Bray-Curtis (AFD) differentiation in molecular ecology: Forecasting, an adjustment (^AA), and comparative performance in selection detection

Geographic genetic differentiation measures are used for purposes such as assessing genetic diversity and connectivity, and searching for signals of selection. Confirmation by unrelated measures can minimize false positives. A popular differentiation measure, Bray-Curtis, has been used increasingly in molecular ecology, renamed AFD (hereafter called BCAFD). Critically, BCAFD is expected to be partially independent of the commonly used Hill “Q-profile” measures. BCAFD needs scrutiny for potential biases, by examining limits on its value, and comparing simulations against expectations. BCAFD has two dependencies on within-population (alpha) variation, undesirable for a between-population (beta) measure. The first dependency is derived from similarity to (Formula presented.) and (Formula presented.). The second dependency is that BCAFD cannot be larger than the highest allele proportion in either location (alpha variation), which can be overcome by data-filtering or by a modified statistic AA or “Adjusted AFD”. The first dependency does not forestall applications such as assessing connectivity or selection, if we know the measure's null behavior under selective neutrality with specified conditions—which is shown in this article for AA, for equilibrium, and nonequilibrium, for the commonly used data type of single-nucleotide-polymorphisms (SNPs) in two locations. Thus, AA can be used in tandem with mathematically contrasting differentiation measures, with the aim of reducing false inferences. For detecting adaptive loci, the relative performance of AA and other measures was evaluated, showing that it is best to use two mathematically different measures simultaneously, and that AA is in one of the best such pairwise criteria. For any application, using AA, rather than BCAFD, avoids the counterintuitive limitation by maximum allele proportion within localities

The introduction of entropy and information methods to ecology by ramon margalef

In ecology and evolution, entropic methods are now used widely and increasingly frequently. Their use can be traced back to Ramon Margalef’s first attempt 70 years ago to use log-series to quantify ecological diversity, including searching for ecologically meaningful groupings within a large assemblage, which we now call the gamma level. The same year, Shannon and Weaver published a generally accessible form of Shannon’s work on information theory, including the measure that we now call Shannon–Wiener entropy. Margalef seized on that measure and soon proposed that ecologists should use the Shannon–Weiner index to evaluate diversity, including assessing local (alpha) diversity and differentiation between localities (beta). He also discussed relating this measure to environmental variables and ecosystem processes such as succession. Over the subsequent decades, he enthusiastically expanded upon his initial suggestions. Finally, 2019 also would have been Margalef’s 100th birthday

Predicting Shannon’s information for genes in finite populations: new uses for old equations

This study provides predictive equations for Shannon’s information in a finite population, which are intuitive and simple enough to see wide scale use in molecular ecology and population genetics. A comprehensive profile of genetic diversity contains three complementary components: numbers of allelic types, Shannon’s information and heterozygosity. Currently heterozygosity has greater resources than Shannon’s information, such as more predictive models and integration into more mainstream genetics software. However, Shannon’s information has several advantages over heterozygosity as a measure of genetic diversity, so it is important to develop Shannon’s information as a new tool for molecular ecology. Past efforts at making forecasts for Shannon’s information in specific molecular ecology scenarios mostly dealt with expectations for Shannon’s information at genetic equilibrium, but dynamic forecasts are also vital. In particular, we must be able to predict loss of genetic diversity when dealing with finite populations, because they risk losing genetic variability, which can have an adverse effect on their survival. We present equations for predicting loss of genetic diversity measured by Shannon’s information. We also provide statistical justification for these models by assessing their fit to data derived from simulations and managed, replicated laboratory populations. The predictive models will enhance the usefulness of Shannon’s information as a measure of genetic diversity; they will also be useful in pest control and conservation

Rapid evolution of leaf physiology in an introduced beach daisy

Photosynthesis is a key biological process. However, we know little about whether plants change their photosynthetic strategy when introduced to a new range. We located the most likely source population for the South African beach daisy Arctotheca populifolia introduced to Australia in the 1930s, and ran a common-garden experiment measuring 10 physiological and morphological leaf traits associated with photosynthesis. Based on predictions from theory, and higher rainfall in the introduced range, we hypothesized that introduced plants would have a (i) higher photosynthetic rate, (ii) lower water-use efficiency (WUE) and (iii) higher nitrogen-use efficiency. However, we found that introduced A. populifolia had a lower photosynthetic rate, higher WUE and lower nitrogen-use efficiency than did plants from Arniston, South Africa. Subsequent site visits suggested that plants in Arniston may be able to access moisture on a rocky shelf, while introduced plants grow on sandy beaches where water can quickly dissipate. Our unexpected findings highlight that: (1) it is important to compare introduced species to their source population for an accurate assessment of evolutionary change; (2) rainfall is not always a suitable proxy for water availability and (3) introduced species often undergo evolutionary changes, but without detailed ecological information we may not be able to accurately predict the direction of these changes

Erratum: Information theory broadens the spectrum of molecular ecology and evolution: (Trends in Ecology and Evolution 32:12, p:948–963, 2017) (Trends in Ecology & Evolution (2017) 32(12) (948–963), (S0169534717302550), (10.1016/j.tree.2017.09.012))

In Sherwin et al. [1], several corrections are required, having been noticed when assisting other researchers to use the methods. In the main text, in Figure III in Box 2, nine subscripts were incorrect (reversing localities 1 and 2). The correct figure is shown below. [Figure presented] On pages 5 and 6 of the supplement, it should be explained that [Formula presented], that is, the averaging happens before conversion to the D scale (see Equations 10 and 11 of Jost [2]). Similarly, on page 8 of the supplement, [Formula presented]. On Page 6 of the supplement, the equation from Dewar et al. [3] is incorrectly transcribed; the correct equation is: [Formula presented] The authors and publisher apologise for any confusion

Tropical plants do not have narrower temperature tolerances, but are more at risk from warming because they are close to their upper thermal limits

Aim: Tropical species are thought to be more susceptible to climate warming than are higher latitude species. This prediction is largely based on the assumption that tropical species can tolerate a narrower range of temperatures. While this prediction holds for some animal taxa, we do not yet know the latitudinal trends in temperature tolerance for plants. We aim to address this knowledge gap and establish if there is a global trend in plant warming risk. Location: Global. Time period: Present–2070. Major taxa studied: Plants. Methods: We used 9,737 records for 1,312 species from the Kew Gardens’ global germination database to quantify global patterns in germination temperature. Results: We found no evidence for a latitudinal gradient in the breadth of temperatures at which plant species can germinate. However, tropical plants are predicted to face the greatest risk from climate warming, because they experience temperatures closer to their upper germination limits. By 2070, over half (79/142) of tropical plant species are predicted to experience temperatures exceeding their optimum germination temperatures, with some even exceeding their maximum germination temperature (41/190). Conversely, 95% of species at latitudes above 45° are predicted to benefit from warming, with environmental temperatures shifting closer to the species’ optimal germination temperatures. Main conclusions: The prediction that tropical plant species would be most at risk under future climate warming was supported by our data, but through a different mechanism to that generally assumed

Rapid reshaping: The evolution of morphological changes in an introduced beach daisy

Thousands of species have been introduced to new ranges worldwide. These introductions provide opportunities for researchers to study evolutionary changes in form and function in response to new environmental conditions. However, almost all previous studies of morphological change in introduced species have compared introduced populations to populations from across the species' native range, so variation within native ranges probably confounds estimates of evolutionary change. In this study, we used micro-satellites to locate the source population for the beach daisy Arctotheca populifolia that had been introduced to eastern Australia. We then compared four introduced populations from Australia with their original South African source population in a common-environment experiment. Despite being separated for less than 100 years, source and introduced populations of A. populifolia display substantial heritable morphological differences. Contrary to the evolution of increased competitive ability hypothesis, introduced plants were shorter than source plants, and introduced and source plants did not differ in total biomass. Contrary to predictions based on higher rainfall in the introduced range, introduced plants had smaller, thicker leaves than source plants. Finally, while source plants develop lobed adult leaves, introduced plants retain their spathulate juvenile leaf shape into adulthood. These changes indicate that rapid evolution in introduced species happens, but not always in the direction predicted by theory

Affiliation history and age similarity predict alliance formation in adult male bottlenose dolphins

Male alliances are an intriguing phenomenon in the context of reproduction since, in most taxa, males compete over an indivisible resource, female fertilization. Adult male bottlenose dolphins (Tursiops aduncus) in Shark Bay, Western Australia, form long-term, multilevel alliances to sequester estrus females. These alliances are therefore critical to male reproductive success. Yet, the long-term processes leading to the formation of such complex social bonds are still poorly understood. To identify the criteria by which male dolphins form social bonds with other males, we adopted a long-term approach by investigating the ontogeny of alliance formation. We followed the individual careers of 59 males for 14 years while they transitioned from adolescence (8-14 years of age) to adulthood (15-21 years old). Analyzing their genetic relationships and social associations in both age groups, we found that the vast majority of social bonds present in adolescence persisted through time. Male associations in early life predict alliance partners as adults. Kinship patterns explained associations during adolescence but not during adulthood. Instead, adult males associated with males of similar age. Our findings suggest that social bonds among peers, rather than kinship, play a central role in the development of adult male polyadic cooperation in dolphins. Multilevel cooperation in adult male bottlenose dolphins is based on friendships that are formed among similarly aged males during their adolescence. Although cooperative behaviors in many animals are found among relatives, this is not the case in dolphins. Our findings reveal the existence of enduring friendships in a complex marine mammal society, similar to those that have been described in many primate species including humans

Evolution of defense and herbivory in introduced plants-Testing enemy release using a known source population, herbivore trials, and time since introduction

The enemy release hypothesis is often cited as a potential explanation for the success of introduced plants; yet, empirical evidence for enemy release is mixed. We aimed to quantify changes in herbivory and defense in introduced plants while controlling for three factors that might have confounded past studies: using a wide native range for comparison with the introduced range, measuring defense traits without determining whether they affect herbivore preferences, and not considering the effect of time since introduction. The first hypothesis we tested was that introduced plants will have evolved lower levels of plant defense compared to their source population. We grew South African (source) and Australian (introduced) beach daisies (Arctotheca populifolia) in a common-environment glasshouse experiment and measured seven defense traits. Introduced plants had more ash, alkaloids, and leaf hairs than source plants, but were also less tough, with a lower C:N ratio and less phenolics. Overall, we found no difference in defense between source and introduced plants. To determine whether the feeding habits of herbivores align with changes in defense traits, we conducted preference feeding trials using five different herbivore species. Herbivores showed no overall preference for leaves from either group. The second hypothesis we tested was that herbivory on introduced plant species will increase through time after introduction to a new range. We recorded leaf damage on herbarium specimens of seven species introduced to eastern Australia and three native control species. We found no change in the overall level of herbivory experienced by introduced plants since arriving in Australia.Conclusion In the field of invasion ecology, we need to rethink the paradigm that species introduced to a new range undergo simple decreases in defenses against herbivores. Instead, plants are likely to employ a range of defense traits that evolve in both coordinated and opposing ways in response to a plethora of different biotic and abiotic selective pressures