Information or entropy analysis of diversity is used extensively in community ecology, and has recently been exploited for prediction and analysis in molecular ecology and evolution. Information measures belong to a spectrum (or q profile) of measures whose contrasting properties provide a rich summary of diversity, including allelic richness (q=0), Shannon information (q=1), and heterozygosity (q=2). We present the merits of information measures for describing and forecasting molecular variation within and among groups, comparing forecasts with data, and evaluating underlying processes such as dispersal. Importantly, information measures directly link causal processes and divergence outcomes, have straightforward relationship to allele frequency differences (including monotonicity that q=2 lacks), and show additivity across hierarchical layers such as ecology, behaviour, cellular processes, and nongenetic inheritance.

Sugar maple (Acer saccharum Marsh.) is the most economically important member of the Hard Maple species complex, a group of related species that occupy a range between Canada and Mexico, which are adapted to distinct ecological niches. Sugar maple has been identified as vulnerable to rapid climate change, and sustainable solutions are needed to support its role in the production of maple sugar, as well as timber and nursery production in the northeastern United States. Genetic relationships among sugar maple and its allies are largely unknown. In the current study, genetic relationships of 278 individuals from six hard maple species were assessed using 17 multi-allelic microsatellite (SSR) loci. Genetic variance was partitioned into separate components for variation within and among populations and within and among species. Most of the divergence among populations (FPT = 0.263) reflected interspecific divergence (FST = 0.169), but provenances within species also differed at nontrivial scales (FPS = 0.113). Estimation and testing of paired interprovenance divergence showed that all population pairs were statistically divergent. Principal coordinates analysis indicated that the pattern of radiation observed among these taxa is broadly compatible with geography.

We deploy Shannon analysis of five ancestrally (ANCE) diagnostic microsatellite loci to explore the patterns of ‘deep’ allelic genetic diversity within the peat moss Sphagnum ×australe Mitt. s.l. cryptic species complex across its Australasian distribution. There is both notable divergence among and considerable allelic overlap within the three allopolyploid lineages of this complex, two gametophytically allodiploid (R1S1 and R2S2) and one gametophytically allotriploid (FR1*S1*). Detailed biogeographic patterns reflect historical differences in genetic isolation and interbreeding. Lineage I (R1S1) occurs in both Australia and New Zealand, while Lineage II (R2S2) and Lineage III (FR1*S1*) are endemic to New Zealand, where Lineage III predominates. Available data suggest that Lineage I arose in Australia, whereas both Lineage II and Lineage III originated in New Zealand. ‘Deep’ allelic diversity provides a pronounced signal of evolutionary radiation within and among the three lineages. We develop a methodology to explore allelic diversity across ploidy levels and elaborate another for scaling additive allele-metric diversity values [0,1], relative to attainable minimal and maximal values, given the sampling frame. We suggest the following taxonomic disposition: gametophytically allodiploid Lineages I and II → S. ×australe; gametophytically allotriploid Lineage III → S. ×antarcticum. Epitypes are designated for both species.

PREMISE OF THE STUDY:The traditional approach used in analyses of population genetic data for historical inference is to average across multiple marker loci, but averaging conflates the different evolutionary signals provided by stable vs. labile markers.METHODS:We used a battery of microsatellites with a wide range of mutation/substitution rates, grouping them into two sets (stable and hypervariable) to provide a more nuanced reconstruction of the population genetics and evolutionary history of the allotriploid peat moss Sphagnum × falcatulum across three disjunct regions.KEY RESULTS:Shannon diversity translation analyses show that the relative apportionment of total within-species allelic diversity (∆WS ) within and among strata ranges widely, both between the two sets and within and among regions. The majority of diversity in the stable set was inherited directly from the ancestors of this genetically complex allopolyploid, but most of the diversity in the hypervariable set has developed post-hybrid-origin.CONCLUSIONS:It is useful to group markers into sets having similar evolutionary lability, with each set being analyzed separately, particularly for allopolyploids. A methodology for determining how to group markers into such sets is presented, which can be applied to the requirements of other studies. Within-individual allelic diversity (ΔWI ) should be addressed in genetic studies on allopolyploids. Allotriploid haplotypes based on a set of nine highly stable microsatellites appear to serve as a clonal-detection set for S. × falcatulum. An additive "allele-metric" diversity approach is introduced, which facilitates a direct comparison of within- and among-stratum diversity components at all levels of diversity.

Current guidance on sourcing native plants to support ecosystem function focuses on the high risk of failure when unsuitable material is used in ecological restoration. However, there is growing recognition that risks may be lower and rewards higher at highly disturbed sites isolated from remnant populations, especially when considering support for pollinators, wildlife, and other ecosystem functions. We developed the first decision support tool using expert opinion to assess suitability of different native plant sources, including horticultural cultivars, in two different planting contexts. We assessed the suitability of 761 sources for 72 commonly sold native species in two different planting contexts (small, isolated, highly disturbed sites vs. large, undisturbed sites near remnant populations). Information on genetic and adaptive backgrounds of sources was strikingly lacking, forcing us to exclude one‐third of sources from our assessment. While only 3% of cultivars received high suitability scores for use in large, undisturbed sites near remnant populations, 52% received high suitability scores in small, isolated, highly disturbed sites. However, nearly 25% of cultivars had floral or leaf traits that differed from wild plants in ways that may compromise their ability to support pollinators and other wildlife. Forbs and cultivars lacking genetic diversity and source information were most likely to have altered traits. We recommend that native plant breeders and sellers work together to ensure ecosystem function, adaptation, and diversity information is available to consumers, that consumers request this information to drive demand, and that researchers further investigate how context influences risks and benefits of different sources.

Premise of the Study Flowering initiation, duration and magnitude, and degree of flowering synchrony within a population can affect the reproductive fitness of individuals. We examined the flowering phenology within a population of the tropical dry forest Guanacaste tree (Enterolobium cyclocarpum) to gauge the impact of phenological variation among trees on fruit production and progeny vigor. Methods We monitored the flowering phenology of 93 trees weekly during 2005, 2006, and 2007, using a scale based on the percentage of the crown with open flowers. We also monitored fruit production for each tree in 2005, 2006, 2007, and 2008. Finally, we evaluated the relationship between phenological variation and progeny performance. Key Results Ten measures of flowering phenology and synchrony among flowering trees, based on the number of weeks when anthesis of the crown exceeded 50%, were used to develop four phenological profiles. These profiles were correlated with significant differences in fruit production and progeny vigor. Trees with flowers in >50% of their crown for at least 2 weeks produced more fruits and more vigorous progeny than trees with other profiles. Trees also tended to produce the same phenological profile among years than predicted by chance. Conclusions Guanacaste trees vary significantly in the initiation of anthesis, duration and magnitude of flowering, and degree of synchrony among trees. Trees also tend to maintain the same flowering profile among years. Finally, the flowering behavior of E. cyclocarpum leads to significant differences in fruit and seed production, germination, and early progeny growth.

Polyploidy (whole-genome duplication) is common in vascular plants, but the modes of establishment and persistence, as well as the ecological consequences, of polyploidy remain vague. Highbush blueberry (Vaccinium corymbosum L.) is an ecologically and economically important understory shrub with an unclear species definition, coexisting in sympatric populations of diploid and tetraploid cytotypes. This study analyzes differences in bloom time between sympatric diploid and tetraploid V. corymbosum in natural populations, testing the potential for these cytotypes to interbreed and contributing to the formation and continuity of ploidy-level diversification within this species. Ploidal level was confirmed through DNA flow cytometry of sympatric plants from two populations in New Jersey, USA. Flower bloom date and corolla size were recorded over a 3-year period. Diploid corollas were 32% smaller than tetraploid corollas, making them easily identifiable in the field. Ploidy accounted for 55%–69% of the variati...

The use of diversity metrics has a long history in population ecology, while population genetic work has been dominated by variance-derived metrics instead, a technical gap that has slowed cross-communication between the fields. Interestingly, Rao’s Quadratic Entropy (RQE), comparing elements for ‘degrees of divergence’, was originally developed for population ecology, but has recently been deployed for evolutionary studies. We here translate RQE into a continuous diversity analogue, and then construct a multiply nested diversity partition for alleles, individuals, populations, and species, each component of which exhibits the behavior of proper diversity metrics, and then translate these components into [0,1]—scaled form. We also deploy non-parametric statistical tests of the among-stratum components and novel tests of the homogeneity of within-stratum diversity components at any hierarchical level. We then illustrate this new analysis with eight nSSR loci and a pair of close Australian marsupial (Antechinus) congeners, using both ‘different is different’ and ‘degree of difference’ distance metrics. The total diversity in the collection is larger than that within either species, but most of the within-species diversity is resident within single populations. The combined A. agilis collection exhibits more diversity than does the combined A. stuartii collection, possibly attributable to localized differences in either local ecological disturbance regimes or differential levels of population isolation. Beyond exhibiting different allelic compositions, the two congeners are becoming more divergent for the arrays of allele sizes they possess.

We used the globally widespread genus Ophiognomonia as a model system to investigate climatic niche patterns in fungi, characterizing the climatic profiles of 28 species with seven temperature and seven precipitation variables. Using a novel version of Spatial Evolutionary and Ecological Vicariance Analysis (SEEVA), designed to deal with continuous and correlated variables, we examined well-sampled phyletic splits of a multi-gene phylogeny. We evaluated the degree to which phyletic divergence has been associated with climatic niche divergence between sister lineages, permitting elucidation of climatic associations in evolutionary context. From the 14 inter-correlated climatic variables, we extracted four principal axes, accounting for 93.2% of the climatic variation, with axes broadly labelled as: polarity, tropicality, winter mildness and aridity. We also analysed the two single variables maximum monthly temperature and precipitation. We detected climatic associations that were compatible with both niche conservatism and niche divergence within the phylogeny, and different cladistic bifurcations associated with different climatic splits. As might have been anticipated, geographic separation (or lack thereof) of phylogenetic splits was correlated with climate niche divergence (or conservation). This elaborated SEEVA method provides a visual and statistically solid basis for characterizing climatic niche divergence that should prove useful for elucidation of many other taxonomic groups.

Lyme disease is a major vector-borne bacterial disease in the USA. The disease is caused by Borrelia burgdorferi, and transmitted among hosts and humans, primarily by blacklegged ticks (Ixodes scapularis). The ~25 B. burgdorferi genotypes, based on genotypic variation of their outer surface protein C (ospC), can be phenotypically separated as strains that primarily cause human diseases—human invasive strains (HIS)—or those that rarely do. Additionally, the genotypes are non-randomly associated with host species. The goal of this study was to examine the extent to which phenotypic outcomes of B. burgdorferi could be explained by the host communities fed upon by blacklegged ticks. In 2006 and 2009, we determined the host community composition based on abundance estimates of the vertebrate hosts, and collected host-seeking nymphal ticks in 2007 and 2010 to determine the ospC genotypes within infected ticks. We regressed instances of B. burgdorferi phenotypes on site-specific characteristics of host communities by constructing Bayesian hierarchical models that properly handled missing data. The models provided quantitative support for the relevance of host composition on Lyme disease risk pertaining to B. burgdorferi prevalence (i.e. overall nymphal infection prevalence, or NIPAll) and HIS prevalence among the infected ticks (NIPHIS). In each year, NIPAll and NIPHIS was found to be associated with host relative abundances and diversity. For mice and chipmunks, the association with NIPAll was positive, but tended to be negative with NIPHIS in both years. However, the direction of association between shrew relative abundance with NIPAll or NIPHIS differed across the two years. And, diversity (H') had a negative association with NIPAll, but positive association with NIPHIS in both years. Our analyses highlight that the relationships between the relative abundances of three primary hosts and the community diversity with NIPAll, and NIPHIS, are variable in time and space, and that disease risk inference, based on the role of host community, changes when we examine risk overall or at the phenotypic level. Our discussion focuses on the observed relationships between prevalence and host community characteristics and how they substantiate the ecological understanding of phenotypic Lyme disease risk.

Background and AimsAllopolyploids exhibit both different levels and different patterns of genetic variation than are typical of diploids. However, scant attention has been given to the partitioning of allelic information and diversity in allopolyploids, particularly that among homeologous monoploid components of the hologenome. Sphagnum × falcatulum is a double allopolyploid peat moss that spans a considerable portion of the Holantarctic. With monoploid genomes from three ancestral species, this organism exhibits a complex evolutionary history involving serial inter-subgeneric allopolyploidizations.MethodsStudying populations from three disjunct regions [South Island (New Zealand); Tierra de Fuego archipelago (Chile, Argentina); Tasmania (Australia)], allelic information for five highly stable microsatellite markers that differed among the three (ancestral) monoploid genomes was examined. Using Shannon information and diversity measures, the holoploid information, as well as the information within and among the three component monoploid genomes, was partitioned into separate components for individuals within and among populations and regions, and those information components were then converted into corresponding diversity measures.Key ResultsThe majority (76 %) of alleles detected across these five markers are most likely to have been captured by hybridization, but the information within each of the three monoploid genomes varied, suggesting a history of recurrent allopolyploidization between ancestral species containing different levels of genetic diversity. Information within individuals, equivalent to the information among monoploid genomes (for this dataset), was relatively stable, and represented 83 % of the grand total information across the Holantarctic, with both inter-regional and inter-population diversification each accounting for about 5 % of the total information.ConclusionsSphagnum × falcatulum probably inherited the great majority of its genetic diversity at these markers by reticulation, rather than by subsequent evolutionary radiation. However, some post-hybridization genetic diversification has become fixed in at least one regional population. Methodology allowing statistical analysis of any ploidy level is presented.

Reconstructing evolutionary history for emerging species complexes is notoriously difficult, with newly isolated taxa often morphologically cryptic and the signature of reproductive isolation often restricted to a few genes. Evidence from multiple loci and genomes is highly desirable, but multiple inputs require 'common currency' translation. Here we deploy a Shannon information framework, converting into diversity analogue, which provides a common currency analysis for maternally inherited haploid and bi-parentally inherited diploid nuclear markers, and then extend that analysis to construction of minimum-spanning networks for both genomes. The new approach is illustrated with a quartet of cryptic congeners from the sexually deceptive Australian orchid genus Chiloglottis, still in the early stages of speciation. Divergence is more rapid for haploid plastids than for nuclear markers, consistent with the effective population size differential (N(ep) < (N(en)), but divergence patterns are broadly correlated for the two genomes. There are nevertheless intriguing discrepancies between the emerging plastid and nuclear signals of early phylogenetic radiation of these taxa, and neither pattern is entirely consistent with the available information on the sexual cues used by the orchids to lure the pollinators enforcing reproductive isolation. We describe possible extensions of this methodology to multiple ploidy levels and other types of markers, which should increase the range of application to any taxonomic assemblage in the very early stages of reproductive isolation and speciation.

The Columbia Basin once supported a diversity of native fishes and large runs of anadromous salmonids that sustained substantial fisheries and cultural values. Extensive land conversion, watershed disruptions, and subsequent fishery declines have led to one of the most ambitious restoration programs in the world. Progress has been made, but restoration is expensive (exceeding US$300M/year), and it remains unclear whether habitat actions, in particular, can be successful. A comprehensive approach is needed to guide cost-effective habitat restoration. Four elements that must be addressed simultaneously are (1) a scientific foundation from landscape ecology and the concept of resilience, (2) broad public support, (3) governance for collaboration and integration, and (4) a capacity for learning and adaptation. Realizing these in the Columbia Basin will require actions to rebalance restoration goals to include diversity, strengthen linkages between science and management, increase public engagement, work across traditional ecological and social boundaries, and learn from experience.

Transgenic crops expressing Bacillus thuringiensis (Bt) toxins have been widely and successfully deployed for the control of target pests, while allowing a substantial reduction in insecticide use. The evolution of resistance (a heritable decrease in susceptibility to Bt toxins) can pose a threat to sustained control of target pests, but a high-dose refuge (HDR) management strategy has been key to delaying countervailing evolution of Bt resistance. The HDR strategy relies on the mating frequency between susceptible and resistant individuals, so either partial dominance of resistant alleles or nonrandom mating in the pest population itself could elevate the pace of resistance evolution. Using classic Wright-Fisher genetic models, we investigated the impact of deviations from standard refuge model assumptions on resistance evolution in the pest populations. We show that when Bt selection is strong, even deviations from random mating and/or strictly recessive resistance that are below the threshold of detection can yield dramatic increases in the pace of resistance evolution. Resistance evolution is hastened whenever the order of magnitude of model violations exceeds the initial frequency of resistant alleles. We also show that the existence of a fitness cost for resistant individuals on the refuge crop cannot easily overcome the effect of violated HDR assumptions. We propose a parametrically explicit framework that enables both comparison of various field situations and model inference. Using this model, we propose novel empiric estimators of the pace of resistance evolution (and time to loss of control), whose simple calculation relies on the observed change in resistance allele frequency.

The distribution and abundance of genetic diversity in plant populations is initiated by sexually asymmetric propagule dispersal through pollen and seeds. Because these processes occur serially, it is not transparent how each contributes to subsequent patterns of genetic diversity. Using combined seedling/seed coat assay for naturally distributed seedlings of Quercus lobata Née, we extracted male and female gametic genotypes, and then assessed (wind-vectored) paternal and (gravity- and animal-vectored) maternal contributions to spatially distributed allelic diversity. We evaluated 200 naturally recruited seedlings from 4 open patches away from any adult canopies (denoted ‘open’), and 174 seedlings from 14 patches immediately beneath adult canopies (denoted ‘canopy’). The open patches included 19 % long distant dispersal events of >1 km while the canopy patches contained seedlings from one tree overhead. For each patch type, we partitioned average allelic diversity for six microsatellite loci for the whole study site (γ) into separate within-patch (α) and among-patch (β) components, translated into among-patch divergence (δ). We found that α-diversity resulting from seed dispersal was much less than that from pollen dispersal in both patch types, while total γ-diversity across the site was similar. Divergence (δ) among canopy patches was significantly greater than δ among open patches. We then evaluated spatial genetic autocorrelation (kinship) patterns for both open and canopy strata, separately for male and female gametes. Female gametes showed sharply declining kinship with increasing distance for canopy patches and modestly for open patches. In sharp contrast, male gametes from both patches showed only subtle decline of kinship, but seedlings still showed significant structure across patch types. On balance, sexual asymmetry in propagule dispersal shapes both the abundance and distribution of allelic diversity, with pollen dispersal promoting overall diversity but reducing spatial structure, but seed-dispersal reduces overall diversity and markedly increases spatial genetic structure.

PREMISE OF THE STUDY:Variation in a species is a blend of adaptive, random, and migratory responses. Pitch pine (Pinus rigida), a highly variable eastern conifer, has occupied multiple glacial refugia, whose harsh conditions favored adaptations enhancing subsequent dispersal and recolonization of newly deglaciated sites. We assessed phenotypic diversity in long-term growth trials to elucidate both the adaptations and likely refugia.METHODS:Pitch pine progeny from 31 areas were grown in common gardens in six locations, from eastern Massachusetts to Korea.KEY RESULTS:Survival increased with source latitude, but seedlings from southern latitudes were tallest in the first (postplanting) year, but that advantage dissipated in later years. Progeny from northern latitudes were precocious, highly fecund, had smaller seeds, and more seeds per cone. Seed mass decreased with latitude in both parents and progeny. Serotinous cones were notably common in the New Jersey Pine Plains and Acadia National Park. Various disease agents and frost burn exhibited latitudinal trends that were nonlinear, with a break in the regression slope at about 40°N latitude. Cluster analysis identified both northern and southern groups, largely split between unglaciated and deglaciated terrain, but with Acadia and the Pine Plains as unique outliers. Within the southern group, provenances were organized into contiguous subgroups, but geographic structure was less evident in the northern group.CONCLUSIONS:The present range of pitch pine was colonized by migrants from at least three different refugia, including at least one on the exposed continental shelf during the Last Glacial Maximum.

Foraging movements of animals shape their efficiency in finding food and their exposure to the environment while doing so. Our goal was to test the optimal foraging theory prediction that territorial acorn woodpeckers (Melanerpes formicivorus) should forage closer to their ‘central place’ in years of high resource availability and further afield when resources are less available. We used genetic data on acorns stored in caching sites (granaries) and adult trees for two oak species (Quercus lobata and Quercus agrifolia) to track acorn movements across oak savanna habitat in central California. We also compared the patterns of trees these territorial bird groups foraged upon, examining the effective numbers of source trees represented within single granaries (α), the effective number of granaries (β), the diversity across all granaries (γ), and the overlap (ω) in source trees among different granaries, both within and across years.

Borrelia burgdorferi s.s., the bacterium that causes Lyme disease in North America, circulates among a suite of vertebrate hosts and their tick vector. The bacterium can be differentiated at the outer surface protein C (ospC) locus into 25 genotypes. Wildlife hosts can be infected with a suite of ospC types but knowledge on the transmission efficiencies of these naturally infected hosts to ticks is still lacking. To evaluate the occupancy and detection of ospC types in wildlife hosts, we adapted a likelihood-based species patch occupancy model to test for the occurrence probabilities (ψ – “occupancy”) and transmission efficiencies (ε – “detection”) of each ospC type. We detected differences in ospC occurrence and transmission efficiencies from the null models with HIS (human invasive strains) types A and K having the highest occurrence estimates, but both HIS and non-HIS types having high transmission efficiencies. We also examined ospC frequency patterns with respect to strains known to be invasive in humans across the host species and phylogenetic groups. We found that shrews and to a lesser extent, birds, were important host groups supporting relatively greater frequencies of HIS to non-HIS types. This novel method of simultaneously assessing occurrence and transmission of ospC types provides a powerful tool in assessing disease risk at the genotypic level in naturally infected wildlife hosts and offers the opportunity to examine disease risk at the community level.

In theory, conservation genetics predicts that forest fragmentation will reduce gene dispersal, but in practice, genetic and ecological processes are also dependent on other population characteristics. We used Bayesian genetic analyses to characterize parentage and propagule dispersal in Heliconia acuminata L. C. Richard (Heliconiaceae), a common Amazonian understory plant that is pollinated and dispersed by birds. We studied these processes in two continuous forest sites and three 1‐ha fragments in Brazil's Biological Dynamics of Forest Fragments Project. These sites showed variation in the density of H. acuminata. Ten microsatellite markers were used to genotype flowering adults and seedling recruits and to quantify realized pollen and seed dispersal distances, immigration of propagules from outside populations, and reproductive dominance among parents. We tested whether gene dispersal is more dependent on fragmentation or density of reproductive plants. Low plant densities were associated with elevated immigration rates and greater propagule dispersal distances. Reproductive dominance among inside‐plot parents was higher for low‐density than for high‐density populations. Elevated local flower and fruit availability is probably leading to spatially more proximal bird foraging and propagule dispersal in areas with high density of reproductive plants. Nevertheless, genetic diversity, inbreeding coefficients and fine‐scale spatial genetic structure were similar across populations, despite differences in gene dispersal. This result may indicate that the opposing processes of longer dispersal events in low‐density populations vs. higher diversity of contributing parents in high‐density populations balance the resulting genetic outcomes and prevent genetic erosion in small populations and fragments.

Adaptive radiation and reproductive isolation can determine the biogeographic structure of any species. We examine patterns of biotic variation in Embothrium coccineum, a Proteaceae tree that spans 20° of latitude and is both morphologically and genetically highly variable. We aim to (1) explore the correspondence between these biotic patterns and current geographic and climatic gradients, and (2) determine whether and how those patterns are likely to respond to changing climate. We conducted separate principal component analyses on biotic and abiotic sets of variables for 34 populations of Embothrium coccineum, accounting for a large fraction of the total variation in each. We then used canonical correlation analyses to optimise the match of those gradients onto each other. Smaller, rounder leaves and particular alleles typify the colder and drier parts of the range, whereas larger, lanceolate leaves and other alleles typify warmer and moister areas. Finally, we mapped biotic profiles onto a predicted climatic landscape, on the basis of doubling of CO2 projections. The climatic regime is predicted to shift geographically, but this lineage has successfully responded to repeated and dramatic climatic shifts since the Oligocene, and it should also be able to move and adapt quickly enough to meet the present challenge. More generally, our analytic approach can be extended to analysis of biotic and abiotic patterns in other species facing climatic challenges. Where there is enough biogeographic variation to provide adaptively relevant substrate, and where propagule dispersal is sufficiently extensive to keep up with the pace of spatial climatic shift, such taxa should be able to cope with shifting climate.