Microsatellites or Single Sequence Repeats (SSRs) are extensively employed in plant genetics studies, using both low and high throughput genotyping approaches. Motivated by the importance of these sequences over the last decades this review aims to address some theoretical aspects of SSRs, including definition, characterization and biological function. The methodologies for the development of SSR loci, genotyping and their applications as molecular markers are also reviewed. Finally, two data surveys are presented. The first was conducted using the main database of Web of Science, prospecting for articles published over the period from 2010 to 2015, resulting in approximately 930 records. The second survey was focused on papers that aimed at SSR marker development, published in the American Journal of Botany's Primer Notes and Protocols in Plant Sciences (over 2013 up to 2015), resulting in a total of 87 publications. This scenario confirms the current relevance of SSRs and indicates their continuous utilization in plant science.

/pdf/microsatellite-markers-what-they-mean-and-why-they-are-so-mp9gfvp8kq.pdf

Microsatellite markers: what they mean and why they are so useful.

Introduction. Ecologically Meaningful Germination Studies. Types of Seed Dormancy. Germination Ecology of Seeds with Nondeep Physiological Dormancy. Germination Ecology of Seeds with Morphophysiological Dormancy. Germination Ecology of Seeds with Physical Dormancy. Germination Ecology of Seeds in the Persistent Seed Bank. Causes of Within-Species Variations in Seed Dormancy and Germination Characteristics. A Geographical Perspective on Germination Ecology: Tropical and Subtropical Zones. A Geographical Perspective on Germination Ecology: Temperate and Arctic Zones. Germination Ecology of Plants with Specialized Life Cycles and/or Habitats. Biogeographical and Evolutionary Aspects of Seed Dormancy. Subject Index.

A Definitive Book on Seed Ecology@@@Seeds: Ecology, Biogeography, and Evolution of Dormancy and Germination

http://web-facstaff.sas.upenn.edu/~seyfarth/Publications/Seyfarth%26Cheney-CurrOpinionNeuro.pdf

The evolution of language from social cognition

The number of times an organism reproduces (i.e., its mode of parity) is a fundamental life-history character, and evolutionary and ecological models that compare the relative fitnesses of different modes of parity are common in life-history theory and theoretical biology. Despite the success of mathematical models designed to compare intrinsic rates of increase (i.e., density-independent growth rates) between annual-semelparous and perennial-iteroparous reproductive schedules, there is widespread evidence that variation in reproductive allocation among semelparous and iteroparous organisms alike is continuous. This study reviews the ecological and molecular evidence for the continuity and plasticity of modes of parity-that is, the idea that annual-semelparous and perennial-iteroparous life histories are better understood as endpoints along a continuum of possible strategies. I conclude that parity should be understood as a continuum of different modes of parity, which differ by the degree to which they disperse or concentrate reproductive effort in time. I further argue that there are three main implications of this conclusion: (1) that seasonality should not be conflated with parity; (2) that mathematical models purporting to explain the general evolution of semelparous life histories from iteroparous ones (or vice versa) should not assume that organisms can only display either an annual-semelparous life history or a perennial-iteroparous one; and (3) that evolutionary ecologists should base explanations of how different life-history strategies evolve on the physiological or molecular basis of traits underlying different modes of parity.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.3341

Between semelparity and iteroparity: Empirical evidence for a continuum of modes of parity.

The term 'life-history theory' is a familiar label in several disciplines. Life-history theory has its roots in evolutionary models of the fitness consequences of allocating energy to reproduction, growth and self-maintenance across the life course. Increasingly, the term is also used in the conceptual framing of psychological and social-science studies. As a scientific paradigm expands its range, its parts can become conceptually isolated from one another, even to the point that it is no longer held together by a common core of shared ideas. Here, we investigate the literature invoking the term 'life-history theory' using quantitative bibliometric methods based on patterns of shared citation. Results show that the literature up to and including 2010 was relatively coherent: it drew on a shared body of core references and had only weak cluster divisions running along taxonomic lines. The post-2010 literature is more fragmented: it has more marked cluster boundaries, both between the human and non-human literatures, and within the human literature. In particular, two clusters of human research based on the idea of a fast-slow continuum of individual differences are bibliometrically isolated from the rest. We also find some evidence suggesting a decline over time in the incidence of formal modelling. We point out that the human fast-slow continuum literature is conceptually closer to the non-human 'pace-of-life' literature than it is to the formal life-history framework in ecology and evolution.

https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2019.0040

The evolution of life-history theory: a bibliometric analysis of an interdisciplinary research area.

Supergenes are genomic regions containing sets of tightly linked loci that control multi-trait phenotypic polymorphisms under balancing selection. Recent advances in genomics have uncovered significant variation in both the genomic architecture as well as the mode of origin of supergenes across diverse organismal systems. Although the role of genomic architecture for the origin of supergenes has been much discussed, differences in the genomic architecture also subsequently affect the evolutionary trajectory of supergenes and the rate of degeneration of supergene haplotypes. In this review, we synthesize recent genomic work and historical models of supergene evolution, highlighting how the genomic architecture of supergenes affects their evolutionary fate. We discuss how recent findings on classic supergenes involved in governing ant colony social form, mimicry in butterflies, and heterostyly in flowering plants relate to theoretical expectations. Furthermore, we use forward simulations to demonstrate that differences in genomic architecture affect the degeneration of supergenes. Finally, we discuss implications of the evolution of supergene haplotypes for the long-term fate of balanced polymorphisms governed by supergenes.

/pdf/the-genomic-architecture-and-evolutionary-fates-of-2ambfgl968.pdf

The Genomic Architecture and Evolutionary Fates of Supergenes.

The genomic architecture and evolutionary fates of supergenes

Graduate teaching assistants (GTAs) are used extensively as undergraduate science lab instructors at universities, yet they often have having minimal instructional training and little is known about effective training methods. This blind randomized control trial study assessed the impact of two training regimens on GTA teaching effectiveness. GTAs teaching undergraduate biology labs (n = 52) completed five hours of training in either inquiry-based learning pedagogy or general instructional "best practices". GTA teaching effectiveness was evaluated using: (1) a nine-factor student evaluation of educational quality; (2) a six-factor questionnaire for student learning; and (3) course grades. Ratings from both GTAs and undergraduates indicated that indicated that the inquiry-based learning pedagogy training has a positive effect on GTA teaching effectiveness.

/pdf/inquiry-based-training-improves-teaching-effectiveness-of-5aswx3g0zi.pdf

Inquiry-based training improves teaching effectiveness of biology teaching assistants.

Semelparity and iteroparity are considered to be distinct and alternative life-history strategies, where semelparity is characterized by a single, fatal reproductive episode, and iteroparity by repeated reproduction throughout life. However, semelparous organisms do not reproduce instantaneously; typically reproduction occurs over an extended time period. If variation in reproductive allocation exists within such a prolonged reproductive episode, semelparity may be considered iteroparity over a shorter time scale. This continuity hypothesis predicts that “semelparous” organisms with relatively low probability of survival after age at first reproduction will exhibit more extreme semelparity than those with high probability of adult survival. This contrasts with the conception of semelparity as a distinct reproductive strategy expressing a discrete, single, bout of reproduction, where reproductive phenotype is expected to be relatively invariant. Here, we manipulate expected season length—and thus expected adult survival—to ask whether Lobelia inflata, a classic “semelparous” plant, exhibits plasticity along a semelparous-iteroparous continuum. Groups of replicated genotypes were manipulated to initiate reproduction at different points in the growing season in each of three years. In lab and field populations alike, the norm of reaction in parity across a season was as predicted by the continuity hypothesis: as individuals bolted later, they showed shorter time to, and smaller size at first reproduction, and multiplied their reproductive organs through branching, thus producing offspring more simultaneously. This work demonstrates that reproductive effort occurs along a semelparous-iteroparous continuum within a “semelparous” organism, and that variation in parity occurs within populations as a result of phenotypic plasticity.

https://link.springer.com/content/pdf/10.1186%2F1471-2148-14-90.pdf

The continuum between semelparity and iteroparity: plastic expression of parity in response to season length manipulation in Lobelia inflata

Seed heteromorphism is the reproductive strategy characterized by the simultaneous production of multiple seed types. While comparing heteromorphic to monomorphic strategies is mathematically simple, there is no explicit test for assessing which ratio of seed morphs minimizes fitness variance, and hence offers a basis for comparing different heteromorphic strategies. Such a test may be particularly valuable when more than two distinct morphs are present, since many strategies may have equivalent geometric fitnesses. As noted by Gillespie (1974), in these cases avoiding rare but evolutionarily important instances of severe reductions in fitness involves the minimization of variation in fitness-i.e., risk. Here I compute the optimal proportions of two or more seed morphs for heteromorphic strategies that either: (1) minimize total fitness variance; or (2) maximize the fitness-risk ratio-i.e., the "extra" fitness accrued per unit of "extra" fitness variance. This work thereby provides a testable null hypothesis to estimate the optimal frequencies of seed morphs when multiple heteromorphic strategies have evolved in environments with severe fitness risks. Moreover, it also permits the calculation of expected seed morph frequencies when more than two seed morphs are produced.

/pdf/minimal-risk-seed-heteromorphism-proportions-of-seed-morphs-48pvgpl63o.pdf

P. William Hughes

Papers

The Genomic Architecture and Evolutionary Fates of Supergenes.

The genomic architecture and evolutionary fates of supergenes

Inquiry-based training improves teaching effectiveness of biology teaching assistants.

The continuum between semelparity and iteroparity: plastic expression of parity in response to season length manipulation in Lobelia inflata

Minimal-Risk Seed Heteromorphism: Proportions of Seed Morphs for Optimal Risk-Averse Heteromorphic Strategies.