scholarly journals Conceptual and empirical advances in Neotropical biodiversity research

2017 ◽  
Author(s):  
Alexandre Antonelli ◽  
María Ariza ◽  
James Albert ◽  
Tobias Andermann ◽  
Josué Azevedo ◽  
...  
Keyword(s):  
Island Biogeography ◽  
Molecular Data ◽  
Ecological Interactions ◽  
Biodiversity Data ◽  
Spatial And Temporal Scales ◽  
Complex Processes ◽  
Climatic Evolution ◽  
The Rich ◽  
Taxonomic Studies ◽  
American Tropics

The outstanding biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in the generation of biodiversity data, many questions remain to be answered. In this review, we first summarize some of the knowns and unknowns about Neotropical biodiversity, and discuss how human impact may have drastically affected some of the patterns observed today. We then link biodiversity to landscape, and outline major advances in biogeographical research. In particular, we argue that it is crucial to test the effect of landscape and climatic evolution to biotic diversification and distribution in order to achieve a comprehensive understanding of current patterns. In this context, it is also important to consider extant and extinct taxa, as well as to use probabilistic and parametric methods that explicitly include landscape evolution models. We subsequently explore different scales in Neotropical biogeography, focusing on the intersection between biogeography and community ecology, both of which often address similar questions from different angles. The concepts of community assembly, island biogeography, neutral processes, and ecological interactions are then discussed as important components of the complex processes that determine the patterns observed today. Single-taxon and cross-taxonomic studies are complementary and greatly needed, but achieving synthesis remains challenging. Finally, we argue that phylogenetic approaches hold great potential to connect across taxonomic, spatial and temporal scales, despite current difficulties to generate and cross-analyze large volumes of molecular data. We conclude by outlining major prospects and hindrances for further advancing our knowledge on the rich Neotropical biodiversity.

scholarly journals Conceptual and empirical advances in Neotropical biodiversity research

2017 ◽  
Author(s):  
Alexandre Antonelli ◽  
María Ariza ◽  
James Albert ◽  
Tobias Andermann ◽  
Josué Azevedo ◽  
...  
Keyword(s):  
Island Biogeography ◽  
Molecular Data ◽  
Ecological Interactions ◽  
Biodiversity Data ◽  
Spatial And Temporal Scales ◽  
Complex Processes ◽  
Climatic Evolution ◽  
The Rich ◽  
Taxonomic Studies ◽  
American Tropics

The outstanding biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in the generation of biodiversity data, many questions remain to be answered. In this review, we first summarize some of the knowns and unknowns about Neotropical biodiversity, and discuss how human impact may have drastically affected some of the patterns observed today. We then link biodiversity to landscape, and outline major advances in biogeographical research. In particular, we argue that it is crucial to test the effect of landscape and climatic evolution to biotic diversification and distribution in order to achieve a comprehensive understanding of current patterns. In this context, it is also important to consider extant and extinct taxa, as well as to use probabilistic and parametric methods that explicitly include landscape evolution models. We subsequently explore different scales in Neotropical biogeography, focusing on the intersection between biogeography and community ecology, both of which often address similar questions from different angles. The concepts of community assembly, island biogeography, neutral processes, and ecological interactions are then discussed as important components of the complex processes that determine the patterns observed today. Single-taxon and cross-taxonomic studies are complementary and greatly needed, but achieving synthesis remains challenging. Finally, we argue that phylogenetic approaches hold great potential to connect across taxonomic, spatial and temporal scales, despite current difficulties to generate and cross-analyze large volumes of molecular data. We conclude by outlining major prospects and hindrances for further advancing our knowledge on the rich Neotropical biodiversity.

scholarly journals ExTaxsI: an exploration tool of biodiversity molecular data

2020 ◽  
Author(s):  
Giulia Agostinetto ◽  
Anna Sandionigi ◽  
Adam Chahed ◽  
Alberto Brusati ◽  
Elena Parladori ◽  
...  
Keyword(s):  
Molecular Data ◽  
Data Availability ◽  
Future Research ◽  
Distribution Data ◽  
Biodiversity Data ◽  
Related Information ◽  
New Information ◽  
Starting Point ◽  
Key Factor ◽  
New Research

AbstractBackgroundThe increasing availability of multi omics data is leading to continually revise estimates of existing biodiversity data. In particular, the molecular data enable to characterize novel species yet unknown and to increase the information linked to those already observed with new genomic data. For this reason, the management and visualization of existing molecular data, and their related metadata, through the implementation of easy to use IT tools have become a key point for the development of future research. The more users are able to access biodiversity related information, the greater the ability of the scientific community to expand the knowledge in this area.ResultsIn our research we have focused on the development of ExTaxsI (Exploring Taxonomies Information), an IT tool able to retrieve biodiversity data stored in NCBI databases and provide a simple and explorable visualization. Through the three case studies presented here, we have shown how an efficient organization of the data already present can lead to obtaining new information that is fundamental as a starting point for new research. Our approach was also able to highlight the limits in the distribution data availability, a key factor to consider in the experimental design phase of broad spectrum studies, such as metagenomics.ConclusionsExTaxI can easily produce explorable visualization of molecular data and its metadata, with the aim to help researchers to improve experimental designs and highlight the main gaps in the coverage of available data.

New species of Crella (Pytheas) Topsent, 1890 and Crellomima Rezvoi, 1925 (Crellidae, Poecilosclerida, Demospongiae) from Chilean shallow and Argentinean deep waters, with a synthesis on the known phylogenetic relationships of crellid sponges

Zootaxa ◽  
2021 ◽  
Vol 5052 (3) ◽  
pp. 353-379
Author(s):  
JULIO C.C. FERNANDEZ ◽  
MARIANELA GASTALDI ◽  
GERMÁN ZAPATA-HERNÁNDEZ ◽  
LUIS M. PARDO ◽  
FABIANO L. THOMPSON ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Molecular Data ◽  
Southern Chile ◽  
Deep Waters ◽  
Molecular Phylogenetic ◽  
Molecular Phylogenies ◽  
Taxonomic Studies ◽  
Phylogenetic Affinities

Here, we describe four new species of Crellidae Dendy, 1922 and discuss characters and relationships from published molecular phylogenies including crellid sponges. New species proposed are Crella (Pytheas) chiloensis Fernandez, Gastaldi, Pardo & Hajdu, sp. nov., from southern Chile (15 m depth), C. (P.) desventuradae Fernandez, Gastaldi, Zapata-Hernández & Hajdu, sp. nov., from Desventuradas Archipelago (10–20 m depth), Crella (P.) santacruzae Fernandez, Gastaldi, Thompson & Hajdu, sp. nov., from deep waters off Argentina (750 m depth) and Crellomima sigmatifera Fernandez, Gastaldi & Hajdu, sp. nov., from the Chilean fjords region (ca. 20 m depth). These new species are set apart from each other and from known species mainly due to aspects of their spiculation. Chelae microscleres and acanthostyles supply characters that might be used to infer phylogenetic relationships and to verify the monophyly of Crella Gray, 1867 and Crellidae, which has seemingly been contradicted by preliminary molecular data available in the systematics’ literature. Our own interpretation of phylogenetic affinities, in the light of morphological characters from previous taxonomic studies, argues for a classification reassessment of materials (vouchers) included in these molecular phylogenies, especially in the case of Crella incrustans (Carter, 1885). We argue that currently available molecular phylogenetic outcomes for crellid sponges are not supportive of the polyphyly of Crella and Crellidae.  

scholarly journals Chronic infections can shape epidemic exposure: Pathogen co-occurrence networks in the Serengeti lions

2018 ◽  
Author(s):  
Nicholas M. Fountain-Jones ◽  
Craig Packer ◽  
Maude Jacquot ◽  
F. Guillaume Blanchet ◽  
Karen Terio ◽  
...  
Keyword(s):  
Community Ecology ◽  
Molecular Data ◽  
Competitive Interactions ◽  
Random Structure ◽  
Disease Dynamics ◽  
Wild Populations ◽  
Chronic Infections ◽  
Spatial And Temporal Scales ◽  
Combine Network ◽  
African Lions

AbstractPathogens are embedded in a complex network of microparasites that can collectively or individually alter disease dynamics and outcomes. Chronic pathogens, for example, can either facilitate or compete with subsequent pathogens thereby exacerbating morbidity and mortality. Pathogen interactions are ubiquitous in nature, but poorly understood, particularly in wild populations. We report here on ten years of serological and molecular data in African lions, leveraging comprehensive demographic and behavioral data to utilize pathogen networks to test if chronic infections shape infection by acute pathogens. We combine network and community ecology approaches to assess broad network structure and characterize associations between pathogens across spatial and temporal scales. We found significant non-random structure in the lion-pathogen co-occurrence network and identified potential facilitative and competitive interactions between acute and chronic pathogens. Our results provide a novel insight for untangling the complex associations underlying pathogen co-occurrence networks.

scholarly journals Taxonomic Studies of Some often Over-Looked Diaporthomycetidae and Sordariomycetidae

2021 ◽  
Author(s):  
Huang Shi-Ke ◽  
Kevin D. Hyde ◽  
Ausana Mapook ◽  
Sajeewa S.N. Maharachchikumbura ◽  
D. Jayarama Bhat ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Type Species ◽  
New Genus ◽  
Molecular Data ◽  
New Combinations ◽  
Number Of Species ◽  
New Family ◽  
Taxonomic Studies

Abstract Sordariomycetes is an earlier and one of the widely distributed class of Ascomycota. The class was initially classified based on morphology in having inoperculate and unitunicate asci. With the development of DNA based phylogenetic analysis, several undetermined or polyphyletic members of Sordariomycetes were reclassified. However, not all species belonging to this class have been sequenced and analyzed. There are a number of species, especially those old and poorly studied ones which have never been sequenced before and not even recollected again for further taxonomic verification. One of the main objective in this study is to revise and update the taxonomy of several well-known old and poorly studied species whose classification are still obscure. Herein, we re-examined the type materials and/or authentic specimens together to explore 74 relatively poorly-studied genera, which mainly belong to Boliniales, Calosphaeriales, Chaetosphaeriales, Jobellisiales, and Sordariales classified under Diaporthomycetidae and Sordariomycetidae. We provide descriptions, notes, figures and/or drawings and discussed their phylogenetic relationships. As a result, the monotypic Jobellisiales is transferred from Hypocreomycetidae to Diaporthomycetidae. Based on phylogenetic analysis, the polyphyletic Lasiosphaeriaceae is divided into five families, Bombardiaceae (Apodospora, Bombardia, Bombardioidea and Fimetariella), Lasiosphaeriaceae (Anopodium, Bellojisia, Corylomyces, Lasiosphaeria, Mammaria and Zopfiella), Lasiosphaeridaceae (Lasiosphaeris), Strattoniaceae (Strattonia) and Zygospermellaceae (Episternus and Zygospermella). In addition, a new family Neoschizotheciaceae is established based on Neoschizothecium. Analysis of the type species of Boothiella, Stellatospora, Sulcatistroma and Tengiomyces placed them in Sordariaceae, Chaetomiaceae, Hypocreales and Coronophorales, respectively. We classify the genera lacking molecular data based on their morphology and expect them to be recollected; that is, Kacosphaeria in Calosphaeriales; Arnium, Biconiosporella, Camptosphaeria, Diffractella, Emblemospora, Eosphaeria, Periamphispora, Ramophialophora, Synaptospora and Tripterosporella in Sordariales; Conidiotheca in Sordariomycetes; Copromyces, Effetia, Endophragmiella and Tulipispora are accommodated in Ascomycota. Besides, we establish a new genus Neoschizothecium based on phylogenetic analysis. New combinations proposed include: Camaropella amorpha, Cam. microspora, Cam. plana, Cladorrhinum grandiusculum, Cla. leucotrichum, Cla. terricola, Cla. olerum, Helminthosphaeria plumbea, Immersiella hirta, Jugulospora minor, Lasiosphaeris arenicola, Neoschizothecium aloides, Neo. carpinicola, Neo. conicum, Neo. curvisporum, Neo. fimbriatum, Neo. glutinans, Neo. inaequale, Neo. minicaudum, Neo. selenosporum, Neo. tetrasporum, Neurospora autosteira, Podospora brunnescens, P. flexuosa, P. jamaicensis, P. hamata, P. macrospora, P. spinosa, Strattonia petrogale and Triangularia microsclerotigena, T. nannopodalis, T. praecox, T. samala, T. tarvisina, T. unicaudata, T. yaeyamensis. New epithets are proposed for Apiorhynchostoma apiosporum and Podospora dacryoidea.

scholarly journals Classification of Cephalotaxus Species Based on rbcL Sequences

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 585f-586
Author(s):  
Donglin Zhang ◽  
Michael A. Dirr ◽  
Robert A. Price
Keyword(s):  
Ornamental Plants ◽  
Distinct Species ◽  
Molecular Data ◽  
Correct Identification ◽  
Drought Tolerant ◽  
Identification Of Species ◽  
Sun And Shade ◽  
The Aesthetic ◽  
Taxonomic Studies

Cephalotaxus species are needle evergreens offering the aesthetic qualities of Taxus, yew, yet are heat- and drought-tolerant, sun- and shade-adaptable, and resist deer browsing. They are adaptable to nursery and garden cultivation in USDA hardiness zones (5)6–9. Unfortunately, the various species are frequently confused in the American nursery trade due to their extreme similarity in morphology. Recently, molecular data have been widely applied in the taxonomic studies, especially DNA sequencing. The chloroplast gene rbcL of Cephalotaxus has been sequenced for determining species relationships. The preliminary results show that C. oliveri Mast. has 10 base changes from C. drupacea Sieb. et Zucc., while only one base difference occurred between C. drupacea and C. harringtonia (Forbes) Koch. There are between one and 10 base substitutions among C. fortunei Hooker, C. koreana Nakai, and C. sinensis (Rehd. et Wils.) Li. Compared with other closely related conifers, Cephalotaxus has a substantial number of differences among species except between C. drupacea and C. harringtonia, which may not be distinct species. Detailed data relative to gene sequencing, growth morphology, and horticultural characteristics should lead to correct identification of species and great horticultural uses. Furthermore, the method of rbcL sequence can be applied to distinguish other morphologically homogeneous ornamental plants.

scholarly journals rotl, an R package to interact with the Open Tree of Life data

2016 ◽  
Author(s):  
François Michonneau ◽  
Joseph W. Brown ◽  
David Winter
Keyword(s):  
Data Structures ◽  
R Package ◽  
Tree Of Life ◽  
Biodiversity Data ◽  
Life Data ◽  
Taxonomic Information ◽  
Source Data ◽  
R Packages ◽  
The Rich ◽  
Tools And Methods

1. While phylogenies have been getting easier to build, it has been difficult to re-use, combine, and synthesize the information they provide because published trees are often only available as image files, and taxonomic information is not standardized across studies. 2. The Open Tree of Life (OTL) project addresses these issues by providing a digital tree that encompasses all organisms, built by combining taxonomic information and published phylogenies. The project also provides tools and services to query and download parts of this synthetic tree, as well as the source data used to build it. Here, we present rotl, an R package to search and download data from the Open Tree of Life directly in R. 3. rotl uses common data structures allowing researchers to take advantage of the rich set of tools and methods that are available in R to manipulate, analyze, and visualize phylogenies. Here, and in the vignettes accompanying the package, we demonstrate how rotl can be used with other R packages to analyze biodiversity data. 4. As phylogenies are being used in a growing number of applications, rotl facilitates access to phylogenetic data, and allows their integration with statistical methods and data sources available in R.

Scalable Semisupervised Functional Neurocartography Reveals Canonical Neurons in Behavioral Networks

2016 ◽  
Vol 28 (8) ◽  
pp. 1453-1497 ◽  
Author(s):  
E. Paxon Frady ◽  
Ashish Kapoor ◽  
Eric Horvitz ◽  
William B. Kristan Jr.
Keyword(s):  
Neural Activity ◽  
Large Scale ◽  
Feature Space ◽  
Brain Regions ◽  
Machine Learning Techniques ◽  
Intersubject Variability ◽  
High Dimensions ◽  
Spatial And Temporal Scales ◽  
Canonical Neurons ◽  
The Rich

Large-scale data collection efforts to map the brain are underway at multiple spatial and temporal scales, but all face fundamental problems posed by high-dimensional data and intersubject variability. Even seemingly simple problems, such as identifying a neuron/brain region across animals/subjects, become exponentially more difficult in high dimensions, such as recognizing dozens of neurons/brain regions simultaneously. We present a framework and tools for functional neurocartography—the large-scale mapping of neural activity during behavioral states. Using a voltage-sensitive dye (VSD), we imaged the multifunctional responses of hundreds of leech neurons during several behaviors to identify and functionally map homologous neurons. We extracted simple features from each of these behaviors and combined them with anatomical features to create a rich medium-dimensional feature space. This enabled us to use machine learning techniques and visualizations to characterize and account for intersubject variability, piece together a canonical atlas of neural activity, and identify two behavioral networks. We identified 39 neurons (18 pairs, 3 unpaired) as part of a canonical swim network and 17 neurons (8 pairs, 1 unpaired) involved in a partially overlapping preparatory network. All neurons in the preparatory network rapidly depolarized at the onsets of each behavior, suggesting that it is part of a dedicated rapid-response network. This network is likely mediated by the S cell, and we referenced VSD recordings to an activity atlas to identify multiple cells of interest simultaneously in real time for further experiments. We targeted and electrophysiologically verified several neurons in the swim network and further showed that the S cell is presynaptic to multiple neurons in the preparatory network. This study illustrates the basic framework to map neural activity in high dimensions with large-scale recordings and how to extract the rich information necessary to perform analyses in light of intersubject variability.

scholarly journals Fire, landscape heterogeneity and wildlife management in Australia's tropical savannas: introduction and overview

2005 ◽  
Vol 32 (5) ◽  
pp. 369 ◽  
Author(s):  
Peter J. Whitehead ◽  
Jeremy Russell-Smith ◽  
John C. Z. Woinarski
Keyword(s):  
Wildlife Management ◽  
Woody Plants ◽  
Charles Darwin ◽  
Structural Integrity ◽  
Landscape Heterogeneity ◽  
Northern Australia ◽  
Spatial And Temporal Scales ◽  
Wildlife Populations ◽  
The Rich ◽  
Trees And Shrubs

Despite an apparent structural integrity, the savanna landscapes of northern Australia are in flux. Important elements of the fauna have contracted in range and are less abundant than in the relatively recent past. Vegetation patterns are changing as populations of some important woody plants decline in some parts of the savannas while, in other places, different trees and shrubs are substantially increasing in density. These sorts of changes are occurring in lands under all tenures and subject to a variety of management goals and practices, including conservation reserves. Fire, large grazing animals and, more recently, invasive plants have all been implicated as drivers of adverse change. An important general, albeit inadequately tested, theory about apparently widespread faunal decline is that these influences have, jointly or separately, compromised landscape heterogeneity. It has been proposed that resource-rich patches that sustain savanna fauna through seasonal and longer-term peaks and troughs have been reduced in number, become more widely separated in space and time, or have been reduced in quality so that wildlife dependent on the rich patches struggle to use them effectively. The issues connected with these ideas were explored in a conference on fire and savanna management at Charles Darwin University in July 2003. Congruent with the theme of the symposium in which they were presented – Managing for Heterogeneity – the subset of papers presented here is diverse in origins, issues, perspectives and the spatial and temporal scales with which they deal. We consider that they make an important contribution to debate about conservation and development in northern Australia. Not because they answer the important questions, but because they illustrate the need for a shift in emphasis: from tentative exploration of pattern and weak inference about process to a harder-edged examination of the features of savanna habitats that influence their capacity to support viable wildlife populations.

DNA barcodes of fish of the Scotia Sea, Antarctica indicate priority groups for taxonomic and systematics focus

2008 ◽  
Vol 20 (3) ◽  
pp. 253-262 ◽  
Author(s):  
J. Rock ◽  
F.O. Costa ◽  
D.I. Walker ◽  
A.W. North ◽  
W.F. Hutchinson ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Molecular Classification ◽  
Molecular Data ◽  
Species Level ◽  
Scotia Sea ◽  
Life History Stages ◽  
Additional Sequence ◽  
Taxonomic Framework ◽  
Taxonomic Studies

AbstractWe analysed cytochrome oxidase I (COI) barcodes for 35 putative fish species collected in the Scotia Sea, and compared the resultant molecular data with field-based morphological identifications, and additional sequence data obtained from GenBank and the Barcode of Life Data System (BOLD). There was high congruence between morphological and molecular classification, and COI provided effective species-level discrimination for nearly all putative species. No effect of geographic sampling was observed for COI sequence variation. For two families, including the Liparidae and Zoarcidae, for which morphological field identification was unable to resolve taxonomy, DNA barcoding revealed significant species-level divergence. However, the dataset lacked sufficient sensitivity for resolving species within theBathydracoandArtedidracogenera. Analysis of cytochromebfor these two genera also failed to resolve taxonomic identity. The data are discussed in relation to emergent priorities for additional taxonomic studies. We emphasize the utility of DNA barcoding in providing a valuable taxonomic framework for fundamental population studies through assigning life history stages or other morphologically ambiguous samples to parental species.

Sign in / Sign up

Export Citation Format

Share Document