A far-reaching and influential view in evolutionary biology claims that species are cohesive units held together by gene flow. Biologists have recognized empirical problems facing this view; after sharpening the expression of the view, we present novel conceptual problems for it. At the heart of these problems is a distinction between two importantly different concepts of cohesion, what we call integrative and response cohesion. Acknowledging the distinction problematizes both the explanandum of species cohesion and the explanans of (...) class='Hi'>gene flow that are central to the view we discuss. We conclude by tracing four broader implications for the study and conceptualization of species. (shrink)

A recent analysis of the genomes of Darwin's finches revealed extensive interspecies allele sharing throughout the history of the radiation and identified a key locus responsible for morphological evolution in this group. The radiation of Darwin's finches on the Galápagos archipelago has long been regarded as an iconic study system for field ecology and evolutionary biology. Coupled with an extensive history of field work, these latest findings affirm the increasing acceptance of introgressive hybridization, or gene flow between species, (...) as a significant contributor to adaptive evolution. Here, we review and discuss these findings in relation to both classical work on Darwin's finches and contemporary work showing similar evolutionary signatures in other biological systems. The continued unification of genomic data with field biology promises to further elucidate the molecular basis of adaptation in Darwin's finches and well beyond. (shrink)

This paper brings needed clarity to the influential view that species are cohesive entities held together by gene flow, and then develops an empirical argument against that view: Neglected data suggest gene flow is neither necessary nor sufficient for species cohesion. Implications are discussed. ‡I'm grateful to Rob Wilson, Alex Rueger and Lindley Darden for important comments on earlier drafts, and to Joseph Nagel, Heather Proctor, Ken Bond, members of the DC History and Philosophy of Biology (...) reading group, and audience members at the November 2006 meeting of the PSA, for helpful comments or discussion. Social Sciences and Humanities Research Council of Canada fellowship 752-2005-1208 supported research. †To contact the author, please write to: Philosophy Department, University of Wisconsin–Madison, 5185 Helen C. White Hall, 600 North Park Street, Madison, WI 53706; e-mail: [email protected]. (shrink)

We identify two processes by which humans increase genetic exchange among groups of individuals: by affecting the distribution of groups and dispersal patterns across a landscape, and by affecting interbreeding among sympatric or parapatric groups. Each of these processes might then have two different effects on biodiversity: changes in the number of taxa through merging or splitting of groups, and the extinction/extirpation of taxa through effects on fitness. We review the various ways in which humans are affecting genetic exchange, and (...) highlight the difficulties in predicting the impacts on biodiversity. Gene flow and hybridization are crucially important evolutionary forces influencing biodiversity. Humans alter natural patterns of genetic exchange in myriad ways, and these anthropogenic effects are likely to influence the genetic integrity of populations and species. We argue that taking a gene-centric view towards conservation will help resolve issues pertaining to conservation and management.Editor's suggested further reading in BioEssays A systemic view of biodiversity and its conservation: Processes, interrelationships, and human culture Abstract. (shrink)

Evolution is a continuous trial and error process in which most lineages go extinct without leaving fossil remains. Many of these lineages would be closely related and occasionally hybridized with lineages that gave rise to extant species. Hence, it is likely that one can find genetic signatures of these ancient introgression events in present‐day genomes, so‐called ghost introgression. The increasing availability of high‐quality genome assemblies for non‐model organisms and the development of more sophisticated methods for detecting introgression will undoubtedly reveal (...) more cases of ghost introgression, indicating that the Tree of Life is even more reticulated than assumed. The presence of ghost introgression has important consequences for the study of numerous evolutionary processes, including adaptation, speciation, and macroevolutionary patterns. In addition, detailed studies of introgressed regions could provide insights into the morphology of the extinct lineage, providing an unexpected link between genomics and the fossil record. Hence, new methods that take into account ghost introgression will need to be developed. (shrink)

The political systems of the Roman Republic were based almost entirely on tradition, “the way of the ancestors”, rather than on a written constitution. While the founders of the American Republic looked to ancient Rome as a primary model for their enterprise, nevertheless, in line with the rationalist spirit of their age, the American founders attempted to create a rational set of rules that would guide the conduct of American politics, namely, the US Constitution.These two examples offer a striking case (...) of the ideal types, famously delineated by Michael Oakeshott in “Rationalism in Politics” and elsewhere, between politics as a practice grounded in tradition and politics as a system based on principles flowing from abstract reasoning.This book explores how the histories of the two republics can help us to understand Oakeshott’s claims about rational versus traditional politics. Through examining such issues we may come to understand better not only Oakeshott’s critique of rationalism, but also modern constitutional theory, issues in the design of the European Union, and aspects of the revival of republicanism. (shrink)

Imprecise definition of key terms in the “public participation” domain have hindered the conduct of good research and militated against the development and implementation of effective participation practices. In this article, we define key concepts in the domain: public communication, public consultation, and public participation. These concepts are differentiated according to the nature and flow of information between exercise sponsors and participants. According to such an information flow perspective, an exercise’s effectiveness may be ascertained by the efficiency with (...) which full, relevant information is elicited from all appropriate sources, transferred to all appropriate recipients, and combined to give an aggregate/consensual response. Key variables that may theoretically affect effectiveness—and on which engagement mechanisms differ—are identified and used to develop a typology of mechanisms. The resultant typology reveals four communication, six consultation, and four participation mechanism classes. Limitations to the typology are discussed, and future research needs identified. (shrink)

We defend a realistic attitude towards biological species. We argue that two species are not different species because they differ in intrinsic features, be they phenotypic or genomic, but because they are separated with regard to gene flow. There are no intrinsic species essences. However, there are relational ones. We argue that bearing a gene flow relation to conspecifics may serve as the essence of a species. Our view of the species as a Gene-Flow (...) Community differs from Mayr’s definition of the species as a reproductive community. In a reproductive community, each organism is able to successfully reproduce with each other. However, there are species in which geographically distant organisms lost their ability to successfully reproduce, due to strong genetic adaptations to the respective local environmental conditions. Despite this loss of the ability to mutually reproduce, they are still bound by gene flow via continuous intermediate populations. This replacement of Mayr’s notion of an interbreeding potential as a criterion for species membership has important implications for the treatment of populations in allopatry and sympatry. (shrink)

Minimal genetic pre-formationism is defended, in that primacy is ascribed to DNA in the structuring of molecules through molecular codes. This together with the importance of such codes for stability and variation in living systems makes DNA categorically different from other causal factors. It is argued that post-transcriptional and post-translational processing in protein synthesis does not rob DNA of this structuring role. Notions of structuring causal powers that may vary in degree, of arbitrary molecular codes that are more or less (...) realized, of partial templating and of genetic information as a subspecies of mechanistic information are brought in to support this and to rival causal and semantic notions of information. It is concluded that the primacy of genes in their structuring of molecules goes together with parity between genes and non-genetic causal factors in regulation of living systems. This is seen to hold independently of the radical reconceptualization of organism cum environment that has been suggested in developmental systems theory. (shrink)

Written for non-experts, this volume introduces the mechanisms that underlie reticulate evolution. Chapters are either accompanied with glossaries that explain new terminology or timelines that position pioneering scholars and their major discoveries in their historical contexts. The contributing authors outline the history and original context of discovery of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infectious heredity. By applying key insights from the areas of molecular (phylo)genetics, microbiology, virology, ecology, systematics, immunology, epidemiology (...) and computational science, they demonstrate how reticulate evolution impacts successful survival, fitness and speciation. Reticulate evolution brings forth a challenge to the standard Neo-Darwinian framework, which defines life as the outcome of bifurcation and ramification patterns brought forth by the vertical mechanism of natural selection. Reticulate evolution puts forward a pattern in the tree of life that is characterized by horizontal mergings and lineage crossings induced by symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infective heredity, making the “tree of life” look more like a “web of life.” On an epistemological level, the various means by which hereditary material can be transferred horizontally challenges our classic notions of units and levels of evolution, fitness, modes of transmission, linearity, communities, and biological individuality. The case studies presented examine topics including the origin of the eukaryotic cell and its organelles through symbiogenesis; the origin of algae through primary and secondary symbiosis and dinoflagellates through tertiary symbiosis; the superorganism and holobiont as units of evolution; how endosymbiosis induces speciation in multicellular life forms; transferrable and non-transferrable plasmids and how they symbiotically interact with their host; the means by which pro- and eukaryotic organisms transfer genes laterally (bacterial transformation, transduction and conjugation as well as transposons and other mobile genetic elements); hybridization and divergence with gene flow in sexually-reproducing individuals; current (human) microbiome and viriome studies that impact our knowledge concerning the evolution of organismal health and acquired immunity; and how symbiosis and symbiogenesis can be modelled in computational evolution. (shrink)

Liberal proponents of genetic engineering maintain that developing human germline modification technologies is morally desirable because it will result in a net improvement in human health and well-being. Skeptics of germline modification, in contrast, fear evolutionary harms that could flow from intervening in the human germline, and worry that such programs, even if well intentioned, could lead to a recapitulation of the scientifically and morally discredited projects of the old eugenics. Some bioconservatives have appealed as well to the value (...) of retaining our “given” human biological nature as a reason for restraining the development and use of human genetic modification technologies even where they would tend to increase well-being. In this article, I argue that germline intervention will be necessary merely to sustain the levels of genetic health that we presently enjoy for future generations—a goal that should appeal to bioliberals and bioconservatives alike. This is due to the population-genetic consequences of relaxed selection pressures in human populations caused by the increasing efficacy and availability of conventional medicine. This heterodox conclusion, which I present as a problem of intergenerational justice, has been overlooked in medicine and bioethics due to certain misconceptions about human evolution, which I attempt to rectify, as well as the sordid history of Darwinian approaches to medicine and social policy, which I distinguish from the present argument. (shrink)

The universally recognized backbone of molecular biology describes the flow of genetic information from deoxyribonucleic acid (DNA) to ribonucleic acid (RNA) to protein or gene product, that is, DNA is transcribed into another nucleic acid (RNA), which is single stranded, next some types of RNA are in turn translated into proteins. Translation of nucleic acids to proteins is literally a translation from the genomic language to the metabolic language. Codons formed of a sequence of three nucleic acids summon (...) a specific amino acid. Translation from codons to proteins, that is, protein synthesis, takes place by specialized machinery comprising mRNA, ribosomes, and free amino acids. Inferring the structure of DNA opened the door for tremendous advances in understanding the role of genes in creating life, directing replication, and ongoing metabolic processes responsible for maintaining life at both the cellular and organism level. (shrink)

First the ‘Weismann barrier’ and later on Francis Crick’s ‘central dogma’ of molecular biology nourished the gene-centric paradigm of life, i.e., the conception of the gene/genome as a ‘central source’ from which hereditary specificity unidirectionally flows or radiates into cellular biochemistry and development. Today, due to advances in molecular genetics and epigenetics, such as the discovery of complex post-genomic and epigenetic processes in which genes are causally integrated, many theorists argue that a gene-centric conception of the organism (...) has become problematic. Here, we first explore the causal implications of the following two central dogma-related issues: (1) widespread reverse transcription—arguing for an extension from ‘DNA-genome’ to RNA-encompassing ‘NA-genome’ and, thus, from traditional DNA-centrism to a broader ‘NA-centrism’; and (2) the absence of a mechanism of reverse translation—arguing for the ‘structural primacy’ of NA-sequence over protein in cellular biochemistry. Secondly, we explore whether this latter conclusion can be extended to a ‘functional primacy’ of NA-sequence over protein in cellular biochemistry, which would imply a limited kind of ‘gene/NA-centrism’ confined to the subcellular level of NA/protein-based biochemistry. Finally, we explore the conditions—and their (non)fulfilment—for a more generalised form of gene-centrism extendable to higher levels of biological organisation. We conclude that the higher we go in the biological hierarchy, the more dubious gene-centric claims become. (shrink)

Higher plant shoot meristems are multicellular structures that are the site of postembryonic organogenesis. Analysis of chimeric plants has indicated that cells in different regions of the meristem can interact with each other so that their activities are coordinated during developmental processes. Correlations have not been demonstrated between events at a molecular level and the interactions observed at a phenotypic level in chimeras. Two recent papers(1,2) address this problem by reporting that expression of the floricaula gene in one region (...) of chimeric snapdragon meristems is sufficient to promote the transition from inflorescence to floral development and to induce the expression of the downstream organ identity genes deficiens and plena throughout the meristem. (shrink)

Admixture, the genetic exchange between differentiated populations appears to be common in the history of species, but has not yet been comparatively studied across mammals. This limits the understanding of its mechanisms and potential role in mammalian evolution. The authors want to summarize the current knowledge on admixture in non‐human primates, and suggest that it is important to establish a comparative framework for this phenomenon in humans. Genetic observations in domesticated mammals and their wild counterparts are discussed, and a brief (...) global overview on other clades is presented. Based on this, some of the consequences of gene flow, including incompatibilities and their genomic footprint, as well as adaptive introgression are discussed, and suggestions for a functional genomics approach are made. It is proposed that the field is moving beyond descriptive observations in single species, to a comprehensive analysis of admixture and its impact. Admixture is becoming an integral part of mammalian evolution. (shrink)

Sympatric speciation illustrates how natural and sexual selection may create new species in isolation without geographic barriers. However, recent genomic reanalyses of classic examples of sympatric speciation reveal complex histories of secondary gene flow from outgroups into the radiation. In contrast, the rich theoretical literature on this process distinguishes among a diverse range of models based on simple genetic histories and different types of reproductive isolating barriers. Thus, there is a need to revisit how to connect theoretical models (...) of sympatric speciation and their predictions to empirical case studies in the face of widespread gene flow. Here, theoretical differences among different types of sympatric speciation and speciation‐with‐gene‐flow models are reviewed and summarized, and genomic analyses are proposed for distinguishing which models apply to case studies based on the timing and function of adaptive introgression. Investigating whether secondary gene flow contributed to reproductive isolation is necessary to test whether predictions of theory are ultimately borne out in nature. (shrink)

Admixture, the genetic exchange between differentiated populations appears to be common in the history of species, but has not yet been comparatively studied across mammals. This limits the understanding of its mechanisms and potential role in mammalian evolution. The authors want to summarize the current knowledge on admixture in non‐human primates, and suggest that it is important to establish a comparative framework for this phenomenon in humans. Genetic observations in domesticated mammals and their wild counterparts are discussed, and a brief (...) global overview on other clades is presented. Based on this, some of the consequences of gene flow, including incompatibilities and their genomic footprint, as well as adaptive introgression are discussed, and suggestions for a functional genomics approach are made. It is proposed that the field is moving beyond descriptive observations in single species, to a comprehensive analysis of admixture and its impact. Admixture is becoming an integral part of mammalian evolution. (shrink)

The standard representation of the Central Dogma (CD) of Molecular Biology conspicuously ignores metabolism. However, both the metabolites and the biochemical fluxes behind any biological phenomenon are encrypted in the DNA sequence. Metabolism constrains and even changes the information flow when the DNA‐encoded instructions conflict with the homeostasis of the biochemical network. Inspection of adaptive virulence programs and emergence of xenobiotic‐biodegradation pathways in environmental bacteria suggest that their main evolutionary drive is the expansion of their metabolic networks towards new (...) chemical landscapes rather than perpetuation and spreading of their DNA sequences. Faulty enzymatic reactions on suboptimal substrates often produce reactive oxygen species (ROS), a process that fosters DNA diversification and ultimately couples catabolism of the new chemicals to growth. All this calls for a revision of the CD in which metabolism (rather than DNA) has the leading role. (shrink)

No later than ~500kya the population of Homo sapiens split into three lin¬eages of independently evolving human populations: Sapiens, Neanderthals and Den¬isovans. After several hundred thousands years, they met several times and interbred with low frequency. Evidence of coupling between them is found in fossil records of Neanderthal – Sapiens offspring and Neanderthal – Denisovans offspring. Moreover, the analysis of ancient and present-day population DNA shows that there were several significant gene flows between populations. Many introgressed sequences from Denisovans (...) and Neanderthals were identified in genomes of currently living populations. All these data, according to biological species definition, may in¬dicate that populations of H. sapiens sapiens and two extinct populations H. sapiens neanderthalensis and H. sapiens denisovensis are one species. Ontological transitions from pre-human beings to humans might have happened before the initial splitting of the Homo sapiens population or after the splitting during evolution of H. sapiens sapiens lineage in Africa. If the ensoulment of the first homo occurred in the evolving populations of H. sapiens sapiens, then occasionally mixed couples created relations that functioned as a family, in which children could have matured. (shrink)

There is increasing evidence for the wide‐spread existence of functionally redundant genetic pathways in developmental processes. However, both their significance and manner of evolution are still matters of debate. I will argue here that redundancy of gene actions may, in fact, be a necessary requirement for the development and evolution of complex life forms. One can view development as a process that transmits information from the egg to the adult organism. Transmission of information is, however, always an error‐prone process, (...) which can only be safeguarded by including redundancies in the message. Molecular examples for well analysed redundant processes indicate that redundancies may best be understood within a conceptual framework of overlaps between different gene functions. (shrink)

Over the decades, there has been substantial empirical evidence showing that the unity of species cannot be maintained by gene flow. The biological species concept is inconclusive on this point. The suggestion is made that the unity of species is maintained rather by selection constantly spreading new alleles throughout the species, or bygene circulation. There is a lack in conceptual distinction between gene flow and gene circulation which lies at the heart of the problem. The (...) concept of gene circulation also sheds some new light on the problem of typology and on such a broad concept as evolution. A new species definition is proposed. (shrink)

This book explains the role of simple biological model systems in the growth of molecular biology. Essentially the whole history of molecular biology is presented here, tracing the work in bacteriophages in E. coli, the role of other prokaryotic systems, and also the protozoan and algal models—Paramecium and Chlamydomonas, primarily—and the move into eukaryotes with the fungal systems Neurospora, Aspergillus and yeast. Each model was selected for its appropriateness for asking a given class of questions, and each spawned its own (...) community of investigators. Some individuals made the transition to a new model over time, and remnant communities of investigators continue to pursue questions in all these models, as the cutting edge of molecular biological research flowed onward from model to model, and onward into higher organisms and, ultimately, mouse and man. (shrink)

Replacements for the self-interest axiom may posit weak to strong theories of sociality. Strong sociality may be useful for positing social cognitive mechanisms and their evolution, but weak sociality may work better for identifying interesting group-level outcomes by focusing on deviations from self-interested psychological assumptions. Such theoretical differences are likely to be based on disciplinary expertise, and the challenge for Darwinian integration is to keep the conversation flowing.

The coexistence of genetically modified (GM) crops and non-GM crops is a myth because the movement of transgenes beyond their intended destinations is a certainty, and this leads to genetic contamination of organic farms and other systems. It is unlikely that transgenes can be retracted once they have escaped, thus the damage to the purity of non-GM seeds is permanent. The dominant GM crops have the potential to reduce biodiversity further by increasing agricultural intensification. There are also potential risks to (...) biodiversity arising from gene flow and toxicity to nontarget organisms from herbicide-resistant (HT) and insect-resistant (Bt) crops. Unless whole regions are declared GM agriculture free, the development of distinct systems of agriculture (GM and non-GM) will be impossible as GM agriculture emerges at the expense of all other forms of production. (shrink)

Our society currently faces many complex and perplexing issues related to biotechnology, including the need to define the outer boundaries of genetic research on human beings and the need to protect individual and group rights to human tissue and the knowledge gained from the study of that tissue. Scientists have increasingly become interested in studying so-called “population isolates” to discover the nature and location of genes that are unique to particular groups. Indigenous peoples are often targeted by scientists because “the (...) relative isolation of the communities ensures minimal gene flow.” Such studies raise a number of issues related to privacy rights, property rights, informed consent, and group rights versus individual rights. These issues recently came to light in a case brought by the Havasupai Tribe and its members over the use of blood samples, handprints, and genealogy information initially taken by researchers at Arizona State University for a diabetes project. These materials were then allegedly used by researchers at ASU and other institutions for a multitude of unauthorized purposes, including research into the frequency of mental health disorders and the origin of human populations. Consequently, the affected members sued for damages under several legal theories. However, underlying all of these claims was the allegation that this unauthorized use of genetic resources and data not only injured the individuals who gave samples, but also caused a collective harm to the Havasupai Tribe and the cultural and spiritual beliefs of its members. (shrink)

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the 'new mechanical philosophy' to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence--namely, whether divergence in the absence of geographic isolation is possible (or significant). (...) Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate--namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive. Show Abstract.. (shrink)

Factors such as subsistence turnover, warfare, or interaction between different groups can be major sources of cultural change in human populations. Global demographic shifts such as the transition to agriculture during the Neolithic and more recently the urbanization and globalization of the twentieth century have been major catalysts for cultural change. Here, we test whether cultural traits such as patri/matrilocality and postmarital migration persist in the face of social upheaval and gene flow during the past 150 years in (...) postcolonial South Africa. The recent history of South Africa has seen major demographic shifts that resulted in the displacement and forced sedentism of indigenous Khoekhoe and San populations. During the expansion of the colonial frontier, the Khoe-San admixed with European colonists and enslaved individuals from West/Central Africa, Indonesia, and South Asia, introducing novel cultural norms. We conducted demographic interviews among Nama and Cederberg communities representing nearly 3,000 individuals across three generations. Despite the history of colonial expansion, and the subsequent incorporation of Khoe-San and Khoe-San-descendant communities into a colonial society with strong patrilocal norms, patrilocality is the least common postmarital residence pattern in our study populations today. Our results suggest that more recent forces of integration into the market economy are likely the primary drivers of change in the cultural traits examined in our study. Birthplace had a strong effect on an individual’s odds of migration, distance moved, and postmarital residence form. These effects are at least partially explained by the population size of the birthplace. Our results suggest that market factors local to birthplaces are important drivers of residence decisions, although the frequency of matrilocal residence and a geographic and temporal cline in migration and residence patterns also indicate the persistence of some historic Khoe-San cultural traits in contemporary groups. (shrink)

This paper proposes a new and testable view about the nature of species and other evolving lineages, according to which they are feedback systems. On this view, it is a mistake to think gene flow, niche sharing, and trait frequency similarities between populations are among variables that interact to cause some further downstream variable that distinguishes evolving lineages from each other, some sort of “species cohesion” for example. Instead, gene flow, niche sharing, similarities between populations, and (...) other causal variables feed into each other—instances of these at earlier times help cause instances of these same variables at later times. And any lineage-identifying cohesion just is the recurrence or cycling of these feedback relations within metapopulations over generations. Such cohesion can then be represented as variable M within multi-dimensional variable spaces, where values of M vary dynamically with the frequency and magnitude of feedback relations. Related conditions for being a species or other evolving lineage are then clarified. To argue for the development and testing of this view, the paper shows how it improves upon others. (shrink)

Indirect identification of innovations in wild populations involves inferring past, unobserved behavioral events. Such historical inference can make simple use of present distribution patterns of differently behaving individuals, but population genetic studies are a potential source of complementary relevant information. Methodological lessons can be taken from phylogeography, that is, molecular approaches to the history of population spatial distribution patterns and gene flows. Opportunities for such studies in primates should increase with the developing population genetic studies used for management and (...) conservation purposes. (shrink)

Recent research into human origins has largely focused on deducing past events and processes from current patterns of genetic variation. Some human genes possess unexpectedly low diversity, seemingly resulting from events of the late Pleistocene. Such anomalies have previously been ascribed to population bottlenecks or selection on genes. For four species of matrilineal whale, evidence suggests that cultural evolution may have reduced the diversity of genes which have similar transmission characteristics to selective cultural traits, through a process called cultural hitchhiking. (...) Cultural evolution is characteristic of human societies and so should be considered as a potential determinant of human genetic diversity. A stochastic simulation of gene and cultural dynamics in an array of hunter-gatherer tribes shows that cultural selection has the potential to severely reduce genetic diversity if: inter-tribe gene flows are reasonably low (<~0.6-15 genes/tribe/generation); cultural evolution changes fitness by >~0.3-3%/generation; and fitness is changed more by cultural innovation within a tribe than cultural assimilation from neighboring tribes. Thus cultural hitchhiking may explain low diversity and short coalescence times in mitochondrial and, especially, Y-linked human genes. (shrink)

Evolutionary investigations of human crania typically take a limited view of cranial diversity as they discount the possibility that human cranial variation could simply be due to the effects of random genetic drift, gene flow and mutation in favor of natural selection and developmental changes. Natural selection alone cannot explain similarities between patterns of cranial and molecular diversity observed in humans. It appears that the amount of phenotypic variance in the human cranium decreases at the population level as (...) a function of distance from Sub‐Saharan Africa much in the same way as observed for human molecular data.1 BioEssays 29:1185–1188, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

Molecular genetic data have greatly improved our ability to test hypotheses about human evolution. During the past decade, a large amount of nuclear and mitochondrial data have been collected from diverse human populations. Taken together, these data indicate that modern humans are a relatively young species. African populations show the largest amount of genetic diversity, and they are the most genetically divergent population. Modern human populations expanded in size first on the African continent. These findings support a recent African origin (...) of modern humans, but this conclusion should be tempered by the possible effects of factors such as gene flow, population size differences, and natural selection. BioEssays 20:126–136, 1998. © 1998 John Wiley & Sons, Inc. (shrink)

This paper examines the ethical andsocial questions that underlie the present UKdiscussion whether GM crops and organicagriculture can co-exist within a given regionor are mutually exclusive. A EuropeanCommission report predicted practicaldifficulties in achieving sufficientseparation distances to guarantee lowerthreshold levels proposed for GM material inorganic produce. Evidence of gene flow betweensome crops and their wild relatives has beena key issue in the recent Government consultation toconsult on whether or not to authorizecommercial planting of GM crops, following theresults of the (...) current UK farm scale trials.The admixture of imported Bt transgenes intolandrace varieties of Mexican maize alsopresents difficulties. An ethical evaluationis made of the claim that organic growersshould expect protection from adventitioustraces of GM constructs in their products. Towhat extent – on either side of the debate –can any particular group in society set upagricultural standards for itself that mayeffectively restrain others from an otherwisejust business? The assumptions behind notionslike ``purity'' and ``contamination'' areexamined, together with their underlying viewsof nature and human intervention. The 2001UK Agriculture and Environmental BiotechnologyCommission report is relevant to theseissues. While the Government wishes to promotethe UK biotechnology industry and is underpressure from US claims of trade restraint, astrong organic lobby demands purity from GMcontamination. Does this adversarial framingof the issues reflect broader public opinionin the UK public consultation? Inarriving at policy decisions, the role of thevirtue of tolerance is considered inpost-modern and Christian ethical contexts. (shrink)

A new set of models has resurrected a role for chromosomal inversions in the formation of new species.1-3 Traditional models, which are generally considered to be unlikely in most cases, had imagined that inversions might aid speciation by directly causing low hybrid fitness. In contrast, the newer models focus on the effect that inversions have on local recombination rates. A test of these models found a strikingly high rate of amino-acid substitution within regions where humans and chimpanzees differ by inversions, (...) suggesting perhaps that our ancestral species underwent a divergence process in which gene flow and inversions played a key role.4 However, it remains uncertain whether this interesting finding is actually consistent with the proposed model. BioEssays 25:825–828, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

This paper elaborates the hypothesis that the unique demography and sociology of Ashkenazim in medieval Europe selected for intelligence. Ashkenazi literacy, economic specialization, and closure to inward gene flow led to a social environment in which there was high fitness payoff to intelligence, specifically verbal and mathematical intelligence but not spatial ability. As with any regime of strong directional selection on a quantitative trait, genetic variants that were otherwise fitness reducing rose in frequency. In particular we propose that (...) the well-known clusters of Ashkenazi genetic diseases, the sphingolipid cluster and the DNA repair cluster in particular, increase intelligence in heterozygotes. Other Ashkenazi disorders are known to increase intelligence. Although these disorders have been attributed to a bottleneck in Ashkenazi history and consequent genetic drift, there is no evidence of any bottleneck. Gene frequencies at a large number of autosomal loci show that if there was a bottleneck then subsequent gene flow from Europeans must have been very large, obliterating the effects of any bottleneck. The clustering of the disorders in only a few pathways and the presence at elevated frequency of more than one deleterious allele at many of them could not have been produced by drift. Instead these are signatures of strong and recent natural selection. (shrink)

Darwin's “mystery of mysteries,” the origin of species, is caused by the evolution of speciation phenotypes, i.e. phenotypic differences that depress gene flow between daughter species during speciation. Postmating, prezygotic (PMPZ) differentiation characterizes many closely related species causing conspecific sperm precedence (CSP), wherein a female preferentially utilizes conspecific over heterospecific sperm in fertilization. Until recently, the components of CSP have been difficult to observe and study in internally fertilizing organisms. Research into the mechanisms of CSP is now progressing (...) rapidly with the help of new innovative research tools. With the recent development of a sperm labeling system enabling distinct labels for different males, direct observations of competing male sperm within the female reproductive tract are possible, revealing multiple PMPZ phenotypes that combine to cause CSP. The discovery of mechanisms underlying CSP predicts an exciting future for studies of PMPZ speciation phenotypes and possible general principles underlying the origin of species. (shrink)

Speciation is an aspect of evolutionary biology that has received little philosophical attention apart from articles mainly by biologists such as Mayr (1988). The role of speciation as a terminus a quo for the individuality of species or in the context of punctuated equilibrium theory has been discussed, but not the nature of speciation events themselves. It is the task of this paper to attempt to bring speciation events into some kind of general scheme, based primarily upon the work of (...) Sergey Gavrilets on adaptive landscapes, using migration rate, or gene flow, as the primary scale, and concluding that adaptive and drift explanations are complementary rather than competing. I propose a distinction between intrinsic and extrinsic selection, and the notion of reproductive reach and argue that speciation modes should be discriminated in terms of gene flow, the nature of selection maintaining reproductive reach, and whether the predominant cause is selective or stochastic. I also suggest that the notion of an adaptive “quasispecies” for asexual species is the primitive notion of species, and that members of reproductively coherent sexual species are additionally coadapted to their mating partners. (shrink)

The introduction of transgenic crops into centers of diversity or areas dominated by traditional agriculture threatens genetic diversity as well as indigenous knowledge and culture. It is further argued that the impacts go beyond genetic changes in heterogeneous native crop varieties to embrace effects on evolutionary processes such as gene flow between native crops and wild relatives, and erosion of local knowledge systems such as folk taxonomies and selection of varieties that thrive in marginal environments in which resourcepoor (...) farmers live. (shrink)

In a typological and racial classification, the hypothesis is to suppose that races have existed at a “pure” level, before migrations would result in a large mixing. In this way of thinking, one forgets that migrations have always existed and thus gene flow too. When groups meet, they may or may not bleed, but they always breed.

Speciation is a central but elusive issue in evolutionary biology. Over the past sixty years, the subject has been studied within a framework conceived by Ernst Mayr and Theodosius Dobzhansky and subsequently developed further by numerous other workers. In this “isolation” theory, the evolution of reproductive isolation is a key element of speciation; natural selection is given only secondary importance while gene flow is considered prohibitive to the process. In this paper, I argue that certain elements in this (...) approach have produced confusion and irreconcilability among students of speciation. The more prominent debates in speciation (i.e., the species definition, sympatry/allopatry, and the role of reinforcement) all derive from an inherent conflict between the “isolation” theory and Darwin's “selection” view on species and speciation (in which disruptive selection is crucial). New data, mainly from field ecology, molecular population genetics, laboratory studies with Drosophila and computer analysis, all suggest that the isolation theory may no longer be the most desirable vantage point from which to explore speciation. Instead, environmental selection in large populations, often unimpeded by ongoing gene flow, appears to be the decisive element. The traditional preoccupation with reproductive isolation has created gaps in our knowledge of several crucial issues, mainly regarding the role of environmental selection and its connection with mate selection. BioEssays 22:1134–1141, 2000. © 2000 John Wiley & Sons, Inc. (shrink)

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the 'new mechanical philosophy' to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence--namely, whether divergence in the absence of geographic isolation is possible (or significant). (...) Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate--namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive. (shrink)

Sexually active male haplochromine cichlid fishes possess pronounced yellow ovoid spots on the anal fm, which mimic eggs of the female and have therefore been called egg dummies (Wickler, 1962b).It is thought that divergence in egg dummy characteristics can considerably reduce gene flow and in this way may trigger off reproductive isolation. Two ways in which egg dummy divergence can develop are described. Both mechanisms may have been operating, at the same time and in the same area, in (...) different species, or possibly even in a single species. (shrink)

Although natural selection might be expected to reduce the incidence and severity of disease, disease persists. Natural selection leads to increases in the mean fitness of populations and so will reduce the frequency of disease-associated alleles, but other evolutionary processes, such as mutation and gene flow, may introduce or increase the frequency of these deleterious alleles. The pleiotropic actions of genes and the epistatic interactions between them complicate the relationship between genotype and phenotype, and may result in the (...) preservation of disease-associated alleles. Deleterious alleles may also be maintained because of linkage to beneficial alleles. The inability of natural selection to eliminate diseases of aging is a reminder that fitness – success in producing progeny, or in contributing genes to the population gene pool – is not equivalent to the absence of disease. Nutritional or psychosocial cues may lead to life history strategies that maximize survival to reproductive maturity at the expense of disease later in life. Natural selection acts on genes, cells, and groups, as well as on organisms; the outcome of evolution reflects selection at different levels of biological organization. Finally, the human environment is constantly changing, largely because of the evolution of our parasites and because of changes in cultural beliefs and practices; genetic evolution is comparatively slow and lags behind environmental change. An evolutionary nosology complements traditional medical nosologies and enhances our understanding of the persistence of disease and the meaning of human variation. (shrink)

The analysis distinguishes two types of standards for defining organic produce; process standards and product standards. Process standards define organic products by the method and means of production. Product standards define organic by the physical quality of the end product. The National Organic Program (NOP) uses process standards as the basis for defining organic. However, the situation is complicated by agricultural production practices, which sometimes result in the migration of NOP prohibited substances from conventional to organic fields. When this interaction (...) alters the value of the product or the costs of production, a production externality is said to exist. Defining organic using process, rather than product standards, influences the burden and character of production externalities. The NOP’s emphasis on process standards reduces the likelihood that production externalities will emerge. (shrink)

The controversy over genetically modified [GM] organisms is often framed in terms of possible hazards for human health. Articles in a previous volume of this *Encyclopedia* give a general overview of GM crops [@Mulvaney2014] and specifically examine human health [@Nordgard2014] and labeling [@Bruton2014] issues surrounding GM organisms. This article explores several other aspects of the controversy: environmental concerns, political and legal disputes, and the aim of "feeding the world" and promoting food security. Rather than discussing abstract, hypothetical GM organisms, this (...) article explores the consequences of the GM organisms that have actually been deployed in the particular contexts that they have been deployed, on the belief that there is little point in discussing GM organisms in an idealized or context-independent way. (shrink)

The central dogma of biology holds that genetic information normally flows from DNA to RNA to protein. As a consequence it has been generally assumed that genes generally code for proteins, and that proteins fulfil not only most structural and catalytic but also most regulatory functions, in all cells, from microbes to mammals. However, the latter may not be the case in complex organisms. A number of startling observations about the extent of non-protein-coding RNA (ncRNA) transcription in the higher eukaryotes (...) and the range of genetic and epigenetic phenomena that are RNA-directed suggests that the traditional view of the structure of genetic regulatory systems in animals and plants may be incorrect. ncRNA dominates the genomic output of the higher organisms and has been shown to control chromosome architecture, mRNA turnover and the developmental timing of protein expression, and may also regulate transcription and alternative splicing. This paper re-examines the available evidence and suggests a new framework for considering and understanding the genomic programming of biological complexity, autopoletic development and phenotypic variation. BioEssays 25:930-939,2003. (C) 2003 Wiley Periodicals, Inc. (shrink)

Not by Genes Alone excellently explains Peter J. Richerson and Robert Boyd's important ideas about human gene-culture co-evolution to a broader audience but remains short of a larger vision of civilization. Several decades ago Ralph Burhoe had seen that fertile possibility in Richerson and Boyd's work. I suggest getting past present reductionistic customs to a scientific perspective having an integral place for virtue. Subsystem agency is part of this view, as is the driving role of abundance, whose ultimate origins (...) are in the mysterious, quintessentially energetic Big Bang. The free-rider problem may not impede higher social organization as inexorably as Richerson and Boyd believe; "the tragedy" of enervating leakage from "the commons" may often be less influential than an invigorating flow of externalities to the commons. Eukaryotic origins mark the origin of inevitable wider sharing as higher living systems evolve. I use a metaphor of flesh and spirit in drawing a parallel between that turning point and the wide sharing that occurs in civilization. This helps solve the enigma of the demographic transition. Why do so many productive participants in first-world societies severely restrict their selfish-gene reproduction to below replacement birth rate? It is not because culture is maladaptive but because civilization's brain and womb have become partially differentiated in distinct populations. Considerations of social boundaries, myths of sacrifice, and human creativity help in understanding how human social evolution taps potentials present in reality. Human beings' diverse vigorous activities—the organized ones and the inadvertent ones, the wise and the foolish, the good and the bad, the carefully thoughtful and the merely playful—provide the ground of being, or primordial soup, for cultural entities that transcend our intentions. If we have it right for the most part and are fortunate, we will continue to emerge at higher levels. (shrink)

The potential to collect brain data more directly, with higher resolution, and in greater amounts has heightened worries about mental and brain privacy. In order to manage the risks to individuals posed by these privacy challenges, some have suggested codifying new privacy rights, including a right to “mental privacy.” In this paper, we consider these arguments and conclude that while neurotechnologies do raise significant privacy concerns, such concerns are—at least for now—no different from those raised by other well-understood data collection (...) technologies, such as gene sequencing tools and online surveillance. To better understand the privacy stakes of brain data, we suggest the use of a conceptual framework from information ethics, Helen Nissenbaum’s “contextual integrity” theory. To illustrate the importance of context, we examine neurotechnologies and the information flows they produce in three familiar contexts—healthcare and medical research, criminal justice, and consumer marketing. We argue that by emphasizing what is distinct about brain privacy issues, rather than what they share with other data privacy concerns, risks weakening broader efforts to enact more robust privacy law and policy. (shrink)