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.

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.

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.

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.

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.

A Cladist is a systematist who seeks a natural classification: some comments on Quinn (2017).

In response to Quinn (Biol Philos, 2017. 10.1007/s10539-017-9577-z) we identify cladistics to be about natural classifications and their discovery and thereby propose to add an eighth cladistic definition to Quinn's list, namely the systematist who seeks to discover natural classifications, regardless of their affiliation, theoretical or methodological justifications.

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.

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).

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.

A review of the Carboniferous and Permian trilobites of Australia.

The first complete review of the Carboniferous and Permian trilobite species found within Australia is presented to assess the current standing of Australian taxa in a modern systematic context. The review consists of four families, 20 genera and 61 known species from the early Tournaisian to Moscovian (358.9 Ma to 304 Ma), throughout New South Wales, Tasmania, Western Australia and Queensland. The revision also includes a revised anatomical nomenclature for Australian Carboniferous trilobites. Emended diagnoses are provided for seven genera and 28 species. The genus Thalabaria is placed within the subfamily Archegoninae, and the genera Australokaskia and Planokaskia are placed within Cummingellinae. The subgenera Brachymetopus (Spinimetopus), Bollandia (Capricornia), Australokaskia (Longilobus) and Australokaskia (Planilobus) are suppressed within Brachymetopus, Bollandia, Australokaskia, respectively. All Brachymetopus (Brachymetopus) maccoyi subspecies are elevated to species. Species of Linguaphillipsia are considered sensu lato until there is adequate revision of the entire genus. New combinations include the following: Aprathia semicircularis is reassigned to Weania; Aprathia applanata is questionably reassigned to Carbonocoryphe; and Phillipsia squamata is tentatively reassigned to Palaeophillipsia. The following have been synonymised: Conophillipsia with Monodechenella; Megaproetus with Pudoproetus; Weberiphillipsia with Palaeophillipsia; Weania (Rosehillia) with Schizophillipsia; Conophillipsia breviceps dungogensis with Monodechenella breviceps; Linguaphillipsia raglanensis with Linguaphillipsia stanvellensis; and Weberiphillipsia girvanensis with Palaeophillipsia collinsi. Carbonocoryphe (Winterbergia) elegans, Carbonocoryphe (Winterbergia) keepitensis and Winterbergia? waterhousei are considered representatives of indeterminate genera.

Spatial variation in the climatic predictors of species compositional turnover and endemism.

Previous research focusing on broad-scale or geographically invariant species-environment dependencies suggest that temperature-related variables explain more of the variation in reptile distributions than precipitation. However, species-environment relationships may exhibit considerable spatial variation contingent upon the geographic nuances that vary between locations. Broad-scale, geographically invariant analyses may mask this local variation and their findings may not generalize to different locations at local scales. We assess how reptile-climatic relationships change with varying spatial scale, location, and direction. Since the spatial distributions of diversity and endemism hotspots differ for other species groups, we also assess whether reptile species turnover and endemism hotspots are influenced differently by climatic predictors. Using New Zealand reptiles as an example, the variation in species turnover, endemism and turnover in climatic variables was measured using directional moving window analyses, rotated through 360°. Correlations between the species turnover, endemism and climatic turnover results generated by each rotation of the moving window were analysed using multivariate generalized linear models applied at national, regional, and local scales. At national-scale, temperature turnover consistently exhibited the greatest influence on species turnover and endemism, but model predictive capacity was low (typically r (2) = 0.05, P < 0.001). At regional scales the relative influence of temperature and precipitation turnover varied between regions, although model predictive capacity was also generally low. Climatic turnover was considerably more predictive of species turnover and endemism at local scales (e.g., r (2) = 0.65, P < 0.001). While temperature turnover had the greatest effect in one locale (the northern North Island), there was substantial variation in the relative influence of temperature and precipitation predictors in the remaining four locales. Species turnover and endemism hotspots often occurred in different locations. Climatic predictors had a smaller influence on endemism. Our results caution against assuming that variability in temperature will always be most predictive of reptile biodiversity across different spatial scales, locations and directions. The influence of climatic turnover on the species turnover and endemism of other taxa may exhibit similar patterns of spatial variation. Such intricate variation might be discerned more readily if studies at broad scales are complemented by geographically variant, local-scale analyses.

Quantifying phytogeographical regions of Australia using geospatial turnover in species composition.

The largest digitized dataset of land plant distributions in Australia assembled to date (750,741 georeferenced herbarium records; 6,043 species) was used to partition the Australian continent into phytogeographical regions. We used a set of six widely distributed vascular plant groups and three non-vascular plant groups which together occur in a variety of landscapes/habitats across Australia. Phytogeographical regions were identified using quantitative analyses of species turnover, the rate of change in species composition between sites, calculated as Simpson's beta. We propose six major phytogeographical regions for Australia: Northern, Northern Desert, Eremaean, Eastern Queensland, Euronotian and South-Western. Our new phytogeographical regions show a spatial agreement of 65% with respect to previously defined phytogeographical regions of Australia. We also confirm that these new regions are in general agreement with the biomes of Australia and other contemporary biogeographical classifications. To assess the meaningfulness of the proposed phytogeographical regions, we evaluated how they relate to broad scale environmental gradients. Physiographic factors such as geology do not have a strong correspondence with our proposed regions. Instead, we identified climate as the main environmental driver. The use of an unprecedentedly large dataset of multiple plant groups, coupled with an explicit quantitative analysis, makes this study novel and allows an improved historical bioregionalization scheme for Australian plants. Our analyses show that: (1) there is considerable overlap between our results and older biogeographic classifications; (2) phytogeographical regions based on species turnover can be a powerful tool to further partition the landscape into meaningful units; (3) further studies using phylogenetic turnover metrics are needed to test the taxonomic areas.

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.

Temporal Geobiotic Mapping: a conceptual mapping technique toward visualising geobiotic areas in cross-section

Geobiota are defined by taxic assemblages (i.e., biota) and their defining abiotic breaks, which are mapped in cross-section to reveal past and future biotic boundaries. We term this conceptual approach Temporal Geobiotic Mapping (TGM) and offer it as a conceptual approach for biogeography. TGM is based on geological cross-sectioning, which creates maps based on the distribution of biota and known abiotic factors that drive their distribution, such as climate, topography, soil chemistry and underlying geology. However, the availability of abiotic data is limited for many areas. Unlike other approaches, TGM can be used when there is minimal data available. In order to demonstrate TGM, we use the well-known area in the Blue Mountains, New South Wales (NSW), south-eastern Australia and show how surface processes such as weathering and erosion affect the future distribution of a Moist Basalt Forest taxic assemblage. Biotic areas are best represented visually as maps, which can show transgressions and regressions of biota and abiota over time. Using such maps, a biogeographer can directly compare animal and plant distributions with features in the abiotic environment and may identify significant geographical barriers or pathways that explain biotic distributions.

Quantifying high resolution transitional breaks in plant and mammal distributions at regional extent and their association with climate, topography and geology.

OBJECTIVES: We quantify spatial turnover in communities of 1939 plant and 59 mammal species at 2.5 km resolution across a topographically heterogeneous region in south-eastern Australia to identify distributional breaks and low turnover zones where multiple species distributions overlap. Environmental turnover is measured to determine how climate, topography and geology influence biotic turnover differently across a variety of biogeographic breaks and overlaps. We identify the genera driving turnover and confirm the versatility of this approach across spatial scales and locations. METHODS: Directional moving window analyses, rotated through 360°, were used to measure spatial turnover variation in different directions between gridded cells containing georeferenced plant and mammal occurrences and environmental variables. Generalised linear models were used to compare taxic turnover results with equivalent analyses for geology, regolith weathering, elevation, slope, solar radiation, annual precipitation and annual mean temperature, both uniformly across the entire study area and by stratifying it into zones of high and low turnover. Identified breaks and transitions were compared to a conservation bioregionalisation framework widely used in Australia. RESULTS/SIGNIFICANCE: Detailed delineations of plant and mammal turnover zones with gradational boundaries denoted subtle variation in species assemblages. Turnover patterns often diverged from bioregion boundaries, though plant turnover adhered most closely. A prominent break zone contained either comparable or greater numbers of unique genera than adjacent overlaps, but these were concentrated in a small subsection relatively under-protected by conservation reserves. The environmental correlates of biotic turnover varied for different turnover zones in different subsections of the study area. Topography and temperature showed much stronger relationships with plant turnover in a topographically complex overlap, relative to a lowland overlap where weathering was most predictive. This method can quantify transitional turnover patterns from small to broad extents, at different resolutions for any location, and complements broad-scale bioregionalisation schemes in conservation planning.