scholarly journals Coat of many colours—DNA reveals polymorphism of mantle patterns and colouration in CaribbeanCyphomaRöding, 1798 (Gastropoda, Ovulidae)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3018 ◽  
Author(s):  
Bastian T. Reijnen ◽  
Sancia E.T. van der Meij
Keyword(s):  
Model Organism ◽  
Incipient Speciation ◽  
Defence Mechanisms ◽  
Balanced Polymorphism ◽  
Reef Degradation ◽  
Rapid Divergence ◽  
The Caribbean ◽  
Morphological Differences ◽  
Physical Defence ◽  
Future Work

The iconic gastropod genusCyphomais commonly observed in the Caribbean, where it lives in association with various octocorallian hosts. Each species in the genusCyphomahas a unique, characteristic mantle pattern and colouration, which separates the valid taxa. Because of its abundance and recognisabilityCyphoma gibbosumhas been used as a model organism in several studies concerning allelochemicals, reef degradation, and physical defence mechanisms. Molecular analyses based on four molecular markers (COI, 16S, H3 and 28S) for threeCyphomaspecies (C. gibbosum,C. mcgintyi,C. signatum) and an unidentified black morph, collected from three localities in the Caribbean, show that they represent morphological varieties of a single, genetically homogeneous species. This outcome is in agreement with previous anatomical studies. As a resultC. mcgintyiandC. signatumare synonymised withC. gibbosum, which is a key result for future work usingC. gibbosumas a model organism. The striking morphological differences in mantle pattern and colouration are hypothesised to be the result of one of three possible scenarios: rapid divergence, supergenes (including balanced polymorphism), or incipient speciation.

Development and Molecular Genetics of Marchantia polymorpha

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Takayuki Kohchi ◽  
Katsuyuki T. Yamato ◽  
Kimitsune Ishizaki ◽  
Shohei Yamaoka ◽  
Ryuichi Nishihama
Keyword(s):  
Model Organism ◽  
Land Plant ◽  
Marchantia Polymorpha ◽  
Annual Review ◽  
Publication Date ◽  
Molecular Tools ◽  
Genetic Redundancy ◽  
Morphological Differences ◽  
Evo Devo ◽  
Basal Position

Bryophytes occupy a basal position in the monophyletic evolution of land plants and have a life cycle in which the gametophyte generation dominates over the sporophyte generation, offering a significant advantage in conducting genetics. Owing to its low genetic redundancy and the availability of an array of versatile molecular tools, including efficient genome editing, the liverwort Marchantia polymorpha has become a model organism of choice that provides clues to the mechanisms underlying eco-evo-devo biology in plants. Recent analyses of developmental mutants have revealed that key genes in developmental processes are functionally well conserved in plants, despite their morphological differences, and that lineage-specific evolution occurred by neo/subfunctionalization of common ancestral genes. We suggest that M. polymorpha is an excellent platform to uncover the conserved and diversified mechanisms underlying land plant development. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Resilience in the Caribbean - Natural Hazards Exposure Assessment and Areas for Future Work

10.1596/36408 ◽  
2020 ◽  
Author(s):  
A.E. Schweikert ◽  
G.L. L'her ◽  
L.G. Nield ◽  
S.W. Kerber ◽  
R.R. Flanagan ◽  
...  
Keyword(s):  
Exposure Assessment ◽  
Natural Hazards ◽  
The Caribbean ◽  
Future Work

scholarly journals Ecological solutions to reef degradation: optimizing coral reef restoration in the Caribbean and Western Atlantic

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2597 ◽  
Author(s):  
Diego Lirman ◽  
Stephanie Schopmeyer
Keyword(s):  
Coral Reef ◽  
Scientific Basis ◽  
Western Atlantic ◽  
Reef Restoration ◽  
Reef Structure ◽  
Reef Degradation ◽  
Complex Engineering ◽  
The Caribbean ◽  
Direct And Indirect Benefits

Reef restoration activities have proliferated in response to the need to mitigate coral declines and recover lost reef structure, function, and ecosystem services. Here, we describe the recent shift from costly and complex engineering solutions to recover degraded reef structure to more economical and efficient ecological approaches that focus on recovering the living components of reef communities. We review the adoption and expansion of the coral gardening framework in the Caribbean and Western Atlantic where practitioners now grow and outplant 10,000’s of corals onto degraded reefs each year. We detail the steps for establishing a gardening program as well as long-term goals and direct and indirect benefits of this approach in our region. With a strong scientific basis, coral gardening activities now contribute significantly to reef and species recovery, provide important scientific, education, and outreach opportunities, and offer alternate livelihoods to local stakeholders. While challenges still remain, the transition from engineering to ecological solutions for reef degradation has opened the field of coral reef restoration to a wider audience poised to contribute to reef conservation and recovery in regions where coral losses and recruitment bottlenecks hinder natural recovery.

scholarly journals Testing species hypotheses for Fridericia magna, an enchytraeid worm (Annelida: Clitellata) with great mitochondrial variation

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Svante Martinsson ◽  
Mårten Klinth ◽  
Christer Erséus
Keyword(s):  
Species Delimitation ◽  
Single Species ◽  
The Other ◽  
Cryptic Speciation ◽  
Incipient Speciation ◽  
Nuclear Markers ◽  
Separate Species ◽  
Mitochondrial Markers ◽  
Morphological Differences ◽  
Barcode Gap

Abstract Background Deep mitochondrial divergences were observed in Scandinavian populations of the terrestrial to semi-aquatic annelid Fridericia magna (Clitellata: Enchytraeidae). This raised the need for testing whether the taxon is a single species or a complex of cryptic species. Results A total of 62 specimens from 38 localities were included in the study, 44 of which were used for species delimitation. First, the 44 specimens were divided into clusters using ABGD (Automatic Barcode Gap Discovery) on two datasets, consisting of sequences of the mitochondrial markers COI and 16S. For each dataset, the worms were divided into six not completely congruent clusters. When they were combined, a maximum of seven clusters, or species hypotheses, were obtained, and the seven clusters were used as input in downstream analyses. We tested these hypotheses by constructing haplowebs for two nuclear markers, H3 and ITS, and in both haplowebs the specimens appeared as a single species. Multi-locus species delimitation analyses performed with the Bayesian BPP program also mainly supported a single species. Furthermore, no apparent morphological differences were found between the clusters. Two of the clusters were partially separated from each other and the other clusters, but not strongly enough to consider them as separate species. All 62 specimens were used to visualise the Scandinavian distribution, of the species, and to compare with published COI data from other Fridericia species. Conclusion We show that the morphospecies Fridericia magna is a single species, harbouring several distinct mitochondrial clusters. There is partial genetic separation between some of them, which may be interpreted as incipient speciation. The study shows the importance of rigorous species delimitation using several independent markers when deep mitochondrial divergences might give the false impression of cryptic speciation.

scholarly journals Lepidochitona pseudoliozonis, una nueva especie de quitón (Polyplacophora: Ischnochitonidae) del norte del Caribe

2015 ◽  
Vol 63 (2) ◽  
pp. 369 ◽  
Author(s):  
Cedar I. García-Ríos
Keyword(s):  
Puerto Rico ◽  
New Species ◽  
Cytochrome Oxidase ◽  
Mitochondrial Gene ◽  
Florida Keys ◽  
Cytochrome Oxidase I ◽  
Type Locality ◽  
Gene Coding ◽  
The Caribbean ◽  
Morphological Differences

<p>The genus <em>Lepidochitona</em> (Gray 1821) contains relatively small chitons with a distinctive girdle, dorsally clothed with non-overlapping calcareous corpuscles. In the Caribbean, it is represented by four species: <em>L. liozonis</em> (Dall, &amp; Simpson, 1901), <em>L. rosea</em> Kaas, 1972, <em>L. rufoi</em> García-Ríos, 2010 and <em>L. bullocki</em> García-Ríos, 2011. A rutinary morphological inspection of 10 specimens of a <em>Lepidochitona</em> species from the Florida Keys was concordant with <em>L. liozonis </em>(the only species of the genus informed for Florida). They did not show many morphological differences that could justify its separation from the specimens from Puerto Rico (the type locality). However, the comparison of sequences of the mitochondrial gene coding for cytochrome oxidase I (COI) of <em>L. liozonis </em>from Puerto Rico and the Florida specimens showed a divergence of 14%. This divergence is incompatible with a reproductively connected species. In addition to their genetic differences, the new species differs from <em>L</em>. <em>liozonis</em> in having bigger size, longer marginal spicules and a postmucronal slope very concave.</p>

scholarly journals Terrestrial Isopoda (Crustacea, Oniscidea) from the coasts of Costa Rica, with descriptions of three new species

2018 ◽  
Vol 66 (1-1) ◽  
pp. 187 ◽  
Author(s):  
Stefano Taiti ◽  
Giuseppe Montesanto ◽  
José A. Vargas
Keyword(s):  
New Species ◽  
Costa Rica ◽  
Pacific Coast ◽  
Caribbean Sea ◽  
The Pacific ◽  
The Caribbean ◽  
Morphological Differences ◽  
Three New Species ◽  
Halophilic Species ◽  
Caribbean Populations

Abstract: Seven species of terrestrial isopods are recorded from the coasts of the Pacific and Caribbean sides of Costa Rica. Three species (Buchnerillo neotropicalis, Hawaiioscia nicoyaensis and Trichorhina biocellata) are described as new and two species (Tylos niveus and Armadilloniscus cf. caraibicus) are newly recorded from the country. The poorly known species T. niveus is also illustrated. At present the total number of terrestrial isopod species recorded from Costa Rica is 30. Interestingly four typical littoral halophilic species (Ligia baudiniana, Tylos wegeneri, T. niveus and A. cf. caraibicus) are present on both the Pacific coast of Costa Rica and on the coasts of the lands encompassed by the Caribbean Sea. With the sole exception of A. cf. caraibicus, no morphological differences could be detected from the Pacific and Caribbean populations of those species. Rev. Biol. Trop. 66(Suppl. 1): S187-S210. Epub 2018 April 01. 

scholarly journals Morphological and genetic divergence between Mediterranean and Caribbean populations of Madracis pharensis (Heller 1868) (Scleractinia, Pocilloporidae): too much for one species?

Zootaxa ◽  
2018 ◽  
Vol 4471 (3) ◽  
pp. 473
Author(s):  
FRANCESCA BENZONI ◽  
ROBERTO ARRIGONI ◽  
MICHAEL L . BERUMEN ◽  
MARCO TAVIANI ◽  
PIM BONGAERTS ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Species Boundaries ◽  
East Atlantic ◽  
Coral Genus ◽  
The Caribbean ◽  
The Mediterranean ◽  
Morphological Differences ◽  
Central Atlantic ◽  
Caribbean Populations ◽  
Study Species

The colonial stony coral genus Madracis is cosmopolitan, lives in shallow and deep water habitats, and includes zooxanthellate, azooxanthellate and facultative symbiotic species. One of its species, Madracis pharensis, has been recorded from the Mediterranean and East Atlantic, where it forms small knobby and facultative zooxanthellate colonies (also named M. pharensis f. pharensis), and from the tropical Caribbean, where it also occurs in a massive and zooxanthellate form (named M. pharensis f. luciphila by some). These two forms have been previously found to host different Symbiodinium species. In this study, species boundaries and phylogenetic relationships between these two Madracis pharensis forms (from the Mediterranean Sea and the Caribbean), M. senaria, and the Indo-west Pacific M. kirbyi were analyzed through an integrated systematics approach, including corallite dimensions, micromorphology and two molecular markers (ITS and ATP8). Significant genetic and morphological differences were found between all the examined Madracis species, and between M. pharensis from the Mediterranean Sea and M. pharensis f. luciphila from the Caribbean in particular. Based on these results, the latter does not represent a zooxanthellate ecomorph of the former but a different species. Its identity remains to be ascertained and its relationship with the Caribbean M. decactis, with which it bears morphologic resemblance, must be investigated in further studies. Overall, the presence of cryptic Madracis species in the Easter and Central Atlantic Ocean remains to be evaluated. 

scholarly journals A novel deep learning scheme for morphology-based classification of mycobacterial infection in unstained macrophages

2019 ◽  
Author(s):  
Xinzhuo Zhao ◽  
Yanqing Bao ◽  
Lin Wang ◽  
Wei Qian ◽  
Jianjun Sun
Keyword(s):  
Deep Learning ◽  
Bacterial Infections ◽  
Morphological Changes ◽  
Model Organism ◽  
Bacterial Pathogen ◽  
Mycobacterial Infection ◽  
Fine Tuning ◽  
Great Promise ◽  
Morphological Differences ◽  
Guided Propagation

AbstractObjectiveMycobacterium tuberculosis (Mtb) is an airborne, contagious bacterial pathogen that causes widespread infections in humans. Using Mycobacterium marinum (Mm), a surrogate model organism for Mtb research, the present study develops a deep learning-based scheme that can classify the Mm-infected and uninfected macrophages in tissue culture solely based on morphological changes.MethodsA novel weak-and semi-supervised learning method is developed to detect and extract the cells, firstly. Then, transfer learning and fine-tuning from the CNN is built to classify the infected and uninfected cells.ResultsThe performance is evaluated by accuracy (ACC), sensitivity (SENS) and specificity (SPEC) with 10-fold cross-validation. It demonstrates that the scheme can classify the infected cells accurately and efficiently at the early infection stage. At 2 hour post infection (hpi), we achieve the ACC of 0.923 ± 0.005, SENS of 0.938 ± 0.020, and SPEC of 0.905 ± 0.019, indicating that the scheme has detected significant morphological differences between the infected and uninfected macrophages, although these differences are hardly visible to naked eyes. Interestingly, the ACC at 12 and 24 hpi are 0.749 ± 0.010 and 0.824 ± 0.009, respectively, suggesting that the infection-induced morphological changes are dynamic throughout the infection. Finally, deconvolution with guided propagation maps the key morphological features contributing to the classification.SignificanceThis proof-of-concept study provides a novel venue to investigate bacterial pathogenesis in a macroscopic level and has a great promise in diagnosis of bacterial infections.

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