The development and diversification of Precambrian life

During the past decade, important strides have been made toward deciphering the paleobiology of the Precambrian Eon, the earliest seven-eighths of Earth history. This progress has accured chiefly from micropaleontological and organic geochemical studies of fine-grained, ancient cherts. Although understanding of the early biota—of its composition, diversity, paleocology and evolution—still remains far from adequate, three particularly significant generalizations have emerged: (i) Living systems were extant earlier than about 3000 m.y. ago; (ii) between about 3000 and 1000 m.y. ago, the Earth's biota was dominated by prokaryotic blue-green algae; and (iii) the development of the nucleated, eukaryotic cell type somewhat earlier than 1000 m.y. ago led to a stage of rapid diversification that culminated with the appearance of megascopic life near the close of the Precambrian. Consideration of these generalizations, and of the evidence bearing on them provides a ‘state-of-the-art’ assessment of the current status of Precambrian paleobiology.     

Geographic range size, life history and rates of diversification in Australian mammals

Abstract What causes species richness to vary among different groups of organisms? Two hypotheses are that large geographical ranges and fast life history either reduce extinction rates or raise speciation rates, elevating a clade's rate of diversification. Here we present a comparative analysis of these hypotheses using data on the phylogenetic relationships, geographical ranges and life history of the terrestrial mammal fauna of Australia. By comparing species richness patterns to null models, we show that species are distributed nonrandomly among genera. Using sister‐clade comparisons to control for clade age, we then find that faster diversification is significantly associated with larger geographical ranges and larger litters, but there is no evidence for an effect of body size or age at first breeding on diversification rates. We believe the most likely explanation for these patterns is that larger litters and geographical ranges increase diversification rates because they buffer species from extinction. We also discuss the possibility that positive effects of litter size and range size on diversification rates result from elevated speciation rates.     

A model for the evolutionary diversification of religions

We address the problem of cultural diversification by studying selection on cultural ideas that colonize human hosts and using diversification of religions as a conceptual example. In analogy to studying the evolution of pathogens or symbionts colonizing animal hosts, we use models for host-pathogen dynamics known from theoretical epidemiology. In these models, religious content colonizes individual humans. Rates of transmission of ideas between humans, i.e., transmission of cultural content, and rates of loss of ideas (loss of belief) are determined by the phenotype of the cultural content, and by interactions between hosts carrying different ideas. In particular, based on the notion that cultural non-conformism can be negative frequency-dependent (for example, religion can lead to oppression of lower classes and emergence of non-conformism and dissent once a religious belief has reached dominance), we assume that the rate of loss of belief increases as the number of humans colonized by a particular religious phenotype increases. This generates frequency-dependent selection on cultural content, and we use evolutionary theory to show that this frequency dependence can lead to the emergence of coexisting clusters of different cultural types. The different clusters correspond to different cultural traditions, and hence our model describes the emergence of distinct descendant cultures from a single ancestral culture in the absence of any geographical isolation.     

Phylogenetic evidence for pollinator-driven diversification of angiosperms

Since Darwin, the diversity of flowers has been attributed to selection by pollinators. Although pollinators commonly act as selective agents on floral traits, determining the extent to which they have influenced angiosperm diversification requires a historical perspective. Here we review recent studies that combine species-level phylogenies with pollinator data and show that pollinator shifts are common, being associated with at least a quarter of documented divergence events. However, shift frequency and directionality vary extensively, owing to variation in intrinsic factors such as floral features and phylogenetic history, as well as extrinsic factors such as interactions with local pollinator assemblages. Despite technical advances, phylogenies remain limited in their power to distinguish among various pollinator-driven evolutionary processes.     

Flavonoid diversification in the polemoniaceae

Analysis of species representing most sections of all the genera in the family Polemoniaceae showed a range of variation in flavonoids comparable to variation already documented for gross morphological features, karyotypes and pollen grains. Three main groups of flavonoids predominate: (A) common flavonols (kaempferol, quercetin, myricetin); (B) 6-methoxyflavonols (patuletin, eupalitin, eupatolitin); and (C) C-glycosylflavones (apigenin and luteolin based). Cobaea, Loeselia], Polemonium, Allophyllum, Collomia and Gymnosteris have predominantly Group A flavonoids; Bonplandia, Ipomopsis and Eriastrum have predominantly Group B flavonoids; Phlox, Microsteris and Leptodactylon have predominantly Group C flavonoids; while the remaining genera (Cantua, Huthia, Gilia, Langloisia, Navarretia and Linanthus) either have flavonoids of all three groups, or some species within a genus have flavonoids of one group, while other species have flavonoids of another group. Linanthus, Gilia and Navarretia (3 of the larger genera in the family) show great flavonoid diversity, while Langloisia (4 species) has 2 species with Group A flavonoids and the other two species have Group B pigments. Two rare hydroxycoumarins, one being daphnetin, were detected in five genera but they proved to be only of limited systematic interest.     

Whole-tree methods for detecting differential diversification rates

Prolific cladogenesis, adaptive radiation, species selection, key innovations, and mass extinctions are a few examples of biological phenomena that lead to differential diversification among lineages. Central to the study of differential diversification rates is the ability to distinguish chance variation from that which requires deterministic explanation. To detect diversification rate variation among lineages, we propose a number of methods that incorporate information on the topological distribution of species diversity from all internal nodes of a phylogenetic tree. These whole-tree methods (M(Pi), M(Sigma), and M(R)) are explicitly connected to a null model of random diversification--the equal-rates Markov (ERM) random branching model--and an alternative model of differential diversification: M(Pi) is based on the product of individual nodal ERM probabilities; M(Sigma) is based on the sum of individual nodal ERM probabilities, and M(R) is based on a transformation of ERM probabilities that corresponds to a formalized system that orders trees by their relative symmetry. These methods have been implemented in a freely available computer program, SYMMETREE, to detect clades with variable diversification rates, thereby allowing the study of biological processes correlated with and possibly causal to shifts in diversification rate. Application of these methods to several published phylogenies demonstrates their ability to contend with relatively large, incompletely resolved trees. These topology-based methods do not require estimates of relative branch lengths, which should facilitate the analysis of phylogenies, such as supertrees, for which such data are unreliable or unavailable.     

Fluctuating natural selection accounts for the evolution of diversification bet hedging

Natural environments are characterized by unpredictability over all time scales. This stochasticity is expected on theoretical grounds to result in the evolution of ‘bet-hedging’ traits that maximize the long term, or geometric mean fitness even though such traits do not maximize fitness over shorter time scales. The geometric mean principle is thus central to our interpretation of optimality and adaptation; however, quantitative empirical support for bet hedging is lacking. Here, I report a quantitative test using the timing of seed germination—a model diversification bet-hedging trait—in Lobelia inflata under field conditions. In a phenotypic manipulation study, I find the magnitude of fluctuating selection acting on seed germination timing—across 70 intervals throughout five seasons—to be extreme: fitness functions for survival are complex and multimodal within seasons and significantly dissimilar among seasons. I confirm that the observed magnitude of fluctuating selection is sufficient to account for the degree of diversification behaviour characteristic of individuals of this species. The geometric mean principle has been known to economic theory for over two centuries; this study now provides a quantitative test of optimality of a bet-hedging trait in nature.     

Evolutionary diversification of the flowers in angiosperms

Angiosperms and their flowers have greatly diversified into an overwhelming array of forms in the past 135 million years. Diversification was shaped by changes in climate and the biological environment (vegetation, interaction with other organisms) and by internal structural constraints and potentials. This review focuses on the development and structural diversity of flowers and structural constraints. It traces floral diversification in the different organs and organ complexes (perianth, androecium, gynoecium) through the major clades of extant angiosperms. The continuously improved results of molecular phylogenetics provide the framework for this endeavor, which is necessary for the understanding of the biology of the angiosperms and their flowers. Diversification appears to work with innovations and modifications of form. Many structural innovations originated in several clades and in special cases could become key innovations, which likely were hot spots of diversification. Synorganization between organs was an important process to reach new structural levels, from which new diversifications originated. Complexity of synorganization reached peaks in Orchidaceae and Apocynaceae with the independent evolution of pollinaria. Such a review throughout the major clades of angiosperms also shows how superficial and fragmentary our knowledge on floral structure in many clades is. Fresh studies and a multidisciplinary approach are needed.     

The life cycle of the amoeboid alga Synchroma grande (Synchromophyceae, Heterokontophyta)--highly adapted yet equally equipped for rapid diversification in benthic habitats

Synchroma grande (Synchromophyceae, Heterokontophyta) is a marine amoeboid alga, which was isolated from a benthic habitat. This species has sessile cell stages (amoeboid cells with lorica and cysts) and non‐sessile cell stages (migrating and floating amoebae) during its life cycle. The different cell types and their transitions within the life cycle are described, as are their putative functions. Cell proliferation was observed only in cells attached to the substrate but not in free‐floating or migrating cells. We also characterised the phagotrophy of the meroplasmodium in comparison to other amoeboid algae and the formation of the lorica. The functional adaptations of S. grande during its life cycle were compared to the cell stages of other amoeboid algae of the red and green chloroplast lineages. S. grande was found to be highly adapted to the benthic habitat. One sexual and two asexual reproductive strategies (haplo‐diploid life cycle) support the ability of this species to achieve rapid diversification and high adaptivity in its natural habitat.     

Genome diversification within a clonal population of pandemic Vibrio parahaemolyticus seems to depend on the life circumstances of each individual bacteria

Background

New strains of Vibrio parahaemolyticus that cause diarrhea in humans by seafood ingestion periodically emerge through continuous evolution in the ocean. Influx and expansion in the Southern Chilean ocean of a highly clonal V. parahaemolyticus (serotype O3:K6) population from South East Asia caused one of the largest seafood-related diarrhea outbreaks in the world. Here, genomics analyses of isolates from this rapidly expanding clonal population offered an opportunity to observe the molecular evolutionary changes often obscured in more diverse populations.

Results

Whole genome sequence comparison of eight independent isolates of this population from mussels or clinical cases (from different years) was performed. Differences of 1366 to 217,729 bp genome length and 13 to 164 bp single nucleotide variants (SNVs) were found. Most genomic differences corresponded to the presence of regions unique to only one or two isolates, and were probably acquired by horizontal gene transfer (HGT). Some DNA gain was chromosomal but most was in plasmids. One isolate had a large region (8,644 bp) missing, which was probably caused by excision of a prophage. Genome innovation by the presence of unique DNA, attributable to HGT from related bacteria, varied greatly among the isolates, with values of 1,366 (ten times the number of highest number of SNVs) to 217,729 (a thousand times more than the number of highest number of SNVs).

Conclusions

The evolutionary forces (SNVs, HGT) acting on each isolate of the same population were found to differ to an extent that probably depended on the ecological scenario and life circumstances of each bacterium.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1385-8) contains supplementary material, which is available to authorized users.     

Emerging technologies for metabolite generation and structural diversification

Multiple technologies have emerged for structural diversification and efficient production of metabolites of drug molecules. These include expanded use of enzymatic and bioorganic transformations that mimic biological systems, biomimetic catalysis and electrochemical techniques. As this field continues to mature the breadth of transformations is growing beyond simple oxidative processes due in part to parallel development of more efficient catalytic methods for functionalization of unactivated scaffolds. These technologies allow for efficient structural diversification of both aromatic and aliphatic substrates in many cases via single step reactions without the use of protecting groups.     

Isologous diversification for robust development of cell society.

Isologous diversification, proposed for cell differentiation, is shown to be stable against molecular and other external fluctuations, where amplification of noise-induced slight difference between cells leads to a noise-tolerant society with differentiated cell types. It is a general consequence of interacting cells with biochemical networks and cell divisions, as is confirmed by several model simulations. According to the theory, differentiation proceeds first by loss of synchrony of intracellular oscillations as the number of cells increases. Then the chemical composition of the cells is differentiated. The differentiated compositions become inherited by the next generation, and lead to determined cell types. As a result of successive occurrence of the cell differentiation, the cell society will be composed of different cell types. The whole developmental process is robust not only against molecular fluctuations but also against the removal of a cluster of cells. This robustness is a remarkable feature of isologous diversification, in contrast to the conventional threshold-type mechanism for development. As a testable consequence of the theory, we also discuss interaction-dependent tumor formation and negative correlation between growth speed and chemical diversity.     

Models for the molybdenum hydroxylases

 This commentary reviews structural, spectroscopic, and chemical models for the molybdenum hydroxylases. It briefly describes the current state of modeling and identifies areas where model chemistry may play a future role in understanding these enzymes. Received: 28 April 1997 / Accepted: 20 August 1997     

A new timeframe for the diversification of Japan’s mammals

Aim The main Japanese islands are land‐bridge islands divided by the biogeographic division Blakiston’s Line and represent two natural laboratories for studying land‐bridge diversification. Colonization of the current mammal fauna has been dated to the middle to late Pleistocene using fossil evidence. The purpose of this paper is to apply a molecular clock to the genetic divergences between Japanese mammalian taxa and their sister mainland taxa to test the late Pleistocene land‐bridge colonization hypothesis. Location The main Japanese islands (Kyushu, Shikoku, Honshu and Hokkaido). Methods I used mitochondrial DNA (cytochrome b) and a species tree approach to estimate the divergence times of 24 Japanese non‐volant terrestrial mammal taxa and their mainland sister taxa using the program *beast . I then tested for evidence of non‐simultaneous divergence among these taxon‐pairs by controlling for expected coalescent stochasticity using the program Ms Bayes . Results Divergence events between taxa on Japan and their mainland sister taxa were significantly older than expected under the current paradigm, which is based on fossil data. Consistent with the land‐bridge colonization hypothesis, there was evidence of multiple divergence events. Main conclusions These results implicate a colonization timeframe that is older than posited by the current paradigm based on fossil evidence. However, these results are still consistent with the land‐bridge colonization hypothesis. Multiple periods of land‐bridge connectivity may account for the current mammalian fauna in Japan. In addition, half of the divergence time estimates in the Honshu–Shikoku–Kyushu region were clumped around 2.4 Ma, which might suggest a dramatic interchange period, concordant with a period of significant global cooling, when the first land bridge may have connected Japan to the mainland.     

Phylogenetic status and timescale for the diversification of Steno and Sotalia dolphins

Molecular data have provided many insights into cetacean evolution but some unsettled issues still remain. We estimated the topology and timing of cetacean evolutionary relationships using bayesian and maximum likelihood analyses of complete mitochondrial genomes. In order to clarify the phylogenetic placement of Sotalia and Steno within the Delphinidae, we sequenced three new delphinid mitogenomes. Our analyses support three delphinid clades: one joining Steno and Sotalia (supporting the revised subfamily Stenoninae); another placing Sousa within the Delphininae; and a third, the Globicephalinae, which includes Globicephala, Feresa, Pseudorca, Peponocephala and Grampus. We also conclude that Orcinus does not belong in the Globicephalinae, but Orcaella may be part of that subfamily. Divergence dates were estimated using the relaxed molecular clock calibrated with fossil data. We hypothesise that the timing of separation of the marine and Amazonian Sotalia species (2.3 Ma) coincided with the establishment of the modern Amazon River basin.     

Allozyme evidence for the origin and diversification of Gossypium barbadense L.

Summary Gossypium barbadense L. is a commercially important cotton species of tropical South American origin presently grownin many regions of the world. The species is morphologically diverse, consisting of a wide range of wild (or feral), commensal, landrace, and highly improvedcommercial forms. We performed allozyme analysis on 153 accessions representing the spectrum of G. barbadense diversityto ascertain the geographic origin of the species, its patterns of diffusion subsequent to domestication, and to reveal infraspecific relationships. Levels ofgenetic variation in G. barbadense are moderate. Of 59 loci scored, 24 were polymorphic, with a mean number of alleles perlocus of 1.69 and an average panmictic heterozygosity of 0.062. Principal component analysis revealed geographic clustering of accessions into six relativelydiscrete regions. Gene frequencies at many loci are significantly heterogeneous among these regions, with an average G _STof 0.272. Northwestern South America contains the greatest genetic variability; we suggest that this region is the ancestral home of the species. The data indicate separate diffusion pathways from this region into Argentina-Paraguay and into eastern and northern South America east of the Andes. Caribbean Island and Central American forms appear to be derived from the latter. These diffusion pathways are in accordance with morphological evidence and historical record. In contrast to expectations based on geographic proximity, Pacific Island forms have their closest affinity to accessions from eastern South America. Advanced cultivated stocks seem largely derived from western Andean material, but also contain introgressed G. hirsutum germ plasm. Introgression was relatively high (22%–50% of accessions) in commercial stocks and in forms from Argentina-Paraguay and various Pacific Islands, but was conspicuously low or absent in material from Central America and the Caribbean, where commensal and commercial forms of both species are sympatric.