How many processes are responsible for phenotypic evolution?

SUMMARY In addressing phenotypic evolution, this article reconsiders natural selection, random drift, developmental constraints, and internal selection in the new extended context of evolutionary developmental biology. The change of perspective from the "evolution of phenotypes" toward an "evolution of ontogenies" (evo-devo perspective) affects the reciprocal relationships among these different processes. Random drift and natural selection are sibling processes: two forms of post-productional sorting among alternative developmental trajectories, the former random, the latter nonrandom. Developmental constraint is a compound concept; it contains even some forms of natural ("external" and "internal") selection. A narrower definition ("reproductive constraints") is proposed. Internal selection is not a selection caused by an internal agent. It is a form of environment-independent selection depending on the level of the organism's internal developmental or functional coordination. Selection and constraints are the main deterministic processes in phenotypic evolution but they are not opposing forces. Indeed, they are continuously interacting processes of evolutionary change, but with different roles that should not be confused.     

How many birds are there?

Attempts to assess the magnitude of global biodiversity have focused on estimating species richness. However, this is but one component of biodiversity, and others, such as numbers of individuals or biomass, are at least as poorly known and just as important to quantify. Here, we use a variety of methods to estimate the global number of individuals for a single taxon, birds. The different methods yield surprisingly consistent estimates of a global bird population of between 200 billion and 400 billion individuals (1 billion=109). We discuss some of the implications of this figure.     

How many species are there?

How many species are there is a question receiving more attention from biologists and reasons for this are suggested. Different methods of answering this question are examined and include: counting all species; extrapolations from known faunas and regions; extrapolations from samples; methods using ecological models; censusing taxonomists' views. Most of these methods indicate that global totals of 5 to 15 million species are reasonable. The implications of much higher estimates of 30 million species or more are examined, particularly the question of where these millions of species might be found.     

How many SNPs are enough?

Since the days of allozyme analysis, we have been enamored with the idea that if we just had enough polymorphic mendelian loci, we could gauge the inbreeding level of individuals by measuring heterozygosity and simultaneously measure the degree of genetic relatedness between pairs of individuals. Given Mendel’s Laws, we have always known that we would need numerous independently segregating loci to achieve any reasonable degree of accuracy. Santure et al. (2010, this issue) use a 771 marker SNP panel to assess heterozygosity levels and to assess pairwise relatedness, and compare both with theoretical expectations obtained from a carefully recorded pedigree of a zebra finch breeding colony, as a function of increasing numbers of SNP markers. They also compare the SNP results with those from a 20‐locus microsatellite panel, showing that adding SNPs to a fairly large microsatellite panel improves accuracy, but given an existing panel of 125 SNPs, little is to be gained by adding microsatellites. They show that the accuracy available for estimating individual levels of inbreeding is somewhat limited. They also show that the average pairwise relatedness measures bracket pedigree relationship very nicely, but the variances for individual pairs remain substantial, even with a very large panel.     

How many membrane proteins are there?

One of the basic issues that arises in functional genomics is the ability to predict the subcellular location of proteins that are deduced from gene and genome sequencing. In particular, one would like to be able to readily specify those proteins that are soluble and those that are inserted in a membrane. Traditional methods of distinguishing between these two locations have relied on extensive, time-consuming biochemical studies. The alternative approach has been to make inferences based on a visual search of the amino acid sequences of presumed gene products for stretches of hydrophobic amino acids. This numerical, sequence-based approach is usually seen as a first approximation pending more reliable biochemical data. The recent availability of large and complete sequence data sets for several organisms allows us to determine just how accurate such a numerical approach could be, and to attempt to minimize and quantify the error involved. We have optimized a statistical approach to protein location determination. Using our approach, we have determined that surprisingly few proteins are misallocated using the numerical method. We also examine the biological implications of the success of this technique.     

How many species of Cladocera are there?

An estimation of the number of taxa within families, genera and local faunas of Cladocera reveals that only c. 129 species (17% of all known species) may be considered as sufficiently well described (valid species), and c. 146 as rather well described (fair species) but needing further study using modern methods of investigation. The status of all other species is vague. The families Chydoridae, Daphniidae and Sididae and genera Diaphanosoma, Daphnia, (including Daphniopsis), Megafenestra, Scapholeberis, Eurycercus, Chydorus, Ephemeroporus and Pleuroxus have been comparatively studied best. The largest number of valid species is known from Europe, North America, Australia and South America, and the smallest number from Africa. Presence of large number of vague species of Cladocera negatively affects faunistic, zoogeographic, and ecological studies of continental waters.Dedicated to the memory of Professor D. J. Frey     

How many hydrogen-bonded α-turns are possible?

The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employing the methods of ab initio MO theory in vacuum (HF/6-31G*, B3LYP/6-311?+?G*) and in solution (CPCM/HF/6-31G*). Only few α-turn structures with glycine and alanine backbones fulfill the geometry criteria for the i←(i?+?4) hydrogen bond satisfactorily. The most stable representatives agree with structures found in the Protein Data Bank. There is a general tendency to form additional hydrogen bonds for smaller pseudocycles corresponding to β- and γ-turns with better hydrogen bond geometries. Sometimes, this competition weakens or even destroys the i←(i?+?4) hydrogen bond leading to very stable double β-turn structures. This is also the reason why an “ideal” α-turn with three central amino acids having the perfect backbone angle values of an α-helix could not be localized. There are numerous hints for stable α-turns with a distance between the \( {{\hbox{C}}_\alpha } \)-atoms of the first and fifth amino acid smaller than 6-7 Å, but without an i←(i?+?4) hydrogen bond.     

How many conservation units are there for the endangered grassland earless dragons?

Species are the most commonly recognised unit for conservation management, yet significant variation can exist below the level of taxonomic recognition and there is a lack of consensus around how a species might be defined. This definition has particular relevance when species designations are used to apportion conservation effort and when definitions might be made through legislation. Here, we use microsatellite DNA analyses to test the proposition that the last remaining populations of the endangered grassland earless dragon (Tympanocryptis pinguicolla) harbour substantial cryptic genetic variation. Our study provides strong evidence that long historical isolation and the recent impacts of urbanization, have led to genetic differentiation in microsatellite DNA allele frequencies and high numbers of private alleles among three genetic clusters. This differentiation is partially concordant with previous mitochondrial DNA analyses, which show the two regions (Canberra and Monaro) where this species exists, to be reciprocally monophyletic, but differs through the identification of a third genetic cluster that splits a northern Canberra cluster from that of southern Canberra. Our data also identify a stark contrast in population genetic structure between clusters such that high levels of genetic structure are evident in the highly urbanised Canberra region but not in the largely rural Monaro region. We conclude that this species, like many reptiles, harbours considerable cryptic variation and currently comprises three distinct and discrete units. These units could be classified as separate species for the purpose of conservation under the relevant Australian and international Acts drawing management appropriate to that status.     

How many species of flowering plants are there?

We estimate the probable number of flowering plants. First, we apply a model that explicitly incorporates taxonomic effort over time to estimate the number of as-yet-unknown species. Second, we ask taxonomic experts their opinions on how many species are likely to be missing, on a family-by-family basis. The results are broadly comparable. We show that the current number of species should grow by between 10 and 20 per cent. There are, however, interesting discrepancies between expert and model estimates for some families, suggesting that our model does not always completely capture patterns of taxonomic activity. The as-yet-unknown species are probably similar to those taxonomists have described recently—overwhelmingly rare and local, and disproportionately in biodiversity hotspots, where there are high levels of habitat destruction.     

How many signal peptides are there in bacteria?

Over the last 5 years proteogenomics (using mass spectroscopy to identify proteins predicted from genomic sequences) has emerged as a promising approach to the high‐throughput identification of protein N‐termini, which remains a problem in genome annotation. Comparison of the experimentally determined N‐termini with those predicted by sequence analysis tools allows identification of the signal peptides and therefore conclusions on the cytoplasmic or extracytoplasmic (periplasmic or extracellular) localization of the respective proteins. We present here the results of a proteogenomic study of the signal peptides in Escherichia coli K‐12 and compare its results with the available experimental data and predictions by such software tools as SignalP and Phobius. A single proteogenomics experiment recovered more than a third of all signal peptides that had been experimentally determined during the past three decades and confirmed at least 31 additional signal peptides, mostly in the known exported proteins, which had been previously predicted but not validated. The filtering of putative signal peptides for the peptide length and the presence of an eight‐residue hydrophobic patch and a typical signal peptidase cleavage site proved sufficient to eliminate the false‐positive hits. Surprisingly, the results of this proteogenomics study, as well as a re‐analysis of the E. coli genome with the latest version of SignalP program, show that the fraction of proteins containing signal peptides is only about 10%, or half of previous estimates.     

How many flowering plants are pollinated by animals?

It is clear that the majority of flowering plants are pollinated by insects and other animals, with a minority utilising abiotic pollen vectors, mainly wind. However there is no accurate published calculation of the proportion of the ca 352 000 species of angiosperms that interact with pollinators. Widely cited figures range from 67% to 96% but these have not been based on firm data. We estimated the number and proportion of flowering plants that are pollinated by animals using published and unpublished community‐level surveys of plant pollination systems that recorded whether each species present was pollinated by animals or wind. The proportion of animal‐pollinated species rises from a mean of 78% in temperate‐zone communities to 94% in tropical communities. By correcting for the latitudinal diversity trend in flowering plants, we estimate the global number and proportion of animal pollinated angiosperms as 308 006, which is 87.5% of the estimated species‐level diversity of flowering plants. Given current concerns about the decline in pollinators and the possible resulting impacts on both natural communities and agricultural crops, such estimates are vital to both ecologists and policy makers. Further research is required to assess in detail the absolute dependency of these plants on their pollinators, and how this varies with latitude and community type, but there is no doubt that plant–pollinator interactions play a significant role in maintaining the functional integrity of most terrestrial ecosystems.