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.

Historical biogeographical patterns in continental Australia: congruence among areas of endemism of two major clades of eucalypts.

Published phylogenies of two eucalypt clades, red bloodwoods Corymbia subgenus Corymbia and eudesmids Eucalyptus subgenus Eudesmia (Myrtaceae), were combined for an analysis of historical biogeographical area relationships within continental Australia. The method of paralogy-free subtree analysis was used to eliminate geographical paralogy; the paralogy-free subtrees were coded as characters for parsimony analysis to find the minimal and area cladogram, which proved to be informative of a continent-wide pattern. The eucalypt fossil record and molecular dating studies allow an interpretation of the biogeographical history in terms of major vicariance events that date from the early Paleogene. The summary area cladogram shows the wet jarrah forest region of South-West Western Australia, a region of high endemism, as the earliest to differentiate from all other areas, isolated by marine inundation across southern Australia and climatic cooling in the Late Eocene-Early Oligocene. From about this time, regionalization continued, with warmer conditions and monsoonal climate developing in central and northern Australia, and cooling in the south-east. Northern and eastern humid and semi-humid areas were related as a track, but with increased aridity in the interior of the continent, the monsoonal climate contracted northwards. The Australian Monsoon Tropics (AMT: Kimberley, Top End, Arnhem, Cape York and inland north-east Queensland) differentiated from eastern areas (Queensland wet tropics to McPherson-Macleay). Our results also show all arid and semi-arid regions as related, suggestive of a historically cohesive interior biota rather than repeated colonizations of the interior from the periphery of the continent. Climate largely differentiates hot arid areas in the north (Pilbara, Northern and Central deserts) from arid areas in the south (south-west interzone, Wheatbelt, Goldfields and Great Victoria Desert). © The Willi Hennig Society 2010.

Trémaux on species: a theory of allopatric speciation (and punctuated equilibrium) before Wagner.

Pierre Trémaux's 1865 ideas on speciation have been unjustly derided following his acceptance by Marx and rejection by Engels, and almost nobody has read his ideas in a charitable light. Here we offer an interpretation based on translating the term sol as "habitat," in order to show that Trémaux proposed a theory of allopatric speciation before Wagner and a punctuated equilibrium theory before Gould and Eldredge, and we translate the relevant discussion from the French. We believe he may have influenced Darwin's revision to the third edition of the Origin on rates of evolution. We also suggest that Gould's dismissal of Trémaux is motivated by concern that others might think punctuated equilibrium theory was tainted by a connection with Trémaux.

IS FARRIS OPTIMIZATION PERFECT?: THREE-TAXON STATEMENTS AND MULTIPLE BRANCHING.

- The three-taxon approach to phylogenetic analysis separates the universe of cladograms into a larger number of classes of solutions showing decreasing degrees of fit to data than does conventional Farris optimization. The three-taxon approach applies to character analysis Nelson and Platnick's interpretation 2 of multiple branching in cladograms.

CLADISTIC AND BIOGEOGRAPHIC ANALYSIS OF THE "BLUE ASH' EUCALYPTS.

Abstract- A cladistic analysis of the "blue ash" eucalypts (Eucalyptus, Myrtaceae) is presented. Five equally parsimonious trees were found, and a strict consensus tree constructed. A revised informal classification, recognizing five series (Planchonianinae, Sphaerocarpinae, Piperitinae, Fraxininae and Haemastominae, informal subgenus Monocalyptus) is based on the consensus cladogram. A biogeographic analysis applies a new implementation of Assumptions 0 and 1, coding data in the form of three-area statements and using parsimony analysis. These results are used to evaluate hand resolution of Assumption 2. In comparison, Brooks parsimony analysis did not produce area cladograms that best fit the data. Series and subseries were analysed separately for area relationships, which showed a repeated pattern across the blue ash clade; combining all the data in one analysis was seen as equivalent to confounding paralogy and orthology in molecular studies. A resolved area cladogram is presented for southeastern Australia.

OUTGROUPS AND ONTOGENY.

Abstract- Common themes in some recent expositions of character phylogeny are attempts to prove that outgroup comparison is a method of the greatest generality, and that the ontogenetic criterion reduces to outgroup comparison. Another common theme is that pattern cladistics is wrongheaded in suggesting that ontogenetic data have a unique value for studies of character phylogeny. Analysis of particular examples that have been offered as proof of the themes shows them to be flawed and without significance. Arguments against pattern cladistics and the relevance of ontogeny stem from a concern for ideological purity and not for objective appraisal of relevant evidence.