A review of the Entocytheridae (Ostracoda) of the world: updated bibliographic and species checklists and global georeferenced database, with insights into host specificity and latitudinal patterns of species richness

Crustaceana ◽  
2014 ◽  
Vol 87 (8-9) ◽  
pp. 923-951 ◽  
Author(s):  
Alexandre Mestre ◽  
Juan S. Monrós ◽  
Francesc Mesquita-Joanes
Keyword(s):  
Species Richness ◽  
Host Specificity ◽  
Current Knowledge ◽  
Free Access ◽  
Global Biodiversity Information Facility ◽  
Species List ◽  
Biogeographic History ◽  
Richness Pattern ◽  
History Of ◽  
Taxonomic Groups

The creation of biodiversity datasets freely available for the scientific community is a valuable task to stimulate global research on biodiversity. Among others, the Global Biodiversity Information Facility (GBIF) is a remarkable resource providing free online access to biodiversity data on many diverse taxonomic groups (including Ostracoda) from both terrestrial and marine ecosystems. More specific databases for Ostracoda georeferenced data have been built (e.g., NACODe and OMEGA), some with freely available data. However, the Entocytheridae, a family of ostracods living commensal on other crustaceans, with 220 living species, representing the third non-marine ostracod family in number of species, has been remarkably under-represented in the currently available biodiversity databases. To cover this gap, we present here a free-access world database of Entocytheridae published in GBIF and review the current knowledge of the group by updating a bibliographic and species checklists of the Entocytheridae. We also analyse the host specificity of the group and the latitudinal species richness pattern in North and Central America (including 186 spp.). The current database includes 3509 georeferenced records from 220 species, in contrast to just 44 entocytherid georeferenced records previously published in GBIF. In addition, the updated species list accounts for 43 species and 2 genera that were not included in the previous compendium on Entocytheridae published by Hart & Hart in 1974, so as 40 species not included in the 2013 Checklist provided by the Catalogue of Life. We show that the specialisation in one unique host species is not the rule in Entocytheridae, and evidence an unusual latitudinal pattern of species richness in North and Central American entocytherids, most probably related to the biogeographic history of their hosts.

scholarly journals Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals

2011 ◽  
Vol 366 (1576) ◽  
pp. 2414-2425 ◽  
Author(s):  
T. Jonathan Davies ◽  
Lauren B. Buckley
Keyword(s):  
Species Richness ◽  
Phylogenetic Diversity ◽  
Diversity Indices ◽  
Environmental Predictors ◽  
Terrestrial Mammals ◽  
Extinction Rates ◽  
Biogeographic History ◽  
Shared Ancestry ◽  
History Of ◽  
Dispersal Events

Phylogenetic diversity (PD) captures the shared ancestry of species, and is increasingly being recognized as a valuable conservation currency. Regionally, PD frequently covaries closely with species richness; however, variation in speciation and extinction rates and/or the biogeographic history of lineages can result in significant deviation. Locally, these differences may be pronounced. Rapid recent speciation or high temporal turnover of lineages can result in low PD but high richness. In contrast, rare dispersal events, for example, between biomes, can elevate PD but have only small impact on richness. To date, environmental predictors of species richness have been well studied but global models explaining variation in PD are lacking. Here, we contrast the global distribution of PD versus species richness for terrestrial mammals. We show that an environmental model of lineage diversification can predict well the discrepancy in the distribution of these two variables in some places, for example, South America and Africa but not others, such as Southeast Asia. When we have information on multiple diversity indices, conservation efforts directed towards maximizing one currency or another (e.g. species richness versus PD) should also consider the underlying processes that have shaped their distributions.

Eritreo-Arabian Affinities of the Socotran Flora as Revealed from the Molecular Phylogeny of Aerva (Amaranthaceae)

2006 ◽  
Vol 31 (3) ◽  
pp. 560-570 ◽  
Author(s):  
Mike Thiv ◽  
Mats Thulin ◽  
Norbert Kilian ◽  
H. Peter Linder
Keyword(s):  
Indian Ocean ◽  
Sequence Data ◽  
Plastid Dna ◽  
Molecular Dating ◽  
Tropical Asia ◽  
Biogeographic Patterns ◽  
Dna Sequence Data ◽  
Biogeographic History ◽  
History Of ◽  
Taxonomic Groups

We investigated the colonization of the Indian Ocean archipelago of Socotra through phylogenetic analysis of Aerva (Amaranthaceae) based on nuclear and plastid DNA sequence data. The biogeographic history of the genus was tracked using ancestral area reconstructions and molecular dating. Three independent colonization lineages from the Eritreo-Arabian subregion of the Sudano-Zambesian Region were revealed: one endemic clade comprising Aerva revoluta / A. microphylla and once within A. lanata and A. javanica. Our results provide further support for the dominance of Eritreo-Arabian affinities in the flora of Socotra, in contrast to more rare affinities to Madagascar, the Mascarenes, southern Africa, and tropical Asia. Our data point towards colonization via dispersal, rather than a vicariance origin of the island elements. The overall biogeographic patterns of Aerva show only limited concordance with other taxonomic groups distributed on Indian Ocean islands.

The “Cobra-preta” of São Tomé Island, Gulf of Guinea, is a new species of Naja Laurenti, 1768 (Squamata: Elapidae)

Zootaxa ◽  
2017 ◽  
Vol 4324 (1) ◽  
pp. 121 ◽  
Author(s):  
LUIS M. P. CERÍACO ◽  
MARIANA P. MARQUES ◽  
ANDREAS SCHMITZ ◽  
AARON M. BAUER
Keyword(s):  
New Species ◽  
Conservation Status ◽  
Molecular Data ◽  
Oceanic Islands ◽  
Gulf Of Guinea ◽  
Biogeographic History ◽  
History Of ◽  
Morphological And Molecular Data ◽  
Taxonomic Groups ◽  
A New Species

The Cobra-Preta (black snake in Portuguese) of Sao Tomé Island in the Gulf of Guinea has historically been referred to as Naja (Boulengerina) melanoleuca (Squamata: Elapidae). Its presence on the island has been traditionally explained as an introduction from the mainland by Portuguese settlers, supposedly to control the rat population. This explanation has been widely accepted by local authorities and even international conservation agencies. The taxonomic identity of this snake has remained undisputed by all taxonomists who have published about it, with the exception of L. Capocaccia in 1961. Arguments supporting the human introduction hypothesis are weak and are contradicted by historical, morphological and molecular data. Further, the biogeographic history of the Gulf of Guinea oceanic islands and recent insights on the taxonomic identity and evolutionary history of other taxonomic groups occurring there suggest that the Cobra-Preta, in fact, represents a distinct lineage of the melanoleuca group, endemic to São Tomé. We here describe the Cobra Preta as a new species. The new species differs from N. (B.) melanoleuca, its sister species, by a distinct coloration ventral pattern and the type of contact of the sublingual scales. Data on the toxicology, distribution, ecology, folklore and conservation status of the new species are presented. 

scholarly journals The biogeographic history of eelpouts and related fishes: linking phylogeny, environmental change, and patterns of dispersal in a globally distributed fish group

2021 ◽  
Author(s):  
Scott Hotaling ◽  
Marek L. Borowiec ◽  
Luana S.F. Lins ◽  
Thomas Desvignes ◽  
Joanna L. Kelley
Keyword(s):  
Continental Drift ◽  
Data Sets ◽  
Evolutionary Origins ◽  
Biogeographic History ◽  
History Of ◽  
Fish Group ◽  
Polar Ocean ◽  
Taxonomic Groups ◽  
Key Events ◽  
Globally Distributed

AbstractModern genetic data sets present unprecedented opportunities to understand the evolutionary origins of taxonomic groups comprising hundreds to thousands of species. When the timing of key events are known, it is also possible to investigate biogeographic history in the context of major phenomena (e.g., continental drift). In this study, we investigated the biogeographic history of the suborder Zoarcoidei, a globally distributed fish group that includes species inhabiting both poles and multiple taxa that produce antifreeze proteins to survive chronic subfreezing temperatures. We first generated a multi-locus, time-calibrated phylogeny for the group. We then used biogeographic modeling to reconstruct ancestral ranges across the tree and quantify the type and frequency of biogeographic events (e.g., founder, dispersal). With these results, we considered how the cooling of the Southern and Arctic Oceans, which reached their present-day subfreezing temperatures 10-15 million years ago (Mya) and 2-3 Mya, respectively, may have shaped the evolutionary history of Zoarcoidei, with an emphasis on the most speciose and widely distributed family, eelpouts (family Zoarcidae). Our phylogenetic results clarified standing issues in the Zoarcoidei taxonomy and showed that the group began to diversify in the Oligocene ∼31-32 Mya, with the center of origin for all families in north temperate waters. Within-area speciation was the most common biogeographic event in the group’s history (80% of all events) followed by dispersal (20%). Finally, we found mixed evidence for polar ocean cooling underpinning Zoarcoidei diversification, with support limited to eelpout speciation in the Southern Ocean over the last 10 million years.

Coevolutionary patterns and diversification of avian malaria parasites in African sunbirds (Family Nectariniidae)

Parasitology ◽  
2014 ◽  
Vol 142 (5) ◽  
pp. 635-647 ◽  
Author(s):  
ELVIN J. LAURON ◽  
CLAIRE LOISEAU ◽  
RAURI C. K. BOWIE ◽  
GREG S. SPICER ◽  
THOMAS B. SMITH ◽  
...  
Keyword(s):  
Host Specificity ◽  
Avian Malaria ◽  
Malaria Parasites ◽  
Biogeographic History ◽  
History Of ◽  
Host Parasite ◽  
East West ◽  
Parasite Assemblages ◽  
Coevolutionary History ◽  
Avian Malaria Parasites

SUMMARYThe coevolutionary relationships between avian malaria parasites and their hosts influence the host specificity, geographical distribution and pathogenicity of these parasites. However, to understand fine scale coevolutionary host–parasite relationships, robust and widespread sampling from closely related hosts is needed. We thus sought to explore the coevolutionary history of avianPlasmodiumand the widespread African sunbirds, family Nectariniidae. These birds are distributed throughout Africa and occupy a variety of habitats. Considering the role that habitat plays in influencing host-specificity and the role that host-specificity plays in coevolutionary relationships, African sunbirds provide an exceptional model system to study the processes that govern the distribution and diversity of avian malaria. Here we evaluated the coevolutionary histories using a multi-gene phylogeny for Nectariniidae and avianPlasmodiumfound in Nectariniidae. We then assessed the host–parasite biogeography and the structuring of parasite assemblages. We recoveredPlasmodiumlineages concurrently in East, West, South and Island regions of Africa. However, severalPlasmodiumlineages were recovered exclusively within one respective region, despite being found in widely distributed hosts. In addition, we inferred the biogeographic history of these parasites and provide evidence supporting a model of biotic diversification in avianPlasmodiumof African sunbirds.

scholarly journals Updated estimates of biotic diversity and endemism for Madagascar

Oryx ◽  
2005 ◽  
Vol 39 (1) ◽  
pp. 73-77 ◽  
Author(s):  
Steven M. Goodman ◽  
Jonathan P. Benstead
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Research Team ◽  
Field Research ◽  
The Past ◽  
Biotic Diversity ◽  
Wide Range ◽  
History Of ◽  
Taxonomic Groups ◽  
Biodiversity Information

Madagascar is a critical priority for international conservation efforts, based on almost unparalleled levels of endemism, species diversity, and human threat. Field research conducted over the past two decades has greatly expanded knowledge of the island's biota, making it difficult for any single research team to maintain up to date estimates of biodiversity and endemism across taxonomic groups. The recent publication of The Natural History of Madagascar, a synthesis by nearly 300 contributors from a wide range of disciplines, provides the means to update these estimates. Here, we summarize biodiversity information presented in the volume by providing revised estimates of species richness, endemism, and state of knowledge of a wide variety of taxonomic groups occurring on the island.

scholarly journals The BHL-Plazi Partnership: Getting data from the 1800s directly into 21st century, reused digital accessible knowledge

2021 ◽  
Vol 5 ◽  
Author(s):  
Diego Alvares ◽  
Marcus Guidoti ◽  
Felipe Simoes ◽  
Carolina Sokolowicz ◽  
Donat Agosti
Keyword(s):  
Data Mining ◽  
Service Providers ◽  
Nuclear Research ◽  
Free Access ◽  
Digital Repository ◽  
Global Biodiversity Information Facility ◽  
European Organization ◽  
Governmental Organization ◽  
Access To Data ◽  
Taxonomic Groups

Plazi is a Swiss non-governmental organization dedicated to the liberation of data imprisoned in flat, dead-end formats such as PDFs. In the process, the data therein is annotated and exported in various formats, following field-specific standards, facilitating free access and reutilization by several other service providers and end-users. This data mining and enhancement process allows for the rediscovery of the known biodiversity since the knowledge on known taxa is published into an ever-growing corpus of papers, chapters and books, inaccessible to the state-of-the-art service providers, such as Global Biodiversity Information Facility (GBIF). The data liberated by Plazi focuses on taxonomic treatments, which carry the unit of knowledge about a taxon concept in a given publication and can be considered the building block of taxonomic science. Although these extracted taxonomic treatments can be found in Plazi’s TreatmentBank and Biodiversity Literature Repository (BLR), hosted in the European Organization for Nuclear Research (CERN) digital repository Zenodo, data included in treatments (e.g., material citations and treatment citations) can also be found in other applications as well, such as Plazi’s Synospecies, Zenodeo, and GBIF. Plazi’s efforts result in more Findable, Accessible, Interoperable, and Reusable (FAIR) biodiversity literature, improving, enhancing and enabling access to data included therein as digital accessible data, otherwise almost unreachable. The Biodiversity Heritage Library (BHL), on the other hand, provides a pivotal service by digitizing heritage literature and current literature for which BHL negotiates permission, and provides free access to otherwise inaccessible sources. In 2021, BHL and Plazi signed a Statement of Collaboration, aiming to combine the efforts of both institutions to contribute even further to FAIR-ifying biodiversity literature and data. In a collaborative demonstration project, we selected the earliest volumes and issues of the Revue Suisse de Zoologie in order to conduct a pilot study that combines the efforts of both BHL and Plazi. The corpus is composed of eight volumes (tomes), 24 issues (numbers) and 98 papers, including a total of over 5000 pages and 200 images. To process this material, BHL assigned CrossRef Digital Object Identifiers (DOI) to these already digitally accessible publications. Plazi created a template to be used in GoldenGate-Imagine, indicating key parameters used for tailored data mining of these articles, and customized to the journal’s graphic layout characteristics at that time. Then, we proceeded with quality control steps to provide fit-for-use data for BLR and GBIF by ensuring that the data was correctly annotated and eliminating potential data transit blockages at Plazi’s built-in data gatekeeper. The data was then subsequently reused by GBIF. Finally, we present here the summary of the obtained results, highlighting the number of key publication attributes aforementioned (pages, images), but also including a drill-down into the different taxonomic groups, countries and collections of origin of the studied material, and more. All the data is available via the Plazi statistics, the Biodiversity Literature Repository Website and community at Zenodo, the Zenodeo APIs and GBIF where the data is being reused.

scholarly journals Stones in the road prevents effective implementation of eDNA-based freshwater quality monitoring in the Iberian Peninsula

2021 ◽  
Vol 4 ◽  
Author(s):  
Álvaro Fueyo ◽  
Javier Granero-Castro ◽  
Beatriz Villazán Peñalosa ◽  
Yaisell Borrell Pichs
Keyword(s):  
Iberian Peninsula ◽  
Dna Sequences ◽  
Mitochondrial Gene ◽  
Freshwater Ecosystems ◽  
Freshwater Species ◽  
Sequence Coverage ◽  
Global Biodiversity Information Facility ◽  
Species List ◽  
Family Level ◽  
Taxonomic Groups

The Water Framework Directive (WFD) monitoring requires the use of stressor-specific Multimetric Indices, intercalibrated and validated at river basin level, such as the IBMWP, which is one of the most widely used indices for the biomonitoring of rivers in the Iberian Peninsula. This qualitative index is based on the identification mainly at family level of 125 groups of macroinvertebrates. Currently, molecular biomonitoring systems (biomonitoring 2.0) is widely considered as a good alternative to conduct water quality assessments. The problem comes with the requirement of having complete DNA sequences databases for the targeted species within the indicator groups. In order to know the percentage of sequence coverage of the different taxonomic groups, is needed to know the number of freshwater species in each group. The fact that currently it is only necessary to identify them morphologically at family level to calculate the index means that there are no exhaustive lists of lower taxonomic ranges. In this study, we have studied the available taxonomic databases at species level for river macroinvertebrates in the Iberian Peninsula. For this purpose, species geographically referred to the Iberian Peninsula were extracted from three sources: two European (Freshwaterecology.info database and Weigand et al. (2019)) and one Iberian database/list (Múrria et al. 2020). The resultant species list was compared with GBIF (Global Biodiversity Information Facility) using its tool “Species Matching” to find synonyms and fuzzy names. The similarities and differences between databases were studied (considering the synonyms but not the fuzzy names) and a new list of 3586 species was constructed. Our analysis revealed that from 125 taxonomic groups covered by the IBMWP, there are no species collected for 11 of them (9%) and for another 34 groups (27%) there are less than 5 species collected in the databases. Then, using the BAGS software, all sequences of the mitochondrial gene COX1 were mined from BOLD database. From the 3586 species in the list, only 1900 (53%) have at least one sequence in BOLD. Therefore, conducting biomonitoring 2.0 in Iberian freshwater ecosystems is far from effective today. We need to overcome two big obstacles to reach the goal of using molecular biomonitoring in the Iberian Peninsula: a complete taxonomic list of quality indicators species by groups, and to sequence DNA barcodes from all relevant species.

Paleontology and stratigraphy of Middle Eocene rock units in the southern Green River and Uinta Basins, Wyoming and Utah

2017 ◽  
Vol 4 ◽  
pp. 1-53 ◽  
Author(s):  
Paul Murphey ◽  
K.E. Townsend ◽  
Anthony Friscia ◽  
James Westgate ◽  
Emmett Evanoff ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Middle Eocene ◽  
Green River Basin ◽  
Green River ◽  
Scientific Exploration ◽  
History Of ◽  
Climatic History ◽  
Field Excursion ◽  
Land Mammal ◽  
Bridger Formation

The Bridger Formation is restricted to the Green River Basin in southwest Wyoming, and the Uinta and Duchesne River Formations are located in the Uinta Basin in Utah. These three rock units and their diverse fossil assemblages are of great scientific importance and historic interest to vertebrate paleontologists. Notably, they are also the stratotypes from oldest to youngest for the three middle Eocene North American Land Mammal Ages—the Bridgerian, Uintan, and Duchesnean. The fossils and sediments of these formations provide a critically important record of biotic, environmental, and climatic history spanning approximately 10 million years (49 to 39 Ma). This article provides a detailed field excursion through portions of the Green River and Uinta Basins that focuses on locations of geologic, paleontologic, and historical interest. In support of the field excursion, we also provide a review of current knowledge of these formations with emphasis on lithostratigraphy, biochronology, depositional, and paleoenvironmental history, and the history of scientific exploration.

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