scholarly journals An Analysis of the Street Tree Population of Greater Melbourne at the Beginning of the 21st Century

2006 ◽  
Vol 32 (4) ◽  
pp. 155-163
Author(s):  
Stephen Frank ◽  
Glenn Waters ◽  
Russell Beer ◽  
Peter May
Keyword(s):  
Data Sets ◽  
Botanical Composition ◽  
Future Studies ◽  
Prunus Cerasifera ◽  
Tree Population ◽  
Tree Inventory ◽  
Street Tree ◽  
The Family ◽  
Family Level ◽  
Prunus Spp

An audit of the street tree population of Melbourne, Victoria, Australia, was undertaken to establish its size and botanical composition as a reference point for future studies. The 31 independent municipalities that comprise metropolitan Melbourne were approached to provide information on their respective street tree populations. Where available, data from individual municipalities on population, area, and total street length were also collected. Of the 31 municipalities surveyed, 23 had undertaken some form of street tree inventory or audit. These individual data sets were combined into a single database. Data queries were then undertaken to obtain a range of information. A total of 922,353 trees, comprising 1127 taxa, were captured in this superset of data. Australian native plants made up the majority of the trees with 60% of the total. Of the Australian native taxa, wattles (Acacia spp.), gums or eucalypts (Eucalyptus spp.), paperbarks (Melaleuca spp.), bottlebrush (Callistemon spp.), and Queensland brush box (Lophostemon confertus [R. Br.] Peter G. Wilson and Waterhouse) comprised 394,730 individuals (43% of all trees). Of the exotic taxa, Prunus spp. were the most common with 86,227 individuals (9% of the total). Queensland brush box was the most common taxon surveyed with 61,959 individuals. Purple-leaf cherry plum (Prunus cerasifera Ehrh. ‘Nigra’) was the most common exotic taxon with 35,402 individuals. An analysis of the diversity of this population showed that it meets a set of minimum diversity criteria apart from the dominance of the Myrtaceae at the family level.

scholarly journals Nuclear and mitochondrial phylogenomics of the Diplostomoidea and Diplostomida (Digenea, Platyhelminthes)1

2018 ◽  
Author(s):  
Sean A. Locke ◽  
Alex Van Dam ◽  
Monica Caffara ◽  
Hudson Alves Pinto ◽  
Danimar López-Hernández ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Rapid Radiation ◽  
Mt Dna ◽  
Future Studies ◽  
Higher Taxa ◽  
The Family ◽  
Family Level ◽  
Genome Phylogeny ◽  
Mt Genome ◽  
A New Species

AbstractHigher systematics within the Digenea, Carus 1863 have been relatively stable since a phylogenetic analysis of partial nuclear ribosomal markers (rDNA) led to the erection of the Diplostomida Olson, Cribb, Tkach, Bray, and Littlewood, 2003. However, recent mitochondrial (mt) genome phylogenies suggest this order might be paraphyletic. These analyses show members of two diplostomidan superfamilies are more closely related to the Plagiorchiida La Rue, 1957 than to other members of the Diplostomida. In one of the groups implicated, the Diplostomoidea Poirier, 1886, a recent phylogeny based on mt DNA also indicates the superfamily as a whole is non-monophyletic. To determine if these results were robust to additional taxon sampling, we analyzed mt genomes from seven diplostomoids in three families. To choose between phylogenetic alternatives based on mt genomes and the prior rDNA-based topology, we also analyzed hundreds of ultra-conserved elements (UCEs) assembled from shotgun sequencing. The Diplostomida was paraphyletic in the mt genome phylogeny, but supported in the UCE phylogeny. We speculate this mitonuclear discordance is related to ancient, rapid radiation in the Digenea. Both UCEs and mt genomes support the monophyly of the Diplostomoidea and show congruent relationships within it. The Cyathocotylidae Mühling, 1898 are early diverging descendants of a paraphyletic clade of Diplostomidae Poirier, 1886, in which were nested members of the Strigeidae Railliet, 1919; the results support prior suggestions that the Crassiphialinae Sudarikov, 1960 will rise to the family level. Morphological traits of diplostomoid metacercariae appear to be more useful for differentiating higher taxa than those of adults. We describe a new species of Cotylurus Szidat, 1928, resurrect a species of Hysteromorpha Lutz, 1931, and find support for a species of Alaria Schrank, 1788 of contested validity. Complete rDNA operons are provided as a resource for future studies.

The anatomy of an unstable node: a Levantine relict precipitates phylogenomic dissolution of higher-level relationships of the armoured harvestmen (Arachnida: Opiliones: Laniatores)

2019 ◽  
Author(s):  
Shlomi Aharon ◽  
Jesus A. Ballesteros ◽  
Audrey R. Crawford ◽  
Keyton Friske ◽  
Guilherme Gainett ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Signal ◽  
Future Studies ◽  
Phylogenetic Placement ◽  
Unstable Node ◽  
The Family ◽  
Family Level ◽  
The Matrix ◽  
Tree Topologies ◽  
Unstable Position

After tumultuous revisions to the family-level systematics of Laniatores (the armored harvestmen), the basally branching family Phalangodidae presently bears a disjunct and irregular distribution, attributed to the fragmentation of Pangea. One of the curious lineages assigned to Phalangodidae is the monotypic Israeli genus Haasus, the only Laniatores species that occurs in Israel, and whose presence in the Levant has been inferred to result from biogeographic connectivity with Eurasia. Recent surveys of Israeli caves have also yielded a new troglobitic morphospecies of Haasus. Here, we describe this new species as Haasus naasane sp. nov. So as to test the biogeographic affinity of Haasus, we sequenced DNA from both species and RNA from Haasus naasane sp. nov., to assess their phylogenetic placement. Our results showed that the new species is clearly closely related to Haasus judaeus, but Haasus itself is unambiguously nested within the largely Afrotropical family Pyramidopidae. In addition, the Japanese ‘phalangodid’ Proscotolemon sauteri was recovered as nested within the Southeast Asian family Petrobunidae. Phylogenomic placement of Haasus naasane sp. nov. in a 1550-locus matrix indicates that Pyramidopidae has an unstable position in the tree of Laniatores, with alternative partitioning of the matrix recovering high nodal support for mutually exclusive tree topologies. Exploration of phylogenetic signal showed the cause of this instability to be a considerable conflict between partitions, suggesting that the basal phylogeny of Laniatores may not yet be stable to addition of taxa. We transfer Haasus to Pyramidopidae (new familial assignment). Additionally, we transfer Proscotolemon to the family Petrobunidae (new familial assignment). Future studies on basal Laniatores phylogeny should emphasise the investigation of small-bodied and obscure groups that superficially resemble Phalangodidae.

Street Tree Diversity in Massachusetts, USA

2020 ◽  
Vol 46 (1) ◽  
pp. 27-43
Author(s):  
F.D. Cowett ◽  
Nina Bassuk
Keyword(s):  
New York ◽  
Tree Species ◽  
Tree Diversity ◽  
Asian Longhorned Beetle ◽  
Street Trees ◽  
Tree Population ◽  
Tree Inventory ◽  
Street Tree ◽  
Tree Survival ◽  
Considerable Work

Pests, disease, and climate change pose major challenges to street tree survival, and diversity in tree species and genera is widely considered to promote the sustainability of municipal street tree populations. Conversely, the lack of sufficient diversity in street tree population was judged a contributing factor in the death and removal of thousands of street trees in Worcester, Massachusetts, that state’s second most populous city, due to an infestation of the Asian longhorned beetle (ALB, Anoplophora glabripennis). Therefore, reducing the dominance of prevalent street tree species and genera and increasing tree species and genera diversity are considered vital to sustainable street tree management and to the preservation of the ecosystem services and social benefits that street trees provide. This paper assesses street tree diversity in Massachusetts by analyzing a nonrandom sample of collated municipal street tree inventory data stratified by plant hardiness zones. Consistent with results previously found for Connecticut, New Jersey, New York, and Pennsylvania, results in Massachusetts indicate that a relatively small number of species and genera dominate the composition of most municipal street tree populations, including in particular Acer spp. (maple), one of the ALB’s favorite host genera. There is accordingly a need for greater species and genus diversity in municipal street tree populations statewide. While there may be a trend towards increased street tree diversity and reduction in the dominance of Acer spp., considerable work remains to be done.

scholarly journals Exploring phylogenomic relationships within Myriapoda: should high matrix occupancy be the goal?

2015 ◽  
Author(s):  
Rosa Fernandez ◽  
Gregory D Edgecombe ◽  
Gonzalo Giribet
Keyword(s):  
Sister Group ◽  
Molecular Data ◽  
Taxon Sampling ◽  
Molecular Evidence ◽  
Data Sets ◽  
The Family ◽  
Family Level ◽  
Conserved Genes ◽  
Bayesian Mixture ◽  
Bayesian Mixture Models

Myriapods are one of the dominant terrestrial arthropod groups including the diverse and familiar centipedes and millipedes. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes in many species) or on maximizing matrix occupancy (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed forty Illumina transcriptomes representing three myriapod classes (Diplopoda, Chilopoda and Symphyla); twenty-five transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Eight supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at three levels of mean gene occupancy per taxon (50%, 75% and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in two alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but two nodes remained in conflict in the different analyses despite dense taxon sampling at the family level, situating the order Scolopendromorpha as sister group to a morphologically-anomalous grouping of Lithobiomorpha + Geophilomorpha in a subset of analyses. Interestingly, this anomalous result was obtained for all analyses conducted with the most complete matrix (90% of occupancy), being at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) or with the matrices optimizing phylogenegic informativeness and the most conserved genes, but also with previous hypotheses based on morphology, development or other molecular data sets. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.

A multi-gene molecular phylogeny regarding the two phylogenetically close genera Hydropus and Leucoinocybe (Agaricales, Basidiomycota), new for Turkey

Nova Hedwigia ◽  
2020 ◽  
Vol 111 (3) ◽  
pp. 429-448
Author(s):  
Oğuzhan Kaygusuz ◽  
Hana Ševčíková ◽  
Eliseo Battistin ◽  
Brahim Türkekul
Keyword(s):  
New Records ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Data Sets ◽  
New Genera ◽  
New Host ◽  
Natural Classification ◽  
Future Studies ◽  
Line Drawings ◽  
The Family

The taxonomy and phylogeny of Hydropus subalpinus and Leucoinocybe lenta were investigated on the basis of morphological features and multi-gene molecular analysis (nrITS, nrLSU, tef-1α data sets) in order to elucidate the taxonomic status of these two rare species, and delineate a natural classification within the family Porotheleaceae. The results reinforced the conclusion that Hydropus and Leucoinocybe represent independent genera separate from Clitocybula, Gerronema , Lignomphalia, Megacollybia, Porotheleum and Trogia. The genus Leucoinocybe in the analysis proves to be a monophyletic group, while the genus Hydropus is polyphyletic. In addition, this is the first report of Leucoinocybe lenta growing in forests of the relict endemic Liquidambar orientalis and Fagus orientalis is recorded as a new host for Hydropus subalpinus. The study describes Hydropus subalpinus and Leucoinocybe lenta as new records and Hydropus and Leucoinocybe as new genera records for Turkish mycobiota. Detailed description of the morphological characters, line drawings of salient micromorphological features and color photographs of these species are provided, and comparisons with phenetically similar and phylogenetically related species are presented. This survey provides hopefully useful information for future studies on the phylogeny and diversity of Hydropus and Leucoinocybe, and reveals the need for more molecular studies on collections of the Hydropoid clade.

scholarly journals OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 564
Author(s):  
Rodrigo García-López ◽  
Fernanda Cornejo-Granados ◽  
Alonso A. Lopez-Zavala ◽  
Andrés Cota-Huízar ◽  
Rogerio R. Sotelo-Mundo ◽  
...  
Keyword(s):  
Hypervariable Region ◽  
Total Abundance ◽  
Optimal Production ◽  
Future Studies ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
The Family ◽  
Family Level ◽  
Rearing Conditions ◽  
Diversity Profiles

The interplay between shrimp immune system, its environment, and microbiota contributes to the organism’s homeostasis and optimal production. The metagenomic composition is typically studied using 16S rDNA profiling by clustering amplicon sequences into operational taxonomic units (OTUs) and, more recently, amplicon sequence variants (ASVs). Establish the compatibility of the taxonomy, α, and β diversity described by both methods is necessary to compare past and future shrimp microbiota studies. Here, we used identical sequences to survey the V3 16S hypervariable-region using 97% and 99% OTUs and ASVs to assess the hepatopancreas and intestine microbiota of L. vannamei from two ponds under standardized rearing conditions. We found that applying filters to retain clusters >0.1% of the total abundance per sample enabled a consistent taxonomy comparison while preserving >94% of the total reads. The three sets turned comparable at the family level, whereas the 97% identity OTU set produced divergent genus and species profiles. Interestingly, the detection of organ and pond variations was robust to the clustering method’s choice, producing comparable α and β-diversity profiles. For comparisons on shrimp microbiota between past and future studies, we strongly recommend that ASVs be compared at the family level to 97% identity OTUs or use 99% identity OTUs, both using tailored frequency filters.

Robustness of classification and ordination techniques applied to Macroinvertebrate communities from the La Trobe River, Victoria

1990 ◽  
Vol 41 (4) ◽  
pp. 493 ◽  
Author(s):  
R Marchant
Keyword(s):  
Data Sets ◽  
Macroinvertebrate Communities ◽  
Full Data ◽  
Data Set ◽  
Raw Data ◽  
Genus Level ◽  
The Family ◽  
Ordination Techniques ◽  
Family Level

The robustness of site groupings produced by ordination (DECORANA) and classification (TWINSPAN) techniques to variations in the quality of the raw data was investigated, using two data sets on macroinvertebrate communities from the La Trobe River. Ordinations or classifications based on the presence or absence of species were not substantially different from those based on actual abundance levels. However, when taxonomic discrimination was reduced from the species (or genus) level to the family level, distortions occurred in the resulting ordinations and classifications. In addition, ordinations based on 10 replicates per sample were little different from those based on a subset of 5 or 6 of these replicates; fewer than 4 replicates did not adequately represent the patterns present in the full data set.

scholarly journals Unearthing LTR retrotransposon gag genes co-opted in the deep evolution of eukaryotes

2021 ◽  
Author(s):  
Jianhua Wang ◽  
Guan-Zhu Han
Keyword(s):  
Gene Expression ◽  
Selective Pressure ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Cellular Functions ◽  
The Family ◽  
Family Level ◽  
Gene Expression Analyses ◽  
Comprehensive Picture ◽  
Gypsy Retrotransposons

Abstract LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes, and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.

scholarly journals The Role of Botanical Families in Medicinal Ethnobotany: A Phylogenetic Perspective

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 163
Author(s):  
Airy Gras ◽  
Oriane Hidalgo ◽  
Ugo D’Ambrosio ◽  
Montse Parada ◽  
Teresa Garnatje ◽  
...  
Keyword(s):  
Diversity Indices ◽  
Specific Level ◽  
Medicinal Uses ◽  
The Family ◽  
Family Level ◽  
Phylogenetic Level ◽  
Molecular Phylogenetic ◽  
Quantitative Analyses ◽  
Medicinal Flora

Studies suggesting that medicinal plants are not chosen at random are becoming more common. The goal of this work is to shed light on the role of botanical families in ethnobotany, depicting in a molecular phylogenetic frame the relationships between families and medicinal uses of vascular plants in several Catalan-speaking territories. The simple quantitative analyses for ailments categories and the construction of families and disorders matrix were carried out in this study. A Bayesian approach was used to estimate the over- and underused families in the medicinal flora. Phylogenetically informed analyses were carried out to identify lineages in which there is an overrepresentation of families in a given category of use, i.e., hot nodes. The ethnobotanicity index, at a specific level, was calculated and also adapted to the family level. Two diversity indices to measure the richness of reported taxa within each family were calculated. A total of 47,630 use reports were analysed. These uses are grouped in 120 botanical families. The ethnobotanicity index for this area is 14.44% and the ethnobotanicity index at the family level is 68.21%. The most-reported families are Lamiaceae and Asteraceae and the most reported troubles are disorders of the digestive and nutritional system. Based on the meta-analytic results, indicating hot nodes of useful plants at the phylogenetic level, specific ethnopharmacological research may be suggested, including a phytochemical approach of particularly interesting taxa.

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