Did the evolution of the phytoplankton fuel the diversification of the marine biosphere?

We discuss the possible links between the fossil record of marine biodiversity, nutrient availability and primary productivity. The parallelism of the fossil records of marine phytoplankton and faunal biodiversity implicates the quantity (primary productivity) and quality (stoichiometry) of phytoplankton as being critical to the diversification of the marine biosphere through the Phanerozoic. The relatively subdued marine biodiversity of the Palaeozoic corresponds to a time of relatively low macronutrient availability and poor food quality of the phytoplankton as opposed to the diversification of the Modern Fauna through the Mesozoic–Cenozoic. Increasing nutrient runoff to the oceans through the Phanerozoic resulted from orogeny, the emplacement of Large Igneous Provinces (LIPs), the evolution of deep-rooting forests and the appearance of more easily decomposable terrestrial organic matter that enhanced weathering. Positive feedback by bioturbation of an expanding benthos played a critical role in evolving biogeochemical cycles by linking the oxidation of dead organic matter and the recycling of nutrients back to the water column where they could be re-utilized. We assess our conclusions against a recently published biogeochemical model for geological time-scales. Major peaks of marine diversity often occur near rising or peak fluxes of silica, phosphorus and dissolved reactive oceanic phosphorus; either major or minor ⁸⁷Sr/⁸⁶Sr peaks; and frequently in the vicinity of major (Circum-Atlantic Magmatic Province) and minor volcanic events, some of which are associated with Oceanic Anoxic Events. These processes appear to be scale-dependent in that they lie on a continuum between biodiversification on macroevolutionary scales of geological time and mass extinction.     

The rôle of the plastome in evolution of the genusOenothera

In the subgenusEuoenothera, five plastid types can be identified. The same major groups of genome complexes as established byCleland, stand out when attention is focused on the co-operation between genomes and plastomes.Experiments on plastid competition and plastid-genotype compatibility lead to an unambiguous interpretation of phylogenetic relations within the subgenus.Based on a paper read at the XI International Congress of Genetics, The Hague, of which an abstract has been published in theProceedings, Vol. I, p. 131–132 (1963).     

Can the theory of evolution be falsified?

In this paper we discuss the epistemological positions of evolution theories. A sharp distinction is made between the theory that species evolved from common ancestors along specified lines of descent (here called the theory of common descent), and the theories intended as causal explanations of evolution (e.g. Lamarck's and Darwin's theory). The theory of common descent permits a large number of predictions of new results that would be improbable without evolution. For instance, (a) phylogenetic trees have been validated now; (b) the observed order in fossils of new species discovered since Darwin's time could be predicted from the theory of common descent; (c) owing to the theory of common descent, the degrees of similarity and difference in newly discovered properties of more or less related species could be predicted. Such observations can be regarded as attempts to falsify the theory of common descent. We conclude that the theory of common descent is an easily-falsifiable & often-tested & still-not-falsified theory, which is the strongest predicate a theory in an empirical science can obtain. Theories intended as causal explanations of evolution can be falsified essentially, and Lamarck's theory has been falsified actually. Several elements of Darwin's theory have been modified or falsified: new versions of a theory of evolution by natural selection are now the leading scientific theories on evolution. We have argued that the theory of common descent and Darwinism are ordinary, falsifiable scientific theories.     

On the evolution of fish–coral interactions

The biodiversity of tropical reefs is typified by the interaction between fishes and corals. Despite the importance of this ecological association, coevolutionary patterns between these two animal groups have yet to be critically evaluated. After compiling a large dataset on the prevalence of fish–coral interactions, we found that only a minority of fish species associate strongly with live corals (~5%). Furthermore, we reveal an evolutionary decoupling between fish and coral lineage trajectories. While fish lineages expanded in the Miocene, the bulk of coral diversification occurred in the Pliocene/Pleistocene. Most importantly, we found that coral association did not drive major differences in fish diversification. These results suggest that the Miocene fish diversification is more likely related to the development of novel, wave-resistant reef structures and their associated ecological opportunities. Macroevolutionary patterns in reef fishes are thus more strongly correlated with the expansion of reefs than with the corals themselves.     

What determines the rate of sequence evolution?

High rates of amino-acid sequence evolution have sometimes been considered to be diagnostic for genes undergoing adaptive change. However, two recent studies have shown that rapid evolution of amino-acid sequence can also be congruent with neutrality.     

The evolution of the “Con Artist”

A series of game-theoretical models for the evolution of, what in the folk literature has become known as, the “Confidence Artist” is presented. Con artists are assumed to be noncooperators who move between groups and “prey” on naive cooperators. Cooperators learn about con artists by either direct experience or via cultural transmission about the identity (or behavior) of such individuals. Three types of transmission rules about con artists are modeled: 1) transmission rate that is independent of the frequency of con artists in the metapopulation; 2) transmission such that cooperators, with some probability, can learn about particular con artists who have entered their group; and 3) a type of frequency dependent transmission such that cooperators can identify con artists in proportion to their frequency in the metapopulation.In general, cultural transmission works against con artists by 1) decreasing the critical between travel patch travel time to invade a metapopulation of cooperators or 2) decreasing the equilibrial frequency of con artists (compared to the case of no cultural transmission). Depending on the mode of cultural transmission, con artists may exist at relatively high or low frequencies.     

Beyond the frog: the evolution of homology models of human IKKβ

Nuclear Factor κ B is implicated in tumor progression and chronic inflammatory diseases and is regulated by IκB kinase β (IKKβ). The crystal structure of IKKβ has been recently solved for Xenopus laevis. Homology models of human IKKβ have been developed prior to and after the crystal structure was solved. Here, we compare four models of human IKKβ and evaluate their performance in both broad and focused library docking studies.     

What are the genomic drivers of the rapid evolution of PRDM9?

Mammalian Prdm9 has been proposed to be a key determinant of the positioning of chromosome double-strand breaks during meiosis, a contributor to speciation processes, and the most rapidly evolving gene in human, and other animal, genomes. Prdm9 genes often exhibit substantial variation in their numbers of encoded zinc fingers (ZFs), not only between closely related species but also among individuals of a species. The near-identity of these ZF sequences appears to render them very unstable in copy number. The rare sequence differences, however, cluster within ZF sites that determine the DNA-binding specificity of PRDM9, and these substitutions are frequently positively selected. Here, possible drivers of the rapid evolution of Prdm9 are discussed, including selection for efficient pairing of homologous chromosomes or for recombination of deleterious linked alleles, and selection against depletion of recombination hotspots or against disease-associated genome rearrangement.     

Can kin selection facilitate the evolution of the genetic program of senescence?

The theory of adaptive senescence, or phenoptosis (“altruistic suicide” of the organism), implies that mutations enhancing mortality growth with age (“senescence genes”) can be favored by selection under some circumstances, although the nature of these circumstances and the frequency of their occurrence are not clear. Here I demonstrate by means of computer simulation that senescence genes can spread in the population’s gene pool via the mechanism of kin selection if two conditions are met. First, the population must have high viscosity (low intermixing), which provides positive correlation between spatial proximity of individuals and their relatedness, an important precondition for kin selection. Second, prior to acquisition of the senescence genes, there must be a sufficiently fast decline in the reproductive potential with age, while viability should decrease slower or remain constant. These conditions are probably met in some territorial and social species with severe competition for social rank and mating partners.     

The evolution of generalization? Parasitoid flies and the perils of inferring host range evolution from phylogenies

It is widely assumed that high resource specificity predisposes lineages toward greater likelihood of extinction and lower likelihood of diversification than more generalized lineages. This suggests that host range evolution in parasitic organisms should proceed from generalist to specialist, and specialist lineages should be found at the 'tips' of phylogenies. To test these hypotheses, parsimony and maximum likelihood methods were used to reconstruct the evolution of host range on a phylogeny of parasitoid flies in the family Tachinidae. In contrast to predictions, most reconstructions indicated that generalists were repeatedly derived from specialist lineages and tended to occupy terminal branches of the phylogeny. These results are critically examined with respect to hypotheses concerning the evolution of specialization, the inherent difficulties in inferring host ranges, our knowledge of tachinid-host associations, and the methodological problems associated with ancestral character state reconstruction. Both parsimony and likelihood reconstructions are shown to provide misleading results and it is argued that independent evidence, in addition to phylogenetic trees, is needed to inform models of the evolution of host range and the evolutionary consequences of specialization.     

Molecular evolution of the NF-κB signaling system

The mechanisms of innate immunity in vertebrates show certain overall resemblances to immune mechanisms of insects. Two hypotheses have been proposed to explain these resemblances. (1) According to the evolutionary continuity hypothesis, innate immune mechanisms evolved in the common ancestor of vertebrates and insects and have been conserved since that time. (2) In the independent-evolution hypothesis, the mechanisms of innate immunity in vertebrates evolved independently from invertebrate immune mechanisms. Phylogenetic analysis of five gene families (Pelle, Rel, IkappaB, Toll, and TRAF) whose members are involved in NF-kappaB signaling in vertebrates and insects were used to decide between these hypotheses. The phylogenies of the Rel and TRAF families strongly supported independent evolution of immune functions in vertebrates and invertebrates, and, except for a possible case in the Pelle family, orthologous molecules having immune functions in both vertebrates and invertebrates were not found. The results suggest that NF-kappaB represents an ancient, generalized signaling system that has been co-opted for immune system roles independently in vertebrate and insect lineages.     

Can receiver psychology explain the evolution of aposematism?

The evolution of aposematism is difficult to explain because: (1) new aposematic morphs will be relatively rare and thus risk extinction during predator education; and (2) aposematic morphs lack the protection of crypsis, and thus appear to invite attacks. I describe a simple method for evaluating whether rare aposematic morphs may be selectively advantaged by their effects on predator psychologies. Using a simulated virtual predator, I consider the advantages that might accrue to dispersed and aggregated morphs if aposematic prey can cause neophobic avoidance, accelerate avoidance learning and decelerate predator forgetting. Simulations show that aposematism is very hard to explain unless there are particular combinations of ecological and psychological factors. If prey are dispersed throughout a locality then aposematism will be favoured only if (1) there is neophobia, learning effects and forgetting or if (2) there are learning effects and warning signals reduce forgetting rates. However, the best scenario for aposematic advantage involves learning rates, forgetting and neophobia when prey are aggregated. Prey aggregation has two important effects. First, it is a highly effective way to maximize the per capita benefits of the neophobia. Second, after an attack on a single prey the benefits of learnt aversions will be immediately conferred on the surviving members of an aggregation without the diluting effects of forgetting. Aggregation therefore provides good protection against forgetting. The simulations thus provide new insights into the complexities of aposematic protection and suggest some important directions for empirical work. Copyright 2001 The Association for the Study of Animal Behaviour.     

Was the evolution of plastid genetic machinery discontinuous?

The plastid nucleoid consists of plastid DNA and various, mostly uncharacterized, DNA-binding proteins. The plastid DNA undoubtedly originated from an ancestral cyanobacterial genome, but the origin of the nucleoid proteins appears complex. Initial biochemical analysis of these proteins, as well as comparative genome informatics, suggest that proteins of eukaryotic origin replaced most of the original prokaryotic proteins during the evolution of plastids in the lineage of green plants.     

Climatic influences on the evolution of early Homo?

The nature of the human fossil record is less than ideal for the generation of precise correlations between environmental variables and patterns of evolution in specific lineages. Nonetheless, a critical look at what can and cannot be said from individual fossil morphology and the correlation of specific environmental proxies with specific hominin fossils may lead to a greater understanding of the degree of certainty with which we should embrace environmental hypotheses for the evolution of Homo. Climate shifts have been implicated in both the origin of the genus and its dispersal from Africa. Here, I consider three areas in which a climatic influence has been posited to explain evolutionary shifts in the genus Homo: the origin and dispersal of the genus from Africa; geography, climate and body size in early Homo, and the influence of climate-induced sea level rise on morphological isolation in H. erectus. Each of the data sets is far from ideal, and interpretations of each of the data sets are fraught with issues of equifinality. Of the three hypotheses discussed, the clearest link is seen between latitudinal variation (and presumably temperature) and body size in H. erectus. Similarly, climate-induced sea level change seems a reasonable isolating mechanism to explain the pattern of cranial variation in later Asian H. erectus, but the distribution could also reflect incompletely sampled clinal variation. Alternatively, only equivocal support is found for the influence of climate on the differentiation of H. erectus from H. habilis (as proxied by body/brain size scaling), and therefore the dispersal of the genus Homo cannot be as clearly linked to changes in body size and shape as it has been in the past. These preliminary data suggest that an emphasis on understanding local adaptation before looking at global (and specific) level change is critical to elucidating the importance of climatic factors on the evolution of the genus Homo.