Life-History Divergence In Chinook Salmon: Historic Contingency And Parallel Evolution

By jointly considering patterns of genetic and life-history diversity in over 100 populations of Chinook salmon from California to British Columbia, we demonstrate the importance of two different mechanisms for life history evolution. Mapping adult run timing (the life-history trait most commonly used to characterize salmon populations) onto a tree based on the genetic data shows that the same run-time phenotypes exist in many different genetic lineages. In a hierarchical gene diversity analysis, differences among major geographic and ecological provinces explained the majority (62%) of the overall GST, whereas run-time differences explained only 10%. Collectively, these results indicate that run-timing diversity has developed independently by a process of parallel evolution in many different coastal areas. However, genetic differences between coastal populations with different run timing from the same basin are very modest (GST \u3c 0.02), indicating that evolutionary divergence of this trait linked to reproductive isolation has not led to parallel speciation, probably because of ongoing gene flow. A strikingly different pattern is seen in the interior Columbia River Basin, where run timing and other correlated life-history traits map cleanly onto two divergent genetic lineages (GST ~ 0.15), indicating that some patterns of life-history diversity have a much older origin. Indeed, genetic data indicate that in the interior Columbia Basin, the two divergent lineages behave essentially as separate biological species, showing little evidence of genetic contact in spite of the fact that they co-migrate through large areas of the river and ocean and in some locations spawn in nearly adjacent areas

Reliable effective number of breeders/adult census size ratios in seasonal-breeding species: Opportunity for integrative demographic inferences based on capture-mark-recapture data and multilocus genotypes

The ratio of the effective number of breeders (Nb) to the adult census size (Na), Nb/Na, approximates the departure from the standard capacity of a population to maintain genetic diversity in one reproductive season. This information is relevant for assessing population status, understanding evolutionary processes operating at local scales, and unraveling how life-history traits affect these processes. However, our knowledge on Nb/Na ratios in nature is limited because estimation of both parameters is challenging. The sibship frequency (SF) method is adequate for reliable Nb estimation because it is based on sibship and parentage reconstruction from genetic marker data, thereby providing demographic inferences that can be compared with field-based information. In addition, capture–mark–recapture (CMR) robust design methods are well suited for Na estimation in seasonal-breeding species. We used tadpole genotypes of three pond-breeding amphibian species (Epidalea calamita, Hyla molleri, and Pelophylax perezi, n = 73–96 single-cohort tadpoles/species genotyped at 15–17 microsatellite loci) and candidate parental genotypes (n = 94–300 adults/species) to estimate Nb by the SF method. To assess the reliability of Nb estimates, we compared sibship and parentage inferences with field-based information and checked for the convergence of results in replicated subsampled analyses. Finally, we used CMR data from a 6-year monitoring program to estimate annual Na in the three species and calculate the Nb/Na ratio. Reliable ratios were obtained for E. calamita (Nb/Na = 0.18–0.28) and P. perezi (0.5), but in H. molleri, Na could not be estimated and genetic information proved insufficient for reliable Nb estimation. Integrative demographic studies taking full advantage of SF and CMR methods can provide accurate estimates of the Nb/Na ratio in seasonal-breeding species. Importantly, the SF method provides results that can be readily evaluated for reliability. This represents a good opportunity for obtaining robust demographic inferences with wide applications for evolutionary and conservation research

Anomalous thermal maturities caused by carbonaceous sediments

Sedimentary rocks such as coal and carbonaceous mudstone which contain abundant carbonaceous matter are characterized by thermal conductivity much lower than that exhibited by other common rock types, by a factor of 5–10. As a result, temperature gradients in such sediments can range up to 0.25 °Cm -1 even under conditions of average heat flow. When such steep gradients extend over a significant sedimentary thickness, temperatures of underlying rock units are elevated, causing both organic and inorganic phases to record what seem to be anomalously high levels of thermal maturity. This carbonaceous blanket insulating effect may help to explain unusual levels of maturity observed at shallow depths in the Appalachian Basin, Michigan Basin and other regions of the world with significant carbonaceous strata.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73579/1/j.1365-2117.1994.tb00074.x.pd

Luscious: A High Quality Dessert Pear for the North

This bulletin contains a brief introduction to the Luscious desert pear

Combining demographic and genetic factors to assess population vulnerability in stream species

Accelerating climate change and other cumulative stressors create an urgent need to understand the influence of environmental variation and landscape features on the connectivity and vulnerability of freshwater species. Here, we introduce a novel modeling framework for aquatic systems that integrates spatially explicit, individual-based, demographic and genetic (demogenetic) assessments with environmental variables. To show its potential utility, we simulated a hypothetical network of 19 migratory riverine populations (e.g., salmonids) using a riverscape connectivity and demogenetic model (CDFISH). We assessed how stream resistance to movement (a function of water temperature, fluvial distance, and physical barriers) might influence demogenetic connectivity, and hence, population vulnerability. We present demographic metrics (abundance, immigration, and change in abundance) and genetic metrics (diversity, differentiation, and change in differentiation), and combine them into a single vulnerability index for identifying populations at risk of extirpation. We considered four realistic scenarios that illustrate the relative sensitivity of these metrics for early detection of reduced connectivity: (1) maximum resistance due to high water temperatures throughout the network, (2) minimum resistance due to low water temperatures throughout the network, (3) increased resistance at a tributary junction caused by a partial barrier, and (4) complete isolation of a tributary, leaving resident individuals only. We then applied this demogenetic framework using empirical data for a bull trout (Salvelinus confluentus) metapopulation in the upper Flathead River system, Canada and USA, to assess how current and predicted future stream warming may influence population vulnerability. Results suggest that warmer water temperatures and associated barriers to movement (e.g., low flows, dewatering) are predicted to fragment suitable habitat for migratory salmonids, resulting in the loss of genetic diversity and reduced numbers in certain vulnerable populations. This demogenetic simulation framework, which is illustrated in a web-based interactive mapping prototype, should be useful for evaluating population vulnerability in a wide variety of dendritic and fragment

Guidelines for genetic data analysis

The IWC Scientific Committee recently adopted guidelines for quality control of DNA data. Once data have been collected, the next step is to analyse the data and make inferences that are useful for addressing practical problems in conservation and management of cetaceans. This is a complex exercise, as numerous analyses are possible and users have a wide range of choices of software programs for implementing the analyses. This paper reviews the underlying issues, illustrates application of different types of genetic data analysis to two complex management problems (involving common minke whales and humpback whales), and concludes with a number of recommendations for best practices in the analysis of population genetic data. An extensive Appendix provides a detailed review and critique of most types of analyses that are used with population genetic data for cetaceans.Publisher PDFPeer reviewe

Comparison of three techniques for genetic estimation ofeffective population size in a critically endangered parrot

Understanding the current population size of small, spatially aggregating populations of species is essential for their conservation. Reliable estimates of the effective population size (Ne) can be used to provide an early warning for conservation managers of the risks to genetic viability of small populations. Critically endangered, migratory swift parrots Lathamus discolor exist in a single panmictic population in Australia. In their Tasmanian breeding range, they are at severe risk of predation by introduced sugar gliders, exacerbated by deforestation. We used three genetic approaches to estimate Ne using DNA samples genotyped by microsatellite markers and existing life-history data of swift parrots. Based on all samples, we revealed small contemporary Ne estimates across methods (range: 44-140), supporting the need to urgently address threatening processes. Using the 0.5 Ne/N ratio calculated from demographic data suggests that the minimum potential contemporary population size is below 300 individual swift parrots. This is considerably lower than the published estimates derived from expert elicitation, and accords with modeled estimates of extinction risk in this species. Our study has important implications for other threatened species with unknown population sizes and demonstrates that by utilizing available genetic data, reasonable estimates of Ne can be derived.This work was funded by the Loro Parque Fundaci on, theAustralian Research Council (DP140104202), and a crowd-funding campaign“The parrot, the possum and the parda-lote”. This research also received support from theAustralian Government’s National Environmental ScienceProgram through the Threatened Species Recovery Hub, andfrom Australia Awards through the Endeavour Scholarshipsand Fellowships (ERF-PDR-6086-2017

Temporal migration rates affect the genetic structure of populations in the biennial Erysimum mediohispanicum with reproductive asynchrony

Funding was provided by projects CGL2009-07487/BOS and CGL2016-77720-P (AEI/FEDER, UE) to F.X.P., by the Impact Fellow programme from the University of Stirling to M.A. and by the Portuguese Foundation for Science and Technology (SFRH/BPD/111015/2015) to A.J.M.-P.We are grateful to Armando Caballero, Juan Pedro Martínez Camacho, Mario Vallejo-Marin, Mohammed Bakkali, Robin S. Waples, Xavier Thibert-Plante and Antonio Castilla for their comments and discussions on a previous draft of the manuscript. Esperanza Manzano, Leticia Ayllón and Rocío Gómez assisted in the laboratory. The EVOFLOR discussion group stimulated the development of this study. We thank the Sierra Nevada National Park headquarters for the permits and the support during our samplings in the field. We thank Bioportal at the University of Oslo and Residencia de Estudiantes de la Universidad de Zaragoza in Jaca for logistic support. We also thank the staff of the laboratory of molecular ecology (LEM) of the EBD-CSIC for assistance.Migration is a process with important implications for the genetic structure of populations. However, there is an aspect of migration seldom investigated in plants: migration between temporally isolated groups of individuals within the same geographic population. The genetic implications of temporal migration can be particularly relevant for semelparous organisms, which are those that reproduce only once in a lifetime after a certain period of growth. In this case, reproductive asynchrony in individuals of the same population generates demes of individuals differing in their developmental stage (non-reproductive and reproductive). These demes are connected by temporal migrants, that is, individuals that become annually asynchronous with respect to the rest of individuals of their same deme. Here, we investigated the extent of temporal migration and its effects on temporal genetic structure in the biennial plant Erysimum mediohispanicum. To this end, we conducted two independent complementary approaches. First, we empirically estimated temporal migration rates and temporal genetic structure in four populations of E. mediohispanicum during three consecutive years using nuclear microsatellites markers. Second, we developed a demographic genetic simulation model to assess genetic structure for different migration scenarios differing in temporal migration rates and their occurrence probabilities. We hypothesized that genetic structure decreased with increasing temporal migration rates due to the homogenizing effect of migration. Empirical and modelling results were consistent and indicated a U-shape relationship between genetic structure and temporal migration rates. Overall, they indicated the existence of temporal genetic structure and that such genetic structure indeed decreased with increasing temporal migration rates. However, genetic structure increased again at high temporal migration rates. The results shed light into the effects of reproductive asynchrony on important population genetic parameters. Our study contributes to unravel the complexity of some processes that may account for genetic diversity and genetic structure of natural populations.AEI/FEDER, UE CGL2009-07487/BOS CGL2016-77720-PImpact Fellow programme from the University of StirlingPortuguese Foundation for Science and Technology SFRH/BPD/111015/201

Species abundance dynamics under neutral assumptions: a Bayesian approach to the controversy

1. Hubbell's 'Unified Neutral Theory of Biodiversity and Biogeography' (UNTB) has generated much controversy about both the realism of its assumptions and how well it describes the species abundance dynamics in real communities. 2. We fit a discrete-time version of Hubbell's neutral model to long-term macro-moth (Lepidoptera) community data from the Rothamsted Insect Survey (RIS) light-traps network in the United Kingdom. 3. We relax the assumption of constant community size and use a hierarchical Bayesian approach to show that the model does not fit the data well as it would need parameter values that are impossible. 4. This is because the ecological communities fluctuate more than expected under neutrality. 5. The model, as presented here, can be extended to include environmental stochasticity, density-dependence, or changes in population sizes that are correlated between different species