The performance of morphological characters in broad-scale phylogenetic analyses

In view of their propositional content (i.e. they can be right or wrong), character statements (i.e. statements that predicate characters of organisms) are treated as low-level hypotheses. The thesis of the present study is that such character statements, as do more complex scientific theories, come with variable scope. The scope of a hypothesis, or theory, is the domain of discourse over which the hypothesis, or theory, ranges. A character statement is initially introduced within the context of a certain domain of discourse that is defined by the scale of the initial phylogenetic analysis. The doctrine of 'total evidence' requires the inclusion of previously introduced characters in subsequent studies. As a consequence, the initial scope of character statements is widened to the extent that the scale of subsequent analyses is broadened. Scope expansion for character statements may result in incomplete characters, in the subdivision of characters, or in ambiguity of reference (indeterminacy of the extension of anatomical terms). Character statements with a wide scope are desirable because they refer to characters with the potential to resolve deep nodes in phylogenetic analyses. Care must be taken to preserve referential unambiguity of anatomical terms if the originally restricted scope of a character statement is expanded to match a broad-scale phylogenetic analysis.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 297–308.     

ONTOGENY AND THE HIERARCHY OF TYPES

Abstract— The long history of belief in a parallelism between ontogeny and a hierarchical order of natural things is reviewed. The meaning of von Baerian recapitulation is analyzed and its implications for cladistic methodology are discussed at two levels: ontogeny and homology. The basic problem inherent in the purported parallelism is that the order of natural things (i.e., the taxic approach to homology) is part of the "world of being" of Platonic ideas, whereas ontogeny and phylogeny (i.e., the transformational approach to homology) belong to Plato's "world of becoming." These two "genera of existence," as Plato put it, being and becoming, are incompatible but complementary views of nature.     

Ontogeny–a way forward for systematics, a way backward for phylogeny

In the history of biology, the term 'evolution' has carried a dual meaning, viz. ontogeny (the unfolding of the germ) versus phylogeny (descent with modification). A problem in modern biology is the question of whether it is ontogeny which creates phylogeny, or whether it is phylogeny which moulds ontogeny. The paper explores the relationship of ontogeny to phylogeny in the context of 'pattern cladism'. The conclusion is that the analysis of ontogeny provides a direct method for classification ('a way forward for systematics'), which is a logical prerequisite for a phylogenetic interpretation of ontogenetic sequences ('a way backward for phylogeny'). The ontogenetic process of growth, subdivision and differentiation is related to the 'morphogenetic tree theory' on the basis of Von Baer's "laws of individual development". This conceptual relation shows that ontogeny creates phylogeny in an upward direction within the morphogenetic tree, whereas phylogeny (by means of natural selection) moulds ontogeny in a downward direction. A conflict originates with the conventions of Linnaean classification if ontogenetic divergence is proposed as a causal agent in the origin of higher taxa. It is proposed to solve this conflict by viewing individual organisms (or reproductive communities) not as constituents, but as representatives of higher taxa.     

The K+/H+ antiporter LeNHX2 increases salt tolerance by improving K+ homeostasis in transgenic tomato

The endosomal LeNHX2 ion transporter exchanges H⁺ with K⁺ and, to lesser extent, Na⁺. Here, we investigated the response to NaCl supply and K⁺ deprivation in transgenic tomato (Solanum lycopersicum L.) overexpressing LeNHX2 and show that transformed tomato plants grew better in saline conditions than untransformed controls, whereas in the absence of K⁺ the opposite was found. Analysis of mineral composition showed a higher K⁺ content in roots, shoots and xylem sap of transgenic plants and no differences in Na⁺ content between transgenic and untransformed plants grown either in the presence or the absence of 120 mm NaCl. Transgenic plants showed higher Na⁺/H⁺ and, above all, K⁺/H⁺ transport activity in root intracellular membrane vesicles. Under K⁺ limiting conditions, transgenic plants enhanced root expression of the high‐affinity K⁺ uptake system HAK5 compared to untransformed controls. Furthermore, tomato overexpressing LeNHX2 showed twofold higher K⁺ depletion rates and half cytosolic K⁺ activity than untransformed controls. Under NaCl stress, transgenic plants showed higher uptake velocity for K⁺ and lower cytosolic K⁺ activity than untransformed plants. These results indicate the fundamental role of K⁺ homeostasis in the better performance of LeNHX2 overexpressing tomato under NaCl stress.     

Peribacteroid space acidification: a marker of mature bacteroid functioning in Medicago truncatula nodules

Legumes form a symbiotic interaction with Rhizobiaceae bacteria, which differentiate into nitrogen‐fixing bacteroids within nodules. Here, we investigated in vivo the pH of the peribacteroid space (PBS) surrounding the bacteroid and pH variation throughout symbiosis. In vivo confocal microscopy investigations, using acidotropic probes, demonstrated the acidic state of the PBS. In planta analysis of nodule senescence induced by distinct biological processes drastically increased PBS pH in the N₂‐fixing zone (zone III). Therefore, the PBS acidification observed in mature bacteroids can be considered as a marker of bacteroid N₂ fixation. Using a pH‐sensitive ratiometric probe, PBS pH was measured in vivo during the whole symbiotic process. We showed a progressive acidification of the PBS from the bacteroid release up to the onset of N₂ fixation. Genetic and pharmacological approaches were conducted and led to disruption of the PBS acidification. Altogether, our findings shed light on the role of PBS pH of mature bacteroids in nodule functioning, providing new tools to monitor in vivo bacteroid physiology.     

The braincases of mosasaurs and Varanus, and the relationships of snakes

The braincase structure of the mosasaur Platecarpus is described in detail and compared to that of Varanus and snakes. The braincase of mosasaurs and Varanus is found to be closely similar in most respects other than the consequences of obliteration of the metakinetic axis in mosasaurs. Neither Varanus, nor mosasaurs, approach snakes in braincase structure. The hypothesis of a sister-group relationship of snakes and mosasauroids is discussed in the light of how hypotheses of homology, or synapomorphy, can be established on an empirical, i.e. testable and potentially falsifiable basis. The establishment of homology qua synapomorphy is recognized as a procedure involving at least two levels of generalization. The most basic level is the conjecture of similarity of constituent elements of two or more organisms. Such conjectures of similarity maintain their testability, and falsifiability, only if established by reference to topographical equivalence, or equivalence of connectivity.     

Endosymbiont metacommunities,mtDNA diversity and the evolution of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex

Bemisia tabaci, an invasive pest that causes crop damage worldwide, is a highly differentiated species complex, divided into biotypes that have mainly been defined based on mitochondrial DNA sequences. Although endosymbionts can potentially induce population differentiation, specialization and indirect selection on mtDNA, studies have largely ignored these influential passengers in B. tabaci, despite as many as seven bacterial endosymbionts have been identified. Here, we investigate the composition of the whole bacterial community in worldwide populations of B. tabaci, together with host genetic differentiation, focusing on the invasive B and Q biotypes. Among 653 individuals studied, more than 95% of them harbour at least one secondary endosymbiont, and multiple infections are very common. In addition, sequence analyses reveal a very high diversity of facultative endosymbionts in B. tabaci, with some bacterial genus being represented by more than one strain. In the B and Q biotypes, nine different strains of bacteria have been identified. The mtDNA‐based phylogeny of B. tabaci also reveals a very high nucleotide diversity that partitions the two ITS clades (B and Q) into six CO1 genetic groups. Each genetic group is in linkage disequilibrium with a specific combination of endosymbionts. All together, our results demonstrate the rapid dynamics of the bacterial endosymbiont–host associations at a small evolutionary scale, questioning the role of endosymbiotic communities in the evolution of the Bemisia tabaci species complex and strengthening the need to develop a metacommunity theory of inherited endosymbionts.     

A revision of Aceratherium blanfordi Lydekker, 1884 (Mammalia: Rhinocerotidae) from the Early Miocene of Pakistan: postcranials as a key

Rhinocerotids are particularly abundant and diversified in Neogene deposits of the Indian subcontinent, but their systematics is far from being well defined. Based on the revision of old collections and new findings from the Early Miocene of the Bugti Hills and Zinda Pir, Pakistan, ‘Aceratherium blanfordi Lydekker, 1884’ is a chimera, consisting of two dentally convergent but postcranially distinct rhinocerotid taxa: Pleuroceros blanfordi and Mesaceratherium welcommi sp. nov. Postcranial features appear to be much more diagnostic than craniodental morphology in this case. A phylogenetic analysis based on 282 morphological characters scored for 28 taxa (four outgroups and ingroup including both taxa of interest and a ‘branching group’) strengthens this statement and supports Pleuroceros and Mesaceratherium as monophyletic genera within Rhinocerotinae. Both genera are recognized for the first time outside Europe. In the Bugti Hills, P. blanfordi and M. welcommi are part of an exceptionally diversified rhinocerotid fauna, with up to nine species associated in the same locality (Kumbi 4f). This rhinocerotid assemblage confirms the earliest Miocene age (Agenian/Aquitanian) of the upper member of the Chitarwata Formation as a whole. Coeval homotaxic rhinocerotid faunas from Europe (France, Czech Republic) and East Africa (Uganda, Kenya) support broad and sustainable rhinocerotid interchanges amongst South Asia, Europe, and Africa under compatible environmental conditions throughout earliest Miocene times. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 139–194.