Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genes

This report describes a set of 21 polymerase chain reaction primers and amplification conditions developed to barcode practically any teleost fish species according to their mitochondrial cytochrome b and nuclear rhodopsin gene sequences. The method was successfully tested in more than 200 marine fish species comprising the main Actinopterygii family groups. When used in phylogenetic analyses, its combination of two genes with different evolutionary rates serves to identify fish at the species level. We provide a flow diagram indicating our validated polymerase chain reaction amplification conditions for barcoding and species identification applications as well as population structure or haplotyping analyses, adaptable to high‐throughput analyses.     

Habitat utilization by hippopotamus in the Mara River*

The results are presented of a 2-month study of the Mara River hippopotamus population in the Serengeti National Park and the Maasai Mara Game Reserve. A method for correcting aerial counts of hippos in turbid rivers and based on herd behaviour characteristics is described. There were an estimated 1927 hippos at an average density of 16-1/km in the area censused. The population became more dispersed and the mean group size decreased from thirty to fifteen after a rise in water level. The value of comparisons between populations in various terms of expression of density, and mean group sizes, are discussed. The amount of day living space, defined as areas preferred or utilizable by hippo during the day, and productivity of the food plants are seen to be very important factors in hippo habitat utilization, and as constraints on population increase. Hippo use of the habitat and the effects of hippo on the vegetation at various distances from the river were quantified, and a cycle of vegetational changes suggested which may be associated with the effects of hippo grazing and fire in other parts of Africa. Groups were found to consist of nearly equal numbers of males and females. There was no evidence of territorial behaviour either on land or in the water. A number of observations on social interactions and defaecating behaviour are described and indicate that olfactory communication is very important in interactions between hippos. Hippo society is unstable due to climatic influences, but a dominance hierarchy including males and females exists in the groups. Males appear less firmly attached to groups than females, but a male is normally the dominant animal in a group.     

The evolution of the basicranium in the Henophidia (Reptilia: Serpentes)

In lizards, a short Vidian canal pierces the base of the basipterygoid process. In snakes, the anterior opening of the primitively short Vidian canal lies on the dorsal surface of the basisphenoid, trapped in an intracranial position by downgrowths of the frontal and parietal which meet the lateral edges of the basisphenoid-parasphenoid complex. This condition is observed in anilioid snakes which retain other primitive features in the braincase: the paroccipital process and the spheno-occipital tubercle (Aniliidae only) and participation of the basioccipital in the apertura lateralis of the recessus scalae tympani.
Subsequent evolution within booid snakes shows a shift of the anterior opening of the Vidian canal around the anterior edge of the basisphenoid, thus acquiring a secondary extracranial position. This occurs in parallel within boine and pythonine snakes. Dinilysia shows a parallel development of die condition observed in advanced booid snakes. Pseudoboa , with its short Vidian canal opening in-tracranially, demonstrates that caenophidians originated from a basal henophidian or pre-henophidian stock. The Acrochordidae show a basicranium that can be interpreted as either primitive henophidian or primitive caenophidian.     

The Gegenbaur Transformation: a paradigm change in comparative biology

The leading experts in the development of phylogenetic systematics, Walter Zimmermann and Willi Hennig, formulated their research program in opposition to (neo-) idealistic morphology as expounded by authors such as Wilhelm Troll and Adolf Naef. Idealistic morphology was synonymous with systematic morphology for Naef, who wanted it to be strictly kept separate and independent of phylogenetics. Naef conceded, however, that the natural system researched by systematic morphology is to be causally explained by the theory of descent with modification. Naef went on to compile a dictionary that would regulate the translation of the language of systematic morphology into the language of phylogenetics. The switch from idealistic morphology to phylogenetic morphology is paradigmatically exemplified in the two editions (1859, 1870) of Carl Gegenbaur's Grundzüge der vergleichenden Anatomie. This paper traces the development of phylogenetic systematics from Gegenbaur through the work of Adolf Naef to Walter Zimmermann and Willi Hennig. Hennig added to Naef's systematic morphology the dimension of time, which required an ontological replacement: Naef's natural system, a nested hierarchy of intensionally defined sets subject to the membership relation, was replaced by Hennig's phylogenetic system, an enkaptic hierarchy subject to the part-to-whole relation.     

Embryonic development and endosymbiont transmission mode in the symbiotic clam Lucinoma aequizonata (Bivalvia: Lucinidae)

Summary

Lucinoma aequizonata is a large lucinid clam which lives in reducing mud around 500 m deep. Adults harbor intracellular chemoautotrophic sulfur-oxidizing bacteria in specialized gill cells called bacteriocytes. The embryonic and early larval development of L. aequizonata is described by using light and scanning electron microscopy. Gametes were obtained by injection of 0.2ml of 4 mM serotonin solution in seawater into the posterior adductor muscle. The oocytes, 200 μm in diameter, are surrounded by a glycoprotein capsule which gives to the egg a total diameter of 500μm. The development which occurs at 10°C is slow. The first polar body is detected 2.5 h after contact between sperm and oocytes (T_o+2.5 h), and the first cleavage begins 10 h later (T_o+12.5 h). The following successive cleavages produce a nonciliated morula, then a ciliated gastrula which begins to rotate within the egg-capsule at T_o+4.5 days. At this stage, the first shell pellicle appears on the dorsal side of the embryo. At T₀+8 days, the trochophore larvae develop discrete ciliary bands which constitute the prototroch. Typical straight-hinge veligers, D-shaped larvae, hatch from the egg-capsule 12 days after fertilization. The newly hatched larvae are 240 μm in length and 200μm in height, and the straight hinge 150μm long. To elucidate the symbiont transmission mode, two symbiont-specific primers were designed and used in amplifications by PCR. This primer set was unsuccessful in amplifying symbiont DNA targets from mature gonads, spawned oocytes, eggs, and veligers whereas successful amplifications were obtained from symbiont-containing gill tissues. These data rule out the vertical transmission mode and strongly suggest that the symbionts are environmentally transmitted to the new host generation in L. aequizonata as for all tropical lucinids examined to date.