Polyploidy is genetic hence may cause non-adaptive radiations, whereas pseudopolyploidy is genomic hence may cause adaptive non-radiations.

There are two ways eukaryotes double number of chromosomes: (1) whole genome duplication (polyploidy), in which all nuclear DNA is replicated, and (2) karyotypic fission (pseudopolyploidy), in which all chromosomes are physically bifurcated. We contrast polyploidy with pseudopolyploidy, highlighting when it is crucial to look at genetic vs. genomic levels. We review history of pseudopolyploidy, including recent mechanisms by which chromosomal bifurcation may occur and outline methods for detecting such genomic changes. We then delve into the evolutionary implications, with particular focus on adaptive potential, of these two forms of doubling chromosome numbers. We address the common assertion that polyploidy induces adaptive radiations, which contains three fallacies. First, while polyploidy causes quantum speciation, evolutionary theory implies that these radiations should be non-adaptive. Polyploidy causes reproductive isolation, minute effective population sizes, and increased mutation rates, which all imply a diminished role for selection. Second, due to lack of karyotyping in recent decades and lack of distinction between genomic and genetic effects, it is usually impossible to detect pseudopolyploids. Third, pseudopolyploids lack minority cytotype exclusion because they readily backcross with their progenitors, which thereby means no reproductive isolation for newly formed pseudopolyploids. Pseudopolyploidy will thereby not result in radiations until pseudopolyploid descendants undergo subsequent chromosome rearrangements or grow new centromeres. Pseudopolyploids may have a modest selective advantage over their progenitors due to diminished linkage disequilibrium. Thus, pseudopolyploidy may induce adaptive non-radiations. We encourage a renaissance of karyotyping to distinguish between these two mechanisms and a renaissance in genomic perspectives in evolution.

Maternal influences on early development: preferred temperature prior to oviposition hastens embryogenesis and enhances offspring traits in the Children's python, Antaresia childreni.

Embryonic life is particularly sensitive to its surroundings, and the developmental environment can have long-lasting effects on offspring. In oviparous species, the impacts of the developmental environment on offspring traits are mostly examined during development within the egg. However, as more than 25% of the development of squamate reptiles can occur prior to oviposition, we explored the effect of thermal conditions on development prior to oviposition in an oviparous snake species, the Children's python (Antaresia childreni). We housed gravid female pythons under three thermal cycles: an optimal regime that reflected maternal preference in a non-constrained environment (constant preferred body temperature of gravid females, T(set)=31.5°C) and two mildly suboptimal regimes that shared the same mean temperature of 27.7°C, but differed in the duration at T(set). In one of the constraining regimes, females had access to T(set) for 4 h daily whereas in the other regime, females never reached T(set) (maximal temperature of 29.0°C). Thermal treatments were maintained throughout gravidity in all three groups, but, after oviposition, all eggs were incubated at T(set) until hatching. Compared with the optimal regime, the two suboptimal regimes had a longer duration of gravidity, which resulted in delayed hatching. Between the two suboptimal regimes, gravidity was significantly shorter in the treatment that included time at T(set). Furthermore, suboptimal regimes influenced offspring traits at hatching, including body morphology, antipredator behavior, strength and metabolism. However, partial access to maternal T(set) significantly enhanced several offspring traits, including performance. Our results demonstrate the importance of time at T(set) on early development and suggest an adaptive significance of maternal thermoregulation prior to oviposition.

Commentary: Do we have a consistent terminology for species diversity? The fallacy of true diversity.

There is no single best index that can be used to answer all questions about species diversity. Entropy-based diversity indices, including Hill's indices, cannot account for geographical and phylogenetic structure. While a single diversity index arises if we impose several constraints-most notably that gamma diversity be completely decomposed into alpha and beta diversity-there are many ecological questions regarding species diversity for which it is counterproductive, requiring decomposability. Non-decomposable components of gamma diversity may quantify important intrinsic ecological properties, such as resilience or nestedness.

Prediction of Arctic plant phenological sensitivity to climate change from historical records.

The pace of climate change in the Arctic is dramatic, with temperatures rising at a rate double the global average. The timing of flowering and fruiting (phenology) is often temperature dependent and tends to advance as the climate warms. Herbarium specimens, photographs, and field observations can provide historical phenology records and have been used, on a localised scale, to predict species' phenological sensitivity to climate change. Conducting similar localised studies in the Canadian Arctic, however, poses a challenge where the collection of herbarium specimens, photographs, and field observations have been temporally and spatially sporadic. We used flowering and seed dispersal times of 23 Arctic species from herbarium specimens, photographs, and field observations collected from across the 2.1 million km2 area of Nunavut, Canada, to determine (1) which monthly temperatures influence flowering and seed dispersal times; (2) species' phenological sensitivity to temperature; and (3) whether flowering or seed dispersal times have advanced over the past 120 years. We tested this at different spatial scales and compared the sensitivity in different regions of Nunavut. Broadly speaking, this research serves as a proof of concept to assess whether phenology-climate change studies using historic data can be conducted at large spatial scales. Flowering times and seed dispersal time were most strongly correlated with June and July temperatures, respectively. Seed dispersal times have advanced at double the rate of flowering times over the past 120 years, reflecting greater late-summer temperature rises in Nunavut. There is great diversity in the flowering time sensitivity to temperature of Arctic plant species, suggesting climate change implications for Arctic ecological communities, including altered community composition, competition, and pollinator interactions. Intraspecific temperature sensitivity and warming trends varied markedly across Nunavut and could result in greater changes in some parts of Nunavut than in others.

Decomposing multilocus linkage disequilibrium.

We present a mathematically precise formulation of total linkage disequilibrium between multiple loci as the deviation from probabilistic independence and provide explicit formulas for all higher-order terms of linkage disequilibrium, thereby combining J. Dausset et al.'s 1978 definition of linkage disequilibrium with H. Geiringer's 1944 approach. We recursively decompose higher-order linkage disequilibrium terms into lower-order ones. Our greatest simplification comes from defining linkage disequilibrium at a single locus as allele frequency at that locus. At each level, decomposition of linkage disequilibrium is mathematically equivalent to number theoretic compositions of positive integers; i.e., we have converted a genetic decomposition into a mathematical decomposition.

Normalized mutual entropy in biology: quantifying division of labor.

Division of labor is one of the primary adaptations of sociality and the focus of much theoretical work on self-organization. This work has been hampered by the lack of a quantitative measure of division of labor that can be applied across systems. We divide Shannon's mutual entropy by marginal entropy to quantify division of labor, rendering it robust over changes in number of individuals or tasks. Reinterpreting individuals and tasks makes this methodology applicable to a wide range of other contexts, such as breeding systems and predator-prey interactions.

Neo-Lamarckian medicine.

Darwinian medicine is the treatment of disease based on evolution. The underlying assumption of Darwinian medicine is that traits are coded by genes, which are often assumed to be sequences of DNA nucleotides. The quantitative genetic ramification of this perspective is that traits, including disease susceptibility, are either caused by genes or by the environment, with genotype-by-environment interactions usually considered statistical artefacts. I emphasize also examining those epigenetic signals that can be altered by environmental perturbations and then transmitted to subsequent generations. Although seldom studied, environmentally-alterable meiotically-heritable epigenetic signals exist and provide a mechanism underlying genotype-by-environment interactions. Environment of a parent can affect its descendants by heritably altering epigenetic signals. Neo-Lamarckian medicine is the application of these evolutionary epigenetic notions to diseases and could have enormous public health and environmental policy implications. If industrial contaminants adversely affect organisms by meiotically-heritably altering their epigenetic signals, then cleaning up these contaminants will not remedy the problem. Once contaminants have adversely altered an individual's epigenetic signals, this harm will be transmitted to future generations even if they are not exposed to the contaminant. Exposure to environmental shocks such as free radicals or other carcinogens can alter cytosine methylation patterns on regulatory genes. This can cause cancer by up-regulating genes for cell division or by down-regulating tumour suppressor genes. Environmentally-alterable meiotically-heritable epigenetic signals could also underlie other diseases, such as diabetes, Prader-Willi syndrome, and many complex diseases. If environmentally-altered meiotically-heritable epigenetic effects are widespread - which is an important open empirical question - they have the potential to alter paradigmatic views of evolutionary medicine and the putative dichotomy of nature versus nurture. Neo-Lamarckian medicine would thereby shift emphasis from cure to prevention of diseases.

Kin recognition by roots occurs in cycads and probably in conifers.

Kin recognition by the roots of Cycas edentata was recently demonstrated. Our extensive literature search revealed this to be the first report of kin recognition in any spermatophyte other than angiosperms. Based on this new validation that the phenomenon occurs among phylogenetically diverse taxa, we conclude that kin recognition by roots may be an ancient phenomenon.

Mean annual precipitation explains spatiotemporal patterns of Cenozoic mammal beta diversity and latitudinal diversity gradients in North America.

Spatial diversity patterns are thought to be driven by climate-mediated processes. However, temporal patterns of community composition remain poorly studied. We provide two complementary analyses of North American mammal diversity, using (i) a paleontological dataset (2077 localities with 2493 taxon occurrences) spanning 21 discrete subdivisions of the Cenozoic based on North American Land Mammal Ages (36 Ma--present), and (ii) climate space model predictions for 744 extant mammals under eight scenarios of future climate change. Spatial variation in fossil mammal community structure (ß diversity) is highest at intermediate values of continental mean annual precipitation (MAP) estimated from paleosols (∼ 450 mm/year) and declines under both wetter and drier conditions, reflecting diversity patterns of modern mammals. Latitudinal gradients in community change (latitudinal turnover gradients, aka LTGs) increase in strength through the Cenozoic, but also show a cyclical pattern that is significantly explained by MAP. In general, LTGs are weakest when continental MAP is highest, similar to modern tropical ecosystems in which latitudinal diversity gradients are weak or undetectable. Projections under modeled climate change show no substantial change in ß diversity or LTG strength for North American mammals. Our results suggest that similar climate-mediated mechanisms might drive spatial and temporal patterns of community composition in both fossil and extant mammals. We also provide empirical evidence that the ecological processes on which climate space models are based are insufficient for accurately forecasting long-term mammalian response to anthropogenic climate change and inclusion of historical parameters may be essential.

Single cell heterogeneity: why unstable genomes are incompatible with average profiles.

Multi-level heterogeneity is a fundamental but underappreciated feature of cancer. Most technical and analytical methods either completely ignore heterogeneity or do not fully account for it, as heterogeneity has been considered noise that needs to be eliminated. We have used single-cell and population-based assays to describe an instability-mediated mechanism where genome heterogeneity drastically affects cell growth and cannot be accurately measured using conventional averages. First, we show that most unstable cancer cell populations exhibit high levels of karyotype heterogeneity, where it is difficult, if not impossible, to karyotypically clone cells. Second, by comparing stable and unstable cell populations, we show that instability-mediated karyotype heterogeneity leads to growth heterogeneity, where outliers dominantly contribute to population growth and exhibit shorter cell cycles. Predictability of population growth is more difficult for heterogeneous cell populations than for homogenous cell populations. Since "outliers" play an important role in cancer evolution, where genome instability is the key feature, averaging methods used to characterize cell populations are misleading. Variances quantify heterogeneity; means (averages) smooth heterogeneity, invariably hiding it. Cell populations of pathological conditions with high genome instability, like cancer, behave differently than karyotypically homogeneous cell populations. Single-cell analysis is thus needed when cells are not genomically identical. Despite increased attention given to single-cell variation mediated heterogeneity of cancer cells, continued use of average-based methods is not only inaccurate but deceptive, as the "average" cancer cell clearly does not exist. Genome-level heterogeneity also may explain population heterogeneity, drug resistance, and cancer evolution.

Evolutionary developmental biology in cycad phenology.

We recently described lack of phenotypic plasticity in reproductive organ development and substantial plasticity in vegetative organ development for the cycad Cycas micronesica. Is there an evo-devo explanation for the disparity in phenotypic plasticity of vegetative vs. reproductive organs? Despite modularity, might evolution of cycad phenology be controlled more by drift than selection?

Phenotypic covariance structure and its divergence for acoustic mate attraction signals among four cricket species.

The phenotypic variance-covariance matrix (P) describes the multivariate distribution of a population in phenotypic space, providing direct insight into the appropriateness of measured traits within the context of multicollinearity (i.e., do they describe any significant variance that is independent of other traits), and whether trait covariances restrict the combinations of phenotypes available to selection. Given the importance of P, it is therefore surprising that phenotypic covariances are seldom jointly analyzed and that the dimensionality of P has rarely been investigated in a rigorous statistical framework. Here, we used a repeated measures approach to quantify P separately for populations of four cricket species using seven acoustic signaling traits thought to enhance mate attraction. P was of full or almost full dimensionality in all four species, indicating that all traits conveyed some information that was independent of the other traits, and that phenotypic trait covariances do not constrain the combinations of signaling traits available to selection. P also differed significantly among species, although the dominant axis of phenotypic variation (p(max)) was largely shared among three of the species (Acheta domesticus, Gryllus assimilis, G. texensis), but different in the fourth (G. veletis). In G. veletis and A. domesticus, but not G. assimilis and G. texensis, p(max) was correlated with body size, while p(max) was not correlated with residual mass (a condition measure) in any of the species. This study reveals the importance of jointly analyzing phenotypic traits.

Sex reduces genetic variation: a multidisciplinary review.

For over a century, the paradigm has been that sex invariably increases genetic variation, despite many renowned biologists asserting that sex decreases most genetic variation. Sex is usually perceived as the source of additive genetic variance that drives eukaryotic evolution vis-à-vis adaptation and Fisher's fundamental theorem. However, evidence for sex decreasing genetic variation appears in ecology, paleontology, population genetics, and cancer biology. The common thread among many of these disciplines is that sex acts like a coarse filter, weeding out major changes, such as chromosomal rearrangements (that are almost always deleterious), but letting minor variation, such as changes at the nucleotide or gene level (that are often neutral), flow through the sexual sieve. Sex acts as a constraint on genomic and epigenetic variation, thereby limiting adaptive evolution. The diverse reasons for sex reducing genetic variation (especially at the genome level) and slowing down evolution may provide a sufficient benefit to offset the famed costs of sex.

Multi-way multi-group segregation and diversity indices.

BACKGROUND: How can we compute a segregation or diversity index from a three-way or multi-way contingency table, where each variable can take on an arbitrary finite number of values and where the index takes values between zero and one? Previous methods only exist for two-way contingency tables or dichotomous variables. A prototypical three-way case is the segregation index of a set of industries or departments given multiple explanatory variables of both sex and race. This can be further extended to other variables, such as disability, number of years of education, and former military service. METHODOLOGY/PRINCIPAL FINDINGS: We extend existing segregation indices based on Euclidean distance (square of coefficient of variation) and Boltzmann/Shannon/Theil index from two-way to multi-way contingency tables by including multiple summations. We provide several biological applications, such as indices for age polyethism and linkage disequilibrium. We also provide a new heuristic conceptualization of entropy-based indices. Higher order association measures are often independent of lower order ones, hence an overall segregation or diversity index should be the arithmetic mean of the normalized association measures at all orders. These methods are applicable when individuals self-identify as multiple races or even multiple sexes and when individuals work part-time in multiple industries. CONCLUSIONS/SIGNIFICANCE: The policy implications of this work are enormous, allowing people to rigorously test whether employment or biological diversity has changed.

Species richness and the analytic geometry of latitudinal and altitudinal gradients.

Extensive empirical work has shown that species richness decreases roughly exponentially or quadratically with latitude. What appears to be a latitudinal gradient in fact may simply be a negative correlation of latitude with area at that latitude, due to convergence of lines of meridian at the poles. There is simply less area at high latitudes, which means fewer niches and fewer opportunities for speciation, hence diminished biodiversity at high latitudes. Similarly, analytic geometry of a cone shows that species number should decrease linearly with altitude on a conical mountain. Here, I provide an explicit mathematical model of the area hypothesis of species richness along latitude and altitude gradients. I re-analyze a previously published latitudinal gradient dataset and show that species number is a linear function of the predicted area and that species number is more fully explained by predicted area than by a quadratic function of latitude. However, analytic geometry is not needed if precise measures of area are known.

Theory for why dioecious plants have equal length sex chromosomes.

Dioecy and sex chromosomes almost certainly evolved from ancestral hermaphrodites that only possessed autosomes. There is a growing body of evidence that genes for female or male function were then epigenetically suppressed in some of these hermaphrodites, creating the first males or females and nascent sex chromosomes. The incipient sex-determining epigenetic signals, such as cytosine methylation, then drove Muller's ratchet in many animals, resulting in shorter Y chromosomes. Based on this theory of sex chromosome evolution and limited data on gametophyte gene expression, I argue that plants should be largely immune from Muller's ratchet and therefore retain their ancestral state of equal length sex chromosomes, unless they incur chromosomal rearrangements or large-scale insertions of duplicated genomes. Usually heteromorphic sex chromosomes canalize dioecy, but extensive polyploidy or polysomy can provide an escape from this canalized dioecy. This theory implies that dioecy due to heteromorphic sex chromosomes should be evolutionarily ephemeral in bryophytes and homosporous pteridophytes because of their extraordinarily high incidences of polyploidy. And, if anything, these very high incidences of polyploidy are responsible for translocation or gradual addition of beneficial genes, rather than gradual reduction in the length of a sex chromosome.

Colony response to graded resource changes: an analytical model of the influence of genotype, environment, and dominance.

Successful social groups must respond dynamically to environmental changes. However, a flexible group response requires the coordination of many individuals. Here we offer a static analytical model that integrates variation in environment-based cues for performance of a task with genetically and environmentally based variation in individual responses, and predicts the resultant colony behavior for that task. We also provide formulae for computing effective number of alleles in a haplo-diploid colony founded by any number of parents. Variable colony resources combined with variation among worker phenotypes generate known patterns of colony flexibility, allowing us to explicitly test how the number of loci, dominance/codominance, and the phenotype's environment influences group response. Our model indicates that the number of loci strongly influences colony behavior. For one or two loci, the proportion of workers foraging for pollen remain constant over vast increases in colony pollen stores, but then drops dramatically when the pollen stores increase past a specific threshold. As the number of loci controlling pollen foraging increases, graded increases in pollen stores result in a graded drop in the proportion of the worker population foraging for pollen. The effect of number of alleles is less strong, a result we discuss in light of the fact that a low number of effective alleles are expected in a colony. Comparisons of our model with empirical honey bee (Apis mellifera) data indicate that worker foraging response to pollen stores is driven by one or two loci, each with dominant allelic effects. The growing body of evidence that genotype has strong effects on task performance in social insect colonies, and the variation in within-colony genetic diversity across social insect taxa, make our model broadly applicable in explaining social group coordination.