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.     

The role of size-specific predation in the evolution and diversification of prey life histories

Some of the best empirical examples of life-history evolution involve responses to predation. Nevertheless, most life-history theory dealing with responses to predation has not been formulated within an explicit dynamic food-web context. In particular, most previous theory does not explicitly consider the coupled population dynamics of the focal species and its predators and resources. Here we present a model of life-history evolution that explores the evolutionary consequences of size-specific predation on small individuals when there is a trade-off between growth and reproduction. The model explicitly describes the population dynamics of a predator, the prey of interest, and its resource. The selective forces that cause life-history evolution in the prey species emerge from the ecological interactions embodied by this model and can involve important elements of frequency dependence. Our results demonstrate that the strength of the coupling between predator and prey in the community determines many aspects of life-history evolution. If the coupling is weak (as is implicitly assumed in many previous models), differences in resource productivity have no effect on the nature of life-history evolution. A single life-history strategy is favored that minimizes the equilibrium resource density (if possible). If the coupling is strong, then higher resource productivities select for faster growth into the predation size refuge. Moreover, under strong coupling it is also possible for natural selection to favor an evolutionary diversification of life histories, possibly resulting in two coexisting species with divergent life-history strategies.     

Complex life cycles drive community assembly through immigration and adaptive diversification

Most animals undergo ontogenetic niche shifts during their life. Yet, standard ecological theory builds on models that ignore this complexity. Here, we study how complex life cycles, where juvenile and adult individuals each feed on different sets of resources, affect community richness. Two different modes of community assembly are considered: gradual adaptive evolution and immigration of new species with randomly selected phenotypes. We find that under gradual evolution complex life cycles can lead to both higher and lower species richness when compared to a model of species with simple life cycles that lack an ontogenetic niche shift. Thus, complex life cycles do not per se increase the scope for gradual adaptive diversification. However, complex life cycles can lead to significantly higher species richness when communities are assembled trough immigration, as immigrants can occupy isolated peaks of the dynamic fitness landscape that are not accessible via gradual evolution.     

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.     

Evolutionary diversification of the auditory organ sensilla in Neoconocephalus katydids (Orthoptera: Tettigoniidae) correlates with acoustic signal diversification over phylogenetic relatedness and life history

Neoconocephalus Tettigoniidae are a model for the evolution of acoustic signals as male calls have diversified in temporal structure during the radiation of the genus. The call divergence and phylogeny in Neoconocephalus are established, but in tettigoniids in general, accompanying evolutionary changes in hearing organs are not studied. We investigated anatomical changes of the tympanal hearing organs during the evolutionary radiation and divergence of intraspecific acoustic signals. We compared the neuroanatomy of auditory sensilla (crista acustica) from nine Neoconocephalus species for the number of auditory sensilla and the crista acustica length. These parameters were correlated with differences in temporal call features, body size, life histories and different phylogenetic positions. By this, adaptive responses to shifting frequencies of male calls and changes in their temporal patterns can be evaluated against phylogenetic constraints and allometry. All species showed well‐developed auditory sensilla, on average 32–35 between species. Crista acustica length and sensillum numbers correlated with body size, but not with phylogenetic position or life history. Statistically significant correlations existed also with specific call patterns: a higher number of auditory sensilla occurred in species with continuous calls or slow pulse rates, and a longer crista acustica occurred in species with double pulses or slow pulse rates. The auditory sensilla show significant differences between species despite their recent radiation, and morphological and ecological similarities. This indicates the responses to natural and sexual selection, including divergence of temporal and spectral signal properties. Phylogenetic constraints are unlikely to limit these changes of the auditory systems.     

Phylogenetic approaches for studying diversification

Estimating rates of speciation and extinction, and understanding how and why they vary over evolutionary time, geographical space and species groups, is a key to understanding how ecological and evolutionary processes generate biological diversity. Such inferences will increasingly benefit from phylogenetic approaches given the ever‐accelerating rates of genetic sequencing. In the last few years, models designed to understand diversification from phylogenetic data have advanced significantly. Here, I review these approaches and what they have revealed about diversification in the natural world. I focus on key distinctions between different models, and I clarify the conclusions that can be drawn from each model. I identify promising areas for future research. A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment. This will not only improve our understanding of diversification; it will also present a new perspective to the use of phylogenies in community ecology, the science of interaction networks and conservation biology, and might shift the current focus in ecology on equilibrium biodiversity theories to non‐equilibrium theories recognising the crucial role of history.     

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.     

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.     

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.