Ronald Brady and the cladists.

Ronald Brady was the first philosopher to defend pattern cladistics as an independent scientific field. That independence was achieved through the decoupling of biological systematics from phylogenetics--that is, inferred evolutionary processes (e.g. character transformation). Brady saw parallels between biological systematics and Wolfgang von Goethe's Morphology, an empirical scientific field that incorporates human observation and perception to discover coherent morphological structures. Goethe's Morphology and pre-Darwinian systematics were independent from evolutionary narratives, a tradition that continued into the 20th Century through the work of biologists such as Agnes Arber. Most importantly, Brady provided the philosophical and historical foundations to an independent systematics by demonstrating the links between phenomenology, Goethe's Morphology and comparative biology.

Temporal area approach for distributional data in biogeography.

A structural approach to temporality in distributional data for use in palaeobiogeography is described herein. Pre-established areas in the distributional data matrix are split temporally, allowing a single geographical space to have multiple iterations [e.g. Area A (Lower Devonian), Area A (Middle Devonian)]. The resulting temporal matrix will allow the representation and capture of any differing relationships through time. Designed primarily for Parsimony Analysis of Endemicity (PAE) and biotic similarity analyses, this approach simply structures distributional data within a temporal partition, meaning that numerical methods can be used to assess relationships between areas to find a branching diagram. Created through the application of the temporal matrix to a given analysis, Temporal Area Approach (TAAp) is a structural approach that facilitates exploration of the data rather than being a hypothesis-driven model following analysis. Understanding the behaviour of non-phylogenetic palaeobiogeographical data and reducing the prevalence of temporal artefacts will lead to more robust area classifications.

Do phytogeographic patterns reveal biomes or biotic regions?

We present the largest comparative biogeographical analysis that has complete coverage of Australia's geography (20 phytogeographical subregions), using the most complete published molecular phylogenies to date of large Australian plant clades (Acacia, Banksia and the eucalypts). Two distinct sets of areas within the Australian flora were recovered, using distributional data from the Australasian Virtual Herbarium (AVH) and the Atlas of Living Australia (ALA): younger Temperate, Eremaean and Monsoonal biomes, and older southwest + west, southeast and northern historical biogeographical regions. The analyses showed that by partitioning the data into two sets, using either a Majority or a Frequency method to select taxon distributions, two equally valid results were found. The dataset that used a Frequency method discovered general area cladograms that resolved patterns of the Australian biomes, whereas if widespread taxa (Majority method, with >50% of occurrences outside a single subregion) were removed the analysis then recovered historical biogeographical regions. The study highlights the need for caution when processing taxon distributions prior to analysis as, in the case of the history of Australian phytogeography, the validity of both biomes and historical areas have been called into question.

What is Intuitive Taxonomic Practice?

Scotland and Steel (2015) recently explored the idea of character compatibility, examining the issue from the perspective of a particular model, "a simple and extreme model in which each character either fits perfectly on some tree, or is entirely random $\ldots$,." (Scotland and Steel 2015, p. 492, abstract). They suggested that character compatibility, when formalized as a phylogenetic method, captured what they believed was the "intuitive taxonomic practice of recognizing taxa based on conserved nonhomoplastic characters" (Scotland and Steel 2015, p. 493). Although we agree that there is much to be said for compatibility analysis, and "it has largely been set aside, initially in favour of maximum parsimony, and, more recently, by model-based methods for inferring phylogeny from DNA sequence data" (Scotland and Steel 2015, p. 493), their use of the expression "intuitive taxonomic practice" attracted our attention. Below we discuss in more detail what "intuitive taxonomic practice" might be and relate that understanding to recent progress in the history of biology, specifically the history of systematics (taxonomy), and finally sketch out a proposal that might satisfy those of us who retain an interest in capturing in a more rigorous way what "intuitive taxonomic practice" might have been. [Compatibility methods; monothetic taxa; polythetic taxa."History is what we have to struggle to remember even when legend [myth] is more pleasing" (Adam Gopnik, The New Yorker, 23 November 2015).

Aphyly: identifying the flotsam and jetsam of systematics.

Many taxon names in any classification will be composed of taxa that have yet to be demonstrated as monophyletic, that is, characterized by synapomorphies. Such taxa might be called aphyletic, the flotsam and jetsam in systematics, simply meaning they require taxonomic revision. The term aphyly is, however, the same as, if not identical to, Hennig's "Restkörper" and Bernardi's merophyly. None of these terms gained common usage. We outline Hennig's use of "Restkörper" and Bernardi's use of merophyly and compare it to aphyly. In our view, application of aphyly would avoid the oft made assumption that when a monophyletic group is discovered from within an already known and named taxon, then the species left behind are rendered paraphyletic. By identifying the flotsam and jetsam in systematics, we can focus on taxa in need of attention and avoid making phylogenetic faux pas with respect to their phylogenetic status.

Establishing a Framework for a Natural Area Taxonomy.

The identification of areas of endemism is essential in building an area classification, but plays little role in how natural areas are discovered. Rather area monophyly, derived from cladistics, is essential in the discovery of natural area classifications or area taxonomy. We propose Area Taxonomy to be a new sub-discipline of historical biogeography, one that can be revised and debated, and which has its own area nomenclature. Separately to area taxonomy, we outline how natural areas may be discovered by transcribing the concepts of homology and monophyly from biological systematics to historical biogeography, in the form of area homologues, area homologies and area monophyly.

From Correlation to Causation: What Do We Need in the Historical Sciences?

Changes in the methodology of the historical sciences make them more vulnerable to unjustifiable speculations being passed off as scientific results. The integrity of historical science is in peril due the way speculative and often unexamined causal assumptions are being used to generate data and underpin the identification of correlations in such data. A step toward a solution is to distinguish between plausible and speculative assumptions that facilitate the inference from measured and observed data to causal claims. One way to do that is by comparing these assumptions against a well-attested set of aspects of causation, such as the so-called "Bradford Hill Criteria" (BHC). The BHC do not provide a test for causation or necessary and sufficient conditions for causation but do indicate grounds for further investigation. By revising the BHC to reflect the needs and focus of historical sciences, it will be possible to assess the cogency of methods of investigation. These will be the Historical Sciences Bradford Hill Criteria (HSBHC). An application to one area in historical science is used to demonstrate the effectiveness of the HSBHC, namely biogeography. Four methods are assessed in order to show how the HSBHC can be used to examine the assumptions between our data and the causal biogeographical processes we infer.

Does counting species count as taxonomy? On misrepresenting systematics, yet again.

Recent commentary by Costello and collaborators on the current state of the global taxonomic enterprise attempts to demonstrate that taxonomy is not in decline as feared by taxonomists, but rather is increasing by virtue of the rate at which new species are formally named. Having supported their views with data that clearly indicate as much, Costello et al. make recommendations to increase the rate of new species descriptions even more. However, their views appear to rely on the perception of species as static and numerically if not historically equivalent entities whose value lie in their roles as "metrics". As such, their one-dimensional portrayal of the discipline, as concerned solely with the creation of new species names, fails to take into account both the conceptual and epistemological foundations of systematics. We refute the end-user view that taxonomy is on the rise simply because more new species are being described compared with earlier decades, and that, by implication, taxonomic practice is a formality whose pace can be streamlined without considerable resources, intellectual or otherwise. Rather, we defend the opposite viewpoint that professional taxonomy is in decline relative to the immediacy of the extinction crisis, and that this decline threatens not just the empirical science of phylogenetic systematics, but also the foundations of comparative biology on which other fields rely. The allocation of space in top-ranked journals to propagate views such as those of Costello et al. lends superficial credence to the unsupportive mindset of many of those in charge of the institutional fate of taxonomy. We emphasize that taxonomy and the description of new species are dependent upon, and only make sense in light of, empirically based classifications that reflect evolutionary history; homology assessments are at the centre of these endeavours, such that the biological sciences cannot afford to have professional taxonomists sacrifice the comparative and historical depth of their hypotheses in order to accelerate new species descriptions.

The bioregionalisation revival.

The aim of this paper is to review some of the economic drivers of large scale bioregionalisation, using examples from deep sea hydrothermal vent communities, the Antarctic and sub-Antarctic, and Australia. These economic drivers are mainly recent conservation efforts, while early 20th century bioregionalisation was driven by 19th century taxonomy and exploration to assess available biological resources for economic exploitation. Modern regionalisation, particularly of the Antarctic and deep sea hydrothermal vent communities, are driven by conservation studies to protect areas from economic exploitation, rather than biogeographical questions concerning endemism and natural classification.

Implementation as theory, hierarchy as transformation, homology as synapomorphy.

Presently cladistics is based on, and justified by, a computer implementation (Wagner Parsimony) rather than sound methodological or theoretical foundations. In this paper, the recent goals of cladistics that are derived from computer implementations and 'tree-thinking' are discussed. The discussion raises a critical point, namely whether one can dispense with these recent goals and adopt a wholly systematic approach, one herein termed systematic thinking.

Towards an Australian Bioregionalisation Atlas: A provisional area taxonomy of Australia's biogeographical regions.

The large number, definition, varied application and validity of named Australian biogeographical regions reflect their ad hoc development via disparate methods or case study idiosyncracies. They do not represent a coherent system. In order to resolve these uncertainties an Australian Bioregionalisation Atlas is proposed as a provisional hierarchical classification, accounting for all known named areas. This provisional area taxonomy includes a diagnosis, description, type locality and map for each named area within the Australian continent, as well as a first-ever area synonymy. Akin to biological classifications, this Atlas seeks to provision universality, objectivity and stability, such that biogeographers, macroecologists and geographers, can test existing areas as well as proposing novel areas. With such a formalised and comparative system in place, practitioners can analyse the definition and relationships of biotic areas, and putatively minimise ad hoc explanations.

Impediments to taxonomy and users of taxonomy: accessibility and impact evaluation.

There has been much discussion of the "taxonomic impediment". This phrase confuses two kinds of impediment: an impediment to end users imposed by lack of reliable information; and impediments to taxonomy itself, which vary from insufficient funding to low citation rates of taxonomic monographs. In order to resolve both these types of impediment, taxonomy needs to be revitalized through funding and training taxonomists, as well as investing in taxonomic revisions and monographs rather than technological surrogates such as DNA barcoding. © The Willi Hennig Society 2011.

Bioregionalisation of the freshwater zoogeographical areas of mainland China.

Biogeographic regionalisations extract patterns of co-occurrence from different taxa to form a hierarchical system of geographical units of different scales. This system is useful for revealing biogeographic patterns and can be used as the basis for scientific communication between different fields. The history of Chinese freshwater biogeography is not well known to most modern biogeographers and is reviewed herein. We produce the first quantitative bioregionalisation of the freshwater zoogeographic areas of mainland China based on multiple animal groups. The combined occurrence data of amphibians, freshwater fish and freshwater crabs were subjected to cluster and network analyses. The two different methods yielded largely similar results. We propose four freshwater zoogeographical subregions (Beifang, Tarim, China, and the Tibetan subregion), three dominions for the China subregion (Jianghuai, Dongyang, and the new Dian dominion), three provinces for the Dian dominion (West Hengduan, Diannan Highlands and the new Yungui Plateau province) and two provinces for the Dongyang dominion (Zhemin and the new Huanan province) according to the naming rules of ICAN. The endemic areas of each animal group were then individually studied and were found to reflect the bioregionalisation at the subregion level, but differed from each other at the dominion and province level. Our analyses show that: (1) previous intuitive biogeographical studies have found similar areas; (2) there are recurring large scale biogeographic patterns in Chinese freshwater fishes, amphibians and freshwater crabs; and (3) bioregionalisations derived from quantitative methods can be effective for partitioning areas into biogeographically meaningful units.

Quantifying vertebrate zoogeographical regions of Australia using geospatial turnover in the species composition of mammals, birds, reptiles and terrestrial amphibians.

A geospatial analysis of 1,906,302 records of 1938 species of Australian vertebrates has shown that the original regions proposed in the 19th century, namely the Eyrean, Torresian and Bassian still hold. The analysis has shown that the Eyrean region has an east-west divide, forming two, possibly independent arid regions (Eastern Desert and Western Desert provinces), that are shaped by topography and rainfall. A revised and interim zoogeographical area taxonomy of the Australian region is presented herein.