Constraints in naming parts of the Tree of Life

There are now overlapping codes of nomenclature that govern some of the same names of biological taxa. The International Code of Zoological Nomenclature (ICZN) uses the non-evolutionary concept of a "type species" to fix the names of animal taxa to particular ranks in the nomenclatural hierarchy. The PhyloCode, in contrast, uses phylogenetic definitions for supraspecific taxa at any hierarchical level within the Tree of Life (without associating the names to particular ranks), but does not deal with the names of species. Thus, biologists who develop classifications of animals need to use both systems of nomenclature, or else operate without formal rules for the names of some taxa (either species or many monophyletic groups). In addition, the ICZN does not permit the unique naming of many taxa that are considered to be between the ranks of genus and species. Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] provided recommendations for the classification of New World true frogs that utilized the ICZN to provide names for species, and the PhyloCode to provide names for supraspecific taxa. Nonetheless, they created new taxon names that followed both sets of rules, to avoid conflicting classifications. They also recommended that established names for both species and clades be used whenever possible, to stabilize the names of both species and clades under either set of rules, and to avoid conflicting nomenclatures. Dubois [Dubois, A., 2006. Naming taxa from cladograms: a cautionary tale. Mol. Phylogenet. Evol., 42, 317-330] objected to these principles, and argued that the names provided by Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] are unavailable under the ICZN, and that the two nomenclatural systems are incompatible. Here, I argue that he is incorrect in these assertions, and present arguments for retaining the established names of New World true frogs, which are largely compatible under both sets of nomenclatural rules.     

Structural and evolutionary comparisons of four alleles of the mouse Igk-J locus which encodes immunoglobulin kappa light chain joining (J K ) segments

The Igk-J locus of the mouse encodes the immunoglobulin light chain joining (J) segments. Four Igk-J alleles have been described on the basis of restriction enzyme length polymorphisms. The nucleotide sequences of the Igk-J ^a allele (type strain, C.C58), Igk-J ^c allele (type strain, SJL/J), and Igk-J ^d allele (type strain, SK/CamRk) have been determined and are compared with the previously reported Igk-J ^b allele sequence (type strain, BALB/c). The mouse sequences are also compared with published sequences for rat and human J _k sequences. Far more differences were found between the Igk-J ^a allele and the other mouse alleles than between any two of the latter. These result in two amino acid substitutions which distinguish the J2 and J3 ¹ segments of the Igk-J ^a allele from the other three alleles. Use of the Phylogenetic Analysis Using Parsimony program to generate a phylogenetic tree strongly indicates that after divergence from the rat ancestor, there appears to have been an early split between the Igk-J ^a allele and the evolutionary precursor of the other mouse alleles. There also appears to have been far less divergence from the ancestral condition in the Igk-J ^a allele than in the other alleles. Also, the presence of only one convergent mutation among the four mouse alleles provides strong evidence against any crossing over within the Igk-J locus during the history of these alleles. Finally, the differences in rates of evolution of the Igk-J alleles are in marked contrast to the relatively uniform rates of divergence of four alleles of a mouse V _k gene, Igk-VSer.     

Can you hear me now? Range‐testing a submerged passive acoustic receiver array in a Caribbean coral reef habitat

Submerged passive acoustic technology allows researchers to investigate spatial and temporal movement patterns of many marine and freshwater species. The technology uses receivers to detect and record acoustic transmissions emitted from tags attached to an individual. Acoustic signal strength naturally attenuates over distance, but numerous environmental variables also affect the probability a tag is detected. Knowledge of receiver range is crucial for designing acoustic arrays and analyzing telemetry data. Here, we present a method for testing a relatively large‐scale receiver array in a dynamic Caribbean coastal environment intended for long‐term monitoring of multiple species. The U.S. Geological Survey and several academic institutions in collaboration with resource management at Buck Island Reef National Monument (BIRNM), off the coast of St. Croix, recently deployed a 52 passive acoustic receiver array. We targeted 19 array‐representative receivers for range‐testing by submersing fixed delay interval range‐testing tags at various distance intervals in each cardinal direction from a receiver for a minimum of an hour. Using a generalized linear mixed model (GLMM), we estimated the probability of detection across the array and assessed the effect of water depth, habitat, wind, temperature, and time of day on the probability of detection. The predicted probability of detection across the entire array at 100 m distance from a receiver was 58.2% (95% CI: 44.0–73.0%) and dropped to 26.0% (95% CI: 11.4–39.3%) 200 m from a receiver indicating a somewhat constrained effective detection range. Detection probability varied across habitat classes with the greatest effective detection range occurring in homogenous sand substrate and the smallest in high rugosity reef. Predicted probability of detection across BIRNM highlights potential gaps in coverage using the current array as well as limitations of passive acoustic technology within a complex coral reef environment.