The Geography of Evolution and the Evolution of Geography

Insights into the geography of life have played a fundamental role in motivating major developments in evolutionary biology. The focus here is on outlining some of these major developments, specifically in the context of paleontology, by emphasizing the significance of geographic isolation and allopatric speciation, punctuated equilibria, and the Turnover Pulse Hypothesis to evolutionary theory. One of the major debates in evolution concerns the relative contributions of abiotic and biotic factors to macroevolution, and each one of these developments increasingly suggested that it was climatic and geologic factors, rather than competition, that played the primary role in motivating macroevolution. New technical developments, including in the area of Geographic Information Systems, allow continued detailed testing of the relative roles that biotic as opposed to abiotic factors play in causing evolution, and some of the work in this area will also be described.     

The Evolution of Evolution: Reconciling the Problem of Stability

Evolutionary Science has, at least since the publication of Origin, been less concerned with the continuation of species in stable forms, than with the reconfiguration of forms into a host of varieties. So influential has this emphasis been that, over the years, “variation” has become a cardinal desideratum, even taking precedence over the macroevolutionary landscape. This orientation has made it much more difficult to objectively assess the meaning of non-change patterns such as periods of stasis, which appear to be widespread in most species. Yet, if stasis is an expectable outcome of evolutionary activity, this raises the possibility that there may be mechanisms and processes at many causal levels, acting on its behalf, without reference to the impetus toward persistent variation. Researchers have been reluctant to attribute stasis to a macroevolutionary tendency toward ‘stability’ despite the commonality of stasis in many species, and notwithstanding the many biological/behavioral processes that seem inclined to produce and maintain conformance, regulation and consistency. Speciation, paradoxically, is the best evidence for an overriding influence toward stability in that stability would seem to be a necessary condition prior to the development of isolating mechanisms. An alternative macroevolutionary model of biological activity is offered consisting of two tendencies, “variety” counterpoised with “stability” both acting in the service of the persistence of life.     

Evolution of the hydrogenosome

Since its discovery almost 25 years ago the enigmatic hydrogenosome, a redox organelle of anaerobic unicellular eukaryotes, has puzzled evolutionists as to its origin and function. Synthesis of recent molecular, physiological and morphological studies now favours the hypothesis that hydrogenosomes derived from a modification of pre-existing mitochondria, and argues against the previously held view that the hydrogenosome had a polyphyletic origin. These data provide evidence for a more ancient origin of mitochondria than hitherto thought.     

Evolution of the Archaea

Archaea, members of the third domain of life, are bacterial-looking prokaryotes that harbour many unique genotypic and phenotypic properties, testifying for their peculiar evolutionary status. The archaeal ancestor was probably a hyperthermophilic anaerobe. Two archaeal phyla are presently recognized, the Euryarchaeota and the Crenarchaeota. Methanogenesis was the main invention that occurred in the euryarchaeal phylum and is now shared by several archaeal groups. Adaptation to aerobic conditions occurred several times independently in both Euryarchaeota and Crenarchaeota. Recently, many new groups of Archaea that have not yet been cultured have been detected by PCR amplification of 16S ribosomal RNA from environmental samples. The phenotypic and genotypic characterization of these new groups is now a top priority for further studies on archaeal evolution.     

Evolution of the individual

This article studies the transition in evolution from single cells to multicellular organisms as a case study in the origin of individuality. The issues considered are applicable to all major transitions in the units of selection that involve the emergence of cooperation and the regulation of conflict. Explicit genetic models of mutation and selection both within and between organisms are studied. Cooperation among cells increases when the fitness covariance at the level of the organism overcomes within-organism change toward defection. Selection and mutation during development generate significant levels of within-organism variation and lead to variation in organism fitness at equilibrium. This variation selects for gem-line modifiers and other mediators of within-organism conflict, increasing the heritability of fitness at the organism level. The evolution of these modifiers is the first new function at the emerging organism level and a necessary component of the evolution of individuality.     

Evolution of the cytoskeleton

The eukaryotic cytoskeleton appears to have evolved from ancestral precursors related to prokaryotic FtsZ and MreB. FtsZ and MreB show 40-50% sequence identity across different bacterial and archaeal species. Here I suggest that this represents the limit of divergence that is consistent with maintaining their functions for cytokinesis and cell shape. Previous analyses have noted that tubulin and actin are highly conserved across eukaryotic species, but so divergent from their prokaryotic relatives as to be hardly recognizable from sequence comparisons. One suggestion for this extreme divergence of tubulin and actin is that it occurred as they evolved very different functions from FtsZ and MreB. I will present new arguments favoring this suggestion, and speculate on pathways. Moreover, the extreme conservation of tubulin and actin across eukaryotic species is not due to an intrinsic lack of variability, but is attributed to their acquisition of elaborate mechanisms for assembly dynamics and their interactions with multiple motor and binding proteins. A new structure-based sequence alignment identifies amino acids that are conserved from FtsZ to tubulins. The highly conserved amino acids are not those forming the subunit core or protofilament interface, but those involved in binding and hydrolysis of GTP.     

On the Theory of Evolution Versus the Concept of Evolution: Three Observations

Here we address three misconceptions stated by Rice et al. in their observations of our article Paz-y-Mi?o and Espinosa (Evo Edu Outreach 2:655–675, 2009), published in this journal. The five authors titled their note “The Theory of Evolution is Not an Explanation for the Origin of Life.” First, we argue that it is fallacious to believe that because the formulation of the theory of evolution, as conceived in the 1800s, did not include an explanation for the origin of life, nor of the universe, the concept of evolution would not allow us to hypothesize the possible beginnings of life and its connections to the cosmos. Not only Stanley Miller’s experiments of 1953 led scientists to envision a continuum from the inorganic world to the origin and diversification of life, but also Darwin’s own writings of 1871. Second, to dismiss the notion of Rice et al. that evolution does not provide explanations concerning the universe or the cosmos, we identify compelling scientific discussions on the topics: Zaikowski et al. (Evo Edu Outreach 1:65–73, 2008), Krauss (Evo Edu Outreach 3:193–197, 2010), Peretó et al. (Orig Life Evol Biosph 39:395–406, 2009) and Follmann and Brownson (Naturwissenschaften 96:1265–1292, 2009). Third, although we acknowledge that the term Darwinism may not be inclusive of all new discoveries in evolution, and also that creationists and Intelligent Designers hijack the term to portray evolution as ideology, we demonstrate that there is no statistical evidence suggesting that the word Darwinism interferes with public acceptance of evolution, nor does the inclusion of the origin of life or the universe within the concept of evolution. We examine the epistemological and empirical distinction between the theory of evolution and the concept of evolution and conclude that, although the distinction is important, it should not compromise scientific logic.     

The Pattern of Mammalian Evolution and the Relative Rate of Molecular Evolution

The rates of nucleotide substitution at four genes in four orders of eutherian mammals are compared in relative rate tests using marsupial orthologs for reference. There is no evidence of systematic variation in evolutionary rate among the orders. The sequences are used to reconstruct the phylogeny of the orders using maximum likelihood, parsimony and compatibility methods. A branching order of rodent then ungulate then primate and lagomorph is overwhelmingly indicated. The nodes of the nucleotide based cladograms are widely separated in relation to the total lengths of the branches. The assumption of a star phylogeny that underlies Kimura's test for molecular evolutionary rate variation is shown to be invalid for eutherian mammals. Excess variance in nucleotide or amino acid differences between mammalian orders, above that predicted by neutral theory is explained better by variation in divergence time than by variation in evolutionary rate.     

Evolution of the family Lumbriculidae

The structure of the male ducts of numerous representatives of the family Lumbriculidae testifies against the assumption of Stephenson (1930) of an archaism of this family and against the classification of the Oligochaeta based on this fallacy in the papers of Yamaguchi (1953) and Brinkhurst (1971). The genus Dorydrilus Piguet is confirmed as a member of the family Lumbriculidae.     

Evolution of the beta-propeller fold

beta-Propellers are toroidal folds, in which repeated, four-stranded beta-meanders are arranged in a circular and slightly tilted fashion, like the blades of a propeller. They are found in all domains of life, with a strong preponderance among eukaryotes. Propellers show considerable sequence diversity and are classified into six separate structural groups by the SCOP and CATH databases. Despite this diversity, they often show similarities across groups, not only in structure but also in sequence, raising the possibility of a common origin. In agreement with this hypothesis, most propellers group together in a cluster map of all-beta folds generated by sequence similarity, because of numerous pairwise matches, many of which are individually nonsignificant. In total, 45 of 60 propellers in the SCOP25 database, covering four SCOP folds, are clustered in this group and analysis with sensitive sequence comparison methods shows that they are similar at a level indicative of homology. Two mechanisms appear to contribute to the evolution of beta-propellers: amplification from single blades and subsequent functional differentiation. The observation of propellers with nearly identical blades in genomic sequences show that these mechanisms are still operating today.     

Evolution of the sterile caste

Biased sex ratios are expected to affect the conditions of the evolution of worker behaviour in malehaploid populations. In a subsocial, malehaploid species an association to female-biased brood sex ratios favours the evolution of worker behaviour. There are various reasons to expect such an association. The critical worker efficiency threshold required for worker behaviour to evolve is lower when looked at from the viewpoint of the mother than from that of the daughter. In this mother-daughter conflict, the mother can expect some help from her other offspring to resolve the conflict in her favour. In semisocial species the sex ratio biases have a less significant role and the worker behaviour can evolve more easily in malehaploid than in diploid populations. Furthermore, limited dispersal (due to the risks attached to it) is expected to favour worker behaviour in malehaploid but inbreeding in diploid populations. In addition to the genetic mechanisms that determine the critical worker efficiency threshold, it is essential to pay attention to those ecological factors that affect the actual worker efficiency in nature. Several such factors exist but it is not easy to associate them with the common occurrence of eusocial species in the Hymenoptera.     

Evolution of the Multicellular Animals

SYNOPSIS. Molecular sequence analysis is providing new insightsinto the study of metazoan relationships. The use of ribosomalRNA sequences is revising many of the metazoan phylogenies thathave been established traditionally with anatomical and embryologicaldata. Four new findings that seem to be well supported by moleculardata, both from the authors' laboratories and from others, aredescribed and discussed. First, the arthropods are members ofa deep primary clade within the protostomes and are not thesister taxa of either the annelids or the mollusks. Second,the lophophorate animals are clearly protostomes and are containedwithin a lophotrochozoan superclade including the mollusks,annelids, and many other phyla. Third, the arthropods togetherwith all other molting animals comprise a second monophyleticsuperclade within the protostomes, the ecdysozoa. Fourth, theplatyhelminthes are contained within the lophotrochozoan superclade.     

Evolution of the diacylglycerol lipases

Diacylglycerol lipases (DGLs) mainly catalyze “on-demand” biosynthesis of bioactive monoacylglycerols (MAGs) with different long fatty acyl chains, including 2-arachidonoylglycerol (2-AG), 2-linoleoylglycerol (2-LG), 2-oleoylglycerol (2-OG) and 2-palmitoylglycerol (2-PG). Enzymatic characterization of DGLs, their expression and distribution, and functional features has been elucidated from microorganisms to mammals in some extent. In mammals, biosynthesis, degradation and metabolism of these bioactive lipids intertwine and form a complicated biochemical pathway to affect the mammal neuromodulation of central nervous system and also other physiological processes in most peripheral organs and non-nervous tissue cells, and yet we still do not know if the neuromodulatory role of mammal DGL and MAGs is similar to invertebrates. Tracing the evolutionary history of DGLs from microorganisms to vertebrates will be an essential method to infer DGL and MAG research in organisms. In this review, we give an exhaustive explanation of the ancestral origin, divergence and evolutionary pattern through systemic searching of DGL orthologs in different species. Finally, we also summarize our recent work on the structural and functional studies of DGL in order to explore usage of DGLs in industry and the development of inhibitors for clinical intervention.