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.     

Admixture increases diversity in managed honey bees: Reply to De la Rúa et al. (2013)

De la Rúa et al. (2013) express some concerns about the conclusions of our recent study showing that management increases genetic diversity of honey bees (Apis mellifera) by promoting admixture (Harpur et al. 2012). We provide a brief review of the literature on the population genetics of A. mellifera and show that we utilized appropriate sampling methods to estimate genetic diversity in the focal populations. Our finding of higher genetic diversity in two managed A. mellifera populations on two different continents is expected to be the norm given the large number of studies documenting admixture in honey bees. Our study focused on elucidating how management affects genetic diversity in honey bees, not on how to best manage bee colonies. We do not endorse the intentional admixture of honey bee populations, and we agree with De la Rúa et al. (2013) that native honey bee subspecies should be conserved.     

The age of the Middle Ordovician Winneshiek Shale: reply to a critical review by Lindskog & Young (2019) of a paper by Bergström et al. (2018a)

A recent review by Lindskog & Young (2019) of a paper published in Lethaia by Bergström et al. (2018a) contains many errors, misleading statements and unsupported opinions. Their review claims that we did not consider biostratigraphy in our efforts to chemostratigraphically date the Winneshiek Shale. That this is incorrect is shown by the fact that Liu et al. (2017), which contains a two-page review of all fossil evidence that has a bearing on the age of the Winneshiek Shale and was written by Bergström, was cited in Bergström et al. (2018a) and used extensively in our chemostratigraphical age assessment of the unit. Interestingly, recent research provides support for our conclusion regarding the age of the Winneshiek Shale, indicating that at least its upper part is coeval with the Nicholsonograptus fasciculatus Graptolite Zone and the Eoplacognathus pseudoplanus Conodont Zone. In constructing their arguments, Lindskog & Young (2019) provide no alternative interpretations or corrections of scientific value.     

Plankton dynamics under different climate conditions in tropical freshwater systems (a reply to the comment by Sarmento,Amado & Descy, )

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More precisely biased: increasing the number of markers is not a silver bullet in genetic bottleneck testing

In response to our review of the use of genetic bottleneck tests in the conservation literature (Peery et al. 2012, Molecular Ecology, 21 , 3403–3418), Hoban et al. (2013, Molecular Ecology, in press) conducted population genetic simulations to show that the statistical power of genetic bottleneck tests can be increased substantially by sampling large numbers of microsatellite loci, as they suggest is now possible in the age of genomics. While we agree with Hoban and co‐workers in principle, sampling large numbers of microsatellite loci can dramatically increase the probability of committing type 1 errors (i.e. detecting a bottleneck in a stable population) when the mutation model is incorrectly assumed. Using conservative values for mutation model parameters can reduce the probability of committing type 1 errors, but doing so can result in significant losses in statistical power. Moreover, we believe that practical limitations associated with developing large numbers of high‐quality microsatellite loci continue to constrain sample sizes, a belief supported by a literature review of recent studies using next generation sequencing methods to develop microsatellite libraries. conclusion, we maintain that researchers employing genetic bottleneck tests should proceed with caution and carefully assess both statistical power and type 1 error rates associated with their study design.     

Predicting the distribution of non‐vagile taxa: a response to McNyset and Blackburn (2006) and re‐evaluation of Stockman et al. (2006)

This paper addresses the issues raised by McNyset and Blackburn (2006 ) in their response to Stockman et al. (2006 ). Re‐evaluation of our published GARP analyses by McNyset and Blackburn showed that a much improved ecological niche model is obtained for predicting the distribution of the trapdoor spider genus Promyrmekiaphila in central/northern California. The improved niche model results in a substantially reduced omission error rate and a predictive model comparable to models obtained using other methods (GLM and BIOCLIM). However, the improved GARP models have a high commission error rate (> 0.75); consequently, the inferences regarding difficulties in modelling non‐vagile taxa drawn by Stockman et al. remain valid. Finally, we discuss other relatively minor criticisms of our study raised by McNyset and Blackburn and issues related to the peer review of our original paper.     

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.     

Improving Bayesian isotope mixing models: a response to Jackson et al. (2009)

We recently described a Bayesian framework for stable isotope mixing models and provided a software tool, MixSIR, for conducting such analyses (Ecol. Lett., 2008; 11 :470). Jackson et al. (Ecol. Lett., 2009; 12:E1) criticized the performance of our software based on tests using simulated data. However, their simulation data were flawed, rendering claims of erroneous behaviour inaccurate. A re‐evaluation of the MixSIR source code did, however, uncover two minor coding errors, which we have fixed. When data are correctly simulated according to eqns  (1)–(4) in Jackson et al. (2009) , MixSIR consistently and accurately estimated the proportional contribution of prey to a predator diet, and was surprisingly robust to additional unquantified error. Jackson et al. (2009) also suggested we use a Dirichlet prior on the source proportion parameters, which we agree with. Finally, Jackson et al. (2009) propose adding additional error parameters to our mixing model framework. We caution that such increases in model complexity should be evaluated based on data support.     

Tending a complex microbiota requires major immune complexity

Animals maintain complex microbial communities within their guts that fill important roles in the health and development of the host. To what degree a host's genetic background influences the establishment and maintenance of its gut microbial communities is still an open question. We know from studies in mice and humans that external factors, such as diet and environmental sources of microbes, and host immune factors play an important role in shaping the microbial communities (Costello et al. 2012 ). In this issue of Molecular Ecology, Bolnick et al. ( 2014a ) sample the gut microbial community from 150 genetically diverse stickleback isolated from a single lake to provide evidence that another part of the adaptive immune response, the major histocompatibility complex class II (MHCII) receptors of antigen‐presenting cells, may play a role in shaping the gut microbiota of the threespine stickleback, Gasterosteus aculeatus (Bolnick et al. 2014a ). Bolnick et al. ( 2014a ) provide insight into natural, interindividual variation in the diversity of both stickleback MHCII alleles and their gut microbial communities and correlate changes in the diversity of MHCII receptor alleles with changes in the microbiota.     

The number of markers and samples needed for detecting bottlenecks under realistic scenarios,with and without recovery: a simulation‐based study

Detecting bottlenecks is a common task in molecular ecology. While several bottleneck detection methods exist, evaluations of their power have focused only on severe bottlenecks (e.g. to Ne ~10). As a component of a recent review, Peery et al. ( 2012 ) analysed the power of two approaches, the M‐ratio and heterozygote excess tests, to detect moderate bottlenecks (e.g. to Ne ~100), which is realistic for many conservation situations. In this Comment, we address three important points relevant to but not considered in Peery et al. Under moderate bottleneck scenarios, we test the (i) relative advantage of sampling more markers vs. more individuals, (ii) potential power to detect the bottleneck when utilizing dozens of microsatellites (a realistic possibility for contemporary studies) and (iii) reduction in power when postbottleneck recovery has occurred. For the realistic situations examined, we show that (i) doubling the number of loci shows equal or better power than tripling the number of individuals, (ii) increasing the number of markers (up to 100) results in continued additive gains in power, and (iii) recovery after a moderate amount of time or gradual change in size reduces power, by up to one‐half. Our results provide a practical supplement to Peery et al. and encourage the continued use of bottleneck detection methods in the genomic age, but also emphasize that the power under different sampling schemes should be estimated, using simulation modelling, as a routine component of molecular ecology studies.     

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.     

Stem cell competition: how speeding mutants beat the rest

How mutations lead to tumor formation is a central question in cancer research. Although cellular changes that follow the occurrence of common mutations are well characterized, much less is known about their effects on the population level. Now, two recent studies reveal in what way oncogenic aberrations alter stem cell dynamics to provide cells with an evolutionary advantage over their neighbors (Amoyel et al, 2014 ; Baker et al, 2014 ).     

The explanatory power of biogeographical patterns: a reply to de Bruyn et al

Confusion between evidence and hypothesis in biogeographical studies was the focus of our recent Guest Editorial (Parenti & Ebach, 2013, Journal of Biogeography, 40 , 813–820). That editorial was critiqued by de Bruyn et al. (2013, Journal of Biogeography, doi: 10.1111/jbi.12166) to whom we reply briefly here. Despite our shared goals – to understand what lives where and why – we argue from different philosophical premises. Although we may have little common ground, such debate encourages the good health of the field of biogeography.     

Pattern,prediction and parsimony in continental‐scale synthesis of pyromes: a reply to Gosper et al.

We (Murphy et al., 2013; Clarke et al., 2015) have recently developed a framework to understand the spatial distribution of fire regimes and plant fire‐response traits at large spatial scales. We integrated a range of data sources to create a continental‐scale overview of Australian pyromes from which to infer pyrogeographic drivers. Gosper et al. (in press) have criticized our approach, based on our misclassification of a vegetation type (eucalypt woodland), with distinct fire regime, in the Coolgardie bioregion of Western Australia. We argue that the intention of our integrative approach was to develop and refine conceptual models of Australian pyrogeography, not to produce a predictive map of fire regimes, and certainly not to guide local‐scale fire management. Like all models, continental‐scale syntheses of pyromes are imperfect, yet they still represent powerful tools for understanding the drivers of the spatial distribution of fire regimes.     

Enalikter is not an annelid: homology,autapomorphies and the interpretation of problematic fossils

A megacheiran arthropod, Enalikter aphson, was recently described by Siveter et al. (2014) from the mid‐Silurian (late Wenlock) of Herefordshire. Previously, megacheirans had only been recognized from the Cambrian. Struck et al. (2015) considered the body plan of Enalikter to be incompatible with this affinity, arguing that many of the arthropod features were either not present or misinterpreted. Instead, they compared Enalikter to polychaete annelids, identifying characters from numerous polychaete lineages which they considered to be present in Enalikter. A reply to this critique by Siveter et al. (2015) reaffirmed arthropod affinities for Enalikter by presenting additional evidence for key arthropod features, such as arthropodized appendages. Here, we augment Siveter et al. by critically addressing the putative annelid characters of Enalikter presented by Struck et al. and additionally explore the morphological and phylogenetic implications of their hypothesis. We conclude that similarities between Enalikter and polychaetes are superficial and that character combinations proposed by Struck et al. are not present in any annelid, living or extinct. This taxon highlights the importance of using a phylogenetic framework for interpreting fossils that present unusual morphologies, such that proposed shared characters are hypotheses of homology rather than merely phenotypic similarities. Crucially, we argue that autapomorphic characters of subgroups of large taxa (like families or classes within phyla) should not be used to diagnose problematic fossils.     

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.     

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.     

Two are better than one: combining landscape genomics and common gardens for detecting local adaptation in forest trees

Predicting likely species responses to an alteration of their local environment is key to decision‐making in resource management, ecosystem restoration and biodiversity conservation practice in the face of global human‐induced habitat disturbance. This is especially true for forest trees which are a dominant life form on Earth and play a central role in supporting diverse communities and structuring a wide range of ecosystems. In Europe, it is expected that most forest tree species will not be able to migrate North fast enough to follow the estimated temperature isocline shift given current predictions for rapid climate warming. In this context, a topical question for forest genetics research is to quantify the ability for tree species to adapt locally to strongly altered environmental conditions (Kremer et al. 2012 ). Identifying environmental factors driving local adaptation is, however, a major challenge for evolutionary biology and ecology in general but is particularly difficult in trees given their large individual and population size and long generation time. Empirical evaluation of local adaptation in trees has traditionally relied on fastidious long‐term common garden experiments (provenance trials) now supplemented by reference genome sequence analysis for a handful of economically valuable species. However, such resources have been lacking for most tree species despite their ecological importance in supporting whole ecosystems. In this issue of Molecular Ecology, De Kort et al. ( 2014 ) provide original and convincing empirical evidence of local adaptation to temperature in black alder, Alnus glutinosa L. Gaertn, a surprisingly understudied keystone species supporting riparian ecosystems. Here, De Kort et al. ( 2014 ) use an innovative empirical approach complementing state‐of‐the‐art landscape genomics analysis of A. glutinosa populations sampled in natura across a regional climate gradient with phenotypic trait assessment in a common garden experiment (Fig. 1 ). By combining the two methods, De Kort et al. ( 2014 ) were able to detect unequivocal association between temperature and phenotypic traits such as leaf size as well as with genetic loci putatively under divergent selection for temperature. The research by De Kort et al. ( 2014 ) provides valuable insight into adaptive response to temperature variation for an ecologically important species and demonstrates the usefulness of an integrated approach for empirical evaluation of local adaptation in nonmodel species (Sork et al. 2013 ).     

The Hfq chaperone helps the ribosome mature

Ribosome biogenesis is a complex process that is facilitated by a large number of assembly factors. In this issue, Andrade et al ( 2018 ) provide evidence that a widely conserved RNA chaperone, Hfq, acts as a ribosomal assembly factor in bacteria. Hfq is known to support regulation of stress response genes by small RNAs. Andrade et al ( 2018 ) show that the absence of Hfq results in higher levels of immature 30S ribosomes and error‐prone translation, suggesting that Hfq globally affects the quality of protein synthesis when bacteria are under stress.