Monotonicity of Fitness Landscapes and Mutation Rate Control

A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the performance of evolutionary algorithms. Much biological theory in this area is based on Ronald Fisher's work, who used Euclidean geometry to study the relation between mutation size and expected fitness of the offspring in infinite phenotypic spaces. Here we reconsider this theory based on the alternative geometry of discrete and finite spaces of DNA sequences. First, we consider the geometric case of fitness being isomorphic to distance from an optimum, and show how problems of optimal mutation rate control can be solved exactly or approximately depending on additional constraints of the problem. Then we consider the general case of fitness communicating only partial information about the distance. We define weak monotonicity of fitness landscapes and prove that this property holds in all landscapes that are continuous and open at the optimum. This theoretical result motivates our hypothesis that optimal mutation rate functions in such landscapes will increase when fitness decreases in some neighbourhood of an optimum, resembling the control functions derived in the geometric case. We test this hypothesis experimentally by analysing approximately optimal mutation rate control functions in 115 complete landscapes of binding scores between DNA sequences and transcription factors. Our findings support the hypothesis and find that the increase of mutation rate is more rapid in landscapes that are less monotonic (more rugged). We discuss the relevance of these findings to living organisms

Understanding cooperation through fitness interdependence

Some acts of human cooperation are not easily explained by traditional models of kinship or reciprocity. Fitness interdependence may provide a unifying conceptual framework, in which cooperation arises from the mutual dependence for survival or reproduction, as occurs among mates, risk-pooling partnerships and brothers-in-arms

Cross-cultural invariances in the architecture of shame

This set of experiments shows that in 15 traditional small-scale societies there is an extraordinarily close correspondence between (i) the intensity of shame felt if one exhibited specific acts or traits and (ii) the magnitude of devaluation expressed in response to those acts or traits by local audiences, and even foreign audiences. Three important and widely acknowledged sources of cultural variation between communities—}geographic proximity, linguistic similarity, and religious similarity{—}all failed to account for the strength of between-community correlations in the shame{–}devaluation link. This supplies a parallel line of evidence that shame is a universal system, part of our species{’} cooperative biology, rather than a product of cultural evolution.Human foragers are obligately group-living, and their high dependence on mutual aid is believed to have characterized our species{’} social evolution. It was therefore a central adaptive problem for our ancestors to avoid damaging the willingness of other group members to render them assistance. Cognitively, this requires a predictive map of the degree to which others would devalue the individual based on each of various possible acts. With such a map, an individual can avoid socially costly behaviors by anticipating how much audience devaluation a potential action (e.g., stealing) would cause and weigh this against the action{’}s direct payoff (e.g., acquiring). The shame system manifests all of the functional properties required to solve this adaptive problem, with the aversive intensity of shame encoding the social cost. Previous data from three Western(ized) societies indicated that the shame evoked when the individual anticipates committing various acts closely tracks the magnitude of devaluation expressed by audiences in response to those acts. Here we report data supporting the broader claim that shame is a basic part of human biology. We conducted an experiment among 899 participants in 15 small-scale communities scattered around the world. Despite widely varying languages, cultures, and subsistence modes, shame in each community closely tracked the devaluation of local audiences (mean r = +0.84). The fact that the same pattern is encountered in such mutually remote communities suggests that shame{’s match to audience devaluation is a design feature crafted by selection and not a product of cultural contact or convergent cultural evolution

Carbon dating cancer: defining the chronology of metastatic progression in colorectal cancer.

Background: Patients often ask oncologists how long a cancer has been present before causing symptoms or spreading to other organs. The evolutionary trajectory of cancers can be defined using phylogenetic approaches but lack of chronological references makes dating the exact onset of tumours very challenging. Patients and methods: Here, we describe the case of a colorectal cancer (CRC) patient presenting with synchronous lung metastasis and metachronous thyroid, chest wall and urinary tract metastases over the course of 5 years. The chest wall metastasis was caused by needle tract seeding, implying a known time of onset. Using whole genome sequencing data from primary and metastatic sites we inferred the complete chronology of the cancer by exploiting the time of needle tract seeding as an in vivo 'stopwatch'. This approach allowed us to follow the progression of the disease back in time, dating each ancestral node of the phylogenetic tree in the past history of the tumour. We used a Bayesian phylogenomic approach, which accounts for possible dynamic changes in mutational rate, to reconstruct the phylogenetic tree and effectively 'carbon date' the malignant progression. Results: The primary colon cancer emerged between 5 and 8 years before the clinical diagnosis. The primary tumour metastasized to the lung and the thyroid within a year from its onset. The thyroid lesion presented as a tumour-to-tumour deposit within a benign Hurthle adenoma. Despite rapid metastatic progression from the primary tumour, the patient showed an indolent disease course. Primary cancer and metastases were microsatellite stable and displayed low chromosomal instability. Neo-antigen analysis suggested minimal immunogenicity. Conclusion: Our data provide the first in vivo experimental evidence documenting the timing of metastatic progression in CRC and suggest that genomic instability might be more important than the metastatic potential of the primary cancer in dictating CRC fate

The role of citizen science in addressing grand challenges in food and agriculture research

The power of citizen science to contribute to both science and society is gaining increased recognition, particularly in physics and biology. Although there is a long history of public engagement in agriculture and food science, the term ‘citizen science’ has rarely been applied to these efforts. Similarly, in the emerging field of citizen science, most new citizen science projects do not focus on food or agriculture. Here, we convened thought leaders from a broad range of fields related to citizen science, agriculture, and food science to highlight key opportunities for bridging these overlapping yet disconnected communities/fields and identify ways to leverage their respective strengths. Specifically, we show that (i) citizen science projects are addressing many grand challenges facing our food systems, as outlined by the United States National Institute of Food and Agriculture, as well as broader Sustainable Development Goals set by the United Nations Development Programme, (ii) there exist emerging opportunities and unique challenges for citizen science in agriculture/food research, and (iii) the greatest opportunities for the development of citizen science projects in agriculture and food science will be gained by using the existing infrastructure and tools of Extension programmes and through the engagement of urban communities. Further, we argue there is no better time to foster greater collaboration between these fields given the trend of shrinking Extension programmes, the increasing need to apply innovative solutions to address rising demands on agricultural systems, and the exponential growth of the field of citizen science.This working group was partially funded from the NCSU Plant Sciences Initiative, College of Agriculture and Life Sciences ‘Big Ideas’ grant, National Science Foundation grant to R.R.D. (NSF no. 1319293), and a United States Department of Food and Agriculture-National Institute of Food and Agriculture grant to S.F.R., USDA-NIFA Post Doctoral Fellowships grant no. 2017-67012-26999.http://rspb.royalsocietypublishing.orghj2018Forestry and Agricultural Biotechnology Institute (FABI

Cooperation among cancer cells: applying game theory to cancer

Cell cooperation promotes many of the hallmarks of cancer via the secretion of diffusible factors that can affect cancer cells or stromal cells in the tumour microenvironment. This cooperation cannot be explained simply as the collective action of cells for the benefit of the tumour because non-cooperative subclones can constantly invade and free-ride on the diffusible factors produced by the cooperative cells. A full understanding of cooperation among the cells of a tumour requires methods and concepts from evolutionary game theory, which has been used successfully in other areas of biology to understand similar problems but has been underutilized in cancer research. Game theory can provide insights into the stability of cooperation among cells in a tumour and into the design of potentially evolution-proof therapies that disrupt this cooperation

Drivers of Cape Verde archipelagic endemism in keyhole limpets

Oceanic archipelagos are the ideal setting for investigating processes that shape species assemblages. Focusing on keyhole limpets, genera Fissurella and Diodora from Cape Verde Islands, we used an integrative approach combining molecular phylogenetics with ocean transport simulations to infer species distribution patterns and analyse connectivity. Dispersal simulations, using pelagic larval duration and ocean currents as proxies, showed a reduced level of connectivity despite short distances between some of the islands. It is suggested that dispersal and persistence driven by patterns of oceanic circulation favouring self-recruitment played a primary role in explaining contemporary species distributions. Mitochondrial and nuclear data revealed the existence of eight Cape Verde endemic lineages, seven within Fissurella, distributed across the archipelago, and one within Diodora restricted to Boavista. The estimated origins for endemic Fissurella and Diodora were 10.2 and 6.7 MY, respectively. Between 9.5 and 4.5 MY, an intense period of volcanism in Boavista might have affected Diodora, preventing its diversification. Having originated earlier, Fissurella might have had more opportunities to disperse to other islands and speciate before those events. Bayesian analyses showed increased diversification rates in Fissurella possibly promoted by low sea levels during Plio-Pleistocene, which further explain differences in species richness between both genera.FCT - Portuguese Science Foundation [SFRH/BPD/109685/2015, SFRH/BPD/111003/2015]; Norte Portugal Regional Operational Program (NORTE), under the PORTUGAL Partnership Agreement, through the European Regional Development Fund (ERDF) [MARINFO - NORTE-01-0145-FEDER-000031]info:eu-repo/semantics/publishedVersio

Variation in Cooperative Behaviour within a Single City

Human cooperative behaviour, as assayed by decisions in experimental economic dilemmas such as the Dictator Game, is variable across human populations. Within-population variation has been less well studied, especially within industrial societies. Moreover, little is known about the extent to which community-level variation in Dictator Game behaviour relates to community-level variation in real-world social behaviour. We chose two neighbourhoods of the city of Newcastle upon Tyne that were similar in most regards, but at opposite ends of the spectrum in terms of level of socioeconomic deprivation. We administered Dictator Games to randomly-selected residents, and also gathered a large number of more naturalistic measures of cooperativeness. There were dramatic differences in Dictator Game behaviour between the two neighbourhoods, with the mean allocation to the other player close to half the stake in the affluent neighbourhood, and close to one tenth of the stake in the deprived neighbourhood. Moreover, the deprived neighbourhood was also characterised by lower self-reported social capital, higher frequencies of crime and antisocial behaviour, a higher frequency of littering, and less willingness to take part in a survey or return a lost letter. On the other hand, there were no differences between the neighbourhoods in terms of the probability of helping a person who dropped an object, needed directions to a hospital, or needed to make change for a coin, and people on the streets were less likely to be alone in the deprived neighbourhood than the affluent one. We conclude that there can be dramatic local differences in cooperative behaviour within the same city, and that these need further theoretical explanation

LGR5 expression is regulated by EGF in early colorectal adenomas and governs EGFR inhibitor sensitivity.

BACKGROUND LGR5 serves as a co-receptor for Wnt/β-catenin signalling and marks normal intestinal stem cells; however, its role in colorectal cancer (CRC) remains controversial. LGR5 cells are known to exist outside the stem cell niche during CRC progression, and the requirement for epidermal growth factor (EGF) signalling within early adenomas remains to be fully elucidated. METHODS Epidermal growth factor and gefitinib treatments were performed in EGF-responsive LGR5 early adenoma RG/C2 cells. 2D growth assays were measured using an IncuCyte. LGR5 or MEK1/2 silencing studies were executed using siRNA and LGR5 expression was assessed by qRT-PCR and immunoblotting. Ki67 level and cell cycle status were analysed by flow cytometry. RESULTS Epidermal growth factor suppresses expression of LGR5 at both the transcript and protein level in colorectal adenoma and carcinoma cells. Suppression of LGR5 reduces the survival of EGF-treated adenoma cells by increasing detached cell yield but also inducing a proliferative state, as evidenced by elevated Ki67 level and enhanced cell cycle progression. Repression of LGR5 further increases the sensitivity of adenoma cells to EGFR inhibition. CONCLUSIONS LGR5 has an important role in the EGF-mediated survival and proliferation of early adenoma cells and could have clinical utility in predicting response of CRC patients to EGFR therapy

Evolution of in-group favoritism

In-group favoritism is a central aspect of human behavior. People often help members of their own group more than members of other groups. Here we propose a mathematical framework for the evolution of in-group favoritism from a continuum of strategies. Unlike previous models, we do not pre-suppose that players never cooperate with out-group members. Instead, we determine the conditions under which preferential in-group cooperation emerges, and also explore situations where preferential out-group helping could evolve. Our approach is not based on explicit intergroup conflict, but instead uses evolutionary set theory. People can move between sets. Successful sets attract members, and successful strategies gain imitators. Individuals can employ different strategies when interacting with in-group versus out-group members. Our framework also allows us to implement different games for these two types of interactions. We prove general results and derive specific conditions for the evolution of cooperation based on in-group favoritism