We contend that the move away from providing character evidence with phylogenies has diminished fish systematics and systematics in general, and amounts to a crisis. Present practices focus on solutions to matrices rather than on character homology, and rely on algorithms and statistics rather than biology to determine relationships. Optimization procedures in tree-building programs are phenetic and no longer employ homology, the original foundation of cladistics. Evidence for phylogenies is presented in a manner that obscures character conflict and makes meaningful debate difficult. The role of morphological characters has largely been reduced to their optimization and reinterpretation on the revealed "truth" of molecule-based topologies. All of this has resulted in a schism between molecular and morphological phylogeneticists. We examine several examples, focusing on Percomorpha and Gobioidei, to illustrate the shortcomings of recent approaches. We feel that phylogenetics can only move forward by recognizing that molecules are small-scale morphology; molecular data are not substantively different from larger-scale morphological data and should be treated in much the same manner. Careful investigation of homology and transparent presentation of evidence will keep our work and our science relevant. We suggest four measures that need reintroduction to phylogenetic practice in order to bring systematics back to its fundamental principles: (1) examine data quality, character distribution, and evidence; plot characters to identify and examine character conflict, and weigh evidence for homology, (2) explore the nature of character information-data become characters only after they are understood, (3) question assumptions of methods, common practice is not necessarily indicative of the ideal analysis, (4) in particular, question and investigate optimization as a method and what its impact is on character homology and the meaning of synapomorphies; use biology, not algorithms to make homology decisions.Since, in principle, a data matrix containing characters for different minerals can be analyzed with PAUP to obtain a dendrogram, the application of cladistic techniques alone does not make an analysis phylogenetic.
Butterflyfish are colourful, pan-tropical coastal fish that are important and distinctive members of coral reef communities. A successful systematic scheme and a robust phylogeny is considered essential in understanding further their biogeography and ecology, although recent cladistic treatments of butterflyfish phylogeny, based on soft tissue and bone morphology and coded at the generic and subgeneric levels, differ in character coding and subsequently tree topology. This study provides an independent test of the morphologically based hypotheses, using molecular systematic data from two partial mitochondrial gene fragments, cytochrome b (cytb) and small subunit rRNA (rrnS), for 52 ingroup chaetodontids and seven pomacanthids used to root the molecular trees. Individual gene trees were largely compatible and a combined molecular phylogeny, inferred from Bayesian analysis, was used to test alternative hypotheses suggested by morphological analyses. The tree was also used to map the latest morphological matrix in order to evaluate potential synapomorphies for various nodes defining butterflyfish interrelationships. A clade comprised of Chelmon and Coradion was sister group to other chaetodontids. Heniochus and Hemitaurichthys were each resolved as monophyletic groups, and as sister taxa Of the taxa sampled, Prognothodes was resolved as the sister genus to Chaeotodon. Of the ten Chaetodon subgenera sampled, all were monophyletic but their interrelationships differed significantly from that inferred from morphological characters. Lepidochaetodon was the most basal subgenus followed by Exornator and the remaining subgenera. Molecular data support the sister group relationship between Corallochaetodon and Citharoedus suggested by morphology, but major differences occur among the remaining more derived taxa. Chaetodon trifascialis and C. oligacanthus were resolved as sister taxa adding weight to the inclusion of the latter in C. Megaprotodon. Of those pairs of taxa known to hybridize and sampled with molecular data, all were closely related phylogenetically, except those hybrids known to occur in the Rabdophorus subgenus. Two base changes separated C. pelewensis from C.
The assertion that phylogenetic inference algorithms are not authoritarian because results are repeatable, predictable and freely available misses the point that the authority resides in underlying algorithm models that are not cladistic. We show that optimization procedures can group using symplesiomorphy and that optimization is not always equivalent to cladistic argumentation. Because parsimony and Bayesian algorithms can obtain the same answer from the same data set is not evidence that they are Hennigian; examples exist where these methods do not provide the same result from the same data. Using ‘reversals’ as evidence in systematics is problematic because the question, “Reversal to what?” has no straightforward answer. This confusion can be eliminated by recognizing that homologues are the parts of organisms and homologies are the relationships between the parts, and that the latter is a hierarchical concept rather than transformational. We clarify that Hennig’s auxiliary principle pertains to potential synapomorphy, meaning for molecular work that it is the presence of a particular derived nucleotide that is shared in a given position of aligned sequences of two or more taxa that should be considered homologous until proven otherwise, not simply the alignments themselves. We reiterate that not all data are evidence and we specifically reject homoplasy as a source of ‘evidence’ for systematics. We further reject the view that conflict among data should be resolved through methodology. It is the data that should be our primary focus, as it is our attempts to identify and clarify homologues worthy of suggesting relationships (homology) that are primary in systematics.
Two new species of Lates Cuvier are described. Lates lakdiva, new species, from western Sri Lanka, differs from its Indo-Pacific congeners by its lesser body depth, 26.6‒27.6% SL; 5 rows of scales in transverse line between base of third dorsal-fin spine and lateral line; 31‒34 serrae on the posterior edge of the preoperculum; third anal-fin spine longer than second;47‒52 lateral-line scales on body; and greatest depth of maxilla less than eye diameter. Lates uwisara, new species, fromeastern Myanmar, is distinguished by possessing 7 scales in transverse line between base of third dorsal-fin spine and lat-eral line; eye diameter 4.4‒4.7% SL; body depth 28.4‒34.5% SL; and third anal-fin spine shorter than the second. Despitesubstantial genetic variation, L. calcarifer sensu lato is widely distributed, from tropical Australia through Indonesia, Sin-gapore and Thailand, westwards to at least the west coast of India. Caution is urged in translocating Lates in the Indo-Pacific region as other yet unrecognized species likely exist. The status of the type specimens of L. calcarifer is discussed,and a common lectotype designated for L. heptadactylus and L. nobilis. While Lates vacti (type locality Bengal) may bea valid species, L. cavifrons and L. darwiniensis are considered synonyms of L. calcarifer. Plectopomus Goldfuss and Ptertopomus Goldfuss are shown to be incorrect subsequent spellings of Plectropomus Oken.
The composition of the Microdesminae has been inconsistently reported in recent molecular studies. A monophyletic Microdesminae consisting of both Indo-Pacific and New World/Atlantic genera is diagnosed here by the following synapomorphies: maxilla with elongate projection extending anteriorly over ascending processes of premaxilla; palatine medial process absent; single dorsal process on cleithrum; supracleithrum oriented vertically and closely applied to cleithrum; posttemporal with elongate posteroventral process; body slender and elongate, with associated increase in number of vertebrae and median fin rays (total vertebrae 42–66 with 19 or more precaudal vertebrae, total dorsal-fin rays 42–78, anal-fin rays 27–43), slender pelvis with anterior extensions of the pelvic intercleithral cartilage, and decrease in number of pelvic-fin rays (with a spine and 2–4 segmented rays); single dorsal fin; dorsal-fin spines usually 12 or more; predominantly 1:1 relationship between interneural spaces and anterior dorsal-fin pterygiophores; and first (supernumerary) ray on first anal pterygiophore a bilaterally paired, segmented ray. Several of these characters (particularly single dorsal process on cleithrum, posttemporal with elongate posteroventral process) support a possible relationship between microdesmines and Schindleria, as does dorsal gill-arch morphology.
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