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of Biogeography, 2013, 40 , 1010–1012) critiqued our paper on the grounds that our ‘pyric phase’ model was built on outdated views of cultural development, claiming we developed it to be the unifying explanatory framework for all human–fire sciences.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.     

On cladistics and human–ape relationships

The rebuttal of our correspondence (Lehtonen et al., Journal of Biogeography, 2011, 38, 805–808) by J. R. Grehan and J. H. Schwartz (Journal of Biogeography, 2011, 38, 2397–2404) reveals logical inconsistencies in their methodology. Here, we provide a clarification of these issues.     

Just a hypothesis: a reply to Hanski

Hanski's critique of the habitat amount hypothesis (Hanski, 2015, Journal of Biogeography, 42 , 989–993) does not actually constitute a test of the hypothesis, but rather a series of arguments for why he suspects that it is not correct. But the habitat amount hypothesis is exactly that – a hypothesis. It will remain ‘just’ a hypothesis until it has been rigorously tested against empirical data. To facilitate such testing, in Fahrig (2013, Journal of Biogeography, 40 , 1649–1663) I presented specific, testable predictions of the hypothesis. Here, I reiterate the main tests needed, in the hope that some readers will be encouraged to carry them out. I appreciate this opportunity to emphasize that the habitat amount hypothesis needs to be tested against empirical data, and I look forward to seeing the results of such tests.     

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.     

Towards a balanced view of pike in Ireland: a reply to Ensing

In our recent study of the population genetics of pike (Esox lucius) in Ireland (Pedreschi et al., 2014 , Journal of Biogeography, 41 , 548–560), we reported the existence of two main demographic units and showed that these may correspond to two independent and temporally staggered colonization events, the first of which may have been too old to be caused or assisted by human translocations. Ensing (2015, Journal of Biogeography, doi: 10.1111/jbi.12410 ) first used our genotypic data to explore alternative historical scenarios, then attempted to reconcile the ‘two‐wave’ colonization process of Ireland by pike with translocation activities by humans in Neolithic/Bronze age times. Here we illustrate why the evidence base for Ensing's reconstruction is weak and we outline a realistic strategy to better understand the role of pike in Irish freshwater ecosystems.     

Marine island biogeography. Response to comment on ‘Island biogeography: patterns of marine shallow‐water organisms’

In this response we have incorporated data on gastropod and seaweed biodiversity referred to by Ávila et al. (2016, Journal of Biogeography, doi: 10.1111/jbi.12816 ) to allow an updated analysis on marine shallow‐water biogeography patterns. When compared to the biogeography patterns reported in Hachich et al. (2015, Journal of Biogeography, 42 , 1871–1882), we find (1) no differences in the patterns originally reported for reef fish or seaweeds, (2) minor differences in gastropod species–area and species–age patterns and (3) a significant difference for the gastropod species‐isolation pattern. In our original work, we reported that there was limited evidence that gastropod species richness was influenced by island isolation; however, our new analysis reveals a power‐model relationship between these variables. Thus, we are now able to conclude that gastropod species diversity, whose dispersal capacity is intermediate between seaweeds (lowest) and reef fish (highest), is also influenced by island isolation.     

Time and space in biogeography: response to Parenti & Ebach (2013)

A recent Guest Editorial by Parenti & Ebach (2013, Journal of Biogeography, 40, 813–820) disagrees with the methods or interpretations in two of our recent papers. In addition, the authors open a debate on biogeographical concepts, and present an alternative philosophy for biogeographical research in the context of their recently described biogeographical subregion called ‘Pandora’. We disagree with their approach and conclusions, and comment on several issues related to our differing conceptual approaches for biogeographical research; namely, our use of molecular phylogenetic analyses, including time estimates; and Parenti & Ebach's reliance on taxon/general area cladograms. Finally, we re‐examine their ‘tests’ supporting the existence of ‘Pandora’.     

Analysis of stable states in global savannas – a response to Staver and Hansen

Staver & Hansen (2015, Global Ecology and Biogeography, doi: 10.1111/geb.12285) comment on our recent paper (Hanan et al., Global Ecology and Biogeography, 2014, 23 , 259–263) in which we argue that classification and regression tree methods used with remote sensing data to predict tree cover may bias inference of bifurcations in savanna vegetation communities. While we agree with several of their comments, we remain unconvinced that a remote sensing product based on an inherently discontinuous statistical approach can, or should, be used to test for discontinuities.     

Correspondence

Comment on M. Pole (1994): ‘The New Zealand flora—entirely long-distance dispersal?’Journal of Biogeography (1994) 22, 625–635     

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.     

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.     

Outlier detection methods are still effective even using virtual species created with the probabilistic approach

Liu et al. (Journal of Biogeography, 2018, 45 :164–176) presented an approach to detect outliers in species distribution data by developing virtual species created using the threshold approach. Meynard et al. (Journal of biogeography, 2019, 46 :2141–2144) raised concerns about this approach stating that ‘using a probabilistic approach … may significantly change results’. Here we provide a new series of simulations using the two approaches and demonstrate that the outlier detection approach based on pseudo species distribution models was still effective when using the probabilistic approach, although the detection rate was lower than when using the threshold approach.     

Putting biogeography’s cart back behind taxonomy’s horse: a response to Triantis et al.

In a recent paper, two of us discussed diversity patterns and diversification processes in the Azores flora. Triantis et al. (2012, Journal of Biogeography, 39, 1179–1184) challenged our hypothesis that palaeoclimatic differences had an effect on diversification rates and suggested that area, island age and isolation explain diversity patterns. They did not, however, fully address the results from our subsequent paper, in which we showed that diversity patterns evident from phylogeographic studies differ markedly from those suggested by checklists. Checklists are working hypotheses and we suggest that the discrepancies evident between molecular data and checklists may be indicative of deficiencies in our taxonomic understanding of the Azores flora. Patterns of molecular and morphological diversity need to be better understood, and the discrepancies between checklists and molecular data accounted for, before we can establish the relative importance of factors such as palaeoclimate, area, island age or isolation in generating endemic diversity patterns in the Azores flora.     

Pleistocene speciation is not refuge speciation

A number of researchers working on the origin of extant Neotropical biodiversity implicitly and without appropriate proofs assume that Pleistocene speciation should necessarily follow the rules of the refuge hypothesis. A recent example is provided by a study of Neotropical butterflies. Although the analysis showed that these groups experienced their main diversification burst during the last 2.6 million years, coinciding with the Pleistocene glacial cycles (Garzón‐Orduña et al., 2014, Journal of Biogeography, 41 , 1631–1638), a causal link between the speciation chronology and the evolutionary mechanisms proposed by the refuge hypothesis is not provided. Without more detailed studies on the environmental drivers, geographical patterns and speciation modes, establishing a causal link between speciation chronology and a particular speciation model – of which the refuge hypothesis is only one among many possibilities – is too speculative. Here I provide a six‐step conceptual framework for linking the speciation chronology with the environmental drivers and the ecological and evolutionary mechanisms potentially involved.     

New Caledonian biogeography: a reply to Murienne

This note replies to criticisms raised by Murienne (Journal of Biogeography, 2010, doi: 10.1111/j.1365‐2699.2010.02321.x ). Herein it is argued that assuming distributions in New Caledonia are caused by current environmental factors overlooks the possible importance of regional tectonic history for the biogeography.     

Who is the closest extant cousin of humans? Total‐evidence approach to hominid phylogenetics via simultaneous optimization

J. R. Grehan & J. H. Schwartz (Journal of Biogeography, 2009, 36 , 1823–1844) argued that humans (Homo) are more closely related to orangutans (Pongo) than to chimpanzees (Pan), and used this scenario to draw biogeographical conclusions about human origins. They discussed a contradiction between phenotypical and molecular results that has led to a debate about the reliability of genetic versus phenotypic data. The main aim of our study is to test the conflicting phylogenetic hypotheses by a total‐evidence analysis based on simultaneous optimization of extensive phenotypic and molecular data sets. Our results supported the human–chimpanzee clade, without any phenotypical–molecular data conflict, as the same phylogeny emerged both from the total analysis and when the molecular and phenotypic data were analysed separately. Sensitivity analyses showed that the result was not dependent on the parameters chosen for character weighting.     

Termite mounds alter the spatial distribution of African savanna tree species: artefacts and real patterns

In a recent issue (vol. 43) of the Journal of Biogeography, Davies et al. (2015) presented novel analyses of the spatial distribution of tree species around termite mounds in a South African savanna. However, some of their conclusions are not supported by the data. My aim in this correspondence is to point out some limitations of their analyses, stimulate cautious interpretation of their results and suggest better methods for future use.     

The need for richness‐independent measures of turnover when delineating biogeographical regions

Delineating biogeographical regions is one of the primary steps when analysing biogeographical patterns. In their proposed quantitative framework, Kreft & Jetz (2010, Journal of Biogeography, 37 , 2029–2053) recommended the use of the β_sim index to delineate biogeographical regions because this turnover measure is weakly affected by differences in species richness between localities. A recent study by Carvalho et al. (2012, Global Ecology and Biogeography, 21 , 760–771) critiziced the use of β_sim in ecological and biogeographical studies, and proposed the β_‐3 index. Here we used simple numerical examples and an empirical case study (European freshwater fishes) to highlight potential pitfalls associated with the use of β_‐3 for bioregionalization. We show that β_‐3 is not a richness‐independent measure of species turnover. We also show that this index violates the ‘complementarity’ property, namely that localities without species in common have the largest dissimilarity, which is an essential prerequisite for beta diversity studies.     

Less than eight (and a half) misconceptions of spatial analysis

Spatial analyses are indispensable analytical tools in biogeography and macroecology. In a recent Guest Editorial, Hawkins (Journal of Biogeography, 2012, 39 , 1–9) raised several issues related to spatial analyses. While we concur with some points, we here clarify those confounding (1) spatial trends and spatial autocorrelation, and (2) spatial autocorrelation in the response variable and in the residuals. We argue that recognizing spatial autocorrelation in statistical modelling is not only a crucial step in model diagnostics, but that disregarding it is essentially wrong.     

Analysis of stable states in global savannas: is the CART pulling the horse? – a comment

In their recent paper, Hanan et al. (Global Ecology and Biogeography, 2014, 23 , 259–263) argue that the use of classification and regression trees (CARTs) to calibrate global remote sensing datasets, including the MODIS VCF tree‐cover dataset, makes these data inappropriate for analysing the frequency distribution of tree cover. While we agree with their most general point – that the use of remote sensing products should be informed and deliberate – their analysis overlooks a few key aspects of the use of CARTs in generating global tree‐cover data. Firstly, while their presentation of flaws in the use of CARTs is compelling, their use of hypothetical data obscures the reasons why CARTs are a useful tool. Secondly, they do not actually examine the error distributions of the MODIS VCF tree‐cover data. Such an analysis, which we perform, revealed the following: (1) the MODIS VCF product may not be useful for differentiating over small ranges of tree cover (less than c. 10%); (2) that the bimodality of low and high tree cover, with a frequency minimum at intermediate tree cover, is not attributable to bias in MODIS VCF tree‐cover calibrations; and (3) that the MODIS VCF is not well‐resolved below c. 20–30% tree cover, such that MODIS cannot be used with any confidence to evaluate multimodality in tree cover in that range. Further validation and calibration are likely to be helpful and, at low tree cover, necessary for improving MODIS VCF tree‐cover estimates. However, the MODIS VCF – which has facilitated major steps in our ability to examine ecological phenomena at global scales – remains a useful tool for well‐informed ecological analysis.