On some features of historical morphogenesis

The results of the analysis of the diversity dynamics and phylogenetic schemes of various taxa (from species up to classes) show that taxa of different ranks evolved as separate integral natural systems. The main trends in the diversity dynamics of classes and orders are quite different from those of genera and families. The diversity dynamics of genera and families reflect the adaptive essence of these taxonomic categories in the evolution. About five short episodes of mass appearances of genera and families took place in the Phanerozoic. The taxonomic categories of classes and orders are characterized by the archetypes of these groups, and their diversity decreased in the evolution. The appearance of these taxa is not connected with the mass extinctions and changes in the abiotic environment.     

The dynamics of Phanerozoic marine animal diversity agrees with the hyperbolic growth model

Generic diversity dynamics of the Phanerozoic marine animals is far better described by the hyperbolic model, widely used in demography and macrosociology, than by the exponential and logistic models from population dynamics traditionally employed for this purpose. Exponential and logistic models imply zero influence of interactions between taxa on the dynamics of diversity, with the exception of competing for unoccupied ecological space, whereas the hyperbolic model implies non-linear second-order positive feedback in the development of the biota. The hyperbolic human population growth is caused by positive feedback between population size and the rate of technological and cultural development (the more individuals, the more inventors, the more rapid progress, the more rapid growth of the Earth's bearing capacity; the smaller death-rate, the more accelerated growth-rate of the population). Probably there is also non-linear second-order positive feedback between diversity and community structure (the more genera, the higher alpha-diversity, which is defined as average number of genera per community, the more complicated and stable, "buffered" communities, the greater "taxonomic capacity of the environment" and average duration of the existence of genera; extinction rate dencreases, biodiversity growth-rate increases). The simplest mathematical model of biodiversity dynamics based on this assumption is confirmed by empirical data on alpha-diversity dynamics. Progressive complexification of marine communities during the Phanerozoic is also confirmed by the growing evennes of generic abundance distribution in paleocommunities.     

Environmental niche conservatism explains the accumulation of species richness in Mediterranean‐hotspot plant genera

The causes of exceptionally high plant diversity in Mediterranean‐climate biodiversity hotspots are not fully understood. We asked whether a mechanism similar to the tropical niche conservatism hypothesis could explain the diversity of four large genera (Protea, Moraea, Banksia, and Hakea) with distributions within and adjacent to the Greater Cape Floristic Region (South Africa) or the Southwest Floristic Region (Australia). Using phylogenetic and spatial data we estimated the environmental niche of each species, and reconstructed the mode and dynamics of niche evolution, and the geographic history, of each genus. For three genera, there were strong positive relationships between the diversity of clades within a region and their inferred length of occupation of that region. Within genera, there was evidence for strong evolutionary constraint on niche axes associated with climatic seasonality and aridity, with different niche optima for hotspot and nonhotspot clades. Evolutionary transitions away from hotspots were associated with increases in niche breadth and elevated rates of niche evolution. Our results point to a process of “hotspot niche conservatism” whereby the accumulation of plant diversity in Mediterranean‐type ecosystems results from longer time for speciation, with dispersal away from hotspots limited by narrow and phylogenetically conserved environmental niches.     

Rush hour at the Museum – Diversification patterns provide new clues for the success of figs (Ficus L., Moraceae)

Tropical rainforests harbour much of the earth's plant diversity but little is still known about how it evolved and why a small number of plant genera account for the majority. Whether this success is due to rapid turnover or constant evolution for these hyper-diverse plant genera is here tested for the species-rich genus Ficus L. (figs). The pan-tropical distribution of figs makes it an ideal study group to investigate rainforest hyper-diversification patterns. Using a recently published, dated and comprehensive phylogenetic hypothesis, we infer that figs are an old lineage that gradually accumulated species and exhibits very low extinction rates, which corresponds to the ‘museum model’ of evolution. Overall, no major significant shifts in evolutionary dynamics are detected, yet two shifts with lower probability are found. Hemi-epiphytism, monoecy, and active pollination are traits that possibly are associated with the hyper-diversity found in figs, making it possible for the plants to occupy new niches followed by extensive radiation over evolutionary time scales. Figs possess unique diversification patterns compared to other typical rainforest genera.     

Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression

Quantifying the dynamics of intrahost HIV-1 sequence evolution is one means of uncovering information about the interaction between HIV-1 and the host immune system. In the chronic phase of infection, common dynamics of sequence divergence and diversity have been reported. We developed an HIV-1 sequence evolution model that simulated the effects of mutation and fitness of sequence variants. The amount of evolution was described by the distance from the founder strain, and fitness was described by the number of offspring a parent sequence produces. Analysis of the model suggested that the previously observed saturation of divergence and decrease of diversity in later stages of infection can be explained by a decrease in the proportion of offspring that are mutants as the distance from the founder strain increases rather than due to an increase of viral fitness. The prediction of the model was examined by performing phylogenetic analysis to estimate the change in the rate of evolution during infection. In agreement with our modeling, in 13 out of 15 patients (followed for 3–12 years) we found that the rate of intrahost HIV-1 evolution was not constant but rather slowed down at a rate correlated with the rate of CD4+ T-cell decline. The correlation between the dynamics of the evolutionary rate and the rate of CD4+ T-cell decline, coupled with our HIV-1 sequence evolution model, explains previously conflicting observations of the relationships between the rate of HIV-1 quasispecies evolution and disease progression.     

The ecology and evolution of bacteriocins

In this review we focus on the ecological and evolutionary forces that determine the frequency and diversity of colicins inEscherichia coli. To begin, we describe that this killing phenotype is ubiquitous inE. coli, with as many as 50% of the isolates from a population producing colicin toxins, and that each population sampled has its own unique distribution of the more than 20 known colicin types. Next, we explore the dynamics of colicinogeny, which exhibits a typical form of frequency dependence, where the likelihood of successful colicin invasion into a population increases as the initial density of colicinogenic cells increases. We then incorporate thoughts on the evolution of chromosomal resistance to colicins and describe how resistance might influence the dynamics of colicinogen invasion and maintenance and the resulting colicin diversity. The final section deals with a genetic and phylogenetic characterization of colicins and a discussion of the evolutionary mechanisms responsible for generating colicin diversity. In this final section we provide details of the different molecular mechanisms known to play a role in generating colicin diversity, including the two most dominant forces in colincin evolution: recombination and positive, deversifying, selection.     

Diversity dynamics of post‐Palaeozoic crinoids – in quest of the factors affecting crinoid macroevolution

Following the end‐Permian biotic crisis which led to the near extinction of crinoids, this echinoderm class rebounded rapidly during the Mesozoic, resulting in forms with important morphological and behavioural novelties. However, quantitative patterns of crinoid diversity during the Mesozoic remain largely unexplored. Here, we report results of analyses of the evolutionary dynamics of post‐Palaeozoic crinoid genera spanning a time interval between 250 and 70 Myr. We show that crinoids reached their Mesozoic peak of genus‐level richness during the Late Jurassic. We also document a major reorganization of different ecological crinoid groups in the Mesozoic. More specifically, the diversity of sessile forms generally increased towards the mid‐Mesozoic but decreased significantly starting in the Cretaceous, whereas the number of motile crinoid genera increased linearly during the Mesozoic. The possible role of biotic and abiotic factors in crinoid evolution is discussed.     

Influence of evolution on the stability of ecological communities

In randomly assembled communities, diversity is known to have a destabilizing effect. Evolution may affect this result, but our theoretical knowledge of its role is mostly limited to models of small food webs. In the present article, I introduce evolution in a two-species Lotka-Volterra model in which I vary the interaction type and the cost constraining evolution. Regardless of the cost type, evolution tends to stabilize the dynamics more often in trophic interactions than for mutualism or competition. I then use simulations to study the effect of evolution in larger communities that contain all interaction types. Results suggest that evolution usually stabilizes the dynamics. This stabilizing effect is stronger when evolution affects trophic interactions, but happens for all interaction types. Stabilization decreases with diversity and evolution becomes destabilizing in very diverse communities. This suggests that evolution may not counteract the destabilizing effect of diversity observed in random communities.     

Evolution in the block: common elements of 5S rDNA organization and evolutionary patterns in distant fish genera

The 5S rDNA is organized in the genome as tandemly repeated copies of a structural unit composed of a coding sequence plus a nontranscribed spacer (NTS). The coding region is highly conserved in the evolution, whereas the NTS vary in both length and sequence. It has been proposed that 5S rRNA genes are members of a gene family that have arisen through concerted evolution. In this study, we describe the molecular organization and evolution of the 5S rDNA in the genera Lepidorhombus and Scophthalmus (Scophthalmidae) and compared it with already known 5S rDNA of the very different genera Merluccius (Merluccidae) and Salmo (Salmoninae), to identify common structural elements or patterns for understanding 5S rDNA evolution in fish. High intra- and interspecific diversity within the 5S rDNA family in all the genera can be explained by a combination of duplications, deletions, and transposition events. Sequence blocks with high similarity in all the 5S rDNA members across species were identified for the four studied genera, with evidences of intense gene conversion within noncoding regions. We propose a model to explain the evolution of the 5S rDNA, in which the evolutionary units are blocks of nucleotides rather than the entire sequences or single nucleotides. This model implies a "two-speed" evolution: slow within blocks (homogenized by recombination) and fast within the gene family (diversified by duplications and deletions).     

Mollusks in Phanerozoic marine communities: Implications from the analysis of global paleontological databases

Evolutionary history of three mollusk classes (Bivalvia, Gastropoda, and Cephalopoda), regarded as components of the Phanerozoic marine biota, is discussed based on the comparison of dynamics of quantitative parameters obtained from the analysis of the global paleontological databases. The main trends in the evolution of the role of mollusks in Phanerozoic marine ecosystems and relationships between the diversification of this group and biodiversity of paleocommunities are considered. Certain parameters show similarity between the diversity dynamics of mollusks and the whole marine biota, including the paleolatitudinal distribution of diversity. At the same time, mollusk classes differ considerably in certain aspects. The evolutionary history of Bivalvia, Gastropoda, and Cephalopoda was different and determined presumably by deep ecological divergence which occurred as early as the Early Paleozoic adaptive radiation. Bivalves and gastropods followed the trend of a gradual and constant increase in their role in marine communities; they are characterized by high and constantly growing duration of genera, high (and also growing) frequency in paleontological collections. Cephalopods show more chaotic macroevolutionary dynamics, relatively low mean duration of genera and low relative frequency.     

Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria‐phage system

Host–parasite evolutionary interactions are typically considered in a pairwise species framework. However, natural infections frequently involve multiple parasites. Altering parasite diversity alters ecological and evolutionary dynamics as parasites compete and hosts resist multiple infection. We investigated the effects of parasite diversity on host–parasite population dynamics and evolution using the pathogen Pseudomonas aeruginosa and five lytic bacteriophage parasites. To manipulate parasite diversity, bacterial populations were exposed for 24 hours to either phage monocultures or diverse communities containing up to five phages. Phage communities suppressed host populations more rapidly but also showed reduced phage density, likely due to interphage competition. The evolution of resistance allowed rapid bacterial recovery that was greater in magnitude with increases in phage diversity. We observed no difference in the extent of resistance with increased parasite diversity, but there was a profound impact on the specificity of resistance; specialized resistance evolved to monocultures through mutations in a diverse set of genes. In summary, we demonstrate that parasite diversity has rapid effects on host–parasite population dynamics and evolution by selecting for different resistance mutations and affecting the magnitude of bacterial suppression and recovery. Finally, we discuss the implications of phage diversity for their use as biological control agents.     

青藏高原蝇科昆虫生物地理初探

对青藏高原蝇科昆虫进行了生物地理学研究.青藏高原已知蝇科9亚科42属574种,以特有类群占优势.其中特有属占11.9%,特有种占66.2%,文中讨论了该地区区系成分的多源性,特有成份的特异性及青藏高原北缘特有属的起源与演化,特有种的狭域分布现象及理论探讨.讨论了该地区与其它地区间隔分布的多样性及高原蝇科昆虫的适应性.分析了青藏高原的隆起与冰期对蝇科昆虫的作用.青藏高原的横空崛起以及第四纪冰期--间冰期的循环往复,导致该地区生境千差万别,使蝇科区系不仅有地域分异,且垂直差异显著.在此期间,北方物种向南入侵,南北成分交互渗透,高山类群适应进化,使许多特有成分在这里被陶冶、孕育,故而造成了该地区蝇科区系的特有性和物种的多样性.     

物种多样性及环境因子对入侵植物空心莲子草群落稳定性的影响

为探讨外来入侵植物空心莲子草群落稳定性的驱动机制,在中国21°N-37°N范围内设置73个面积为10 mX 10 m的空心莲子草群落样地(陆生39个,水生34个),分别计算其Godron群落稳定性坐标值和4个α-物种多样性指数,并测定各样地的7项环境因子(经度、纬度、海拔、铵态氮、硝态氮、年均温和年均降雨量),采用回归...     

Evolutionary history of the parrotfishes: biogeography,ecomorphology, and comparative diversity

The family Scaridae comprises about 90 species of herbivorous coral reef, rock reef, and seagrass fishes. Parrotfishes are important agents of marine bioerosion who rework the substrate with their beaklike oral jaws. Many scarid populations are characterized by complex social systems including highly differentiated sexual stages, territoriality, and the defense of harems. Here, we test a hypothesis of relationships among parrotfish genera derived from nearly 2 kb of nuclear and mitochondrial DNA sequence. The DNA tree is different than a phylogeny based on comparative morphology and leads to important reinterpretations of scarid evolution. The molecular data suggest a split among seagrass and coral reef associated genera with nearly 80% of all species in the coral reef clade. Our phylogenetic results imply an East Tethyan origin of the family and the recurrent evolution of excavating and scraping feeding modes. It is likely that ecomorphological differences played a significant role in the initial divergence of major scarid lineages, but that variation in color and breeding behavior has triggered subsequent diversification. We present a two-phase model of parrotfish evolution to explain patterns of comparative diversity. Finally, we discuss the application of this model to other adaptively radiating clades.     

Modeling nucleotide evolution at the mesoscale: the phylogeny of the neotropical pitvipers of the Porthidium group (viperidae: crotalinae)

We analyzed the phylogeny of the Neotropical pitvipers within the Porthidium group (including intra-specific through inter-generic relationships) using 1.4 kb of DNA sequences from two mitochondrial protein-coding genes (ND4 and cyt-b). We investigated how Bayesian Markov chain Monte-Carlo (MCMC) phylogenetic hypotheses based on this 'mesoscale' dataset were affected by analysis under various complex models of nucleotide evolution that partition models across the dataset. We develop an approach, employing three statistics (Akaike weights, Bayes factors, and relative Bayes factors), for examining the performance of complex models in order to identify the best-fit model for data analysis. Our results suggest that: (1) model choice may have important practical effects on phylogenetic conclusions even for mesoscale datasets, (2) the use of a complex partitioned model did not produce widespread increases or decreases in nodal posterior probability support, and (3) most differences in resolution resulting from model choice were concentrated at deeper nodes. Our phylogenetic estimates of relationships among members of the Porthidium group (genera: Atropoides, Cerrophidion, and Porthidium) resolve the monophyly of the three genera. Bayesian MCMC results suggest that Cerrophidion and Porthidium form a clade that is the sister taxon to Atropoides. In addition to resolving the intra-specific relationships among a majority of Porthidium group taxa, our results highlight phylogeographic patterns across Middle and South America and suggest that each of the three genera may harbor undescribed species diversity.     

Selection-Driven Extinction Dynamics for Group II Introns in Enterobacteriales

Transposable elements (TEs) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Some TEs were proposed to evolve under a pattern of periodic extinctions-recolonizations, in which elements recurrently invade and quickly proliferate within their host genomes, then start to disappear until total extinction. Depending on the model, TE extinction is assumed to be driven by purifying selection against colonized host genomes (Sel-DE model) or by saturation of host genomes (Sat-DE model). Bacterial group II introns are suspected to follow an extinction-recolonization model of evolution, but whether they follow Sel-DE or Sat-DE dynamics is not known. Our analysis of almost 200 group II intron copies from 90 sequenced Enterobacteriales genomes confirms their extinction-recolonization dynamics: patchy element distributions among genera and even among strains within genera, acquisition of new group II introns through plasmids or other mobile genetic elements, and evidence for recent proliferations in some genomes. Distributions of recent and past proliferations and of their respective homing sites further provide strong support for the Sel-DE model, suggesting that group II introns are deleterious to their hosts. Overall, our observations emphasize the critical impact of host properties on TE dynamics.     

Genus age,provincial area and the taxonomic structure of marine faunas

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf–Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area.     

Originator dynamics

We study the origin of evolution. Evolution is based on replication, mutation, and selection. But how does evolution begin? When do chemical kinetics turn into evolutionary dynamics? We propose "prelife" and "prevolution" as the logical precursors of life and evolution. Prelife generates sequences of variable length. Prelife is a generative chemistry that proliferates information and produces diversity without replication. The resulting "prevolutionary dynamics" have mutation and selection. We propose an equation that allows us to investigate the origin of evolution. In one limit, this "originator equation" gives the classical selection equation. In the other limit, we obtain "prelife." There is competition between life and prelife and there can be selection for or against replication. Simple prelife equations with uniform rate constants have the property that longer sequences are exponentially less frequent than shorter ones. But replication can reverse such an ordering. As the replication rate increases, some longer sequences can become more frequent than shorter ones. Thus, replication can lead to "reversals" in the equilibrium portraits. We study these reversals, which mark the transition from prelife to life in our model. If the replication potential exceeds a critical value, then life replicates into existence.     

Protein dynamics and the diversity of an antibody response

The immune system is remarkable in its ability to produce antibodies (Abs) with virtually any specificity from a limited repertoire of germ line precursors. Although the contribution of sequence diversity to this molecular recognition has been studied for decades, recent models suggest that protein dynamics may also broaden the range of targets recognized. To characterize the contribution of protein dynamics to immunological molecular recognition, we report the sequence, thermodynamic, and time-resolved spectroscopic characterization of a panel of eight Abs elicited to the chromophoric antigen 8-methoxypyrene-1,3,6-trisulfonate (MPTS). Based on the sequence data, three of the Abs arose from unique germ line Abs, whereas the remaining five comprise two sets of siblings that arose by somatic mutation of a common precursor. The thermodynamic data indicate that the Abs recognize MPTS via a variety of mechanisms. Although the spectroscopic data reveal small differences in protein dynamics, the anti-MPTS Abs generally show similar levels of flexibility and conformational heterogeneity, possibly representing the convergent evolution of the dynamics necessary for function. However, one Ab is significantly more rigid and conformationally homogeneous than the others, including a sibling Ab from which it differs by only five somatic mutations. This example of divergent evolution demonstrates that point mutations are capable of fixing significant differences in protein dynamics. The results provide unique insight into how high affinity Abs may be produced that bind virtually any target and possibly, from a more general perspective, how new protein functions are evolved.