The notion of homology in current comparative biology

Current notions on homology, and its recognition, causation, and explanation are reviewed in this report. The focus is primarily on concepts because the formulation of precise definitions of homology has contributed little to our understanding of the issue. Different aspects or concepts of homology have been contrasted, currently the most important ones being the distinction between systematic and biological concepts. The systematic concept of homology focuses on common ancestry and on taxa; the biological concept tries to explain patterns of conservatism in evolution by shared developmental constraints. Similarity or correspondence is generally accepted as a primary criterion in the delimitation of homologues, albeit that this criterion is not without practical and theoretical problems. Apart from similarity, the biological concept of homology also stresses developmental individuality of putative homologous structures. Structural and positional aspects of homology can be separated, with positional homology acquiring an independent status. Similarity, topographic relationships, and ontogenetic development cannot be tests of homology. Within the cladistic paradigm, the most decisive test of homology is that of congruence; proponents of the biological-homology concept have been less concerned with test implications. Adopting a hierarchical view of nature suggests that characters have to be homologized at their appropriate level of organization. A taxic or systematic approach to homology has precedence over a transformational or biological approach. Nevertheless, pattern analysis and process explanations are not independent of each other.     

Ontogenetic systematics: The synthesis of taxonomy, phylogenetics, and evolutionary developmental biology

The main purpose of the present review is to draw attention to growing problems in the modern systematics and phylogenetics which are presently underestimated by the professional community. The dramatic reduction of the importance of ontogeny and morphology in phylogenetic studies of the second part of the 20th century is considered among the major factors of the modern taxonomic and evolutionary paradigm. The deep contradiction of modern approaches, which either merely consider systematics and phylogeny as genealogy or even in a neotypolgical manner irrespective of the evolutionary idea, is demonstrated. Thus, despite the widespread opinion that the evolutionary theory is the major basis for taxonomy, the processes, which in fact caused the origin and formation of the systematic hierarchy are often considered as redundant for the procedure of classification. In this respect, the classical, but well forgotten statement that evolution is a modification of ontogeny is specially highlighted. Tight relationships between evolution, ontogeny, systematics, and phylogenetics are prima facie obvious, but also presently underestimated, although the field of the evo-devo is continuously growing. Paradoxically, even despite the outburst of various molecular ontogenetic approaches, the commonly accepted evolutionary paradigm still lacks a general theory for changes in the shape of organisms. As a step towards the development of such a theory, a synthesis (or more exactly, resynthesis) of still largely independently developing major biological fields, i.e., ontogenetic and evolutionary studies, on the one hand, and traditional taxonomy, on the other hand, a new concept of ontogenetic systematics is proposed. The new concept is intended for integration of supposedly ??immobile?? traditional taxonomy with the dynamics, but predominantly considered as hypothetical, evolutionary field based on the process of ontogeny, which, in contrast to the evolution itself, can be observed in the real time. Therefore, it is concluded that, for instance, the evolution of the main group of living organisms Metazoa, is primarily the evolution of a very limited number of ontogenetic cycles that were formed as early as the Early Cambrian. A significant underestimation of cyclic properties of ontogeny in the evolution and systematics is shown. Using two model groups, echinoderms of the class Ophiuroidea and dorid nudibranch mollusks (Gastropoda: Doridacea), practical importance of the integrative approach developed here is demonstrated. The ??disruption?? of the ancestral ontogenetic cycle and further formation of a new descendant cycle (which implies some continuity of ancestral and descendant characters) is considered to be a major evolutionary pattern. The model proposed implies either progressive (addition of stages and characters) or regressive (reduction of already existing stages and structures) modification of ancestral taxon, the diagnosis of which corresponds to the model of its ontogenetic cycle. In the extreme cases of disruption of the ancestral ontogenetic cycle, adult characters of descendants are substituted by juvenile ancestral features, demonstrating paedomorphoses in the narrow sense. Within the framework of the approach proposed, the evolutionary and ontogenetic models of ancestral ontogenetic cycles of brittle stars and dorid nudibranchs are developed and discussed. Based on the original material of the extinct Paleozoic ophiuroid group Oegophiurida, the origin of key evolutionary novelties is discussed. A major conclusion of the present review is the high necessity of integration of new molecular data with already well-established taxonomic hierarchy and ontogenetic information as a basis for the development of the general theory of transformations of organisms, i.e., the theory of evolution in its true sense.     

Pollen types in Southern New World Convolvulaceae and their taxonomic significance

Pollen morphology from 143 collections representing 11 genera and 75 species of native South American Convolvulaceae was analyzed with LM and SEM. Exine structure and sculpture allow to distinguish three main types, in two of these types some subtypes were recognized. 1) Tectate, microechinate-perforate exine, with ramified columellae. On the basis of apertures three subtypes were distinguished: tricolpate in Aniseia, Bonamia, Convolvulus, Cressa, Dichondra, Merremia and Jacquemontia blanchetii; penta-hexacolpate in Merremia umbellata; and pantoporate with elliptic and circular pores, in Calystegia. 2) Tectate, microechinate-perforate exine with microspines and single columellae in concordant pattern, relates pantocolpate pollen of Jacquemontia and Evolvulus. From pollen data generic status of J. blanchetii should be considered. 3) Semitectate, echinate or gemmate, microechinate-microreticulate exine with single columellae is exclusive of pantoporate pollen of Ipomoea. Four subtypes were recognized in this genera, which are discussed in relation to Austins infrageneric classification.     

The cranial arteries of turtles and their evolutionary significance

In this paper the cranial arteries, cranial arterial foramina, and bony canals of the Cheloniidae, Chelydridae, Pelomedusidae, and Chelidae are described in detail. From skull studies and published material, the general cranial arterial patterns of all the turtle families can be inferred. Sea turtles, the Cheloniidae and Dermochelyidae, possess both a large stapedial artery and a large artery supplying the orbit, which is possibly similar to the primitive cranial arterial pattern for turtles. From a primitive pattern in which stapedial and palatine arteries supply the orbit, the Chelydridae and Testudinidae retained a large stapedial artery and reduced the palatine artery, while the Kinosternidae and Dermatemydidae developed a large palatine artery and reduced the stapedial artery. The Trionychidae and probably the Carettochelyidae evolved a complex arterial pattern in which the stapedial artery was reduced somewhat and the pseudopalatine artery was substituted for the palatine artery. Pleurodires in general retained a large stapedial artery and reduced or eliminated the palatine artery. The Podocneminae, including the Madagascar species, developed a highly modified carotid canal, which is found in no other turtle group. The facts which have been presented should aid in fossil skull studies and in understanding the evolutionary background of recent turtles.     

The population biology and evolutionary significance of Ty elements in Saccharomyces cerevisiae

The basic structure and properties of Ty elements are considered with special reference to their role as agents of evolutionary change. Ty elements may generate genetic variation for fitness by their action as mutagens, as well as by providing regions of portable homology for recombination. The mutational spectra generated by Ty 1 transposition events may, due to their target specificity and gene regulatory capabilities, possess a higher frequency of adaptively favorable mutations than spectra resulting from other types of mutational processes. Laboratory strains contain between 25–35 elements, and in both these and industrial strains the insertions appear quite stable. In contrast, a wide variation in Ty number is seen in wild isolates, with a lower average number/genome. Factors which may determine Ty copy number in populations include transposition rates (dependent on Ty copy number and mating type), and stabilization of Ty elements in the genome as well as selection for and against Ty insertions in the genome. Although the average effect of Ty transpositions are deleterious, populations initiated with a single clone containing a single Ty element steadily accumulated Ty elements over 1,000 generations. Direct evidence that Ty transposition events can be selectively favored is provided by experiments in which populations containing large amounts of variability for Ty1 copy number were maintained for 100 generations in a homogeneous environment. At their termination, the frequency of clones containing 0 Ty elements had decreased to 0.0, and the populations had became dominated by a small number of clones containing >0 Ty elements. No such reduction in variability was observed in populations maintained in a structured environment, though changes in Ty number were observed. The implications of genetic (mating type and ploidy) changes and environmental fluctuations for the long-term persistence of Ty elements within the S. cerevisiae species group are discussed.     

The glutamine synthetases of rhizobia: phylogenetics and evolutionary implications

Glutamine synthetase exists in at least two related forms, GSI and GSII, the sequences of which have been used in evolutionary molecular clock studies. GSI has so far been found exclusively in bacteria, and GSII has been found predominantly in eukaryotes. To date, only a minority of bacteria, including rhizobia, have been shown to express both forms of GS. The sequences of equivalent internal fragments of the GSI and GSII genes for the type strains of 16 species of rhizobia have been determined and analyzed. The GSI and GSII data sets do not produce congruent phylogenies with either neighbor-joining or maximum-likelihood analyses. The GSI phylogeny is broadly congruent with the 16S rDNA phylogeny for the same bacteria; the GSII phylogeny is not. There are three striking rearrangements in the GSII phylograms, all of which might be explained by horizontal gene transfer to Bradyrhizobium (probably from Mesorhizobium), to Rhizobium galegae (from Rhizobium), and to Mesorhizobium huakuii (perhaps from Rhizobium). There is also evidence suggesting intrageneric DNA transfer within Mesorhizobium. Meta-analysis of both GS genes from the different genera of rhizobia and other reference organisms suggests that the divergence times of the different rhizobium genera predate the existence of legumes, their host plants.     

Cognitive ethology and applied philosophy: The significance of an evolutionary biology of mind

The broad field of cognitive ethology, in which internal mental states are inferred from the behavior they explain, is receiving increased attention nowadays from diverse scientists and philosophers. The nature of the results and how they are presented greatly influence how humans assess their place in the natural world and how they view other animals. The attribution of consciousness and intelligence to other animals suggests that they have moral rights. The results of comparative cognitive ethological analyses and how they are presented may play a large role in defining the domain of morally permissible research, and in the development of research strategies including decisions on feeding and housing, treatment, handling, and what happens to animal subjects when the research is completed. Scientists and philosophers interested in the evolution of behavior and mental continuity can have a significant impact on how others view the world.     

The evolutionary biology of sex

In 1861, Charles Darwin wrote "We do not even in the least know the final cause of sexuality; why new beings should be produced by the union of the two sexual elements, instead of by a process of parthenogenesis". It was hardly possible to begin to answer this question at that time, in view of the contemporary lack of knowledge of genetics and cell biology. Since then, research into the cellular basis of reproduction has shown that sexual reproduction is the norm for the majority of eukaryotes, with huge consequences for their biology. The evolution of sex and some of its consequences are the subject of the series of reviews, and a Primer, in this special issue of Current Biology.     

The result of evolutionary limb loss on the complement of motor neurons in a crayfish limb nerve revealed by serial homology

Many macruran decapod crustaceans show sexual dimorphism of abdominal appendages adapted for use as secondary reproductive organs. Not only does the Australian crayfish, Cherax destructor, show no external, abdominal dimorphism, but both males and females have lost the pleopods of the first abdominal segment entirely. The first nerves of the abdominal ganglia of crayfish and lobsters carry the axons of the pleopod motor neurons. We used intracellular cobalt infusion into the first nerves of the first and second abdominal ganglia to reveal the motor neuron complement of these ganglia in males and females. The first nerves of the second abdominal ganglia of both males and females have approximately 37 motor neurons associated with them. The homologous nerves in the first abdominal segment, where there are no pleopods, have only 8 or 9 motor neurons associated with them. The evolutionary implications of this difference are discussed.     

The evolutionary biology of child health

I apply evolutionary perspectives and conceptual tools to analyse central issues underlying child health, with emphases on the roles of human-specific adaptations and genomic conflicts in physical growth and development. Evidence from comparative primatology, anthropology, physiology and human disorders indicates that child health risks have evolved in the context of evolutionary changes, along the human lineage, affecting the timing, growth-differentiation phenotypes and adaptive significance of prenatal stages, infancy, childhood, juvenility and adolescence. The most striking evolutionary changes in humans are earlier weaning and prolonged subsequent pre-adult stages, which have structured and potentiated maladaptations related to growth and development. Data from human genetic and epigenetic studies, and mouse models, indicate that growth, development and behaviour during pre-adult stages are mediated to a notable degree by effects from genomic conflicts and imprinted genes. The incidence of cancer, the primary cause of non-infectious childhood mortality, mirrors child growth rates from birth to adolescence, with paediatric cancer development impacted by imprinted genes that control aspects of growth. Understanding the adaptive significance of child growth and development phenotypes, in the context of human-evolutionary changes and genomic conflicts, provides novel insights into the causes of disease in childhood.     

The morphogenesis of evolutionary developmental biology

The early studies of evolutionary developmental biology (Evo-Devo) come from several sources. Tributaries flowing into Evo-Devo came from such disciplines as embryology, developmental genetics, evolutionary biology, ecology, paleontology, systematics, medical embryology and mathematical modeling. This essay will trace one of the major pathways, that from evolutionary embryology to Evo-Devo and it will show the interactions of this pathway with two other sources of Evo-Devo: ecological developmental biology and medical developmental biology. Together, these three fields are forming a more inclusive evolutionary developmental biology that is revitalizing and providing answers to old and important questions involving the formation of biodiversity on Earth. The phenotype of Evo-Devo is limited by internal constraints on what could be known given the methods and equipment of the time and it has been framed by external factors that include both academic and global politics.     

Novel computational biology methods and their applications to drug discovery

Computational biology methods are now firmly entrenched in the drug discovery process. These methods focus on modeling and simulations of biological systems to complement and direct conventional experimental approaches. Two important branches of computational biology include protein homology modeling and the computational biophysics method of molecular dynamics. Protein modeling methods attempt to accurately predict three-dimensional (3D) structures of uncrystallized proteins for subsequent structure-based drug design applications. Molecular dynamics methods aim to elucidate the molecular motions of the static representations of crystallized protein structures. In this review we highlight recent novel methodologies in the field of homology modeling and molecular dynamics. Selected drug discovery applications using these methods conclude the review.     

The use of evolutionary biology concepts for genome annotation

The past decade has seen the completion of numerous whole-genome sequencing projects, began with bacterial genomes and continued with eukaryotic species from different phyla: fungi, plants and animals. Besides, more biological information are produced and are shared thanks to information exchange systems, and more biological concepts, as well as more bioinformatics tools, are available. In this article, we will describe how the evolutionary biology concepts, as well as computer science, are useful for a better understanding of biology in general and genome annotation in particular. The genome annotation process consists of taking the raw DNA produced, for example, by the genome sequencing projects, adding the layers of analysis and interpretation necessary to extract its biological significance and placing it in the context of our understanding of biological processes. Genome annotation is a multistep process falling into two broad categories: structural and functional annotation.     

Methodological problems in evolutionary biology

One of the major criticisms of optimal foraging theory (OFT) is that it is not testable. In discussions of this criticism opposing parties have confused methodological concepts and used meaningless biological concepts. In this paper we discuss such misunderstandings and show that OFr has an empirically testable, and even well-confirmed, general core theory. One of our main conclusions is that specific model testing should not be aimed at proving optimality, but rather at identifying the context in which certain types of behaviour are optimal. To do this, it is necessary to be aware of the assumptions made in testing a model. The assumptions that are explicitly stated in the literature up to now do not completely cover the actual assumptions made in testing OFT models in practice. We present a more comprehensive set of assumptions. Although all the assumptions play a role in testing models, they are not of equal status. Crucial assumptions concern constraints and the relation between fitness and currency. Therefore, it is essential to make such assumptions testable in practice. We show that a more explicit relationship between OFT modelling and evolutionary theory can help with this. Specifically, phylogeny reconstruction and population dynamic modelling can and should be used to formulate assumptions concerning constraints and currencies.