Morphological Evolution: Bioinspired Methods for Analyzing Bioinspired Robots

To fully understand the evolution of complex morphologies, analyses cannot stop at selection: It is essential to investigate the roles and interactions of multiple processes that drive evolutionary outcomes. The challenges of undertaking such analyses have affected both evolutionary biologists and evolutionary roboticists, with their common interests in complex morphologies. In this paper, we present analytical techniques from evolutionary biology, selection gradient analysis and morphospace walks, and we demonstrate their applicability to robot morphologies in analyses of three evolutionary mechanisms: randomness (genetic mutation), development (an explicitly implemented genotype-to-phenotype map), and selection. In particular, we applied these analytical techniques to evolved populations of simulated biorobots—embodied robots designed specifically as models of biological systems, for the testing of biological hypotheses—and we present a variety of results, including analyses that do all of the following: illuminate different evolutionary dynamics for different classes of morphological traits; illustrate how the traits targeted by selection can vary based on the likelihood of random genetic mutation; demonstrate that selection on two selected sets of morphological traits only partially explains the variance in fitness in our biorobots; and suggest that biases in developmental processes could partially explain evolutionary dynamics of morphology. When combined, the complementary analytical approaches discussed in this paper can enable insight into evolutionary processes beyond selection and thereby deepen our understanding of the evolution of robotic morphologies.

Complete mitochondrial genome of Rhodeus cyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis

Rhodeus cyanorostris Li, Liao & Arai, 2020 is a freshwater fish that is endemic to China and restricted to Chengdu City in Sichuan Province. This study is the first to sequence and characterize the complete mitochondrial genome of R. cyanorostris. The mitogenome of R. cyanorostris is 16580 bp in length, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region (D-loop). The base composition of the sequence is 28.5% A, 27.6% C, 26.4% T, and 17.5% G, with a bias toward A+T. The genome structure, nucleotide composition, and codon usage of the mitogenome of R. cyanorostris are consistent with those of other species of Rhodeus. To verify the molecular phylogeny of the genus Rhodeus, we provide new insights to better understand the taxonomic status of R. cyanorostris. The phylogenetic trees present four major clades based on 19 mitogenomic sequences from 16 Rhodeus species. Rhodeus cyanorostris exhibits the closest phylogenetic relationship with R. pseudosericeus, R. amarus, and R. sericeus. This study discloses the complete mitochondrial genome sequence of R. cyanorostris for the first time and provides the most comprehensive phylogenetic reconstruction of the genus Rhodeus based on whole mitochondrial genome sequences. The information obtained in this study will provide new insights for conservation, phylogenetic analysis, and evolutionary biology research.

Evolutionary Processes in Cancer

Cancer develops through the evolution of somatic cells in multicellular bodies. The familiar dynamics of organismal evolution, including mutations, natural selection, genetic drift, and migration, also occur among the cells of multicellular organisms. In some cases, but not all, these evolutionary processes lead to cancer. This has profound implications for both our understanding of cancer and our treatment of the disease, as well as its prevention. All of our medical interventions impose selective pressures on the heterogeneous populations of billions of cells in tumors, and tend to select for mutant cells that are resistant to the intervention, regardless of whether the intervention is a drug, radiation, the immune system, or anything else that has been tried. We will likely need evolutionary and ecological approaches to cancer to manage its evolution in response to our interventions. The field of the evolutionary biology and ecology of cancer is still young and relatively small. We are in the early stages of translating ideas and tools from evolutionary biology and ecology to study and manage cancers. There is a desperate need for more researchers with expertise in evolutionary biology and ecology to apply their skills and ideas to cancer. Currently, there are far more important questions that need to be addressed than there are people to address them.

Role of TlyA in the Biology of Uncultivable Mycobacteria

TlyA proteins are related to distinct functions in a diverse spectrum of bacterial pathogens including mycobacterial spp. There are several annotated proteins function as hemolysin or pore forming molecules that play an important role in the virulence of pathogenic organisms. Many studies reported the dual activity of mycobacterial TlyA as ‘hemolysin’ and ‘S-adenosylmethionine dependent rRNA methylase’. To act as a hemolysin, a sequence must have a signal sequence and transmembrane segment which helps the protein to enter the extracellular environment. Interestingly, the mycobacterial tlyA has neither a traditional signal sequences of general/sec/tat pathways nor any transmembrane segments are present. Still it can reach the extracellular milieu with the help of non-classical signal mechanisms. Also, retention of tlyA in cultivable mycobacterial pathogens (such as Mycobacterium tuberculosis and M. marinum) as well as uncultivated mycobacterial pathogens despite their extreme reductive evolution (such as M. leprae, M. lepromatosis and M. uberis) suggests its crucial role in evolutionary biology of pathogenic mycobacteria. Numerous virulence factors have been characterised from the uncultivable mycobacteria but the information of TlyA protein is still limited in terms of molecular and structural characterisation. The genomic insights offered by comparative analysis of TlyA sequences and its conserved domains reveal its pore forming activity which further confirms its role as a virulence protein, particularly in uncultivable mycobacteria. Therefore, this review presents a comparative analysis of mycobacterial TlyA family by sequence homology and alignment to improve our understanding of this unconventional hemolysin and RNA methyltransferase TlyA of uncultivable mycobacteria.

Dominance in humans

Dominance captures behavioural patterns found in social hierarchies that arise from agonistic interactions in which some individuals coercively exploit their control over costs and benefits to extract deference from others, often through aggression, threats and/or intimidation. Accumulating evidence points to its importance in humans and its separation from prestige—an alternate avenue to high status in which status arises from information (e.g. knowledge, skill, etc.) or other non-rival goods. In this review, we provide an overview of the theoretical underpinnings of dominance as a concept within evolutionary biology, discuss the challenges of applying it to humans and consider alternative theoretical accounts which assert that dominance is relevant to understanding status in humans. We then review empirical evidence for its continued importance in human groups, including the effects of dominance—independently of prestige—on measurable outcomes such as social influence and reproductive fitness, evidence for specialized dominance psychology, and evidence for gender-specific effects. Finally, because human-specific factors such as norms and coalitions may place bounds on purely coercive status-attainment strategies, we end by considering key situations and contexts that increase the likelihood for dominance status to coexist alongside prestige status within the same individual, including how: (i) institutional power and authority tend to elicit dominance; (ii) dominance-enhancing traits can at times generate benefits for others (prestige); and (iii) certain dominance cues and ethology may lead to mis-attributions of prestige. This article is part of the theme issue ‘The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies’.

The Technological Advance and Application of Coprolite Analysis

Coprolites (mummified or fossilized feces), belonging to the group of ichnofossils, are fossilized remains of feces produced by animals. Various types of data from coprolites provide detailed evidence of the producer’s condition, like diet, intestinal microbiome, virus infection and parasites diseases. In addition, the palaeoenvironment information relevant to producers’ ecological niche can be drawn from taphonomy details the coprolites mirrored. At present, the phylogenetic clues of the producer’s population can be determined by advanced molecular biotechnologies. With the integration of multiple methods and techniques, coprolite has been widely accepted as an ideal material to study the diet, evolution, and palaeoenvironment of producers. In this paper, we reviewed the history of coprolite research, enumerated and interpreted the data recovered from coprolites, and explained their research value to palaeocoprology and evolutionary biology. Finally, we summarized the current directions of coprolite research and looked into its future prospects.

THEWEIGHT: A simple and flexible algorithm for simulating non-ideal, age-structured populations

1. The Wright-Fisher model, which directs how matings occur and how genes are transmitted across generations, has long been a lynchpin of evolutionary biology. This model is elegantly simple, analytically tractable, and easy to implement, but it has one serious limitation: essentially no real species satisfies its many assumptions. With growing awareness of the importance of jointly considering both ecology and evolution in eco-evolutionary models, this limitation has become more apparent, causing many researchers to search for more realistic simulation models. 2. A recently described variation retains most of the Wright-Fisher simplicity but provides greater flexibility to accommodate departures from model assumptions. This generalized Wright-Fisher model relaxes the assumption that all individuals have identical expected reproductive success by introducing a vector of parental weights w that specifies relative probabilities different individuals have of producing offspring. With parental weights specified this way, expectations of key demographic parameters are simple functions of w. This allows researchers to quantitatively predict the consequences of non-Wright-Fisher features incorporated into their models. 3. An important limitation of the Wright-Fisher model is that it assumes discrete generations, whereas most real species are age-structured. Here I show how an algorithm (THEWEIGHT) that implements the generalized Wright-Fisher model can be used to model evolution in age-structured populations with overlapping generations. Worked examples illustrate simulation of seasonal and lifetime reproductive success and show how the user can pick vectors of weights expected to produce a desired level of reproductive skew or a desired Ne/N ratio. Alternatively, weights can be associated with heritable traits to provide a simple, quantitative way to model natural selection. Using THEWEIGHT, it is easy to generate positive or negative correlations of individual reproductive success over time, thus allowing explicit modeling of common biological processes like skip breeding and persistent individual differences. 4. R code is provided to implement basic features of THEWEIGHT and applications described here. However, required coding changes to the Wright-Fisher model are modest, so the real value of the new algorithm is to encourage users to adopt its features into their own or others models.

Monster plants. The vegetal political ecology of Lacandonia schismatica

This paper presents a story about a plant – Lacandonia schismatica  – who subverted disciplinary traditions in botany and reconfigured its geopolitical orders of knowledge. To tell this story, we focus on Lacandonia’s plantiness, Lesley Head and colleagues’s (2012) concept to signify each kind of plant’s unique biophysical characteristics, capacities, and potentialities, and through which they co-produce the world. We trace how L. schismatica intervened in, and (re)configured processes of knowledge production, environmental politics, and identity formation in the Lacandon Forest, Chiapas, Mexico, where it was found. Lacandonia’s plantiness came into being through sudden macromutations; this unexpected but viable plant species participated in reviving an old debate in evolutionary biology: macroevolution versus gradualism. We also analyze how Lacandonia’s plantiness compelled shifts in environmental politics in Chiapas and identity formation in Frontera Corozal, the Chol community where L. schismatica was first located. We conclude with a brief reflection on the implications of vegetal ethics for addressing contemporary environmental crises. 

The First High-Quality Genome Assembly and Data Analysis of the Malaysian mahseer (Tor tambroides)

The Malaysian mahseer (Tor tambroides), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an adult fish on both Illumina and Nanopore platforms. The hybrid genome assembly had resulted in a sum of 1.5 Gb genomic sequence from the 44,726 contigs found with 44 kb N50 length and BUSCO genome completeness of 84.3%. Four types of SSRs had been detected and identified within the genome with a greater AT abundance than that of GC. Predicted protein sequences had been functionally annotated to public databases, namely GO, KEGG and COG. A maximum likelihood phylogenomic tree containing 53 Actinopterygii species and two outgroups was constructed, providing first insights into the genome-based evolutionary relationship of T. tambroides with other ray-finned fish. These data are crucial in facilitating the study of population genomics, species identification, morphological variations, and evolutionary biology, which are helpful in the conservation of this species.

Delayed differentiation of epidermal cells walls can underlie pedomorphosis in plants: the case of pedomorphic petals in the hummingbird-pollinated Caiophora hibiscifolia (Loasaceae, subfam. Loasoideae) species

Background Understanding the relationship between macroevolutionary diversity and variation in organism development is an important goal of evolutionary biology. Variation in the morphology of several plant and animal lineages is attributed to pedomorphosis, a case of heterochrony, where an ancestral juvenile shape is retained in an adult descendant. Pedomorphosis facilitated morphological adaptation in different plant lineages, but its cellular and molecular basis needs further exploration. Plant development differs from animal development in that cells are enclosed by cell walls and do not migrate. Moreover, in many plant lineages, the differentiated epidermis of leaves, and leaf-derived structures, such as petals, limits organ growth. We, therefore, proposed that pedomorphosis in leaves, and in leaf-derived structures, results from delayed differentiation of epidermal cells with respect to reproductive maturity. This idea was explored for petal evolution, given the importance of corolla morphology for angiosperm reproductive success. Results By comparing cell morphology and transcriptional profiles between 5 mm flower buds and mature flowers of an entomophile and an ornitophile Loasoideae species (a lineage that experienced transitions from bee- to hummingbird-pollination), we show that evolution of pedomorphic petals of the ornithophile species likely involved delayed differentiation of epidermal cells with respect to flower maturity. We also found that developmental mechanisms other than pedomorphosis might have contributed to evolution of corolla morphology. Conclusions Our results highlight a need for considering alternatives to the flower-centric perspective when studying the origin of variation in flower morphology, as this can be generated by developmental processes that are also shared with leaves. Graphical Abstract