Do microsatellites reflect genome‐wide genetic diversity in natural populations? A comment on Väli et al. (2008)

A recent study by Väli et al. (2008) highlights that microsatellites will often provide a poor prediction of the genome‐wide nucleotide diversity of wild populations, but does not fully explain why. To clarify and stress the importance of identity disequilibrium and marker variability for correlations between multilocus heterozygosity and genome‐wide genetic variability, we performed a simple simulation with different types of markers, corresponding to microsatellites and SNPs, in populations with different inbreeding history. The importance of identity disequilibrium was apparent for both markers and there was a clear impact of marker variability.     

How to define nativeness in organisms with high dispersal capacities? A comment on Essl et al.

Essl and colleagues documented worldwide invasion patterns in bryophytes, which so far have been neglected in invasion biology. In the absence of historical evidence, Essl and colleagues used criteria such as anomalous geographical distribution, preference for disturbed habitats, and indirect associations with some means of human transport as criteria to identify aliens. Because bryophytes exhibit high long‐distance dispersal capabilities, disjunct distribution patterns are, however, the rule rather than the exception in the group. In our opinion, none of the previously proposed criteria to characterize aliens can be satisfactorily applied to groups like bryophytes, for which historical and fossil records are extremely scarce. We suggest that, in order to validate the conclusions of Essl and colleagues, further taxonomic and phylogeographical studies are needed. This is especially true for island floras, for which recent critical taxonomic work and updated checklists, which compose the primary source of information for biodiversity, are largely missing.     

Does GARP really fail miserably? A response to Stockman et al. (2006)

Stockman et al. (2006 ) found that ecological niche models built using DesktopGARP ‘failed miserably’ to predict trapdoor spider (genus Promyrmekiaphila) distributions in California. This apparent failure of GARP (Genetic Algorithm for Rule‐Set Production) was actually a failure of the authors’ methods, that is, attempting to build ecological niche models using single data points. In this paper, we present a re‐analysis of their original data using standard methods with the data appropriately partitioned into training/testing subsets. This re‐evaluation generated accurate distributional predictions that we contrast with theirs. We address the consequences of model‐building using single data points and the need for a foundational understanding of the principles of ecological niche modelling.     

How many buffalo does it take to change a savanna? A response to Bowman et al. (2008)

Bowman et al. (Journal of Biogeography, 2008, 35 , 1976–1988) aimed to explain observed increases in woody cover on floodplains and savannas of Kakadu National Park using estimates of buffalo (Bubalus bubalis) density as a causal variable. They found that buffalo were a minor model variable and concluded that buffalo are ‘not a major driver of floodplain and eucalypt dynamics’. However, the authors mislabelled the historical density of buffalo on their site, citing a period as high density instead of low density. Further, their results were not contextualized within the substantial body of scientific and historical evidence of the buffalo’s strong influence on vegetation in Kakadu. The authors instead postulated three unanalysed drivers of observed patterns of change: fire regime, rainfall and atmospheric CO₂. We suggest that further analyses of change in woody vegetation should make use of accurate historical records of grazers as well as available data sets on fire history.     

Do Antarctic lichens modify microclimate and facilitate vascular plants in the maritime Antarctic? A comment to Molina‐Montenegro et al. ()

A recent article published by Molina‐Montenegro et al. (Journal of Vegetation Science24: 463) examines the association of Antarctic native plant and lichen species to the lichen Usnea antarctica on Fildes Peninsula, King George Island, maritime Antarctica. The authors report that on two sites, five out of 13 and four out of 11 species of lichens and mosses were spatially associated with U. antarctica, suggesting positive interactions between them. Although Deschampsia antarctica does not grow naturally associated with U. antarctica, Molina‐Montenegro et al. carried out a transplantation experiment to demonstrate that the macrolichen acts as a nurse plant, improving the survival of the grass. Serious conceptual and methodological discrepancies emerge from a critical evaluation of this study, challenging their conclusions. First, we suspect that the author confused some lichen taxa, and we also disagree with macrolichens being treated as cushion plants, because rootless, poikilohydric and poikilothermic thallophytes such as lichens are unable to create a stable, enclave‐like microhabitat as vascular cushion plants do. Indeed, a critical evaluation of some of the micro‐environmental parameters measured indicates that there are no biologically meaningful differences between the U. antarctica thalli and surrounding open areas. Second, the lack of consideration of the life history of the species under study leads to confusion when (a) referring to the succession sequence of species that colonize the studied area and (b) interpreting the putative distribution patterns promoted by Usnea versus the substrate preferences of associated species. Third, the authors intend to demonstrate experimentally that Usnea can facilitate the survival of D. antarctica plants, transplanting adult plants and not seedlings between the lichen thalli, and it is not clear how the grass was planted – between or within the lichens – as at both experimental sites the lichens grow on stones or rocks. Facilitative interactions are present in the Antarctic and may play a pivotal role in the structure and functioning of the fragile Antarctic ecosystems. However, more rigorous and well‐planned research is needed to assess its presence, importance and involved mechanisms.     

Is there really insufficient support for Tilman's R* concept? A comment on Miller et al

Miller et al. (2005), in the American Naturalist (165:439-448), critically reviewed the applicability of Tilman's resource-ratio hypothesis. One of their conclusions was that only eight experimental papers support the R* concept, while five do not. We are familiar with some of the latter studies, and we question this conclusion. Our evaluation shows that 12 of the 13 articles investigated by Miller et al. support R* prediction, while one article does not fit the experimental conditions for a proper test. Moreover, the microbial and aquatic literature contains many more competition experiments consistent with the R* prediction. We therefore conclude that there is strong experimental support for the R* concept, at least from studies with bacteria, phytoplankton, and zooplankton.     

Technical comment on Boersma et al. (2016) Temperature driven changes in the diet preference of omnivorous copepods: no more meat when it's hot? Ecology Letters, 19, 45–53

A recent study concluded that omnivorous plankton will shift from predatory to herbivorous feeding with climate warming, as consumers require increased carbon:phosphorous in their food. Although this is an appealing hypothesis, we suggest the conclusion is unfounded, based on the data presented, which seem in places questionable and poorly interpreted.     

A forest‐specialist carnivore in the middle of the desert?Comments on Anabalon et al. 2019

We present comments on an article recently published in Ecology and Evolution (“High‐resolution melting of the cytochrome B gene in fecal DNA: A powerful approach for fox species identification of the Lycalopex genus in Chile”) by Anabalon et al. that reported the presence of Darwin's fox (Lycalopex fulvipes), a temperate forest specialist, in the hyperarid Atacama Desert of northern Chile. We argue that this putative record lacks ecological support in light of ongoing research on this endangered species, and contains numerous methodological flaws and omissions related to the molecular identification of the species. Based on these issues, we suggest the scientific community and conservation decision‐makers disregard the alleged presence of the Darwin's fox in the Atacama Desert.     

Early human dispersals into the Iberian Peninsula: a comment on Martínez et al.(2010) and Garcia et al. (2011)

Garcia et al. (2011) recently discussed early human dispersals into the Iberian Peninsula, describing several putative lithic artifacts (Martínez et al., 2010) recovered from layer 7 of the Vallpara díssection (Madurell-Malapeira et al., 2010) in Terrassa (Vallès-Penedès Basin, Catalonia, Spain). According to the authors' opinion, such evidence (1) fills a gap in the chronology of early human occupation in Iberia, (2) indicates that these populations had primary and early access to carcasses, and (3) confirms that early human populations were equipped with advanced cultural traits enabling them to survive in unfavourable climatic conditions. We argue below that the record of human activity at Vallparadís (Martínez et al., 2010;Garcia et al., 2011) is doubtful and even that if confirmed, a chronological gap would remain (contra Garcia et al., 2011). Additional remarks on assertions by these authors on the Vallparadís geology, taphonomy and paleonvironment are also provided.     

Where is the Evidence for Assessing Evidence‐Based Restoration? Comments on Ntshotsho et al. (2010)

In their article “Assessing the evidence base for restoration in South Africa,” Ntshotsho et al. attempt to determine whether restoration in South Africa is evidence based by reporting on 10 projects' baseline data collection, goal setting, and monitoring. However, their contribution suffers from two major constraints. First, they confuse assessing the evidence base with assessing whether restoration is evidence based. Truly, assessing the evidence base would entail a systematic review of the quantity and quality of information available as well as the conclusions supported, perhaps in a meta‐analytical framework. Determining if restoration is evidence based would require a survey of project managers to evaluate if they take decisions based on scientific information. Second, Ntshotsho et al. do not clearly distinguish successfully achieving restoration project goals from successfully restoring ecosystems. They largely focus on projects' socioeconomic goals without emphasizing that these goals are, by definition, secondary to ecological goals in determining restoration success. Thus, Ntshotsho et al. provide neither a sound assessment of the evidence base for restoration nor whether restoration is evidence based. To evaluate and encourage evidence‐based restoration in South Africa, we recommend a simple assessment of the basis on which restoration managers make decisions, identification of factors precluding evidence‐based decision‐making, and development of platforms to evaluate the data collected in restoration programs to generate an evidence base from which to make defendable decisions.