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***: An R package that can generate large phylogenetic trees for plants and animals

Plant Diversity 2023年第3期45卷 347-352页

作者： Yi Jin Hong Qian Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China Guizhou Normal UniversityGuiyang 550025China Research and Collections Center Illinois State Museum1011 East Ash StreetSpringfieldIL 62703USA

The previously released packages of the PhyloMaker series(***,***,and ***2) have been broadly used to generate phylogenetic trees for ecological and biogeographical *** these packages can be used to generate phylogenetic trees for any groups of plants and animals for which megatrees are available,they focus on generating phylogenetic trees for plants based on the megatrees provided by the *** to use these packages to generate phylogenetic trees based on other megatrees is not ***,we present a new tool,which is called ‘***’,and a simple R script that can be used to easily generate large phylogenetic trees for both plants and animals at a relatively fast speed.

关键词： Animals Community phylogenetics Megatree Phylogeny Plants species list

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Global patterns of fern species diversity:An evaluation of fern data in GBIF

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Plant Diversity 2022年第2期44卷 135-140页

作者： Hong Qian Jian Zhang Mei-Chen Jiang Research and Collections Center Illinois State Museum1011 East Ash StreetSpringfieldIL 62703USA Zhejiang Tiantong Forest Ecosystem National Observation and Research Station School of Ecological and Environmental SciencesEast China Normal University200241 ShanghaiChina

Despite that several studies have shown that data derived from species lists generated from distribution occurrence records in the Global Biodiversity Information Facility(GBIF)are not appropriate for those ecological and biogeographic studies that require high sampling completeness,because species lists derived from GBIF are generally very incomplete,Suissa et al.(2021)generated fern species lists based on data with GBIF for 100 km×100 km grid cells across the world,and used the data to determine fern diversity hotspots and species richness-climate *** conduct an evaluation on the completeness of fern species lists derived from GBIF at the grid-cell scale and at a larger spatial scale,and determine whether fern data derived from GBIF are appropriate for studies on the relations of species composition and richness with climatic *** show that species sampling completeness of GBIF is low(species diversity and the identification of diversity *** conclude that fern species lists derived from GBIF are generally very incomplete across a wide range of spatial scales,and are not appropriate for studies that require data derived from species lists in high *** present a map showing global patterns of fern species diversity based on complete or nearly complete regional fern species lists.

关键词： Climate Data bias Fern GBIF species diversity species list

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***2:An updated and enlarged R package that can generate very large phylogenies for vascular plants

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Plant Diversity 2022年第4期44卷 335-339页

作者： Yi Jin Hong Qian Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China Guizhou Normal UniversityGuiyang550025China Research and Collections Center Illinois State Museum1011 East Ash StreetSpringfieldIL62703USA

An earlier version of *** has been broadly used to generate phylogenetic trees of vascular plants for botanical,biogeographical and ecological ***,we update and enlarge this package,which is now called‘***2’.With ***2,one can generate a phylogenetic tree for vascular plants based on one of three different botanical nomenclature ***2 can generate phylogenies for very large species lists(the largest species list that we tested included 365,198 species).***2 generates phylogenies at a fast *** provide an example(including a sample species list and an R script to run it)in this paper to show how to use ***2 to generate phylogenetic trees.

关键词： Community phylogenetics Global plants Phylogeny species list Vascular plants V.PhyloMaker

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Dominant Macroalgae in Bahía de Cochinos, Matanzas, Cuba

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American Journal of Plant Sciences 2022年第6期13卷 797-814页

作者： Yusimí Alfonso Patricia González Sánchez Hansel Caballero Aragón Pedro Chevalier Jhoana Díaz-Larrea Ruben Cabrera Acuario Nacional de Cuba La Habana Cuba Unidad Iztapalapa Departamento de Hidrobiología Universidad Autónoma Metropolitana Cd de México México Gabinete de Arqueología Oficina del Historiador de la Ciudad Habana Vieja Cuba

Spatial-temporal variations of macroalgae were analyzed in a study conducted in Cueva de Los Peces (CP) and Punta Perdiz (PP), two dive sites located on the eastern coast of Bahía de Cochinos. The most conspicuous species found from 3 to 20 m depths were present in the biotopes of ridges and shallow and deep terraces. Sampling was carried out in September 2014, and March and October 2016 by autonomous diving and direct methods. Qualitative visual censuses and quantitative analyzes were used to estimate the coverage (%) of the genera according to the AGRRA methodology with the use of the 10 m linear transect and quadrats as the sampling unit. The first list of macroalgae for the area is offered that includes 49 taxa of which 10 were Rhodophyta, 10 Ochrophyta (Phaeophyceae), and 29 Chlorophyta. The dominant genera during the study period were Halimeda, Dictyota, Lobophora, and Udotea. Spatial differences were found regarding the specific composition. Temporal variations were evidenced in terms of the relative abundance of the genera present, which reveals temporal changes in the qualitative structure, where some species replace others. The information obtained is pioneering and can serve as a comparative baseline for future monitoring of the area.

关键词： Cuba Macroalgae Spatial-Temporal Variations species list

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Xylariaceae:Overview and addition to fungal diversity of Gujarat state

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Studies in Fungi 2016年第1期1卷 69-79页

作者： Koyani RD Patel HR Vasava AM Rajput KS Department of Botany Faculty of ScienceThe Maharaja Sayajirao University of BarodaVadodara 390002India

Extensive fieldwork in all 33 districts including different forests of Gujarat state during 2007 to 2014 resulted in the collection of 349 fungal *** them,19 species represented the family Xylariaceae belonging to three genera ***(3 species),Hypoxylon(2 species)and Xylaria(14 species).From these species,Daldinia concentrica,***,Hypoxylon begae,Xylaria curta,***,*** and *** are reported previously,while Daldinia childiae,Hypoxylon rickii,Xylaria apiculata,***,***,***,***,***,***,***,*** and *** are recorded for the first time from *** the species are saprobic except Hypoxylon fragiforme and Xylaria polymorpha,which are exclusively observed on the bark of Bombax ceiba and Lannea coromandelica as well as dead *** distribution,habitat,morphology of the identified species are described in this article.

关键词： Biodiversity mycobiota species list taxonomy Xylariaceae

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