Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo,Evo-Eco and Evolutionary Transitions

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term “evolutionary connectionism” to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions.     

Real‐time monitoring of greenhouse gas emissions with tall chambers reveals diurnal N2O variation and increased emissions of CO2 and N2O from Miscanthus following compost addition

Miscanthus x giganteus's efficacy as an energy crop relies on maintaining low greenhouse gas (GHG) emissions. As demand for Miscanthus is expected to rise to meet bioenergy targets, fertilizers and composts may be employed to increase yields, but will also increase GHG emissions. Manipulation experiments are vital to investigate the consequences of any fertilizer additions, but there is currently no way to measure whole‐plant GHG fluxes from crops taller than 2.5 m, such as Miscanthus, at the experimental plot scale. We employed a unique combination of eddy covariance (EC), soil chambers and an entirely new automated chamber system, SkyBeam, to measure high frequency (ca. hourly) fluxes of carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) from a Miscanthus crop amended with green compost. Untreated controls were also monitored in a fully replicated experimental design. Net ecosystem exchange (NEE) of CO₂ was partitioned into soil respiration (R_s), gross primary productivity (GPP) and ecosystem respiration, and the crop was harvested to determine the effect of compost on crop productivity. Compost increased NEE emissions by 100% (p < .05), which was the result of a 20% increase of R_s (p < .06) and a 32% reduction in GPP (p < .05) and biomass of 37% (p < .06). Methane fluxes were small and unaffected by compost addition. N₂O emissions increased 34% under compost during an emission event; otherwise, fluxes were low and often negative, even under dry conditions. Diurnal variation in N₂O fluxes, with uptake during the day and emission at night was observed. These fluxes displayed a negative relationship with soil temperature and a hitherto undescribed diurnal temperature hysteresis. We conclude that compost addition negatively affected the productivity and environmental effects of Miscanthus cultivation during the first year following application.     

Soil & Water Assessment Tool (SWAT) simulated hydrological impacts of land use change from temperate grassland to energy crops: A case study in western UK

When considering the large‐scale deployment of bioenergy crops, it is important to understand the implication for ecosystem hydrological processes and the influences of crop type and location. Based on the potential for future land use change (LUC), the 10,280 km² West Wales Water Framework Directive River Basin District (UK) was selected as a typical grassland dominated district, and the Soil & Water Assessment Tool (SWAT) hydrology model with a geographic information systems interface was used to investigate implications for different bioenergy deployment scenarios. The study area was delineated into 855 sub‐basins and 7,108 hydrological response units based on rivers, soil type, land use, and slope. Changes in hydrological components for two bioenergy crops (Miscanthus and short rotation coppice, SRC) planted on 50% (2,192 km²) or 25% (1,096 km²) of existing improved pasture are quantified. Across the study area as a whole, only surface run‐off with SRC planted at the 50% level was significantly impacted, where it was reduced by up to 23% (during April). However, results varied spatially and a comparison of annual means for each sub‐basin and scenario revealed surface run‐off was significantly decreased and baseflow significantly increased (by a maximum of 40%) with both Miscanthus and SRC. Evapotranspiration was significantly increased with SRC (at both planting levels) and water yield was significantly reduced with SRC (at the 50% level) by up to 5%. Effects on streamflow were limited, varying between ?5% and +5% change (compared to baseline) in the majority of sub‐basins. The results suggest that for mesic temperate grasslands, adverse effects from the drying of soil and alterations to streamflow may not arise, and with surface run‐off reduced and baseflow increased, there could, depending on crop location, be potential benefits for flood and erosion mitigation.     

The adaptive potential of plant populations in response to extreme climate events

The frequency and magnitude of extreme climate events are increasing with global change, yet we lack predictions and empirical evidence for the ability of wild populations to persist and adapt in response to these events. Here, we used Fisher's Fundamental Theorem of Natural Selection to evaluate the adaptive potential of Lasthenia fremontii, a herbaceous winter annual that is endemic to seasonally flooded wetlands in California, to alternative flooding regimes that occur during El Niño Southern Oscillation (ENSO) events. The results indicate that populations may exhibit greater adaptive potential in response to dry years than wet years, and that the relative performance of populations will change across climate scenarios. More generally, our findings show that extreme climate events can substantially change the potential for populations to adapt to climate change by modulating the expression of standing genetic variation and mean fitness.     

Genetic and Epigenetic Variation across Genes Involved in Energy Metabolism and Mitochondria of Chinese Hamster Ovary Cell Lines

The increasingdemandfor biopharmaceutical products drives the search for efficient cell factories that are able to sustainably support rapid growth, high productivity, and product quality. As these depend on energy generation, here the genomic variation in nuclear genes associated with mitochondria and energy metabolism and the mitochondrial genome of 14 cell lines is investigated. The variants called enable reliable tracing of lineages. Unique sequence variations are observed in cell lines adapted to grow in protein‐free media, enriched in signaling pathways or mitogen‐activated protein kinase 3. High‐producing cell lines bear unique mutations in nicotinamide adenine dinucleotide (NADH) dehydrogenase (ND2 and ND4) and in peroxisomal acyl‐CoA synthetase (ACSL4), involved in lipid metabolism. As phenotypes are determined not only by functional mutations, but also by the exquisite regulation of expression patterns, it is not surprising that ≈50% of the genes investigated here are found to be differentially methylated and thus epigenetically controlled, enabling a clear distinction of high producers, and cells adapted to a minimal, glutamine (Gln)‐free medium. Similar pathways are enriched as those identified by genome variation. This strengthens the hypothesis that these phenomena act together to define cell behavior.     

Improvements in single-use bioreactor film material composition leads to robust and reliable Chinese hamster ovary cell performance

Single-use technologies, in particular disposable bioreactor bags, have become integral within the biopharmaceutical community. However, safety concerns arose upon the identification of toxic leachable compounds derived from the plastic materials. Although the leachable bis(2,4-di-tert-butylphenyl)-phosphate (bDtBPP) has been previously shown to inhibit CHO cell growth, it is critical to determine if other compounds like this are still present in subsequent generations of films for industrial application. This study compares the performance of CHO cells, CHO-K1, and CHO-DP12, cultured in media conditioned in an older single-use bioreactor (SUB) film (F-1) and a newer generation film (F-2) from the same vendor. CHO cells cultured in media conditioned for 7 days in the F-1 film demonstrated significantly reduced growth and antibody productivity profiles when compared to controls and media conditioned for the same time period in the newer F-2 film. Proteomic profiling of CHO cells cultured in the F-1 conditioned media identified differentially expressed proteins involved in oxidative stress response as well as compromised ATP synthesis. These potentially metabolically compromised cells exhibited reduced oxidative phosphorylation activity as well as lower glycolytic metabolism, characteristic of slower growing cells. Nonvolatile and metal leachables analysis of film extracts by LC–MS revealed a reduction in the abundance of the analyzed leachates from F-2 films when compared to F-1 films including bDtBPP, potentially explaining improved CHO cell growth in F-2 conditioned media. Furthermore, in vitro endocrine disruptor testing of the known leachable revealed this molecule to possess the potential to act as an androgen antagonist. This study demonstrates an improvement in the materials composition used in modern generations of SUBs for safe application in the bioprocess.     

Estimating abdominal adipose tissue with DXA and anthropometry

Objective: To identify an anatomically defined region of interest (ROI) from DXA assessment of body composition that when combined with anthropometry can be used to accurately predict intra‐abdominal adipose tissue (IAAT) in overweight/obese individuals. Research Methods and Procedures: Forty‐one postmenopausal women (age, 49 to 66 years; BMI, 26 to 37 kg/m²) underwent anthropometric and body composition assessments. ROI were defined as quadrilateral boxes extending 5 or 10 cm above the iliac crest and laterally to the edges of the abdominal soft tissue. A single‐slice computed tomography (CT) scan was measured at the L3 to L4 intervertebral space, and abdominal skinfolds were taken. Results: Forward step‐wise regression revealed the best predictor model of IAAT area measured by CT (r² = 0.68, standard error of estimate = 17%) to be: IAAT area (centimeters squared) = 51.844 + DXA 10‐cm ROI (grams) (0.031) + abdominal skinfold (millimeters) (1.342). Interobserver reliability for fat mass (r = 0.994; coefficient of variation, 2.60%) and lean mass (r = 0.986, coefficient of variation, 2.67%) in the DXA 10‐cm ROI was excellent. Discussion: This study has identified a DXA ROI that can be reliably measured using prominent anatomical landmarks, in this case, the iliac crest. Using this ROI, combined with an abdominal skinfold measurement, we have derived an equation to predict IAAT in overweight/obese postmenopausal women. This approach offers a simpler, safer, and more cost‐effective method than CT for assessing the efficacy of lifestyle interventions aimed at reducing IAAT. However, this warrants further investigation and validation with an independent cohort.     

Transcriptomic analysis of IgG4 Fc-fusion protein degradation in a panel of clonally-derived CHO cell lines using RNASeq

In this study, we report an investigation of a panel of clonally-derived Chinese hamster ovary (CHO) cell lines exhibiting variability in the proportion of full-length IgG4 Fc-fusion protein produced. The recombinant protein was found to be degraded during cell culture into four shorter “clipped” species (three of the four cleavage sites occurred at arginine residues) and preliminary analyses suggested that a host cell enzyme was responsible for proteolysis. To identify the specific enzyme responsible, RNA sequencing was used to identify gene expression differences between the cell lines with a “high” and “low” clipping phenotype. From this analysis, six protease-encoding genes were found to be significantly upregulated in those cell lines yielding the lowest proportion of full-length IgG4 Fc-fusion protein. Four of these protease candidates were deprioritized after examination of their cleavage site specificity. The remaining enzymes, Adam19 and Furin, were found to be capable of cleavage at arginine residues, and inhibitors for both proteases were added to cell-free media to determine if the product degradation could be reduced. While the Adam19 inhibitor had no impact, Furin inhibitor I (specific for the proprotein convertase family of enzymes) was found to result in a 33–39% increase in complete IgG4 Fc-fusion protein when compared with untreated samples.     

Breeding populations of Little Ringed Plover Charadrius dubius and Ringed Plover Charadrius hiaticula in the United Kingdom in 2007

Capsule: The 2007 national survey of the UK breeding population of Little Ringed Plovers shows a further spread into Scotland and Wales since the previous survey in 1984. In contrast, there has been a significant decrease in the Ringed Plover breeding population.

Aims: To provide new breeding population estimates in the UK and Great Britain for Little Ringed Plover Charadrius dubius and Ringed Plover Charadrius hiaticula in 2007 and investigate changes in breeding distribution and habitat use since 1984.

Methods: Breeding population estimates were made by combining counts of pairs from ‘key sites’ (2?×?2?km tetrads known to be occupied in/since 1984) and estimates of the numbers of pairs away from these sites based on stratified sampling. Survey periods for Little Ringed Plover: 15 April to 15 July, three visits; Ringed Plover: 15 April to 30 June, two visits.

Results: Population estimates, for 2007, of 1239 (95% confidence intervals: 1175–1311) pairs of Little Ringed Plover and 5291 (5106–5478) pairs of Ringed Plovers were calculated for Great Britain, with 5438 (5257–5622) pairs of Ringed Plover estimated in the UK. Counts of Ringed Plover at inland and coastal sites, covered in both 1984 and 2007, decreased by 83% and 53%, respectively. The Little Ringed Plover population has expanded in range northward and westward since 1984. Main habitats used in 2007 by Little Ringed Plover were inland gravel and sand (25.9%) and river shingle (17.8%); and, for Ringed Plover, coastal shingle and sand (38.5% and 13.7%, respectively) and machair plus associated habitats (23.8%) in the Outer Hebrides.

Conclusions: Between 1984 and 2007, the Little Ringed Plover breeding population in the UK increased considerably, expanding northward and westward, with increased use of river shingle habitats. During the same period Ringed Plover breeding numbers in the UK declined considerably in both coast and inland habitats, likely to be due to human disturbance and habitat change, respectively.