Are the dynamics of tropical forests dominated by large and rare disturbance events?

A recent Ecology Letters paper of Fisher et al. (2008) utilized a modelling framework to investigate disturbance effects on forest biomass dynamics. But it contains serious methodological and conceptual errors. Associated conclusions are unlikely to be correct.     

Analytical results on the neutral non-equilibrium allele frequency spectrum based on diffusion theory

The allele frequency spectrum has attracted considerable interest for the simultaneous inference of the demographic and adaptive history of populations. In a recent study, Evans et al. (2007) developed a forward diffusion equation describing the allele frequency spectrum, when the population is subject to size changes, selection and mutation. From the diffusion equation, the authors derived a system of ordinary differential equations (ODEs) for the moments in a Wright–Fisher diffusion with varying population size and constant selection. Here, we present an explicit solution for this system of ODEs with variable population size, but without selection, and apply this result to derive the expected spectrum of a sample for time-varying population size. We use this forward-in-time-solution of the allele frequency spectrum to obtain the backward-in-time-solution previously derived via coalescent theory by Griffiths and Tavaré (1998). Finally, we discuss the applicability of the theoretical results to the analysis of nucleotide polymorphism data.     

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.     

A strong Madagascan rainforest MDE and no equatorward increase in species richness: re-analysis of 'The missing Madagascan mid-domain effect', by Kerr J.T., Perring M. & Currie D.J. (Ecology Letters 9:149-159, 2006)

By reanalysing inaccurately presented data of Kerr et al. (2006) , we refute their claims that area-corrected species richness of endemic Madagascan birds and mammals increases toward the Equator and is best explained by environmental factors, and that the rainforest mid-domain effect (MDE) Lees et al. (1999) demonstrated is artefactual.     

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.     

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.     

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.     

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.     

Non-equilibrium allele frequency spectra via spectral methods

A major challenge in the analysis of population genomics data consists of isolating signatures of natural selection from background noise caused by random drift and gene flow. Analyses of massive amounts of data from many related populations require high-performance algorithms to determine the likelihood of different demographic scenarios that could have shaped the observed neutral single nucleotide polymorphism (SNP) allele frequency spectrum. In many areas of applied mathematics, Fourier Transforms and Spectral Methods are firmly established tools to analyze spectra of signals and model their dynamics as solutions of certain Partial Differential Equations (PDEs). When spectral methods are applicable, they have excellent error properties and are the fastest possible in high dimension; see Press et al. (2007). In this paper we present an explicit numerical solution, using spectral methods, to the forward Kolmogorov equations for a Wright–Fisher process with migration of K populations, influx of mutations, and multiple population splitting events.     

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.     

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.     

Cell kinetic status of haematopoietic stem cells

The haematopoietic stem cell (HSC) population supports a tremendous cellular production over the course of an animal's lifetime, e.g. adult humans produce their body weight in red cells, white cells and platelets every 7 years, while the mouse produces about 60% of its body weight in the course of a 2 year lifespan. Understanding how the HSC population carries this out is of interest and importance, and a first step in that understanding involves the characterization of HSC kinetics. Using previously published continuous labelling data (of Bradford et al. 1997 and Cheshier et al. 1999 ) from mouse HSC and a standard G₀ model for the cell cycle, the steady state parameters characterizing these HSC populations are derived. It is calculated that in the mouse the differentiation rate ranges between about 0.01 and 0.02, the rate of cell re-entry from G₀ back into the proliferative phase is between 0.02 and 0.05, the rate of apoptosis from the proliferative phase is between 0.07 and 0.23 (all units are days⁻¹), and the duration of the proliferative phase is between 1.4 and 4.3 days. These values are compared with previously obtained values derived from the modelling by Abkowitz and colleagues of long-term haematopoietic reconstitution in the cat ( Abkowitz et al. 1996 ) and the mouse ( Abkowitz et al. 2000 ). It is further calculated using the estimates derived in this paper and other data on mice that between the HSC and the circulating blood cells there are between 17 and 19.5 effective cell divisions giving a net amplification of between ~170 000 and ~720 000.     

Pathogen pollution and the emergence of a deadly amphibian pathogen

Imagine a single pathogen that is responsible for mass mortality of over a third of an entire vertebrate class. For example, if a single pathogen were causing the death, decline and extinction of 30% of mammal species (including humans), the entire world would be paying attention. This is what has been happening to the world's amphibians – the frogs, toads and salamanders that are affected by the chytrid fungal pathogen, Batrachochytrium dendrobatidis (referred to as Bd), which are consequently declining at an alarming rate. It has aptly been described as the worst pathogen in history in terms of its effects on biodiversity (Kilpatrick et al. 2010). The pathogen was only formally described about 13 years ago (Longcore et al. 1999), and scientists are still in the process of determining where it came from and investigating the question: why now? Healthy debate has ensued as to whether Bd is a globally endemic organism that only recently started causing high mortality due to shifting host responses and/or environmental change (e.g. Pounds et al. 2006) or whether a virulent strain of the pathogen has rapidly disseminated around the world in recent decades, affecting new regions with a vengeance (e.g. Morehouse et al. 2003; Weldon et al. 2004; Lips et al. 2008). We are finally beginning to shed more light on this question, due to significant discoveries that have emerged as a result of intensive DNA‐sequencing methods comparing Bd isolates from different amphibian species across the globe. Evidence is mounting that there is indeed a global panzootic lineage of Bd (BdGPL) in addition to what appear to be more localized endemic strains (Fisher et al. 2009; James et al. 2009; Farrer et al. 2011). Additionally, BdGPL appears to be a hypervirulent strain that has resulted from the hybridization of different Bd strains that came into contact in recent decades, and is now potentially replacing the less‐virulent endemic strains of the pathogen (Farrer et al. 2011). In a new study published in this issue of Molecular Ecology, Schloegel et al. (2012) identify an additional unique Bd lineage that is endemic to the Atlantic Brazilian rainforests (Bd‐Brazil) and provide striking evidence that the Bd‐Brazil lineage has sexually recombined with the BdGPL lineage in an area where the two lineages likely came into contact as a result of classic anthropogenically mediated ‘pathogen pollution’(see below). Fungal pathogens, including Bd, have the propensity to form recombinant lineages when allopatric populations that have not yet formed genetic reproductive barriers are provided with opportunities to intermingle, and virulent strains may be selected for because they tend to be highly transmissible (Fisher et al. 2012). As Schloegel et al. (2012) point out, the demonstrated ability for Bd to undergo meiosis may also mean that it has the capacity to form a resistant spore stage (as yet undiscovered), based on extrapolation from other sexually reproducing chytrids that all have spore stages.     

Tracing the recombination and colonization history of hybrid species in space and time

Hybrid speciation has long fascinated evolutionary biologists and laymen alike, presumably because it challenges our classical view of evolution as a ‘one‐way street’ leading to strictly tree‐like patterns of ancestry and descent. Homoploid hybrid speciation (HHS) has been a particularly interesting puzzle, as it appears to occur extremely rapidly, perhaps within less than 50 generations ( McCarthy et al. 1995 ; Buerkle et al. 2000 ). Nevertheless, HHS may sometimes involve extended or repeated periods of recombination and gene exchange between populations subject to strong divergent natural selection ( Buerkle & Rieseberg 2008 ). Thus, HHS provides a highly interesting setting for understanding the drivers and tempo of adaptive divergence and speciation in the face of gene flow ( Arnold 2006 ; Rieseberg & Willis 2007 ; Nolte & Tautz 2009). In the present issue of Molecular Ecology, Wang et al. (2011) explore a particularly challenging issue connected to HHS: they attempt to trace the colonization and recombination history of an ancient (several MYA) hybrid species, from admixture and recombination in the ancestral hybrid zone to subsequent range shifts triggered by tectonic events (uplift of the Tibetan plateau) and climatic shifts (Pleistocene ice ages). This work is important because it addresses key issues related to the origin of the standing genetic variation available for adaptive responses (e.g. to climate change) and speciation in temperate species, which are topics of great current interest ( Rieseberg et al. 2003 ; Barrett & Schluter 2008 ; de Carvalho et al. 2010 ).     

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.     

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.     

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.     

Persistence and colonisation as measures of success in bog restoration for aquatic invertebrates: a question of detection

1. van Duinen et al. (Freshwater Biol., 2006) raise an interesting point regarding Mazerolle et al.’s (Freshwater Biol., 2006, 51 , p. 333) conclusion on the ability of invertebrates, especially sedentary species, to colonise newly created bogs pools. We wish to clarify that Mazerolle et al. (2006) targeted large arthropods and the absence of smaller sedentary species was purely a result of sampling design. 2. van Duinen et al. (2006) postulate that colonisation rates by bog specialists should be higher in Canada than in the Netherlands, given the extensive amount of intact peatlands in Canada. Here, we emphasise the importance of taking the regional context into account when assessing restoration success as our study site occurs in a landscape where most bog pools have been drained. 3. An evaluation of restoration efforts should focus on both sedentary and vagile invertebrates, to resolve the importance of persistence and colonisation. Such patterns are difficult to interpret, however, when sampling designs and analyses do not account for the probability of detection: an absence may be due to non‐detection or true absence. We strongly urge investigators to directly estimate detection probability in addition to the parameters of interest (e.g. presence, abundance) to provide the best information possible regarding restoration success.     

Assessing endemism at multiple spatial scales, with an example from the Australian vascular flora

Aim  To develop an approach for assessing the spatial scale of centres of endemism among species level data.
Location Australia.
Methods  Endemism is inherently scale dependent. Therefore, the Corrected Weighted Endemism (CWE) index used by Crisp et al. [ J. Biogeogr. (2001)28:183] is extended to account for species samples in local neighbourhoods as a Spatial CWE index. This then allows an analysis of how the degree of endemism of a location (cell) changes with spatial scale. The quality of the Spatial CWE index results are assessed using three spatial randomizations at the species level with and without preserving species richness and distributional patterns. We show that CWE is equivalent to beta diversity and predict that it should show high rates of change around centres of endemism.
Results  Similar patterns to those found by Crisp et al. using a data set of vascular flora from Australia are retrieved, but the extent to which they are scale dependent is more easily identified. For example, the Central Australian centre discounted by Crisp et al. is identified when a three-cell radius neighbourhood is used. However, the level of endemism in this centre is no greater than in the margins of many of the coastal centres of endemism. Most of the identified centres of endemism are better than random at all scales and are increasingly so as the spatial scale increases. As predicted, the highest rate of change in Spatial CWE (beta diversity) is most often between zero- and one-cell radius neighbours in most centres of endemism.
Main conclusions  The explicit incorporation of geographical space in analyses allows for a greater understanding of the scale-dependence of phenomena, in this case endemism and beta diversity.