Pyrogeography,historical ecology,and the human dimensions of fire regimes

In our 2011 synthesis (Bowman et al., Journal of Biogeography, 2011, 38 , 2223–2236), we argued for a holistic approach to human issues in fire science that we term ‘pyrogeography’. Coughlan & Petty (Journal of Biogeography, 2013, 40 , 1010–1012) critiqued our paper on the grounds that our ‘pyric phase’ model was built on outdated views of cultural development, claiming we developed it to be the unifying explanatory framework for all human–fire sciences. Rather, they suggest that ‘historical ecology’ could provide such a framework. We used the ‘pyric transition’ for multiple purposes but did not offer it as an exclusive explanatory framework for pyrogeography. Although ‘historical ecology’ is one of many useful approaches to studying human–fire relationships, scholars should also look to political and evolutionary ecology, ecosystems and complexity theories, as well as empirical generalizations to build an interdisciplinary fire science that incorporates human, ecological and biophysical dimensions of fire regimes.     

Process,correlation and parameter fitting in species distribution models: a response to Kriticos et al

In a recent article (Dormann et al., 2012, Journal of Biogeography, 39, 2119–2131), we compared different approaches to species distribution modelling and depicted modelling approaches along an axis from purely ‘correlative’ to ‘forward process‐based’ models. In their correspondence, Kriticos et al. (2013, Journal of Biogeography, doi: 10.1111/j.1365‐2699.2012.02791.x ) challenge this view, claiming that our continuum representation neglects differences among models and does not consider the ability of fitted process‐based models to combine the advantages of both process‐based and correlative modelling approaches. Here we clarify that the continuum view resulted from recognition of the manifold differences between models. We also reinforce the point that the current trend towards combining different modelling approaches may lead not only to the desired combination of the advantages but also to the accumulation of the disadvantages of those approaches. This point has not been made sufficiently clear previously.     

Spatial and temporal variation in historic fire regimes in subalpine forests across the Colorado Front Range in Rocky Mountain National Park, Colorado, USA

Aim The historical variability of fire regimes must be understood in the context of drivers of the occurrence of fire operating at a range of spatial scales from local site conditions to broad‐scale climatic variation. In the present study we examine fire history and variations in the fire regime at multiple spatial and temporal scales for subalpine forests of Engelmann spruce–subalpine fir (Picea engelmannii, Abies lasiocarpa) and lodgepole pine (Pinus contorta) of the southern Rocky Mountains. Location The study area is the subalpine zone of spruce–fir and lodgepole pine forests in the southern sector of Rocky Mountain National Park (ROMO), Colorado, USA, which straddles the continental divide of the northern Colorado Front Range (40°20′ N and 105°40′ W). Methods We used a combination of dendroecological and Geographic Information System methods to reconstruct fire history, including fire year, severity and extent at the forest patch level, for c. 30,000 ha of subalpine forest. We aggregated fire history information at appropriate spatial scales to test for drivers of the fire regime at local, meso, and regional scales. Results The fire histories covered c. 30,000 ha of forest and were based on a total of 676 partial cross‐sections of fire‐scarred trees and 6152 tree‐core age samples. The subalpine forest fire regime of ROMO is dominated by infrequent, extensive, stand‐replacing fire events, whereas surface fires affected only 1–3% of the forested area. Main conclusions Local‐scale influences on fire regimes are reflected by differences in the relative proportions of stands of different ages between the lodgepole pine and spruce–fir forest types. Lodgepole pine stands all originated following fires in the last 400 years; in contrast, large areas of spruce–fir forests consisted of stands not affected by fire in the past 400 years. Meso‐scale influences on fire regimes are reflected by fewer but larger fires on the west vs. east side of the continental divide. These differences appear to be explained by less frequent and severe drought on the west side, and by the spread of fires from lower‐elevation mixed‐conifer montane forests on the east side. Regional‐scale climatic variation is the primary driver of infrequent, large fire events, but its effects are modulated by local‐ and meso‐scale abiotic and biotic factors. The low incidence of fire during the period of fire‐suppression policy in the twentieth century is not unique in comparison with the previous 300 years of fire history. There is no evidence that fire suppression has resulted in either the fire regime or current forest conditions being outside their historic ranges of variability during the past 400 years. Furthermore, in the context of fuel treatments to reduce fire hazard, regardless of restoration goals, the association of extremely large and severe fires with infrequent and exceptional drought calls into question the future effectiveness of tree thinning to mitigate fire hazard in the subalpine zone.     

Simplifying the savanna: the trajectory of fire‐sensitive vegetation mosaics in northern Australia

Aim Fire is a key agent in savanna systems, yet the capacity to predict fine‐grained population phenomena under variable fire regime conditions at landscape scales is a daunting challenge. Given mounting evidence for significant impacts of fire on vulnerable biodiversity elements in north Australian savannas over recent decades, we assess: (1) the trajectory of fire‐sensitive vegetation elements within a particularly biodiverse savanna mosaic based on long‐term monitoring and spatial modelling; (2) the broader implications for northern Australia; and (3) the applicability of the methodological approach to other fire‐prone settings. Location Arnhem Plateau, northern Australia. Methods We apply data from long‐term vegetation monitoring plots included within Kakadu National Park to derive statistical models describing the responses of structure and floristic attributes to 15 years of ambient (non‐experimental) fire regime treatments. For a broader 28,000 km² region, we apply significant models to spatial assessment of the effects of modern fire regimes (1995–2009) on diagnostic closed forest, savanna and shrubland heath attributes. Results Significant models included the effects of severe fires on large stems of the closed forest dominant Allosyncarpia ternata, stem densities of the widespread savanna coniferous obligate seeder Callitris intratropica, and fire frequency and related fire interval parameters on numbers of obligate seeder taxa characteristic of shrubland heaths. No significant relationships were observed between fire regime and eucalypt and non‐eucalypt adult tree components of savanna. Spatial application of significant models illustrates that more than half of the regional closed forest perimeters, savanna and shrubland habitats experienced deleterious fire regimes over the study period, except in very dissected terrain. Main conclusions While north Australia’s relatively unmodified mesic savannas may appear structurally intact and healthy, this study provides compelling evidence that fire‐sensitive vegetation elements embedded within the savanna mosaic are in decline under present‐day fire regimes. These observations have broader implications for analogous savanna mosaics across northern Australia, and support complementary findings of the contributory role of fire regimes in the demise of small mammal fauna. The methodological approach has application in other fire‐prone settings, but is reliant on significant long‐term infrastructure resourcing.     

High‐throughput SNPs for all: genotyping‐in‐thousands

Understanding the genetic structure of species is essential for conservation. It is only with this information that managers, academics, user groups and land‐use planners can understand the spatial scale of migration and local adaptation, source‐sink dynamics and effective population size. Such information is essential for a multitude of applications including delineating management units, balancing management priorities, discovering cryptic species and implementing captive breeding programmes. Species can range from locally adapted by hundreds of metres (Pavey et al. 2010 ) to complete species panmixia (Côté et al. 2013 ). Even more remarkable is that this essential information can be obtained without fully sequenced or annotated genomes, but from mere (putatively) nonfunctional variants. First with allozymes, then microsatellites and now SNPs, this neutral genetic variation carries a wealth of information about migration and drift. For many of us, it may be somewhat difficult to remember our understanding of species conservation before the widespread usage of these useful tools. However most species on earth have yet to give us that ‘peek under the curtain’. With the current diversity on earth estimated to be nearly 9 million species (Mora et al. 2011 ), we have a long way to go for a comprehensive meta‐phylogeographic understanding. A method presented in this issue by Campbell and colleagues (Campbell et al. 2015 ) is a tool that will accelerate the pace in this area. Genotyping‐in‐thousands (GT‐seq) leverages recent advancements in sequencing technology to save many hours and dollars over previous methods to generate this important neutral genetic information.     

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.     

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.     

Pyrodiversity interacts with rainfall to increase bird and mammal richness in African savannas

Fire is a fundamental process in savannas and is widely used for management. Pyrodiversity, variation in local fire characteristics, has been proposed as a driver of biodiversity although empirical evidence is equivocal. Using a new measure of pyrodiversity (Hempson et al.), we undertook the first continent‐wide assessment of how pyrodiversity affects biodiversity in protected areas across African savannas. The influence of pyrodiversity on bird and mammal species richness varied with rainfall: strongest support for a positive effect occurred in wet savannas (> 650 mm/year), where species richness increased by 27% for mammals and 40% for birds in the most pyrodiverse regions. Range‐restricted birds were most increased by pyrodiversity, suggesting the diversity of fire regimes increases the availability of rare niches. Our findings are significant because they explain the conflicting results found in previous studies of savannas. We argue that managing savanna landscapes to increase pyrodiversity is especially important in wet savannas.     

A new multivariate zero‐adjusted Poisson model with applications to biomedicine

Recently, although advances were made on modeling multivariate count data, existing models really has several limitations: (i) The multivariate Poisson log‐normal model (Aitchison and Ho, 1989) cannot be used to fit multivariate count data with excess zero‐vectors; (ii) The multivariate zero‐inflated Poisson (ZIP) distribution (Li et al., 1999) cannot be used to model zero‐truncated/deflated count data and it is difficult to apply to high‐dimensional cases; (iii) The Type I multivariate zero‐adjusted Poisson (ZAP) distribution (Tian et al., 2017) could only model multivariate count data with a special correlation structure for random components that are all positive or negative. In this paper, we first introduce a new multivariate ZAP distribution, based on a multivariate Poisson distribution, which allows the correlations between components with a more flexible dependency structure, that is some of the correlation coefficients could be positive while others could be negative. We then develop its important distributional properties, and provide efficient statistical inference methods for multivariate ZAP model with or without covariates. Two real data examples in biomedicine are used to illustrate the proposed methods.     

Tracking the elusive history of diversification in plant–herbivorous insect–parasitoid food webs: insights from figs and fig wasps

The food webs consisting of plants, herbivorous insects and their insect parasitoids are a major component of terrestrial biodiversity. They play a central role in the functioning of all terrestrial ecosystems, and the number of species involved is mind‐blowing (Nyman et al. 2015 ). Nevertheless, our understanding of the evolutionary and ecological determinants of their diversity is still in its infancy. In this issue of Molecular Ecology, Sutton et al. ( 2016 ) open a window into the comparative analysis of spatial genetic structuring in a set of comparable multitrophic models, involving highly species‐specific interactions: figs and fig wasps. This is the first study to compare genetic structure using population genetics tools in a fig‐pollinating wasp (Pleistodontes imperialis sp1) and its main parasitoid (Sycoscapter sp.A). The fig‐pollinating wasp has a discontinuous spatial distribution that correlates with genetic differentiation, while the parasitoid bridges the discontinuity by parasitizing other pollinator species on the same host fig tree and presents basically no spatial genetic structure. The full implications of these results for our general understanding of plant–herbivorous insect–insect parasitoids diversification become apparent when envisioned within the framework of recent advances in fig and fig wasp biology.     

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

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Comment on ‘Island biogeography: patterns of marine shallow‐water organisms’ by Hachich et al., Journal of Biogeography (2015)

In a recent article, Hachich et al. (2015, Journal of Biogeography, 42 , 1871–1882) studied the large‐scale biogeographical patterns of the species–area, species–island age and species–isolation relationships associated with marine shallow‐water groups (reef fish, gastropods and seaweeds) from 11 Atlantic archipelagos. We here express our concerns regarding the data accuracy used to compute the different models that tested the null hypothesis of species richness being independent of the selected variables. In our commentary, we focus mainly on the use of out‐of‐date checklists of gastropod and seaweed species from different archipelagos, but we also point out inaccuracies in some island age estimates and explain our disagreement with the use of the 200 m depth limit for the shallow‐water gastropods and seaweeds.     

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.     

High‐severity fire corroborated in historical dry forests of the western United States: response to Fulé et al.

Accurate assessment of changing fire regimes is important, since climatic change and people may be promoting more wildfires. Government wildland fire policies and restoration programmes in dry western US forests are based on the hypothesis that high‐severity fire was rare in historical fire regimes, modern fire severity is unnaturally high and restoration efforts should focus primarily on thinning forests to eliminate high‐severity fire. Using General Land Office (GLO) survey data over large dry‐forest landscapes, we showed that the proportion of historical forest affected by high‐severity fire was not insignificant, fire severity has not increased as a proportion of total fire area and large areas of dense forest were present historically (Williams & Baker, Global Ecology and Biogeography, 21 , 1042–1052, 2012; W&B). In response, Fulé et al. (Global Ecology and Biogeography, 2013, doi: 10.1111/geb.12136; FE) suggest that our inferences are unsupported and land management based on our research could be damaging to native ecosystems. Here, we show that the concerns of FE are unfounded. Their criticism comes from misquoting W&B, mistaking W&B's methods, misusing evidence (e.g. from Aldo Leopold) and missing substantial available evidence. We also update corroboration for the extensive historical high‐severity fire shown by W&B. We suggest that restoration programmes are misdirected in seeking to reduce all high‐severity fire in dry forests, given findings from spatially extensive GLO data and other sources.     

Macrophyte effects on algal turbidity in subtropical versus temperate lakes: a reply to Dolman (2014)

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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.     

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.     

The predicament of the African wild dog,Lycaon pictus,is less precarious than claimed

In a paper published fifteen years ago, Gorman et al. (Nature 391 , 479–481) made precise claims about how sensitive the African wild dog is to kleptoparasitism by spotted hyaenas Crocuta crocuta and lions Panthera leo. These claims are regularly referred to in the literature, and so far, they have remained unchallenged. However, careful perusal of their paper and analysis of the available data on energy intake and expenditure by wild dogs show that their claims are unfounded. Contrary to Gorman et al., wild dogs can usually take loss of food by kleptoparasitism in their stride. We present the calculations of the energy budget of wild dogs that remain implicit in the paper by Gorman et al.     

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.