Ecdysozoa versus Articulata: clades, artifacts, prejudices

The claim that monophyly of the Ecdysozoa is caused by chance similarities in 18S rDNA sequences ( Wägele et al., J. Zool. Syst. Evol. Res. 37, 211–223, 1999 ) is re-analysed from the cladistic point of view. It is shown that the molecular characters supporting the Ecdysozoa do not behave as 'noisy' in empirical studies that use the sensitivity analysis and character congruence approaches. The 'anti-noise' methodology proposed by Wägele et al. (1999) is unable to identify true misinformative data. The monophyly of the Articulata (= Annelida + Panarthropoda), proposed by Wägele et al. (1999) , is contradicted by all molecular data that support either Ecdysozoa (including Panarthropoda), or Lophotrochozoa (including Annelida), or usually both.     

The missing Madagascan mid-domain effect

Species richness varies enormously across geographical gradients, a well-known phenomenon for which there are many hypothesized explanations. One recent hypothesis uses null models to demonstrate that random re-distribution of species' ranges within a given domain leads to a 'mid-domain effect' (MDE): increasing species richness towards the centre of the area. Madagascar is especially well-suited for empirical evaluation of mid-domain models by virtue of its large endemic fauna and its clearly defined boundaries. Lees et al. [ Biol. J. Linn. Soc. 67 (1999) 529] observed patterns of species richness consistent with MDEs in the Madagascan rainforest (a slim, north–south belt). In this study, we test one-dimensional and two-dimensional mid-domain model predictions for the birds and mammals of the entire island of Madagascar. When only latitudinal extents of species' distribution are considered, patterns of richness in Madagascar show an MDE. However, this pattern disappears for both taxa after accounting for the tendency of latitudinal bands nearer the middle of the country to be larger. Two-dimensional mid-domain model predictions of species richness are qualitatively opposite to observed patterns. Instead, island-wide spatial gradients of species richness in Madagascar relate strongly to patterns of primary productivity and amount of remaining natural habitat. Earlier work that showed a mid-domain peak within the rainforest biome (effectively after controlling for climate and natural habitat) seems likely to have reflected methodological artefacts. The classic case in which MDEs should occur is, in fact, inconsistent with the mid-domain hypothesis.     

Intergenerational reproductive parasitism in a stingless bee

Insect colonies have been traditionally regarded as closed societies comprised of completely sterile workers ruled over by a single once-mated queen. However, over the past 15 years, microsatellite studies of parentage have revealed that this perception is far from the truth ( Beekman & Oldroyd 2008 ). First, we learned that honey bee queens are far more promiscuous than we had previously imagined ( Estoup et al. 1994 ), with one Apis dorsata queen clocked at over 100 mates ( Wattanachaiyingcharoen et al. 2003 ). Then Oldroyd et al. (1994) reported a honey bee colony from Queensland, where virtually all the males were sons of a single patriline of workers – a clear case of a cheater mutant that promoted intra-colonial reproductive parasitism. Then we learned that both bumble bee colonies ( Lopez-Vaamonde et al. 2004 ) and queenless honey bee colonies ( Nanork et al. 2005, 2007 ) are routinely parasitized by workers from other nests that fly in and lay male-producing eggs that are then reared by the victim colony. There is even evidence that in a thelytokous honey bee population, workers lay female-destined eggs directly into queen cells, thus reincarnating themselves as a queen ( Jordan et al. 2008 ). And let us not forget ants, where microsatellite studies have revealed equally bizarre and totally unexpected phenomena (e.g. Cahan & Keller 2003 ; Pearcy et al. 2004 ; Fournier et al. 2005 ). Now, in this issue, Alves et al. (2009) use microsatellites to provide yet another shocking and completely unexpected revelation about the nefarious goings-on in insect colonies: intergenerational reproductive parasitism by stingless bee workers.     

Genetics of personalities: no simple answers for complex traits

Identifying the genes that underlie phenotypic variation in natural populations, and assessing the consequences of polymorphisms at these loci for individual fitness are major objectives in evolutionary biology. Yet, with the exception of a few success stories, little progress has been made, and our understanding of the link between genotype and phenotype is still in its infancy. For example, although body length in humans is largely genetically determined, with heritability estimates greater than 0.8, massive genome‐wide association studies (GWAS) have only been able to account for a very small proportion of this variation ( Gudbjartsson et al. 2008 ). If it is so difficult to explain the genetics behind relatively ‘simple’ traits, can we envision that it will at all be possible to find genes underlying complex behavioural traits in wild non‐model organisms? Some notable examples suggest that this can indeed be a worthwhile endeavour. Recently, the circadian rhythm gene Clock has been associated with timing of breeding in a wild blue tit population ( Johnsen et al. 2007 ; Liedvogel et al. 2009 ) and the Pgi gene to variation in dispersal and flight endurance in Glanville fritillary butterflies ( Niitepold et al. 2009 ). A promising candidate gene for influencing complex animal personality traits, also known as behavioural syndromes ( Sih et al. 2004 ), is the dopamine receptor D4 (DRD4) gene. Within the last decade, polymorphisms in this gene have been associated with variation in novelty seeking and exploration behaviour in a range of species, from humans to great tits ( Schinka et al. 2002 ; Fidler et al. 2007 ). In this issue, Korsten et al. (2010) attempt to replicate this previously observed association in wild‐living birds, and test for the generality of the association between DRD4 and personality across a number of European great tit populations.     

Speciation genetics of biological invasions with hybridization

The negative effects of human‐induced habitat disturbance and modification on multiple dimensions of biological diversity are well chronicled ( Turner 1996 ; Harding et al. 1998 ; Lawton et al. 1998 ; Sakai et al. 2001 ). Among the more insidious consequences is secondary contact between formerly allopatric taxa ( Anderson & Hubricht 1938 ; Perry et al. 2002 ; Seehausen 2006 ). How the secondary contact will play out is unpredictable ( Ellstrand et al. 2010 ), but if the taxa are not fully reproductively isolated, hybridization is likely, and if the resulting progeny are fertile, the eventual outcome is often devastating from a conservation perspective ( Rhymer & Simberloff 1996 ; Wolf et al. 2001 ; McDonald et al. 2008 ). In this issue of Molecular Ecology, Steeves et al. (2010) present an analysis of hybridization between two avian species, one of which is critically endangered and the other of which is invasive. Their discovery that the endangered species has not yet been hybridized to extinction is promising and not what one would necessarily expect from theory.     

First record of Palisada maris-rubri (Ceramiales, Rhodophyta) from the Mediterranean Sea along with three proposed transfers to the genus Palisada

The first occurrence of Palisada maris-rubri (K.W. Nam et Saito) K.W. Nam (Ceramiales, Rhodomelaceae) from the Mediterranean Sea, is reported. To date the species was known only from tetrasporic specimens from the type locality (Ras Muhammed, Sinai, Egypt, Red Sea). Mediterranean thalli share nearly all vegetative and reproductive features with Red Sea specimens showing more robust thalli with axes to 3 mm broad and ultimate branchlets to 1000 µm broad, absence of intercellular spaces between medullary cells and epidermal cells in transverse section with a palisade arrangement. Male and cystocarpic thalli are recorded for the first time. Moreover, the analysis of characters of three species of Chondrophycus previously known from the Mediterranean Sea ( C. patentirameus (Montagne) K.W. Nam, C. tenerrimus (Cremades) G. Furnari et al. and C. thuyoides (Kützing) G. Furnari) led us to conclude that they belong to the genus Palisada . The following new combinations are formally proposed: P. patentiramea (Montagne) Serio et al., P. thuyoides (Kützing) Serio et al., P. tenerrima (Cremades) Serio et al.     

Stream amphibians as metrics of critical biological thresholds in the Pacific Northwest, U.S.A.: a response to Kroll et al.

1. Kroll, Hayes & MacCracken (in press) Concerns regarding the use of amphibians as metrics of critical biological thresholds: a comment on Welsh and Hodgson 2008 . Freshwater Biology, criticised our paper [ Welsh & Hodgson (2008) Amphibians as metrics of critical biological thresholds in forested headwater streams of the Pacific Northwest. Freshwater Biology, 53 , 1470–1488] proposing the use of headwater stream amphibians as metrics of stream status in the Pacific Northwest (PNW). They argued that our analysis of previously published data reflected circular reasoning because we reached the same conclusions as the earlier studies. In fact, we conducted a meta‐analysis to address new questions about the optimum values and thresholds (based on animal densities) for abiotic stream attributes that were found to be important to these amphibians in earlier studies. This is analogous to determining blood pressure thresholds or fat‐to‐weight ratios that facilitate predicting human health based on meta‐analyses of earlier data from studies that found significant correlations between these variables and relative health. 2. Kroll et al. argued that we should not make inference to environmental conditions across the PNW from data collected in California. We collected data from northern California and southern Oregon, the southern extent of the PNW. We made inference to the Klamath‐Siskiyou and North Coast bioregions, and argued that available research on these headwater species indicates that our results have the potential to be applied throughout the PNW with minimal regional adjustments. 3. Kroll et al. contended that we need reproductive success, survival estimates and density estimates, corrected for detection probabilities, to establish relationships between animal density and stream attributes. Reproductive success and survival estimates are important for demographic modelling and life tables, but they are not necessary to demonstrate meaningful relationships with abiotic conditions. Both corrected occupancy estimates and individual detection probabilities are unnecessary, and take multiple sampling efforts per site, or onerous mark release and re‐capture studies, respectively, to determine accurately. 4. Kroll et al. questioned the use of stream amphibians as a surrogate for measuring physical parameters, such as water temperature, claiming that measuring the physical parameters directly is more efficient. Here they misinterpreted the main point of our paper: stream organisms are integrators of what happens in a catchment, and carefully selected species can serve as surrogates for the biotic community and the relative condition of the network environment. 5. Kroll et al. claimed that we demonstrated weak inferences regarding ecosystem processes. We argue that by relating densities of stream amphibians with changes along abiotic environmental gradients that are commonly affected by anthropogenic activities, we are establishing biological links to gradients that represent important ecosystem processes and identifying biometrics that can be used to quantify the status (health) of these gradients.     

Lack of intermediate-scale disturbance data prevents robust extrapolation of plot-level tree mortality rates for old-growth tropical forests

Lloyd et al. (2009) question the methods, concepts and conclusions of Fisher et al. (2008) . We address these assertions, and place our work into a broader context. We demonstrate the veracity of Fisher et al. , and further show that lack of data for intermediate-scale tree mortality disturbance events for old-growth tropical forests might prevent robust extrapolation of forest plot biomass accumulation data, and accurate estimates of distribution parameters such as power-law exponents ( α ).     

Simulation modelling in landscape genetics: on the need to go further

With the emergence of landscape genetics, the basic assumptions and predictions of classical population genetic theories are being re‐evaluated to account for more complex spatial and temporal dynamics. Within the last decade, there has been an exponential increase in such landscape genetic studies ( Holderegger & Wagner 2006 ; Storfer et al. 2010 ), and both methodology and underlying concepts of the field are under rapid and constant development. A number of major innovations and a high level of originality are required to fully merge existing population genetic theory with landscape ecology and to develop novel statistical approaches for measuring and predicting genetic patterns. The importance of simulation studies for this specific research has been emphasized in a number of recent articles (e.g., Balkenhol et al. 2009a ; Epperson et al. 2010 ). Indeed, many of the major questions in landscape genetics require the development and application of sophisticated simulation tools to explore gene flow, genetic drift, mutation and natural selection in landscapes with a wide range of spatial and temporal complexities. In this issue, Jaquiéry et al. (2011) provide an excellent example of such a simulation study for landscape genetics. Using a metapopulation simulation design and a novel ‘scale of phenomena’ approach, Jaquiéry et al. (2011) demonstrate the utility and limitations of genetic distances for inferring landscape effects on effective dispersal.     

Managing for naturalness alone is not an effective way to preserve all the valuable natural features of the Białowieża Forest – a reply to Jaroszewicz et al.

Currently, Brzeziecki et al. 2016 (Journal of Vegetation Science 27: 460–467.) are using data from permanent study plots established in 1936 in Bia?owie?a National Park (NE Poland) to develop theoretical equilibrium tree size distributions and to then compare modelled and actual distributions with a view to assessing the population dynamics of the species involved. As part of their discussion, the authors address the question of possible consequences for the overall diversity of forest ecosystems under strict protection if long‐term trends relating to tree population densities and size structures are maintained. In the overall context of the above, the goal of the present paper is to respond to Jaroszewicz et al. (Journal of Vegetation Science 28: 218–222.) who suggest that the paper of Brzeziecki et al. (2016) is not representative for the whole Bia?owie?a National Park, and that – in this connection – strict protection should not be seen as a cause for concern. In this paper, we show that the data analysed by Brzeziecki et al. (2016) adequately characterize conditions in the wider Park. We also point out that the thorough scientific understanding of the long‐term dynamics of woodland communities under strict protection should indeed be taken into account as efforts are made to arrive at an effective conservation strategy capable of ensuring that the uniquely valuable features of the Bia?owie?a Forest are retained.     

On the International Code of Area Nomenclature (ICAN): a reply to Zaragüeta-Bagils et al.

In 2007 the Systematic and Evolutionary Biogeographical Association (SEBA) wrote and ratified the first draft of the International Code of Area Nomenclature (ICAN), which was posted subsequently on the SEBA website. The ICAN was published, along with an explanatory discussion, by Ebach et al. ( Journal of Biogeography , 35 , 2008, 1153–1157), an article that is the subject of criticism by Zaragüeta-Bagils et al. ( Journal of Biogeography , 36 , 2009, 1617–1618). We welcome discussion of the issues raised by these authors and respond to them briefly here. For many reasons, we reject the proposition that implementation of the ICAN be postponed until it is flawless. The ICAN has already been implemented. Further, it is the nature of nomenclatural codes to be proposed and then revised periodically to suit our applications. Most importantly, standardization of area names in biogeography is long overdue.     

Attractive sinks, or how individual behavioural decisions determine source–sink dynamics

Gundersen et al . (2001 , Source-sink dynamics: how sinks affect demography of sources. Ecol. Lett. , 4, 14–21.) suggested that sinks can severely affect the demography of populations in source habitats. We propose this is a common result when animals lack cues associated with reduced fitness inside sinks and consequently select habitat inappropriately. These attractive sinks can result either from undetected risks of mortality (as in the experiment of Gundersen et al . 2001 ) or from undetected poor breeding probabilities (due to bioaccumulation of pesticides, for instance). Thus, individual habitat choice is a key process underlying source–sink dynamics.     

Management implications of the Macquarie Island trophic cascade revisited: a reply to Dowding et al. (2009)

1. The management of non-indigenous species is not without its complications. In Bergstrom et al. 's (2009) study, we demonstrated that feral cats Felis catus on sub-Antarctic Macquarie Island were exerting top-down control on the feral rabbit Oryctolagus cuniculus population, and that the eradication of the cats led to a substantial increase in rabbit numbers and an associated trophic cascade.
2. Dowding et al. (2009) claim our modelling was flawed for various reasons, but primarily that a reduction in the application of the rabbit control agent, Myxoma virus, coinciding with cat removal, was a major driver of rabbit population release.
3. We explore this proposition (as well as others) by examining rates of Myxoma viral release between 1991 and 2006 (with an attenuation factor for the years, 2003–2006) in association with presence/absence of cats against two estimates of rabbit population size. Myxoma viral release was a significant factor in the lower estimates of rabbit population, but the effect was small, and was not significant for higher rabbit population estimates. By contrast, the presence or absence of cats remained highly significant for both estimates.
4. Synthesis and applications. We re-affirm our position that top-down control of rabbit numbers by cats, prior to their eradication, was occurring on Macquarie Island. Nonetheless, we agree with Dowding et al. (2009) that systems with multiple invasive species represent complex situations that require careful scrutiny. Such scrutiny should occur in advance of, during, and following management interventions.     

Signal transduction meets systems biology: deciphering specificity determinants for protein-protein interactions

Two recent papers (Gao et al . 2008 and Skerker et al . 2008) describe investigations into the specificity of protein–protein interactions that occur during signal transduction by two-component regulatory systems. This MicroCommentary summarizes and provides context for the reported findings. The results offer insights into molecular determinants that provide specificity to maintain signal separation and thus prevent deleterious cross-talk between pathways, as well as the potential extent and nature of interactions that may combine signals to achieve beneficial cross-regulation among pathways. The methods employed are suitable for application to other systems.     

Immune correlates of protection against anthrax

Bacillus anthracis protective antigen (PA) has been produced from a recombinant B. subtilis and its efficacy, when combined with the Ribi adjuvant (MPL-TDW-CWS) or alhydrogel, has been compared with that of the licensed UK human vaccine, in guinea pigs challenged with aerosolized Ames strain spores. Recombinant PA combined with the Ribi adjuvant performed as well as PA from B. anthracis cultures in previous reports ( Ivins & Welkos 1986 ; Ivins et al . 1990 ; Turnbull et al . 1991 ; Jones et al . 1996 ; McBride et al . 1998 ) giving protection in 100% of animals exposed to the highest challenge dose of the Ames strain of B. anthracis that can be administered practically (retained lung doses of approximately 10⁶ spores).
In attempts at identifying markers of protection in immunized individuals, rPA in combination with the Ribi adjuvant induced a marker IgG₂ response in guinea pigs with no significant differences in IgG₁ levels when compared with other vaccine formulations ( McBride et al . 1998 ). In BALBc mice, rPA with the Ribi adjuvant induced a higher IgG_2a response compared with rPA with anhydrogel and the human vaccine.
To examine the role of anti-PA-specific antibodies in protection, guinea pig sera is being passively transferred into guinea pigs and SCID mice, followed by protection.
Similarly, B- and T-lymphocytes from immunized BALB/c mice are being separately and passively transferred into SCID mice with subsequent challenge. The neutralizing ability of the PA-specific antibodies is being studied using an in vitro macrophage lysis assay.     

First case of rabbit haemorrhagic disease in Canada: contaminated flying insect, vs. long-term infection hypothesis

Following the announcement of the first case of rabbit haemorrhagic disease (RHD) in a pet rabbit, housed indoors in Canada for more than 1 year, I submitted an evidence‐based explanation to ProMed explaining how RHD might have caused the death of ‘one’ of the three pet rabbits. I suggested with supporting evidence, that it may have been persistently infected with rabbit haemorrhagic disease virus (RHDV) which may have reactivated to cause the fatal disease. However, in this issue, Peacock et al. have proposed an alternative ‘hypothesis’ for the appearance of RHD in the pet rabbit. They hypothesise that a non‐identified insect or fomite might have become contaminated by a Chinese strain of RHDV somewhere in the US. This insect/fomite then flew or was windborne, from the US to Canada where it entered the house containing three pet rabbits and infected one of them. RHD is non‐endemic and is rarely reported in the US, where it has only been observed in domestic European rabbits, held in rabbitries. My proposal was based on the details provided by ProMed, the veterinary report from Canada, where RHDV has never previously been identified and the epidemiological, ecological and evolutionary history of RHDV which includes serological and phylogenetic evidence that ancestral RHDV lineages circulated before 1984. The flying insect hypothesis of Peacock et al. is based on circumstantial evidence and, I believe, has a lower probability of being correct than my evidence‐based long‐term infection proposal.     

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA

Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, ‘early detection and rapid response’; (ii) for conserving imperilled native species, ‘protection of biodiversity hotspots’; and (iii) for assessing biosecurity risk, ‘an ounce of prevention equals a pound of cure.’ However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism’s DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next‐generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.     

Loss of intestinal nuclei and intestinal integrity in aging C. elegans

The roundworm C. elegans is widely used as an aging model, with hundreds of genes identified that modulate aging (Kaeberlein et al., 2002. Mech. Ageing Dev. 123 , 1115–1119). The development and bodyplan of the 959 cells comprising the adult have been well described and established for more than 25 years ( Sulston & Horvitz, 1977 . Dev. Biol. 56 , 110–156; Sulston et al., 1983. Dev. Biol. 100 , 64–119.). However, morphological changes with age in this optically transparent animal are less well understood, with only a handful of studies investigating the pathobiology of aging. Age‐related changes in muscle ( Herndon et al., 2002 . Nature 419 , 808–814), neurons ( Herndon et al., 2002 ), intestine and yolk granules ( Garigan et al., 2002 . Genetics 161 , 1101–1112; Herndon et al., 2002 ), nuclear architecture ( Haithcock et al., 2005 . Proc. Natl Acad. Sci. USA 102 , 16690–16695), tail nuclei ( Golden et al., 2007 . Aging Cell 6 , 179–188), and the germline ( Golden et al., 2007 ) have been observed via a variety of traditional relatively low‐throughput methods. We report here a number of novel approaches to study the pathobiology of aging C. elegans. We combined histological staining of serial‐sectioned tissues, transmission electron microscopy, and confocal microscopy with 3D volumetric reconstructions and characterized age‐related morphological changes in multiple wild‐type individuals at different ages. This enabled us to identify several novel pathologies with age in the C. elegans intestine, including the loss of critical nuclei, the degradation of intestinal microvilli, changes in the size, shape, and cytoplasmic contents of the intestine, and altered morphologies caused by ingested bacteria. The three‐dimensional models we have created of tissues and cellular components from multiple individuals of different ages represent a unique resource to demonstrate global heterogeneity of a multicellular organism.     

Anthrax lethal factor cleaves the N-terminus of MAPKKS and induces tyrosine/threonine phosphorylation of MAPKS in cultured macrophages

The lethal toxin (LeTx) of Bacillus anthracis is the major virulence factor responsible for the death of infected animals and for cytolysis of cultured macrophages. Its catalytic component, LF, contains the characteristic zinc-binding motif of metalloproteases, it binds zinc and indirect evidence suggests that this hydrolytic activity is essential for LeTx cytotoxicity ( Limpel et al . 1994 ; Kochi et al . 1994 ). To identify substrates of LF, we have used the yeast two-hybrid system, employing an LF inactive mutant as bait. This approach has led to the identification of the MAP kinase kinases (MAPKKs) Mek1 and Mek2 as proteins capable of specific interaction with LF. LF cleaves Mek1 and Mek2 within their N-terminus in vitro and in vivo , hydrolysing a Pro8-Ile9 and a Pro10-Arg11 peptide bond in Mek1 and Mek2, respectively ( Vitale et al . 1998 ), similarly to that found with a different approach by Duesbery et al . (1998) . The removal of the amino terminus of MAPKKs eliminates the 'docking site' involved in the specific interaction with MAPKs and interferes with the phospho-activation of the MAPKs ERK1 and ERK2, which become phosphorylated in cultured macrophages following toxin challenge. We are currently investigating the relevance of MAPKKs cleavage for LeTx cytotoxicity and the consequences for the activity of the MAP pathway.