It's a family act: the geminin triplets take center stage in motile ciliogenesis

The balance between proliferation and differentiation is a fundamental aspect of multicellular life. Perhaps nowhere is this delicate balance more palpable than in the multiciliated cells (MCCs) that line the respiratory tract, the ependyma, and the oviduct. These cells contain dozens to hundreds of motile cilia that beat in a concerted fashion to generate directed fluid flow over the tissue surface. Although MCCs have exited the cell cycle, remarkably, they retain the ability to duplicate their centrioles and to mature those centrioles into ciliary basal bodies—two features, which are known to be normally under strict cell cycle control (Firat‐Karalar & Stearns, 2014 ). How post‐mitotic MCCs retain this ability, remains unclear. In the past several months, four research articles, including one from Terré et al in this issue of The EMBO Journal, have described a vital role for the geminin coiled‐coil domain‐containing protein (Gemc1) in the MCC gene expression program in multiple tissues and organisms, that bring us closer to understanding this question (Kyrousi et al, 2015 ; Zhou et al, 2015 ; Arbi et al, 2016 ; Terré et al, 2016 ).     

Mitochondria just wanna have FUN(DC1)

A fascinating story is unfolding at the interface between mitochondria and the ER. Two new papers, one in this issue of The EMBO Journal (Wu et al, 2016 ) and one in the journal Autophagy (Chen et al, 2016 ), further clarify the role of mitochondrial outer membrane protein FUNDC1 in autophagy and connect it to mitochondrial fission occurring at the interface between mitochondria and the ER.     

Using RAD‐seq to recognize sex‐specific markers and sex chromosome systems

Next‐generation sequencing methods have initiated a revolution in molecular ecology and evolution (Tautz et al. 2010 ). Among the most impressive of these sequencing innovations is restriction site‐associated DNA sequencing or RAD‐seq (Baird et al. 2008 ; Andrews et al. 2016 ). RAD‐seq uses the Illumina sequencing platform to sequence fragments of DNA cut by a specific restriction enzyme and can generate tens of thousands of molecular genetic markers for analysis. One of the many uses of RAD‐seq data has been to identify sex‐specific genetic markers, markers found in one sex but not the other (Baxter et al. 2011 ; Gamble & Zarkower 2014 ). Sex‐specific markers are a powerful tool for biologists. At their most basic, they can be used to identify the sex of an individual via PCR. This is useful in cases where a species lacks obvious sexual dimorphism at some or all life history stages. For example, such tests have been important for studying sex differences in life history (Sheldon 1998 ; Mossman & Waser 1999 ), the management and breeding of endangered species (Taberlet et al. 1993 ; Griffiths & Tiwari 1995 ; Robertson et al. 2006 ) and sexing embryonic material (Hacker et al. 1995 ; Smith et al. 1999 ). Furthermore, sex‐specific markers allow recognition of the sex chromosome system in cases where standard cytogenetic methods fail (Charlesworth & Mank 2010 ; Gamble & Zarkower 2014 ). Thus, species with male‐specific markers have male heterogamety (XY) while species with female‐specific markers have female heterogamety (ZW). In this issue, Fowler & Buonaccorsi ( 2016 ) illustrate the ease by which RAD‐seq data can generate sex‐specific genetic markers in rockfish (Sebastes). Moreover, by examining RAD‐seq data from two closely related rockfish species, Sebastes chrysomelas and Sebastes carnatus (Fig.  1 ), Fowler & Buonaccorsi ( 2016 ) uncover shared sex‐specific markers and a conserved sex chromosome system.     

Reliability of map accuracy assessments: A reply to Roff et al. (2016)

Roff et al. (Ecological Management and Restoration, 17 , 2016, 000) provide a discussion of the criteria expected for the best approach to validation of mapping programs and uses Hunter (Ecological Management & Restoration 17 , 2016, 40) to highlight issues involved. While we support the general principles outlined, we note that the review does not apply the same standards to Sivertsen et al. (Greater Hunter Native Vegetation Mapping Geodatabase Guide (Version 4.0). Office of Environment and Heritage, Department of the Premier and Cabinet, Sydney, Australia, 2011), the original document critiqued by Hunter (Ecological Management & Restoration 17 , 2016, 40). The Hunter (Ecological Management & Restoration 17 , 2016, 40) validation was based on a larger sample size, greater sampling within mapping units and greater representation of landscapes than Sivertsen et al. (Greater Hunter Native Vegetation Mapping Geodatabase Guide (Version 4.0). Office of Environment and Heritage, Department of the Premier and Cabinet, Sydney, Australia, 2011). Survey and validation sites being placed along public roads and lands are common to both the general Office of Environment and Heritage (OEH) and Hunter (Ecological Management & Restoration 17 , 2016, 40) validation methodologies. Thus, the criticisms of Roff et al. (Ecological Management and Restoration, 17 , 2016, 000) of the Hunter (Ecological Management & Restoration 17 , 2016, 40) approach apply equally, if not more, to Sivertsen et al. (Greater Hunter Native Vegetation Mapping Geodatabase Guide (Version 4.0). Office of Environment and Heritage, Department of the Premier and Cabinet, Sydney, Australia, 2011). We outline in the article how the Roff et al. (Ecological Management and Restoration, 17 , 2016, 000) critique was selective and in some cases incorrect in its analysis of issues presented in Hunter (Ecological Management & Restoration 17 , 2016, 40) and did not apply the same criteria to their own work. We conclude by discussing future directions for validating and mapping vegetation communities.     

Mitochondrial DNA mutations in iPS cells: mtDNA integrity as standard iPSC selection criteria?

Somatic cells harbor random heteroplasmic mitochondrial DNA mutations, which are considered to contribute to aging. In this issue of The EMBO Journal, Perales‐Clemente et al ( 2016 ) show that mtDNA mutations, present at low levels in the starting fibroblasts, become enriched in iPS cells and lead to functional defects in iPS‐derived cells. In another recent study, Kang et al ( 2016 ) demonstrated that accumulation of mtDNA mutations of somatic origin in iPSCs is age related.     

DNA binding to SMC ATPases—trapped for release

The SMC/Rad50/RecN proteins are universal DNA‐associated ABC‐type ATPases with crucial functions in genome maintenance. New insights into Rad50–DNA complex structure and cohesin regulation inspire a speculative look at the entire superfamily. Identification of a continuous DNA binding site across the Rad50 dimer interface (Liu et al, 2016 ; Seifert et al, 2016 ) suggests a similar site in cohesin. The localization of this site hints a DNA‐activated mechanism for cohesin removal from chromosomes.     

Coalescing molecular evolution and DNA barcoding

The DNA barcoding concept (Woese et al. 1990 ; Hebert et al. 2003 ) has considerably boosted taxonomy research by facilitating the identification of specimens and discovery of new species. Used alone or in combination with DNA metabarcoding on environmental samples (Taberlet et al. 2012 ), the approach is becoming a standard for basic and applied research in ecology, evolution and conservation across taxa, communities and ecosystems (Scheffers et al. 2012 ; Kress et al. 2015 ). However, DNA barcoding suffers from several shortcomings that still remain overlooked, especially when it comes to species delineation (Collins & Cruickshank 2012 ). In this issue of Molecular Ecology, Barley & Thomson ( 2016 ) demonstrate that the choice of models of sequence evolution has substantial impacts on inferred genetic distances, with a propensity of the widely used Kimura 2‐parameter model to lead to underestimated species richness. While DNA barcoding has been and will continue to be a powerful tool for specimen identification and preliminary taxonomic sorting, this work calls for a systematic assessment of substitution models fit on barcoding data used for species delineation and reopens the debate on the limitation of this approach.     

Ready,Set…Poised!: Polycomb target genes are bound by poised RNA polymerase II throughout differentiation

In embryonic stem cells (ESCs), silent genes with major developmental functions display a unique epigenetic state in which strong and broad binding by Polycomb repressive complexes (PRCs) is accompanied by the presence of poised RNA polymerase II (RNAPII) and activating histone marks (e.g. H3K4me3) (Azuara et al, 2006 ; Bernstein et al, 2006 ; Stock et al, 2007 ; Brookes et al, 2012 ). It has been suggested that the plasticity and broad differentiation potential of pluripotent cells might rely, at least partly, on this unique epigenetic state (Bernstein et al, 2006 ; Stock et al, 2007 ). In their recent study, Pombo and colleagues (Ferrai et al, 2017 ) show that a similar epigenetic state can be found at a subset of major developmental genes throughout the differentiation of ESCs into neurons, providing novel and exciting insights into the molecular basis of cellular plasticity in differentiated cells.     

Positive range–abundance relationships in Indo‐Pacific bird communities

Reeve et al. (2016, Ecography, 39 , 990–997) recently reported negative range–abundance relationships in Indo‐Pacific bird communities and speculated that geographical isolation facilitates the evolution of broad‐niched, small‐ranged and abundant species. We tested this relationship using a large independent data set on range and abundance of birds across New Caledonia (over 4,000 bird census points for 17,300 km²). In contradiction to Reeve et al. (2016, Ecography, 39 , 990–997), we found clear evidence that range–abundance relationships are positive and endemic species have narrower habitat niches than wide‐range species. Our findings are likely valid also for other islands in the Indo‐Pacific.     

A hot topic: the genetics of adaptation to geothermal vents in Mimulus guttatus

Identifying the individual loci and mutations that underlie adaptation to extreme environments has long been a goal of evolutionary biology. However, finding the genes that underlie adaptive traits is difficult for several reasons. First, because many traits and genes evolve simultaneously as populations diverge, it is difficult to disentangle adaptation from neutral demographic processes. Second, finding the individual loci involved in any trait is challenging given the respective limitations of quantitative and population genetic methods. In this issue of Molecular Ecology, Hendrick et al. (2016) overcome these difficulties and determine the genetic basis of microgeographic adaptation between geothermal vent and nonthermal populations of Mimulus guttatus in Yellowstone National Park. The authors accomplish this by combining population and quantitative genetic techniques, a powerful, but labour‐intensive, strategy for identifying individual causative adaptive loci that few studies have used (Stinchcombe & Hoekstra 2008 ). In a previous common garden experiment (Lekberg et al. 2012), thermal M. guttatus populations were found to differ from their closely related nonthermal neighbours in various adaptive phenotypes including trichome density. Hendrick et al. (2016) combine quantitative trait loci (QTL) mapping, population genomic scans for selection and admixture mapping to identify a single genetic locus underlying differences in trichome density between thermal and nonthermal M. guttatus. The candidate gene, R2R3 MYB, is homologous to genes involved in trichome development across flowering plants. The major trichome QTL, Tr14, is also involved in trichome density differences in an independent M. guttatus population comparison (Holeski et al. 2010) making this an example of parallel genetic evolution.     

Novel aspects in the life cycle and biotrophic interactions in Pezizomycetes (Ascomycota,Fungi)

The ascomycete class Pezizomycetes (single order Pezizales) is known for its cup‐shaped fruit bodies and the evolution of edible truffles and morels, but little is known about the ontogeny and ecology of this large and ecologically diverse fungal group. In this issue of Molecular Ecology, Healy et al. ( 2013 ) make a great leap forward by describing and identifying asexual, anamorphic structures that produce mitotic spores in many ectomycorrhiza‐forming truffle and nontruffle species on soil surfaces worldwide (Fig.  1 ). Although such anamorphic forms have been reported sporadically from certain ectomycorrhizal and saprotrophic Pezizomycetes (e.g. Warcup 1990 ), Healy et al. ( 2013 ) demonstrate that these terricolous asexual forms are both taxonomically and geographically more widespread and, in fact, much more common than previously understood. We anticipate that deeper insight into other substrates, provided by molecular analyses of materials such as dead wood and seeds, is likely to reveal numerous anamorphs of saprotrophic and pathogenic Pezizomycetes as well (see Marek et al. 2009 ).     

Demystifying the RAD fad

We are writing in response to the population and phylogenomics meeting review by Andrews & Luikart ( 2014 ) entitled ‘Recent novel approaches for population genomics data analysis’. Restriction‐site‐associated DNA (RAD) sequencing has become a powerful and useful approach in molecular ecology, with several different published methods now available to molecular ecologists, none of which can be considered the best option in all situations. A&L report that the original RAD protocol of Miller et al. ( 2007 ) and Baird et al. ( 2008 ) is superior to all other RAD variants because putative PCR duplicates can be identified (see Baxter et al. 2011 ), thereby reducing the impact of PCR artefacts on allele frequency estimates (Andrews & Luikart 2014 ). In response, we (i) challenge the assertion that the original RAD protocol minimizes the impact of PCR artefacts relative to that of other RAD protocols, (ii) present additional biases in RADseq that are at least as important as PCR artefacts in selecting a RAD protocol and (iii) highlight the strengths and weaknesses of four different approaches to RADseq which are a representative sample of all RAD variants: the original RAD protocol (mbRAD, Miller et al. 2007 ; Baird et al. 2008 ), double digest RAD (ddRAD, Peterson et al. 2012 ), ezRAD (Toonen et al. 2013 ) and 2bRAD (Wang et al. 2012 ). With an understanding of the strengths and weaknesses of different RAD protocols, researchers can make a more informed decision when selecting a RAD protocol.     

As thick as three in a bed

During the evolution of the lichen symbiosis, shifts from one main type of photobiont to another were infrequent (Miadlikowska et al. 2006 ) but some remarkable transitions from green algal to diazotrophic cyanobacterial photobionts are known from unrelated fungal clades within the ascomycetes. Cyanobacterial, including tripartite, associations (green algal and cyanobacterial photobionts in one lichen individual) facilitate these holobionts to live as C‐ and N‐autotrophs. Tripartite lichens are among the most productive lichens, which provide N‐fertilization to forest ecosystems under oceanic climates (Peltigerales) or deliver low, but ecologically significant N‐input into subarctic and alpine soil communities (Lecanorales, Agyriales). In this issue of Molecular Ecology, Schneider et al. (2016) mapped morphometric data against an eight‐locus fungal phylogeny across a transition of photobiont interactions from green algal to a tripartite association and used a phylogenetic comparative framework to explore the role of nitrogen‐fixing cyanobacteria in size differences in the Trapelia–Placopsis clade (Agyriales). Within the group of tripartite species, the volume of cyanobacteria‐containing structures (cephalodia) correlates with thallus thickness in both phylogenetic generalized least squares and phylogenetic generalized linear mixed‐effects analyses, and the fruiting body core volume increased ninefold. The authors conclude that cyanobacterial symbiosis appears to have enabled lichens to overcome size constraints in oligotrophic environments such as rock surfaces. The Trapelia–Placopsis clade analyzed by Schneider et al. (2016) is an exciting example of interactions between ecology, phylogeny and lichen biology including development – from thin crustose green algal microlichens to thick placodioid, tripartite macrolichens: as thick as three in a bed (Scott 1820 ).     

Bacteriophage exclusion,a new defense system

The ability to withstand viral predation is critical for survival of most microbes. Accordingly, a plethora of phage resistance systems has been identified in bacterial genomes (Labrie et al, 2010 ), including restriction‐modification systems (R‐M) (Tock & Dryden, 2005 ), abortive infection (Abi) (Chopin et al, 2005 ), Argonaute‐based interference (Swarts et al, 2014 ), as well as clustered regularly interspaced short palindromic repeats (CRISPR) and associated protein (Cas) adaptive immune system (CRISPR‐Cas) (Barrangou & Marraffini, 2014 ; Van der Oost et al, 2014 ). Predictably, the dark matter of bacterial genomes contains a wealth of genetic gold. A study published in this issue of The EMBO Journal by Goldfarb et al ( 2015 ) unveils bacteriophage exclusion (BREX) as a novel, widespread bacteriophage resistance system that provides innate immunity against virulent and temperate phage in bacteria.     

Homomorphic plant sex chromosomes are coming of age

Sex chromosomes are a very peculiar part of the genome that have evolved independently in many groups of animals and plants (Bull 1983 ). Major research efforts have so far been focused on large heteromorphic sex chromosomes in a few animal and plant species (Chibalina & Filatov 2011 ; Zhou & Bachtrog 2012 ; Bellott et al. 2014 ; Hough et al. 2014 ; Zhou et al. 2014 ), while homomorphic (cytologically indistinguishable) sex chromosomes have largely been neglected. However, this situation is starting to change. In this issue, Geraldes et al. ( 2015 ) describe a small (~100 kb long) sex‐determining region on the homomorphic sex chromosomes of poplars (Populus trichocarpa and related species, Fig.  1 ). All species in Populus and its sister genus Salix are dioecious, suggesting that dioecy and the sex chromosomes, if any, should be relatively old. Contrary to this expectation, Geraldes et al. ( 2015 ) demonstrate that the sex‐determining region in poplars is of very recent origin and probably evolved within the genus Populus only a few million years ago.     

The discovery of Antarctic RNA viruses: a new game changer

Antarctic ecosystems are dominated by micro‐organisms, and viruses play particularly important roles in the food webs. Since the first report in 2009 (López‐Bueno et al. 2009 ), ‘omic’‐based studies have greatly enlightened our understanding of Antarctic aquatic microbial diversity and ecosystem function (Wilkins et al. 2013 ; Cavicchioli 2015 ). This has included the discovery of many new eukaryotic viruses (López‐Bueno et al. 2009 ), virophage predators of algal viruses (Yau et al. 2011 ), bacteria with resistance to phage (Lauro et al. 2011 ) and mechanisms of haloarchaeal evasion, defence and adaptation to viruses (Tschitschko et al. 2015 ). In this issue of Molecular Ecology, López‐Bueno et al. ( 2015 ) report the first discovery of RNA viruses from an Antarctic aquatic environment. High sequence coverage enabled genome variation to be assessed for four positive‐sense single‐stranded RNA viruses from the order Picornavirales. By examining the populations present in the water column and in the lake's catchment area, populations of ‘quasispecies’ were able to be linked to local environmental factors. In view of the importance of viruses in Antarctic ecosystems but lack of data describing them, this study represents a significant advance in the field.     

Aquatic biodiversity assessment for the lazy

The world is covered in DNA. In any ecosystem, extracellular DNA fragments can be found that once formed the genomes of a variety of micro‐ and macroorganisms. A few years ago, it was proposed to use this environmental DNA (eDNA) as a source of information on local vertebrate biodiversity (Ficetola et al. 2008 ; Taberlet et al. 2012 ). This idea offered an elegant solution to take up the gauntlet of rapidly increasing monitoring needs. Coupled with barcoding efforts, it promised to be cost‐efficient in many respects, for example man‐hours and taxonomic expertise. Ecologists and conservation biologists with an interest in aquatic ecosystems have enthusiastically adopted and pioneered this new method, producing dozens of eDNA studies. Most of these studies have, however, focused on a single or a few aquatic species. In this issue of Molecular Ecology, Valentini et al. ( 2016 ) move the field a step further by demonstrating that metabarcoding approaches – which simultaneously target large groups of organisms such as amphibians or fish – can match and sometimes even outperform other inventory methods.     

Artificial intelligence for microbial biotechnology: beyond the hype

It has been a landmark year for artificial intelligence (AI) and biotechnology. Perhaps the most noteworthy of these advances was Google DeepMind’s AlphaFold2 algorithm which smashed records in protein structure prediction (Jumper et al., 2021, Nature, 596, 583) complemented by progress made by other research groups around the globe (Baek et al., 2021, Science, 373, 871; Zheng et al., 2021, Proteins). For the first time in history, AI achieved protein structure models rivalling the accuracy of experimentally determined structures. The power of accurate protein structure prediction at our fingertips has countless implications for drug discovery, de novo protein design and fundamental research in chemical biology. While acknowledging the significance of these breakthroughs, this perspective aims to cut through the hype and examine some key limitations using AlphaFold2 as a lens to consider the broader implications of AI for microbial biotechnology for the next 15 years and beyond.     

Host plant richness explains diversity of ectomycorrhizal fungi: Response to the comment of Tedersoo et al. (2014)

Exploring the relationships between the biodiversity of groups of interacting organisms yields insight into ecosystem stability and function (Hooper et al. 2000 ; Wardle 2006 ). We demonstrated positive relationships between host plant richness and ectomycorrhizal (EM) fungal diversity both in a field study in subtropical China (Gutianshan) and in a meta‐analysis of temperate and tropical studies (Gao et al. 2013 ). However, based on re‐evaluation of our data sets, Tedersoo et al. ( 2014 ) argue that the observed positive correlation between EM fungal richness and EM plant richness at Gutianshan and also in our metastudies was based mainly from (i) a sampling design with inconsistent species pool and (ii) poor data compilation for the meta‐analysis. Accordingly, we checked our data sets and repeated the analysis performed by Tedersoo et al. ( 2014 ). In contrast to Tedersoo et al. ( 2014 ), our re‐analysis still confirms a positive effect of plant richness on EM fungal diversity in Gutianshan, temperate and tropical ecosystems, respectively.