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Neurostimulation techniques allow us to manipulate the activity of nervous systems, and even that of single neurons. In this piece, researchers discuss what they see as the current key bottlenecks to controlling neural biology., (Copyright © 2020. Published by Elsevier Inc.)

Planetary sustainability is in trouble, heading towards what pioneer of evolutionary biology, E.O Wilson, twenty-two years ago called a "bottleneck". Created through the actions of humanity this is an increasingly narrow passage through which only some species can pass, and on which humans depend to provide the sources of re-radiation. What is lost is hard to impossible to restore. Keeping this passage as wide as possible is crucial, but the trends are not yet promising. At a time when those trends appear to be converging to a human and ecological crisis of planetary but finite duration, changed priorities are required whilst at the same time providing opportunity. In particular, strategies, such as experimental governance devised to act in the face of unknowns and uncertain knowledge provide a basis for action to hold open and successfully pass through the bottleneck, a goal which is of the highest importance for humans as we seek to achieve a sustainable future. [ABSTRACT FROM AUTHOR]

Abstract: The present study assesses the degree of genetic structure and the presence of recent genetic bottlenecks in the wild boar population in Portugal. One hundred and ten individuals were sampled after capture during organised legal drive hunts, conducted in 58 municipalities across the continental territory, during the game seasons of 2002/2003 and 2003/2004. Individuals were genetically typed at six microsatellite loci using multiplex PCR amplification. Significant deviations from Hardy–Weinberg equilibrium were found for the total population of wild boar in Portugal. Wild boar population genetic structure was assessed using Bayesian methods, suggesting the existence of three subpopulations (North, Centre and South). Tests were conducted to detect the presence of potential migrants and hybrids between subpopulations. After exclusion of these individuals, three sets of wild boars representative of respective subpopulations were distinguished and tested for the effects of recent bottlenecks. Genetic distances between pairs of subpopulations were quantified using F ST and R ST estimators, revealing a variation of 0.138–0.178 and 0.107–0.198, respectively. On the basis of genetic and distribution data for Portuguese wild boar from the beginning of the 20th century, a model of strong demographic decline and contraction to isolated refuge areas at the national level, followed by a recovery and expansion towards former distribution limits is suggested. Some evidence points to present admixture among subpopulations in contact areas. [Copyright &y& Elsevier]

The pathogenesis of bacteraemia after challenge with one million pneumococci of three isogenic variants was investigated. Sequential analyses of blood samples indicated that most episodes of bacteraemia were monoclonal events providing compelling evidence for a single bacterial cell bottleneck at the origin of invasive disease. With respect to host determinants, results identified novel properties of splenic macrophages and a role for neutrophils in early clearance of pneumococci. Concerning microbial factors, whole genome sequencing provided genetic evidence for the clonal origin of the bacteraemia and identified SNPs in distinct sub-units of F0/F1 ATPase in the majority of the ex vivo isolates. When compared to parental organisms of the inoculum, ex-vivo pneumococci with mutant alleles of the F0/F1 ATPase had acquired the capacity to grow at low pH at the cost of the capacity to grow at high pH. Although founded by a single cell, the genotypes of pneumococci in septicaemic mice indicate strong selective pressure for fitness, emphasising the within-host complexity of the pathogenesis of invasive disease. [ABSTRACT FROM AUTHOR]

The 3′ untranslated genome region (UTR) of arthropod-borne viruses is characterized by enriched direct repeats (DRs) and stem-loop structures. Despite many years of theoretical and experimental study, on-going positive selection on the 3′UTR had never been observed in ‘real-time,’ and the role of the arbovirus 3′UTR remains poorly understood. We observed a lineage-specific 3′UTR sequence pattern in all available Asian lineage of the mosquito-borne alphavirus, chikungunya virus (CHIKV) (1958–2009), including complicated mutation and duplication patterns of the long DRs. Given that a longer genome is usually associated with less efficient replication, we hypothesized that the fixation of these genetic changes in the Asian lineage 3′UTR was due to their beneficial effects on adaptation to vectors or hosts. Using reverse genetic methods, we examined the functional importance of each direct repeat. Our results suggest that adaptation to mosquitoes, rather than to mammalian hosts, is a major evolutionary force on the CHIKV 3′UTR. Surprisingly, the Asian 3′UTR appeared to be inferior to its predicted ancestral sequence for replication in both mammals and mosquitoes, suggesting that its fixation in Asia was not a result of directional selection. Rather, it may have resulted from a population bottleneck during its introduction from Africa to Asia. We propose that this introduction of a 3′UTR with deletions led to genetic drift and compensatory mutations associated with the loss of structural/functional constraints, followed by two independent beneficial duplications and fixation due to positive selection. Our results provide further evidence that the limited epidemic potential of the Asian CHIKV strains resulted from founder effects that reduced its fitness for efficient transmission by mosquitoes there. [ABSTRACT FROM AUTHOR]

Genome wide patterns of nucleotide diversity and recombination reveal considerable variation including hotspots. Some studies suggest that these patterns are primarily dictated by individual locus history related at a broader scale to the population demographic history. Because bottlenecks have occurred in the history of numerous species, we undertook a simulation approach to investigate their impact on the patterns of aggregation of polymorphic sites and linkage disequilibrium (LD). We developed a new index (Polymorphism Aggregation Index) to characterize this aggregation and showed that variation in the density of polymorphic sites results from an interplay between the bottleneck scenario and the recombination rate. Under particular conditions, aggregation is maximized and apparent mutation hotspots resulting in a 50-fold increase in polymorphic sites density can occur. In similar conditions, long distance LD can be detected. [ABSTRACT FROM AUTHOR]

Retroviral insertional mutagenesis (RIM) is a powerful tool for cancer genomics that was combined in this study with deep sequencing (RIM/DS) to facilitate a comprehensive analysis of lymphoma progression. Transgenic mice expressing two potent collaborating oncogenes in the germ line (CD2-MYC, -Runx2) develop rapid onset tumours that can be accelerated and rendered polyclonal by neonatal Moloney murine leukaemia virus (MoMLV) infection. RIM/DS analysis of 28 polyclonal lymphomas identified 771 common insertion sites (CISs) defining a ‘progression network’ that encompassed a remarkably large fraction of known MoMLV target genes, with further strong indications of oncogenic selection above the background of MoMLV integration preference. Progression driven by RIM was characterised as a Darwinian process of clonal competition engaging proliferation control networks downstream of cytokine and T-cell receptor signalling. Enhancer mode activation accounted for the most efficiently selected CIS target genes, including Ccr7 as the most prominent of a set of chemokine receptors driving paracrine growth stimulation and lymphoma dissemination. Another large target gene subset including candidate tumour suppressors was disrupted by intragenic insertions. A second RIM/DS screen comparing lymphomas of wild-type and parental transgenics showed that CD2-MYC tumours are virtually dependent on activation of Runx family genes in strong preference to other potent Myc collaborating genes (Gfi1, Notch1). Ikzf1 was identified as a novel collaborating gene for Runx2 and illustrated the interface between integration preference and oncogenic selection. Lymphoma target genes for MoMLV can be classified into (a) a small set of master regulators that confer self-renewal; overcoming p53 and other failsafe pathways and (b) a large group of progression genes that control autonomous proliferation in transformed cells. These findings provide insights into retroviral biology, human cancer genetics and the safety of vector-mediated gene therapy. [ABSTRACT FROM AUTHOR]

Abstract: Heterologous expression of integral membrane proteins from Helicobacter pylori 26695 in Escherichia coli enabled the identification of 17 candidates for purification and subsequent crystallization. 45% of the purified proteins were contaminated with what was later identified as the multidrug efflux pump (AcrB) of E. coli, and 17% with the succinate dehydrogenase. While additional purification steps ensured removal of succinate dehydrogenase, they failed to remove AcrB completely, leaving picogram amounts present in fractions intended for 3D-crystallization. Two of these targets, the Na+ dependent d-glucose/d-galactose transporter (GluP-HP1174) and the carbon starvation protein A (CstA-HP1168), produced small crystals (<40μm). Crystals from the GluP preparation diffracted to 4.2Å resolution and belonged to the rhombohedral space group H32. Subsequent molecular replacement proved that these crystals were derived from a contaminant, the efflux transporter AcrB. This unexpected crystallization of AcrB from picogram amounts was observed in six new conditions. The systematic occurrence of AcrB in membrane preparations stems from the upregulation of its transcription in response to the stress induced by the expression of a selected target. This, along with its tendency to crystallize in the picogram scale, poses a serious concern in membrane protein expression using heterologous hosts harbouring AcrB. [Copyright &y& Elsevier]

We investigated potential drivers of interest in topic-context and topic-activity combinations, as well as interactions between the different elements of situational interest in evolutionary biology. High school students (n = 982, age 17 years) were asked to rate their interest in two sets of items consisting of topic-context and topic-activity combinations. Rasch modeling, analyses of variance, and descriptive statistics revealed that topics are the dominant dimension and moderate the general level of interest that students express in both topic-context and topic-activity combinations. Qualitative findings from interviews with high school students (n = 6, age 16 years) support this finding. Thus, choice of a particular context, as well as choice of a particular activity, may be less important than previously assumed, since topics are the bottleneck and drive situational interest in topic-context combinations and topic-activity combinations. Implications for evolution education are discussed.

Arabidopsis halleri is a hyperaccumulating pseudo-metallophyte and an emerging model to explore molecular basis of metal tolerance and hyperaccumulation. In this regard, understanding of interacting genes can be a crucial aspect as these interactions regulate several biological functions at molecular level in response to multiple signals. In this current study, we applied a weighted gene co-expression network analysis (WGCNA) on root and shoot RNA-seq data of A. halleri to predict the related scale-free organ specific co-expression networks, for the first time. A total of 19,653 genes of root and 18,081 genes of shoot were grouped into 14 modules and subjected to GO and KEGG enrichment analysis. "Photosynthesis" and "photosynthesis–antenna proteins" were identified as the most enriched and common pathway to both root and shoot. Whereas "glucosinolate biosynthesis," "autophagy," and "SNARE interactions in vesicular transport" were specific to root, and "circadian rhythm" was found to be enriched only in shoot. Later, hub and bottleneck genes were identified in each module by using cytoHubba plugin based on Cytoscape and scoring the relevance of each gene to the topology of the network. The modules with the most significant differential expression pattern across control and treatment (Cd-Zn treatment) were selected and their hub and bottleneck genes were screened to validate their possible involvement in heavy metal stress. Moreover, we combined the analysis of co-expression modules together with protein–protein interactions (PPIs), confirming some genes as potential candidates in plant heavy metal stress and as biomarkers. The results from this analysis shed the light on the pivotal functions to the hyperaccumulative trait of A. halleri, giving perspective to new paths for future research on this species. [ABSTRACT FROM AUTHOR]

In the absence of long-term monitoring data, inferences about extinctions of species and populations are generally based on past observations about the presence of a particular species at specified places and times (sightings). Several methods have been developed to estimate the probability and timing of extinctions from records of such sightings, but they differ in their computational complexity and assumptions about the nature of the sighting record. Here we use simulations to evaluate the performance of seven methods proposed to estimate the upper confidence limit on extinction times under different extinction and sampling scenarios. Our results show that the ability of existing methods to correctly estimate the timing of extinctions varies with the type of extinction (sudden vs. gradual) and the nature of sampling effort over time. When the probability of sampling a species declines over time, many of the methods perform poorly. On the other hand, the simulation results also suggest that as long as the choice of the method is determined by the nature of the underlying sighting data, existing methods should provide reliable inferences about the timing of past extinctions. [ABSTRACT FROM AUTHOR]

Population genetic studies on marine taxa, specifically in the field of phylogeography, have revealed distinct levels of genetic differentiation in widely distributed species, even though they present long planktonic larval development. A set of factors have been identified as acting on gene flow between marine populations, including physical or physiological barriers, isolation by distance, larval behaviour, and geological and demographic events. In this way, the aim of this study was to analyse the genetic variability among populations of the crab species Sesarma rectum Randall, 1840 along the western Atlantic in order to check the levels of genetic diversity and differentiation among populations. To achieve this purpose, mtDNA cytochrome-c oxidase subunit I (COI) (DNA-barcode marker) data were used to compute a haplotype network and a Bayesian analysis for genetic differentiation, to calculate an Analysis of Molecular Variance (AMOVA), and haplotype and nucleotide diversities. Neutrality tests (Tajima's D and Fu's Fs) were accessed, as well as pairwise mismatch distribution under the sudden expansion model. We found sharing of haplotypes among populations of S. rectum along its range of distribution and no significant indication for restricted gene flow between populations separately over 6000 km, supporting the hypothesis of a high dispersive capacity, and/or the absence of strong selective gradients along the distribution. Nevertheless, some results indicated population structure suggesting the presence of two genetic sources (i.e., groups or lineages), probably interpreted as a result of a very recent bottleneck effect due to habitat losses, followed by the beginning of a population expansion. [ABSTRACT FROM AUTHOR]

Finding causal links between genotype and phenotype is a major issue in biology, even more in mitochondrial biology. First of all, mitochondria form complex networks, undergoing fission and fusion and we do not know how such dynamics influence the distribution of mtDNA variants across the mitochondrial network and how they affect the phenotype. Second, the non-Mendelian inheritance of mitochondrial genes can have sex-specific effects and the mechanism of mitochondrial inheritance is still poorly understood, so it is not clear how selection and/or drift act on mtDNA genetic variation in each generation. Third, we still do not know how mtDNA expression is regulated; there is growing evidence for a convoluted mechanism that includes RNA editing, mRNA stability/turnover, post-transcriptional and post-translational modifications. Fourth, mitochondrial activity differs across species as a result of several interacting processes such as drift, adaptation, genotype-by-environment interactions, mitonuclear coevolution and epistasis. This issue will cover several aspects of mitochondrial biology along the path from genotype to phenotype, and it is subdivided into four sections focusing on mitochondrial genetic variation, on the relationship among mitochondria, germ line and sex, on the role of mitochondria in adaptation and phenotypic plasticity, and on some future perspectives in mitochondrial research. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'. [ABSTRACT FROM AUTHOR]

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Aim: Analysis reconstruction networks from two diseases, IBD and NASH and their relationship, based on systems biology methods. Background: IBD and NASH are two complex diseases, with progressive prevalence and high cost for countries. There are some reports on co-existence of these two diseases. In addition, they have some similar risk factors such as age, obesity, and insulin resistance. Therefore, systems biology approach can help to discover their relationship. Methods: DisGeNET and STRING databases were sources of disease genes and constructing networks. Three plugins of Cytoscape software, including ClusterONE, ClueGO and CluePedia, were used to analyze and cluster networks and enrichment of pathways. Based on degree and Betweenness, hubs and bottleneck nodes were defined. Results: Common genes between IBD and NASH construct a network with 99 nodes. Common genes between IBD and NASH were extracted and imported to STRING database to construct PPI network. The resulting network contained 99 nodes and 333 edges. Five genes were selected as hubs: JAK2, TLR2, TP53, TLR4 and STAT3 and five genes were selected as bottleneck including: JAK2, TP53, AGT, CYP3A4 and TLR4. These genes were hubs in analysis network that was constructed from hubs of NASH and IBD networks. Conclusion: Systems biology methods, specifically PPI networks, can be useful for analyzing complicated related diseases. Finding Hub and bottleneck proteins should be the goal of drug designing and introducing disease markers. [ABSTRACT FROM AUTHOR]

Background: The IAEA colony is the only one available for mass rearing of Glossina pallidipes, a vector of human and animal African trypanosomiasis in eastern Africa. This colony is the source for Sterile Insect Technique (SIT) programs in East Africa. The source population of this colony is unclear and its genetic diversity has not previously been evaluated and compared to field populations. Methodology/Principal Findings: We examined the genetic variation within and between the IAEA colony and its potential source populations in north Zimbabwe and the Kenya/Uganda border at 9 microsatellites loci to retrace the demographic history of the IAEA colony. We performed classical population genetics analyses and also combined historical and genetic data in a quantitative analysis using Approximate Bayesian Computation (ABC). There is no evidence of introgression from the north Zimbabwean population into the IAEA colony. Moreover, the ABC analyses revealed that the foundation and establishment of the colony was associated with a genetic bottleneck that has resulted in a loss of 35.7% of alleles and 54% of expected heterozygosity compared to its source population. Also, we show that tsetse control carried out in the 1990's is likely reduced the effective population size of the Kenya/Uganda border population. Conclusions/Significance: All the analyses indicate that the area of origin of the IAEA colony is the Kenya/Uganda border and that a genetic bottleneck was associated with the foundation and establishment of the colony. Genetic diversity associated with traits that are important for SIT may potentially have been lost during this genetic bottleneck which could lead to a suboptimal competitiveness of the colony males in the field. The genetic diversity of the colony is lower than that of field populations and so, studies using colony flies should be interpreted with caution when drawing general conclusions about G. pallidipes biology. [ABSTRACT FROM AUTHOR]

Since its immigration in the Pacific island of New Caledonia in 1942 (i.e. about 240 tick-generations ago), the cattle tick Boophilus microplus has experienced a remarkable adaptive diversification there. In order to better understand the population factors involved, we have investigated the B. microplus population structure on that main host-species, Bos taurus. This study was based microsatellite loci and confirmed that the island colonization came along with a significant bottleneck. Knowledge on B. microplus biology led us to expect B. microplus populations to be composed of highly inbred lineages irregularly dispatched among the individual hosts belonging to the same herds. Instead, this study evidenced a weak inbreeding level and an absence of genetic differentiation within herds. Complementarily, a significant signal of isolation by distance exhibited that human-traffic of cattle does not promote high tick dispersal within the island. Finally, the tick density was found to be about a few hundreds of reproducing adults per squared kilometre, for a gene dispersal range of about a few hundred metres per tick generation. Results are discussed with regard to the evolution of new adaptive changes. [ABSTRACT FROM AUTHOR]

Polymerase chain reaction (PCR) restriction fragment length polymorphism analysis of mitochondrial DNA was applied to the genetic structure and evolutionary history of the more ancestral Pangasianodon hypophthalmus ( n = 82), and the recently speciated catfish Pangasius bocourti ( n = 90) from the Cambodian Mekong River. Both pangasiids were characterized by a lack of genetic population structure that may result from high levels of contemporary gene flow. Genetic diversity was lower in P. hypophthalmus than in P. bocourti. However, a different evolutionary history was inferred for both species based on genealogical and demographic analyses (mismatch analysis, Tajima’s D- and Fu’s FS-tests). The genetic profile of the more ancestral P. hypophthalmus shows indications of a recent population bottleneck, whereas the recently speciated P. bocourti shows signatures of historical population expansion. This study stresses the importance of preserving the migration routes in the Cambodian Mekong basin in order to maintain the genetic diversity and long-term integrity of both species. [ABSTRACT FROM AUTHOR]

Sperm marking provides a key tool for reproductive biology studies, but it also represents a valuable monitoring tool for genetic pest control strategies such as the sterile insect technique. Sperm-marked lines can be generated by introducing transgenes that mediate the expression of fluorescent proteins during spermatogenesis. The homozygous lines established by transgenesis approaches are going through a genetic bottleneck that can lead to reduced fitness. Transgenic SIT approaches have mostly focused on Dipteran and Lepidopteran pests so far. With this study, we provide sperm-marked lines for the Coleopteran pest model organism, the red flour beetle Tribolium castaneum, based on the β2-tubulin promoter/enhancer driving red (DsRed) or green (EGFP) fluorescence. The obtained lines are reasonably competitive and were thus used for our studies on reproductive biology, confirming the phenomenon of 'last-male sperm precedence' and that the spermathecae are deployed for long-term sperm storage, enabling the use of sperm from first mating events even after secondary mating events for a long period of time. The homozygosity and competitiveness of the lines will enable future studies to analyze the controlled process of sperm movement into the long-term storage organ as part of a post-mating cryptic female choice mechanism of this extremely promiscuous species. [ABSTRACT FROM AUTHOR]

Rhynchaenus maculosus is an emerging insect pest with an increasingly serious tendency. Lack of biology information results in the bottleneck of integrated management of this pest. To facilitate an available design of integrated pest management strategy, biology of R. maculosus, including voltinism, life cycle, distribution, and damage has been investigated. Results reveal that R. maculosus is oligophagous and distributes in Heilongjiang, Jilin, and Liaoning provinces, China. This pest produces one generation per year (univoltinism) and overwinters as adults in leaf litter. From mid-April to late-April, active overwintering adults emerge from overwintering sites. The next generation of adult R. maculosus appears from mid-May to early June until mid-August to early September when the beetles move into the overwintering places. The entire time span of adult occurrence ranges from 315.6 ± 3.6 to 336.4 ± 3.2 days (Mean ± SD). Larvae undergo 3 instars with a total duration of 20 to 23 days. R. maculosus larvae feed on Q. wutaishanica and Q. mongolica without host-specific preference between the two host species, but do not harm Q. acutissim. Three species of larval parasites were collected and identified as Braconidae sp., Eulophidae sp., and Ceraphronidae sp. Biological information of R. maculosus provides essential insights for design and implementation of integrated management of this pest. [ABSTRACT FROM AUTHOR]

In the field of bioinformatics, understanding protein secondary structure is very important for exploring diseases and finding new treatments. Considering that the physical experiment-based protein secondary structure prediction methods are time-consuming and expensive, some pattern recognition and machine learning methods are proposed. However, most of the methods achieve quite similar performance, which seems to reach a model capacity bottleneck. As both model design and learning process can affect the model learning capacity, we pay attention to the latter part. To this end, a framework called Multistage Combination Classifier Augmented Model (MCCM) is proposed to solve the protein secondary structure prediction task. Specifically, first, a feature extraction module is introduced to extract features with different levels of learning difficulties. Second, multistage combination classifiers are proposed to learn decision boundaries for easy and hard samples, respectively, with the latter penalizing the loss value of the hard samples and finally improving the prediction performance of hard samples. Third, based on the Dirichlet distribution and information entropy measurement, a sample difficulty discrimination module is designed to assign samples with different learning difficulty levels to the aforementioned classifiers. The experimental results on the publicly available benchmark CB513 dataset show that our method outperforms most state-of-the-art models. [ABSTRACT FROM AUTHOR]

Annual grain crops dominate agricultural landscapes and provide the majority of calories consumed by humanity. Perennial grain crops could potentially ameliorate the land degradation and off-site impacts associated with annual grain cropping. However, herbaceous perennial plants with constitutively high allocation to harvestable seeds are rare to absent in nature. Recent trade-off theory models suggest that rugged fitness landscapes may explain the absence of this form better than sink competition models. Artificial selection for both grain production and multiyear lifespan can lead to more rapid progress in the face of fitness and genetic trade-offs than natural selection but is likely to result in plant types that differ substantially from all current domestic crops. Perennial grain domestication is also likely to require the development of selection strategies that differ from published crop breeding methods, despite their success in improving long-domesticated crops; for this purpose, we have reviewed literature in the areas of population and evolutionary genetics, domestication, and molecular biology. Rapid domestication will likely require genes with large effect that are expected to exhibit strong pleiotropy and epistasis. Cryptic genetic variation will need to be deliberately exposed both to purge mildly deleterious alleles and to generate novel agronomic phenotypes. We predict that perennial grain domestication programs will benefit from population subdivision followed by selection for simple traits in each subpopulation, the evaluation of very large populations, high selection intensity, rapid cycling through generations, and heterosis. The latter may be particularly beneficial in the development of varieties with stable yield and tolerance to crowding. [ABSTRACT FROM AUTHOR]

To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11–16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B) in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary. [ABSTRACT FROM AUTHOR]

Where do the bottlenecks for information and attention lie when our visual system processes incoming stimuli? The human visual system encodes the incoming stimulus and transfers its contents into three major memory systems with increasing time scales, viz., sensory (or iconic) memory, visual short-term memory (VSTM), and long-term memory (LTM). It is commonly believed that the major bottleneck of information processing resides in VSTM. In contrast to this view, we show major bottlenecks for motion processing prior to VSTM. In the first experiment, we examined bottlenecks at the stimulus encoding stage through a partial-report technique by delivering the cue immediately at the end of the stimulus presentation. In the second experiment, we varied the cue delay to investigate sensory memory and VSTM. Performance decayed exponentially as a function of cue delay and we used the time-constant of the exponential-decay to demarcate sensory memory from VSTM. We then decomposed performance in terms of quality and quantity measures to analyze bottlenecks along these dimensions. In terms of the quality of information, two thirds to three quarters of the motion-processing bottleneck occurs in stimulus encoding rather than memory stages. In terms of the quantity of information, the motion-processing bottleneck is distributed, with the stimulus-encoding stage accounting for one third of the bottleneck. The bottleneck for the stimulus-encoding stage is dominated by the selection compared to the filtering function of attention. We also found that the filtering function of attention is operating mainly at the sensory memory stage in a specific manner, i.e., influencing only quantity and sparing quality. These results provide a novel and more complete understanding of information processing and storage bottlenecks for motion processing. [ABSTRACT FROM AUTHOR]

Background: The origin of extraordinarily rich biodiversity in tropical forests is often attributed to evolution under stable climatic conditions over a long period or to climatic fluctuations during the recent Quaternary period. Here, we test these two hypotheses using Dracaena cambodiana, a plant species distributed in paleotropical forests. Methods: We analyzed nucleotide sequence data of two chloroplast DNA (cpDNA: atpB-rbcL and trnD-trnT) regions and genotype data of six nuclear microsatellites from 15 populations (140 and 363 individuals, respectively) distributed in Indochina Peninsular and Hainan Island to infer the patterns of genetic diversity and phylogeographic structure. The population bottleneck and genetic drift were estimated based upon nuclear microsatellites data using the software programs BOTTLENECK and 2MOD. The lineage divergence times and past population dynamics based on cpDNA data were estimated using coalescent-based isolation-with-migration (IMa) and BEAST software programs. Results: A significant phylogeographic structure (NST = 0.876, GST = 0.796, FST-SSR = 0.329, RST = 0.449; NST>GST, RST>FST-SSR, P<0.05) and genetic differentiation among populations were detected. Bottleneck analyses and Bayesian skyline plot suggested recent population reduction. The cpDNA haplotype network revealed the ancestral populations from the southern Indochina region expanded to northward. The most recent ancestor divergence time of D. cambodiana dated back to the Tertiary era and rapid diversification of terminal lineages corresponded to the Quaternary period. Conclusions: The results indicated that the present distribution of genetic diversity in D. cambodiana was an outcome of Tertiary dispersal and rapid divergence during the Quaternary period under limited gene flow influenced by the uplift of Himalayan-Tibetan Plateau and Quaternary climatic fluctuations respectively. Evolutionary processes, such as extinction-recolonization during the Pleistocene may have contributed to the fast diversification in D. cambodiana. [ABSTRACT FROM AUTHOR]

Background: Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin. Results: According to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: 'Irano-Caucasian', 'North Mediterranean Basin' and 'South Mediterranean Basin'. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the 'Irano-Caucasian' gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the 'North Mediterranean Basin' and 'South Mediterranean Basin' to the secondary centre of diversification. Conclusions: A marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the 'Irano-Caucasian' gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits. [ABSTRACT FROM AUTHOR]

Global change biology has been entering a big data era due to the vast increase in availability of both environmental and biological data. Big data refers to large data volume, complex data sets, and multiple data sources. The recent use of such big data is improving our understanding of interactions between biological systems and global environmental changes. In this review, we first explore how big data has been analyzed to identify the general patterns of biological responses to global changes at scales from gene to ecosystem. After that, we investigate how observational networks and space‐based big data have facilitated the discovery of emergent mechanisms and phenomena on the regional and global scales. Then, we evaluate the predictions of terrestrial biosphere under global changes by big modeling data. Finally, we introduce some methods to extract knowledge from big data, such as meta‐analysis, machine learning, traceability analysis, and data assimilation. The big data has opened new research opportunities, especially for developing new data‐driven theories for improving biological predictions in Earth system models, tracing global change impacts across different organismic levels, and constructing cyberinfrastructure tools to accelerate the pace of model‐data integrations. These efforts will uncork the bottleneck of using big data to understand biological responses and adaptations to future global changes. [ABSTRACT FROM AUTHOR]

Spiroplasmas are cell-wall-deficient helical bacteria belonging to the class Mollicutes. Their ability to maintain a helical shape in the absence of cell wall and their motility in the absence of external appendages have attracted attention from the scientific community for a long time. In this review we compare and contrast motility, shape determination and cytokinesis mechanisms of Spiroplasma with those of other Mollicutes and cell-walled bacteria. The current models for rod-shape determination and cytokinesis in cell-walled bacteria propose a prominent role for the cell wall synthesis machinery. These models also involve the cooperation of the actin-like protein MreB and FtsZ, the bacterial homolog of tubulin. However the exact role of the cytoskeletal proteins is still under much debate. Spiroplasma possess MreBs, exhibit a rod-shape dependent helical morphology, and divide by an FtsZ-dependent mechanism. Hence, spiroplasmas represent model organisms for deciphering the roles of MreBs and FtsZ in fundamental mechanisms of non-spherical shape determination and cytokinesis in bacteria, in the absence of a cell wall. Identification of components implicated in these processes and deciphering their functions would require genetic experiments. Challenges in genetic manipulations in spiroplasmas are a major bottleneck in understanding their biology. We discuss advancements in genome sequencing, gene editing technologies, super-resolution microscopy and electron cryomicroscopy and tomography, which can be employed for addressing long-standing questions related to Spiroplasma biology. [ABSTRACT FROM AUTHOR]

Modern biology produces data at a staggering rate. Yet, much of these biological data is still isolated in the text, figures, tables and supplementary materials of articles. As a result, biological information created at great expense is significantly underutilised. The protein motif biology field does not have sufficient resources to curate the corpus of motif-related literature and, to date, only a fraction of the available articles have been curated. In this study, we develop a set of tools and a web resource, 'articles.ELM', to rapidly identify the motif literature articles pertinent to a researcher's interest. At the core of the resource is a manually curated set of about 8000 motif-related articles. These articles are automatically annotated with a range of relevant biological data allowing in-depth search functionality. Machine-learning article classification is used to group articles based on their similarity to manually curated motif classes in the Eukaryotic Linear Motif resource. Articles can also be manually classified within the resource. The 'articles.ELM' resource permits the rapid and accurate discovery of relevant motif articles thereby improving the visibility of motif literature and simplifying the recovery of valuable biological insights sequestered within scientific articles. Consequently, this web resource removes a critical bottleneck in scientific productivity for the motif biology field. Database URL: http://slim.icr.ac.uk/articles/ [ABSTRACT FROM AUTHOR]

The phylogeography of the bark beetle Ips typographus was assessed using five microsatellite markers. Twenty-eight populations were sampled throughout Europe on the host tree Picea abies. I. typographus showed very low levels of genetic diversity, and the study revealed a lack of genetic structure across Europe. No significant barrier to gene flow was found, even though P. abies has a fragmented distribution. A weak but significant effect of isolation by distance was found. These results suggest a high dispersal capacity of I. typographus, which leads to low genetic differentiation between populations. Its high dispersal capacity is likely to have prevented I. typographus from developing important local adaptations to its host, which would have influenced its genetic structure. The nuclear data was compared to previously published mitochondrial data that showed strong differentiation between Central–Northern European populations and Russian–Baltic populations, and a founder effect in Scandinavia, probably reflecting the postglacial history of I. typographus. Discrepancies between nuclear and mitochondrial markers could be due to the maternal inheritance of mitochondrial DNA, and to sex-biased dispersal in I. typographus. The overall low genetic diversity observed on both markers on a large geographical scale is discussed. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 90, 239–246. [ABSTRACT FROM AUTHOR]

Aerobiology is a branch of biology that studies microorganisms passively transferred by the air. Bacteria, viruses, fungal spores, tiny insects, and pollen grains are samples of microorganisms. Pollen grains classification is essential in medicine, agronomy, economy, etc. It is performed traditionally (manually) and automatically. The automated approach is faster, more accurate, cost-effective, and with less human intervention than the manual method. In this paper, we introduce a Residual Cognitive Attention Network (RCANet) for the automated classification of pollen grains microscopic images. The suggested attention block, Ventral-Dorsal Ateetntion Block (VDAB), is designed based on the ventral (temporal) and dorsal (parietal) pathways of the occipital lobe. It is embedded in each Basic Block of the architecture of ResNet18. The VDAB is composed of ventral and dorsal attention blocks. The ventral and dorsal streams detect the structure and location of the pollen grain, respectively. According to the mentioned pathways, the Ventral Attention Block (VAB) extracts the channels related to the shape of the pollen grain, and the Dorsal Attention Block (DAB) is focused on its position. Three publicly pollen grains datasets including the Cretan Pollen Dataset (CPD), Pollen13K, and Pollen23E are employed for experiments. The ResNet18 and the proposed method (RCANet) are trained on the datasets and the proposed RCANet obtained higher performance metrics than the ResNet18 in the test step. It achieved weighted F1-score values of 98.69%, 97.83%, and 98.24% with CPD, Pollen13K, and Pollen23E datasets, respectively. [ABSTRACT FROM AUTHOR]

The hallmarks of aging have been influential in guiding the biology of aging research, with more recent and growing recognition of the interdependence of these hallmarks on age‐related health outcomes. However, a current challenge is personalizing aging trajectories to promote healthy aging, given the diversity of genotypes and lived experience. We suggest that incorporating heterogeneity—including intrinsic (e.g., genetic and structural) and extrinsic (e.g., environmental and exposome) factors and their interdependence of hallmarks—may move the dial. This editorial perspective will focus on one hallmark, namely mitochondrial dysfunction, to exemplify how consideration of heterogeneity and interdependence or crosstalk may reveal new perspectives and opportunities for personalizing aging research. To this end, we highlight heterogeneity within mitochondria as a model. [ABSTRACT FROM AUTHOR]

In recent years, the fields of evolutionary biomechanics and morphology have developed into a deeply quantitative and integrative science, resulting in a much richer understanding of how structural relationships shape macroevolutionary patterns. This issue highlights new research at the conceptual and experimental cutting edge, with a special focus on applying big data approaches to classic questions in form–function evolution. As this issue illustrates, new technologies and analytical tools are facilitating the integration of biomechanics, functional morphology, and phylogenetic comparative methods to catalyze a new, more integrative discipline. Although we are at the cusp of the big data generation of organismal biology, the field is nonetheless still data-limited. This data bottleneck is primarily due to the rate-limiting steps of digitizing specimens, recording and tracking organismal movements, and extracting patterns from massive datasets. Automation and machine-learning approaches hold great promise to help data generation keep pace with ideas. As a final and important note, almost all the research presented in this issue relied on specimens—totaling the tens of thousands—provided by museum collections. Without collection, curation, and conservation of museum specimens, the future of the field is much less bright. [ABSTRACT FROM AUTHOR]

How and under what situations populations adapt to local conditions remains a key question in evolutionary biology. This study tests if the particular morphology of a population of Tree lizards, Urosaurus ornatus, located in a canyon on the margin of the species range represents an adaptation to canyon habitat. Morphology was compared across 40 populations showing that relative hind limb length, tail length, and mass were all outliers for this population. The function of the relatively longer hind limbs, tail, and lower mass was proposed to be for better sprinting ability on the sheer canyon walls that provide the only available habitat structure for this population. Partial least squares regression found significant effects of tail length on top speed on a broad, steep surface. Partial least squares logistic regression identified significant effects of tail length on survival as well in males but not females of this population. Another canyon population of Tree lizards with access to alternative substrates (trees) showed no evidence of selection on the same morphological features. Ancestral state reconstruction using a phylogeny inferred for 21 populations found that the unique morphology of the focal population was evolutionarily derived compared to closely related populations and so likely arose under the present environmental conditions. Population genetic structure also supported the process of adaptive divergence as there was no evidence for migration and/or a recent genetic bottleneck in the focal population. Lizards in this population appear to have responded to selection allowing them to become specialists for running on canyon walls while other canyon populations with access to a greater variety of habitat structure have not. [ABSTRACT FROM AUTHOR]

The Antarctic-South American bank-forming moss Chorisodontium aciphyllum is known for having the oldest sub-fossils of any extant plant in Antarctica as well as extreme survival abilities, making it a candidate species for possible long-term survival in Antarctica. Applying phylogeographic and population genetic methods using the plastid markers trnL-F and rps4 and the nuclear internal transcribed spacer, we investigated the genetic diversity within C. aciphyllum throughout its range. Low genetic variation was found in all loci, both between and within Antarctic and southern South American populations, suggesting a relatively recent (likely within the last million years) colonization of this moss to the Antarctic, as well as a likely severe bottleneck during Pleistocene glaciations in southern South America. We also performed a simple atmospheric transfer modeling approach to study potential colonization rates of small (microscopic/microbial) or spore-dispersed organisms (such as many mosses and lichens). These suggested that the northern Antarctic Peninsula shows potentially regular connectivity from southern South America, with air masses transferring, particularly southbound, between the two regions. We found elevated genetic variation of C. aciphyllum in Elephant Island, also the location of the oldest known moss banks (> 5500 years), suggesting this location to be a genetic hotspot for this species in the Antarctic. [ABSTRACT FROM AUTHOR]

Immunohistochemistry is a crucial method for detecting specific proteins within tissue samples, yet constrained to one biomarker per tissue section. Multiplexed immunofluorescence, while allowing simultaneous visualization of multiple proteins, faces limitations in the number of simultaneous fluorescent labels due to spectral overlap. Although cyclic immunofluorescence techniques have successfully broadened antibody staining capacities in a single tissue sample, they are plagued by time-consuming and labor-intensive procedures, sample degradation risks, and inability to scale beyond thin sections. In this study, we introduce the use of 3D confocal Fluorescence Lifetime Imaging Microscopy as a high-throughput, multiplexed immunofluorescence platform that can differentiate 11 or more biomarkers in 3D tissue volumes. Leveraging both spectral and lifetime information, this approach allows for practical spatial biology in thin sections that can readily scale to larger volumes of tissue. We believe that this highly multiplexed and versatile biomarker imaging platform will significantly expedite cancer research and enable new translational approaches in the future. Confocal Fluorescence Lifetime Imaging Microscopy is introduced for highly multiplexed immunofluorescence, enabling the differentiation of 11+ biomarkers in 3D tissue, a technique with potential for interpreting the spatial heterogeneity of thick tumor samples. [ABSTRACT FROM AUTHOR]

The use of neutron methods in environmental and biological sciences is rapidly emerging and accelerating with the development of new instruments at neutron user facilities. This article, based on a workshop held at Oak Ridge National Laboratory (ORNL), offers insights into the application of neutron techniques in environmental and biological sciences. We highlight recent advances and identify key challenges and potential future research areas. These include soil and rhizosphere processes, root water dynamics, plant-microbe interactions, structure and dynamics of biological systems, applications in synthetic biology and enzyme engineering, next-generation bioproducts, biomaterials and bioenergy, nanoscale structure, and fluid dynamics of porous materials in geochemistry. We provide an outlook on emerging opportunities with an emphasis on new capabilities that will be enabled at the Spallation Neutron Source Second Target Station currently under design at ORNL. The mission of scientific neutron user facilities worldwide is to enable science using state-of-the-art neutron capabilities. We aim to encourage researchers in the environmental and biological research community to explore the unique capability afforded by neutrons at these facilities. [ABSTRACT FROM AUTHOR]

There is a growing interest in empirically exploring the biological underpinnings of political attitudes and behavior. Heritability studies are a primary vehicle for conducting such investigations and data sets rich in political phenotypes are becoming broadly accessible. A bottleneck exists, however, in exploiting these opportunities because they involve a statistical re-tooling for political scientists and require a conceptual shift that has substantial implications for the field's traditional theoretical models. Methodologically, most twin studies rely on structural equation models unfamiliar to political scientists. We show this methodological bottleneck is easily navigable; it is the lesser discussed shift in theoretical assumptions poses the larger problem to integrating biological elements into the study of political attitudes and behavior. To address these issues we provide a detailed introduction to a regression-based method for analyzing genetic influence on political attitudes and behaviors that will be methodologically intuitive to political scientists with even minimum quantitative training. In doing so, we provide a platform for bridging important conceptual divides between political science and behavioral genetics. [ABSTRACT FROM AUTHOR]

This study elucidates the genomic basis of the evolution of pathogens alongside free-living organisms within the family Alcaligenaceae of Betaproteobacteria. Towards that end, the complete genome sequence of the sulfur-chemolithoautotroph Tetrathiobacter kashmirensis WT001T was determined and compared with the soil isolate Achromobacter xylosoxidans A8 and the two pathogens Bordetella bronchiseptica RB50 and Taylorella equigenitalis MCE9. All analyses comprehensively indicated that the RB50 and MCE9 genomes were almost the subsets of A8 and WT001T, respectively. In the immediate evolutionary past Achromobacter and Bordetella shared a common ancestor, which was distinct from the other contemporary stock that gave rise to Tetrathiobacter and Taylorella. The Achromobacter-Bordetella precursor, after diverging from the family ancestor, evolved through extensive genome inflation, subsequent to which the two genera separated via differential gene losses and acquisitions. Tetrathiobacter, meanwhile, retained the core characteristics of the family ancestor, and Taylorella underwent massive genome degeneration to reach an evolutionary dead-end. Interestingly, the WT001T genome, despite its conserved architecture, had only 85% coding density, besides which 578 out of its 4452 protein-coding sequences were found to be pseudogenized. Translational impairment of several DNA repair-recombination genes in the first place seemed to have ushered the rampant and indiscriminate frame-shift mutations across the WT001T genome. Presumably, this strain has just come out of a recent evolutionary bottleneck, representing a unique transition state where genome self-degeneration has started comprehensively but selective host-confinement has not yet set in. In the light of this evolutionary link, host-adaptation of Taylorella clearly appears to be the aftereffect of genome implosion in another member of the same bottleneck. Remarkably again, potent virulence factors were found widespread in Alcaligenaceae, corroborating which hemolytic and mammalian cell-adhering abilities were discovered in WT001T. So, while WT001T relatives/derivatives in nature could be going the Taylorella way, the lineage as such was well-prepared for imminent host-confinement. [ABSTRACT FROM AUTHOR]

Relatively few studies have extensively analysed the genetic diversity of the runner bean through molecular markers. Here, we used six chloroplast microsatellites (cpSSRs) to investigate the cytoplasmic diversity of 331 European domesticated accessions of the scarlet runner bean (Phaseolus coccineus L.), including the botanical varieties albiflorus, bicolor and coccineus, and a sample of 49 domesticated and wild accessions from Mesoamerica. We further explored the pattern of diversity of the European landraces using 12 phenotypic traits on 262 individuals. For 158 European accessions, we studied the relationships between cpSSR polymorphisms and phenotypic traits. Additionally, to gain insights into the role of gene flow and migration, for a subset of 115 accessions, we compared and contrasted the results obtained by cpSSRs and phenotypic traits with those obtained in a previous study with 12 nuclear microsatellites (nuSSRs). Our results suggest that both demographic and selective factors have roles in the shaping of the population genetic structure of the European runner bean. In particular, we infer the existence of a moderate-to-strong cytoplasmic bottleneck that followed the expansion of the crop into Europe, and we deduce multiple domestication events for this species. We also observe an adaptive population differentiation in the phenology across a latitudinal gradient, which suggests that selection led to the diversification of the runner bean in Europe. The botanical varieties albiflorus, bicolor and coccineus, which are based solely on flower colour, cannot be distinguished based on these cpSSRs and nuSSRs, nor according to the 12 quantitative traits. [ABSTRACT FROM AUTHOR]

Landscape genetic approaches offer the promise of increasing our understanding of the influence of habitat features on genetic structure. We assessed the genetic diversity of the endangered golden-cheeked warbler ( Dendroica chrysoparia) across their breeding range in central Texas and evaluated the role of habitat loss and fragmentation in shaping the population structure of the species. We determined genotypes across nine microsatellite loci of 109 individuals from seven sites representing the major breeding concentrations of the species. No evidence of a recent population bottleneck was found. Differences in allele frequencies were highly significant among sites. The sampled sites do not appear to represent isolated lineages requiring protection as separate management units, although the amount of current gene flow is insufficient to prevent genetic differentiation. Measures of genetic differentiation were negatively associated with habitat connectivity and the percentage of forest cover between sites, and positively associated with geographic distance and the percentage of agricultural land between sites. The northernmost site was the most genetically differentiated and was isolated from other sites by agricultural lands. Fragmentation of breeding habitat may represent barriers to dispersal of birds which would pose no barrier to movement during other activities such as migration. [ABSTRACT FROM AUTHOR]

We apply new analytical methods to understand the consequences of population bottlenecks for expected additive genetic variance. We analyze essentially all models for multilocus epistasis that have been numerically simulated to demonstrate increased additive variance. We conclude that for biologically plausible models, large increases in expected additive variance--attributable to epistasis rather than dominance--are unlikely. Naciri-Graven and Goudet (2003) found that as the number of epistatically interacting loci increases, additive variance tends to be inflated more after a bottleneck. We argue that this result reflects biologically unrealistic aspects of their models. Specifically, as the number of loci increases, higher-order epistatic interactions become increasingly important in these models, with an increasing fraction of the genetic variance becoming nonadditive, contrary to empirical observations. As shown by Barton and Turelli (2004), without dominance, conversion of nonadditive to additive variance depends only on the variance components and not on the number of loci per se. Numerical results indicating that more inbreeding is needed to produce maximal release of additive variance with more loci follow directly from our analytical results. which show that high levels of inbreeding (F > 0.5) are needed for significant conversion of higher-order components. We discuss alternative approaches to modeling multilocus epistasis and understanding its consequences. [ABSTRACT FROM AUTHOR]

Wallacean island populations of two Vespertilioninae bats,Myotis muricolaandScotophilus kuhlii, which have similar geographical ranges, showed marked contrast in the amount and pattern of genetic variation. Within islands, genetic variation was on average much higher inM. muricolabut declined from west to east, whereas all populations ofS. kuhliihad uniformly low levels of genetic variation by mammalian standards.S. kuhliishowed little genetic differentiation between islands and estimates of gene flow were substantial whereas island populations ofM. muricoladiffered markedly and there was a strong isolation-by-distance effect associated with the extent of the sea crossing between islands. Furthermore, the lower mean heterozygosity and small genetic distances between eastern island populations ofM. muricolais evidence that there has been a bottleneck associated with the colonization of this area. The attenuation of genetic diversity to the east is also seen in some other mammalian species and may indicate limits to dispersal and have implications for species management. The patterns of variability inS. kuhliimay be a consequence of its strong dispersal capacity and close association with human activity, which, together with other factors, suggest a panmictic population. © 2004 The Linnean Society of London,Biological Journal of the Linnean Society, 2004,83, 421–431. [ABSTRACT FROM AUTHOR]

Evolutionary biology was previously considered a historical science with predictions about evolutionary trajectories believed to be near impossible. The development of high throughput sequencing and data analysis technologies has challenged this belief, and provided an abundance of data that yields novel insights into evolutionary processes. Evolutionary predictions are now increasingly being used to develop fundamental knowledge of evolving systems and/or to demonstrate evolutionary control. Here we investigate the factors that make evolutionary repeatability more or less likely to increase the accuracy of evolutionary predictions. We identify outstanding questions and provide a potential starting point to determine how evolutionary repeatability is affected by genetic relatedness. [ABSTRACT FROM AUTHOR]

Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but analyses of the resulting millions of short sequences remain a major bottleneck for these approaches. Here, we introduce the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 small subunit rDNA (SSU-rDNA) sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories. Results: Our broadly applicable protocol quantified the progress in the description of genetic diversity of ciliates by environmental SSU-rDNA surveys, detected a fundamental historical bias in the tendency to recover already known groups in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but are structured by habitat and geographical location at intermediate geographical scale, as observed for bacteria, plants, and animals. Conclusions: Currently available 'universal' primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought. Network analyses such as presented in this study offer a promising way to guide the design of novel primers and to further explore this vast and structured microbial diversity. [ABSTRACT FROM AUTHOR]

Shape is data and data is shape. Biologists are accustomed to thinking about how the shape of biomolecules, cells, tissues, and organisms arise from the effects of genetics, development, and the environment. Less often do we consider that data itself has shape and structure, or that it is possible to measure the shape of data and analyze it. Here, we review applications of topological data analysis (TDA) to biology in a way accessible to biologists and applied mathematicians alike. TDA uses principles from algebraic topology to comprehensively measure shape in data sets. Using a function that relates the similarity of data points to each other, we can monitor the evolution of topological features—connected components, loops, and voids. This evolution, a topological signature, concisely summarizes large, complex data sets. We first provide a TDA primer for biologists before exploring the use of TDA across biological sub‐disciplines, spanning structural biology, molecular biology, evolution, and development. We end by comparing and contrasting different TDA approaches and the potential for their use in biology. The vision of TDA, that data are shape and shape is data, will be relevant as biology transitions into a data‐driven era where the meaningful interpretation of large data sets is a limiting factor. [ABSTRACT FROM AUTHOR]