparmelia es el género más grande de hongos liquenizados, con alrededor de 800 especies en todo el mundo. Xanthoparmelia es común en los desiertos del centro de México, pero existen pocos estudios moleculares sobre la diversidad de especies en esta región. En este estudio, muestreamos 38 especies de Xanthoparmelia de diferentes partes del mundo, incluidas especies de los matorrales xerófilos del centro de México, para evaluar la diversidad usando una aproximación integrativa. Los análisis filogenéticos moleculares se realizaron combinando los marcadores genéticos ITS, mtSSU y nuLSU. Además, evaluamos nuestros resultados filogenéticos en un contexto de caracteres morfológicos y químicos usados en la taxonomía tradicional. Teniendo en cuenta las evidencias obtenidas a partir de caracteres moleculares, morfológicos y químicos se identificaron un total de 18 linajes de Xanthoparmelia con categoría de especie que aparecen en el centro de México. Sin embargo, muchas especies tradicionalmente circunscritas no formaron grupos monofiléticos. Este conflicto indica que la taxonomía y delimitación de especies en el género Xanthoparmelia requiere revisión y enfatiza la importancia de los datos moleculares para una delimitación más robusta de especies en este género

Using Tree Rings to Predict the Response of Tree Growth to Climate Change in the Continental United States during the Twenty-First Century

In the early 1900s, tree-ring scientists began analyzing the relative widths of annual growth rings preserved in the cross sections of trees to infer past climate variations. Now, many ring-width index (RWI) chronologies, each representing a specific site and species, are archived online within the International Tree-Ring Data Bank (ITRDB). Comparing annual tree-ring-width data from 1097 sites in the continental United States to climate data, the authors quantitatively evaluated how trees at each site have historically responded to interannual climate variations. For each site, they developed a climate-driven statistical growth equation that uses regional climate variables to model RWI values. The authors applied these growth models to predict how tree growth will respond to twenty-first-century climate change, considering four climate projections. Although caution should be taken when extrapolating past relationships with climate into the future, the authors observed several clear and interesting patterns in the growth projections that seem likely if warming continues. Most notably, the models project that productivity of dominant tree species in the southwestern United States will decrease substantially during this century, especially in warmer and drier areas. In the northwest, nonlinear growth relationships with temperature may lead to warming-induced declines in growth for many trees that historically responded positively to warmer temperatures. This work takes advantage of the unmatched temporal length and spatial breath of annual growth data available within the ITRDB and exemplifies the potential of this ever-growing archive of tree-ring data to serve in meta-analyses of large-scale forest ecology

Shotgun Sequencing Decades-Old Lichen Specimens to Resolve Phylogenomic Placement of Type Material

Natural history collections, including name-bearing type specimens, are an important source of genetic information. These data can be critical for appropriate taxonomic revisions in cases where the phylogenetic position of name-bearing type specimens needs to be identified, including morphologically cryptic lichen-forming fungal species. Here, we use high-throughput metagenomic shotgun sequencing to generate genome-scale data from decades-old (i.e., more than 30 years old) isotype specimens representing three vagrant taxa in the lichen-forming fungal genus Rhizoplaca, including one species and two subspecies. We also use data from high-throughput metagenomic shotgun sequencing to infer the phylogenetic position of an enigmatic collection, originally identified as R. haydenii, that failed to yield genetic data via Sanger sequencing. We were able to construct a 1.64 Mb alignment from over 1200 single-copy nuclear gene regions for the Rhizoplaca specimens. Phylogenomic reconstructions recovered an isotype representing Rhizoplaca haydenii subsp. arbuscula within a clade comprising other specimens identified as Rhizoplaca haydenii subsp. arbuscula, while an isotype of R. idahoensis was recovered within a clade with substantial phylogenetic substructure comprising Rhizoplaca haydenii subsp. haydenii and other specimens. Based on these data and morphological differences, Rhizoplaca haydenii subsp. arbuscula is elevated to specific rank as Rhizoplaca arbuscula. For the enigmatic collection, we were able to assemble the nearly complete nrDNA cistron and over 50 Mb of the mitochondrial genome. Using these data, we identified this specimen as a morphologically deviant form representing Xanthoparmelia aff. subcumberlandia. This study highlights the power of high-throughput metagenomic shotgun sequencing in generating larger and more comprehensive genetic data from taxonomically important herbarium specimens

Localization of the Houdinisome (Ejection Proteins) inside the Bacteriophage P22 Virion by Bubblegram Imaging

The P22 capsid is a T=7 icosahedrally symmetric protein shell with a portal protein dodecamer at one 5-fold vertex. Extending outwards from that vertex is a short tail, and putatively extending inwards is a 15-nm-long α-helical barrel formed by the C-terminal domains of portal protein subunits. In addition to the densely packed genome, the capsid contains three “ejection proteins” (E-proteins [gp7, gp16, and gp20]) destined to exit from the tightly sealed capsid during the process of DNA delivery into target cells. We estimated their copy numbers by quantitative SDS-PAGE as approximately 12 molecules per virion of gp16 and gp7 and 30 copies of gp20. To localize them, we used bubblegram imaging, an adaptation of cryo-electron microscopy in which gaseous bubbles induced in proteins by prolonged irradiation are used to map the proteins’ locations. We applied this technique to wild-type P22, a triple mutant lacking all three E-proteins, and three mutants each lacking one E-protein. We conclude that all three E-proteins are loosely clustered around the portal axis, in the region displaced radially inwards from the portal crown. The bubblegram data imply that approximately half of the α-helical barrel seen in the portal crystal structure is disordered in the mature virion, and parts of the disordered region present binding sites for E-proteins. Thus positioned, the E-proteins are strategically placed to pass down the shortened barrel and through the portal ring and the tail, as they exit from the capsid during an infection

The brown parmelioid lichen species in Greenland

Sixteen species of brown parmelioids are reported from Greenland, including one species of Cetrariella, three species of Melanelia, two species of Melanelixia, six species of Melanohalea, and four species of Montanelia. Descriptions and a key are provided

Pleistocene Speciation in North American Lichenized Fungi and the Impact of Alternative Species Circumscriptions and Rates of Molecular Evolution on Divergence Estimates

Pleistocene climatic fluctuations influenced patterns of genetic variation and promoted speciation across a wide range of species groups. Lichens are commonly found in habitats that were directly impacted by glacial cycles; however, the role of Pleistocene climate in driving speciation in most lichen symbionts remains unclear. This uncertainty is due in part to limitations in our ability to accurately recognize independently evolving lichen-forming fungal lineages and a lack of relevant fossil calibrations. Using a coalescent-based species tree approach, we estimated divergence times for two sister clades in the genus Xanthoparmelia (Parmeliaceae) restricted to western North America. We assessed the influence of two different species circumscription scenarios and various locus-specific rates of molecular evolution on divergence estimates. Species circumscriptions were validated using the program BP&P. although speciation was generally supported in both scenarios, divergence times differed between traditional species circumscriptions and those based on genetic data, with more recent estimates resulting from the former. Similarly, rates of evolution for different loci resulted in variable divergence time estimates. However, our results unambiguously indicate that diversification in the sampled Xanthoparmelia clades occurred during the Pleistocene. Our study highlights the potential impact of ambiguous species circumscriptions and uncertain rates of molecular evolution on estimating divergence times within a multilocus species tree frameworkPeer reviewe

Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota)

Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related Glade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which are separated based on distinctive reproductive modes, the former producing soredia but absent in the latter. We reexamined the relationship between these two species using phenotypic characters and molecular sequence data (ITS, GPD, and MCM7sequences) to address species boundaries in this group. In addition to morphological investigations, we used Bayesian clustering to identify potential genetic groups in the H. hypotrypa/H. flavida Glade. We also used a variety of empirical, sequence-based species delimitation approaches, including: the "Automatic Barcode Gap Discovery" (ABGD), the Poisson tree process model (PTP), the General Mixed Yule Coalescent (GMYC), and the multispecies coalescent approach BPP. Different species delimitation scenarios were compared using Bayes factors delimitation analysis, in addition to comparisons of pairwise genetic distances, pairwise fixation indices (FST). The majority of the species delimitation analyses implemented in this study failed to support H. hypotrypa and H. flavida as distinct lineages, as did the Bayesian clustering analysis. However, strong support for the evolutionary independence of H. hypotrypa and H. flavida was inferred using BPP and further supported by Bayes factor delimitation. In spite of rigorous morphological comparisons and a wide range of sequence-based approaches to delimit species, species boundaries in the H. hypotrypa group remain uncertain. This study reveals the potential limitations of relying on distinct reproductive strategies as diagnostic taxonomic characters for Hypogymnia and also the challenges of using popular sequence-based species delimitation methods in groups with recent diversification histories

Whole-genome sequence data uncover widespread heterothallism in the largest group of lichen-forming fungi

Fungal reproduction is regulated by the mating-type (MAT1) locus, which typically comprises two idiomorphic genes. The presence of one or both allelic variants at the locus determines the reproductive strategy in Fungi – homothallism vs. heterothallism. It has been hypothesized that self-fertility via homothallism is widespread in lichen-forming fungi. To test this hypothesis, we characterized the MAT1 locus of 41 genomes of lichen-forming fungi representing a wide range of growth forms and reproductive strategies in the class Lecanoromycetes, the largest group of lichen-forming fungi. Our results show the complete lack of genetic homothallism suggesting that lichens evolved from a heterothallic ancestor. We argue that this may be related to the symbiotic lifestyle of these fungi, and may be a key innovation that has contributed to the accelerated diversification rates in this fungal group

Methodology for Development of a 600-Year Tree-Ring Multi-Element Record for Larch from the Taymir Peninsula, Russia

We developed a long (600-year) dataset for the concentrations of 26 elements in tree rings of larch from the Taymir Peninsula, the northernmost region in the world (ca. 72°N) where trees grow. Tree rings corresponding to the time period from 1300 to 1900 A.D. were studied. Eleven wood strips, each from a different larch tree, were cut into ca. 100 mg samples usually consisting of ten consecutive tree rings (but occasionally five). Between 19 and 40 consecutive samples resulted from each tree, yielding a total of 277 samples. The replication of each time interval ranged from three (for periods 1300-1400 A.D. and 1600-1700 A.D.) to six (for 1450-1600 A.D.). Wood samples were digested with concentrated HNO 3 for measurement of Li, B, Na, Mg, Al, Si, P, Cl, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Rb, Sr, Y, Zr, Nb, Mo, Ag, Cd, Sn, Sb, I, Ba, La, Ce, Nd, W, Au, Pb, Bi, Th, and U using solution Inductively Coupled Plasma Mass Spectrometry (ICPMS). Fourteen elements (V, Co, As, Y, Nb, Mo, Sb, La, Ce, Nd, W, Au, Th, and U) with extremely low concentrations were eliminated from consideration as unreliable. Here we report our sample preparation and measurement procedure, as well as the observed concentrations in tree rings, emphasizing considerations for developing representative and reliable denrodochemical datasets.Нами был получен длительный массив данных (600 лет) концентраций 26 элементов в годичных кольцах лиственницы с полуострова Таймыр, самого северного региона в мире (около 72° с.ш.), где возможен рост деревьев. Изучались годичные кольца, соответствующие промежутку времени с 1300 по 1900 год н.э. Одиннадцать древесных выпилов, по одному для каждой лиственницы, нарезались на образцы массой около 100 мг, которые, как правило, состояли из десяти годичных колец (но в некоторых случаях из пяти). Из каждого дерева было получено от 19 до 40 последовательных образцов, что дало в общей сложности 277 образцов. Повторность для каждого временного интервала варьировала от трех (для периодов 1300-1400 г.н.э. и 1600-1700 г.н.э.) до шести (для периода 1450-1600 г.н.э.). Древесные образцы растворяли в концентрированной HNO 3 для последующего измерения Li, B, Na, Mg, Al, Si, P, Cl, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Rb, Sr, Y, Zr, Nb, Mo, Ag, Cd, Sn, Sb, I, Ba, La, Ce, Nd, W, Au, Pb, Bi, Th и U при помощи масс-спектрометрии с индуктивно связанной плазмой (ICP-MS) для растворов. Четырнадцать элементов (V, Co, As, Y, Nb, Mo, Sb, La, Ce, Nd, W, Au, Th и U) с очень низкими концентрациями были исключены из рассмотрения как недостоверные. В данной статье, основной целью которой являлась отработка методики получения репрезентативных и достоверных дендрохимических данных, приводится использованная нами процедура пробоподготовки и измерений, а также полученные концентрации в годичных кольцах