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Accidental Homo sapiens : genetics, behavior, and free will
\"Two leading scientists reveal how we became the amazing creatures we are--and help us understand the biology that makes human beings uniquely capable of choice.\"--Dust jacket flap.
Book
A Molecular Phylogeny of Living Primates
Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (~8 Mb) from 186 primates representing 61 (~90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.
Journal Article
Evolutionary models in economics: a survey of methods and building blocks
This paper assesses methods and components of formal evolutionary-economic modelling. Methods are broadly classified into evolutionary game theory and selection dynamics, evolutionary computation and multi-agent models, each with relevant subcategories. The components or building blocks are organized into diversity, innovation, selection, bounded rationality, diffusion, path dependency and lock-in, coevolution, multilevel and group selection, and mechanisms of growth. The number of alternatives that has been proposed for each category is vast, making it difficult to comprehend the variety of assumptions and formalizations underlying existing evolutionary-economic models. Our survey aims to clarify for each model component the choice range, formal expressions, associated assumptions, and possible techniques for formalization. Our study is unique in that it provides more information about the formal details of specific model components and is considerably more inclusive than earlier reviews.
Journal Article
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP
Computational efforts to identify functional elements within genomes leverage comparative sequence information by looking for regions that exhibit evidence of selective constraint. One way of detecting constrained elements is to follow a bottom-up approach by computing constraint scores for individual positions of a multiple alignment and then defining constrained elements as segments of contiguous, highly scoring nucleotide positions. Here we present GERP++, a new tool that uses maximum likelihood evolutionary rate estimation for position-specific scoring and, in contrast to previous bottom-up methods, a novel dynamic programming approach to subsequently define constrained elements. GERP++ evaluates a richer set of candidate element breakpoints and ranks them based on statistical significance, eliminating the need for biased heuristic extension techniques. Using GERP++ we identify over 1.3 million constrained elements spanning over 7% of the human genome. We predict a higher fraction than earlier estimates largely due to the annotation of longer constrained elements, which improves one to one correspondence between predicted elements with known functional sequences. GERP++ is an efficient and effective tool to provide both nucleotide- and element-level constraint scores within deep multiple sequence alignments.
Journal Article
A survey on evolutionary computation for complex continuous optimization
Complex continuous optimization problems widely exist nowadays due to the fast development of the economy and society. Moreover, the technologies like Internet of things, cloud computing, and big data also make optimization problems with more challenges including Many-dimensions, Many-changes, Many-optima, Many-constraints, and Many-costs. We term these as 5-M challenges that exist in large-scale optimization problems, dynamic optimization problems, multi-modal optimization problems, multi-objective optimization problems, many-objective optimization problems, constrained optimization problems, and expensive optimization problems in practical applications. The evolutionary computation (EC) algorithms are a kind of promising global optimization tools that have not only been widely applied for solving traditional optimization problems, but also have emerged booming research for solving the above-mentioned complex continuous optimization problems in recent years. In order to show how EC algorithms are promising and efficient in dealing with the 5-M complex challenges, this paper presents a comprehensive survey by proposing a novel taxonomy according to the function of the approaches, including reducing problem difficulty, increasing algorithm diversity, accelerating convergence speed, reducing running time, and extending application field. Moreover, some future research directions on using EC algorithms to solve complex continuous optimization problems are proposed and discussed. We believe that such a survey can draw attention, raise discussions, and inspire new ideas of EC research into complex continuous optimization problems and real-world applications.
Journal Article
The ethical project
In a revolutionary approach to the problems of moral philosophy, Philip Kitcher makes a provocative proposal: Instead of conceiving ethical commands as divine revelations or as the discoveries of brilliant thinkers, we should see our ethical practices as evolving over tens of thousands of years.
Book
Barcoding Nemo: DNA-Based Identifications for the Ornamental Fish Trade
Background: Trade in ornamental fishes represents, by far, the largest route for the importation of exotic vertebrates. There is growing pressure to regulate this trade with the goal of ensuring that species are sustainably harvested and that their point of origin is accurately reported. One important element of such regulation involves easy access to specimen identifications, a task that is currently difficult for all but specialists because of the large number of species involved. The present study represents an important first step in making identifications more accessible by assembling a DNA barcode reference sequence library for nearly half of the ornamental fish species imported into North America. Methodology/Principal Findings: Analysis of the cytochrome c oxidase subunit I (COI) gene from 391 species from 8 coral reef locations revealed that 98% of these species exhibit distinct barcode clusters, allowing their unambiguous identification. Most species showed little intra-specific variation (adjusted mean = 0.21%), but nine species included two or three lineages showing much more divergence (2.19–6.52%) and likely represent overlooked species complexes. By contrast, three genera contained a species pair or triad that lacked barcode divergence, cases that may reflect hybridization, young taxa or taxonomic over-splitting. Conclusions/Significance: Although incomplete, this barcode library already provides a new species identification tool for the ornamental fish industry, opening a realm of applications linked to collection practices, regulatory control and conservation.
Journal Article