Bioinformatics and Genomics

Article commentary

Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica

Editor rating: 8 / 10

Curtis Daehler –– This work provides genetic evidence suggesting the native range of a widely distributed animal that was accidentally spread by humans starting hundreds of years ago.
The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages

Editor rating: 8 / 10

Xavier Pochon –– This study provides the first range-wide phylogeographic study of the banded coral shrimp S. hispidus, extending across more than 27,000 km of the globe. Coalescence analysis brings evidence that an isolated Indo-Pacific lineage evolved from a rare dispersal event from the Atlantic around South Africa via the Benguela Current, thereby colonizing the Indian and Pacific Oceans, followed by dispersal across the Indo-Pacific in the last 200,000 years. Surprisingly, this benthic coral reef associated shrimp shows a single haplotype dominating the largest continuous tropical oceanic expanse on the planet.
Identification and characterization of the cytosine-5 DNA methyltransferase gene family in Salvia miltiorrhiza

Editor rating: 7 / 10

Gerrit Beemster –– Epigenetic regulation is rapidly becoming a new regulatory mechanism in developmental processes and this study is a nice contribution to that field using a non model species.
Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula

Editor rating: 7 / 10

Tatiana Vishnivetskaya –– Metal resistant strain from cold environments could be useful for bioremediation at low temperatures
A bibliometric analysis in gene research of myocardial infarction from 2001 to 2015

Editor rating: 7 / 10

Maria Cristina Albertini –– Important information has been disclosed in the paper.
A simple molecular technique for distinguishing species reveals frequent misidentification of Hawaiian corals in the genus Pocillopora

Editor rating: 8 / 10

Xavier Pochon –– This study developed a simple and cost-effective assay that quickly allows for discrimination amongst coral species in the genus Pocillopora using simple PCR amplification followed by digestion with widely available restriction enzymes. Pocilloporid corals exhibit extreme phenotypic plasticity, making morphological identification of species very challenging. The assay was tested on 691 coral samples collected from across the Hawaiian Archipelago and successfully characterised all six Pocillopora species occurring in Hawaii. Compared to sequence-based identification, this method is simple, rapid and represents a cost saving of nearly 95%. This work will benefit future studies of population structure, ecology, biodiversity, evolution and conservation in this challenging coral genus.
Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs

Editor rating: 7 / 10

Marc Robinson-Rechavi –– This study allows to link natural variation in morphology with genetic divergence in expression patterns, thus helping link ecology to molecular genomics.
An Indo-Pacific damselfish (Neopomacentrus cyanomos) in the Gulf of Mexico: origin and mode of introduction

Editor rating: 7 / 10

Donald Kramer –– Although only dealing with a single invasive species, it is a very thorough and interesting analysis of the potential for oil rigs to move fish (and potentially other marine species) around the world.
Complex versus simple models: ion-channel cardiac toxicity prediction

Editor rating: 8 / 10

Heiko Enderling –– This article discusses the contributions of quantitative models in predicting biology, and makes an important point about the balance of simplicity/complexity/accuracy/usefulness of biophysical models. If simple models capture biological complexity, the use of more detailed models must be properly justified.
Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics

Editor rating: 8 / 10

Todd Vision –– This is a novel and innovative approach to studying the genomic correlates of convergent evolution. It is likely to inspire similar studies in other systems and for other kinds of genomic changes, as well as bioinformatic work to refine and extend the methods.

Discussing these articles

The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages https://t.co/TXOB7dyxro https://t.co/QkZN9Zfxz0

Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula https://t.co/Pe0VoMrmWT

Zhou H, Tan W, Qiu Z, Song Y, Gao S. (2018) A bibliometric analysis in gene research of myocardial infarction from 2001 to 2015. PeerJ 6:e4354 https://t.co/DLzmzAy7tn #CiteSpace https://t.co/9IFzDlxMK6

New paper to ID Pocillopora corals https://t.co/It92AVvX7X

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs Good job @vonStadarhraun https://t.co/SKVXoWQ3Ix via @thePeerJ

new publication: https://t.co/MONo6omrX3 a comprehensive analysis on how a well-defined simple heuristic is as good (if not better) than complex mathematical models, used by FDA and bloated pharma companies, in ion-channel safety pharmacology #mathbiology

234 days ago
Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics https://t.co/z1sFqYaSeP