Population structure in chicory (Cichorium intybus): A successful U.S. weed since the American revolutionary war

Plant invasions are recognized as major drivers of ecosystem change, yet the precise cause of these invasions remains unknown for many species. Frequency and modes of introductions during the first, transport and colonization, stages of the invasion process as well as phenotypic changes due to plasticity or changing genetic diversity and adaptation during later establishment and expansion stages can all influence the “success” of invasion. Here, we examine some of these factors in, and the origin of, a very successful weed, Cichorium intybus (chicory) which was introduced to North America in the 18th century and which now can be found in all 48 continental U.S. states and much of Canada. We genotyped a Eurasian collection of 11 chicory cultivars, nine native populations and a North American collection of 20 introduced wild populations which span the species range (592 individuals in total). To detect the geographic sources of North American chicory populations and to assess the genetic diversity among cultivars, native, and introduced populations, we used both a sequenced cpDNA region and 12 nuclear simple sequence repeat (SSR), microsatellite loci. Four cpDNA haplotypes were identified and revealed clear geographic subdivisions in the chicory native range and an interspecific hybrid origin of Radicchio group. Nuclear data suggested that domesticated lines deliberately introduced to North America were major contributors to extant weedy populations, although unintended sources such as seed contaminants likely also played important roles. The high private allelic richness and novel genetic groups were detected in some introduced populations, suggesting the potential for local adaptation in natural sites such as deserts and nature reserves. Our findings suggest that the current populations of weedy U.S. chicory have evolved primarily from several sources of domesticated and weedy ancestors and subsequent admixture among escaped lineages.     

Sample Size Effects on Estimates of Population Genetic Structure: Implications for Ecological Restoration

The field of ecological restoration is growing rapidly, and the sourcing of suitable seed is a major issue. Information on the population genetic structure of a species can provide valuable information to aid in defining seed collection zones. For a practical contribution from genetics, a rapid approach to delineating seed collection zones using genetic markers (amplified fragment length polymorphisms [AFLPs]) has been developed. Here, we test the effects of sampling regime on the efficacy of this method. Genetic data were collected for an outcrossing seeder, Daviesia divaricata ssp. divaricata, an important species in urban bushland restoration in Perth, Western Australia. The effect of sample size and number of AFLP markers on estimates of genetic variation and population structure was examined in relation to implications for sourcing material for restoration. Three different sample sizes were used (n= 8, 15, and 30) from six urban bushland remnants. High levels of genetic diversity were observed in D. divaricata (87.4% polymorphic markers), with significant population differentiation detected among sampled populations (Θ^B= 0.1386, p < 0.001). Although sample size does not appear to affect the spatial pattern in principle co‐ordinates analysis (PCA) plots, the number of polymorphic loci increased with sample size and estimates of population subdivision (F_ST and Θ^B) and associated confidence intervals decreased with increasing sample size. We recommend using a minimum of 30 plants for sourcing seed for restoration projects.     

Leaf and Soil Nutrients in a Chronosequence of Second‐Growth Forest in Central Amazonia: Implications for Restoration of Abandoned Lands

Subsistence agriculture, cattle ranching, and periodical land abandonment are common land‐use practices in Amazonia. Because changes in land use affect biogeochemical cycles, secondary forests growing after land abandonment develop at varying speeds and spatial patterns, due in part to varying nutrient dynamics. Leaf and soil nutrient concentrations can provide useful information on nutrient cycling processes and strategies of nutrient use by trees that are suitable for introduction to abandoned areas. To understand nutrient dynamics in secondary forests from different regeneration stages, as well as the importance of pioneer species in the regeneration process, we measured the concentration of macronutrients in leaves of three pioneer tree species (Vismia cayennensis, Cecropia sciadophylla, and Bellucia dichotoma) in central Amazon secondary forests. We also measured macronutrients in the topsoil under the trees. We found that type of prior land use, time since abandonment, and number of fire events were significantly correlated with the concentrations of leaf and soil macronutrients, explaining between 10 and 38% of the variation in macronutrient concentrations. The observed patterns suggest that management practices affect the processes involved in N cycling and availability. Of the three pioneer species, C. sciadophylla showed the highest nutrient resorption efficiency and the highest leaf nutritional quality. We suggest that these two features determine a higher potential of C. sciadophylla for natural regeneration and restoration of abandoned lands.     

Movement Patterns of a Native and Non‐native Frugivore in Hawaii and Implications for Seed Dispersal

Avian frugivores historically played important roles as seed dispersers across the Hawaiian Islands, but presently, the ‘ōma‘o (Myadestes obscurus) is the only extant native frugivore in the wild on the Island of Hawaii. During recent decades, the introduced generalist Japanese White‐eye (Zosterops japonicus) has become the most common bird in Hawaii. The movements of avian frugivores largely dictate how far seeds get dispersed and into what kinds of microhabitats. This study compares the movement patterns and diet of the ‘ōma‘o to the Japanese White‐eye to understand how a native differs from a non‐native frugivore in the type and distances of seeds dispersed. Radiotelemetry was conducted on nine ‘ōma‘o and nine Japanese White‐eyes in a system of natural forest fragments (kīpuka) created by lava flows. Japanese White‐eyes disperse seeds approximately twice as far as ‘ōma‘o; during the time of gut passage, ‘ōma‘o move a mean distance of 98.1 m, and Japanese White‐eyes move 170.1–194.8 m. However, the ‘ōma‘o disperses the seeds of at least seven different native fruit species compared with two dispersed by Japanese White‐eyes. Japanese White‐eyes were found to disperse seeds smaller than 1.5 mm, whereas the ‘ōma‘o dispersed seeds up to 6 mm in diameter. Despite their ecological differences, both birds distribute certain seeds within and among kīpuka and likely facilitate primary succession of fruiting plants in the young lava matrix. However, this study suggests that if the ‘ōma‘o were extirpated, a smaller‐bodied generalist cannot entirely substitute for the ecological role played by the native frugivore.     

Comparative phylogeography and demographic history of two marsupials of the Atlantic Forest in eastern Brazil

The Atlantic Forest biodiversity hotspot in eastern South America has been the focus of several phylogeographic studies concerning relationships between populations and areas and how taxa respond to environmental changes. We infer and compare the demographic and biogeographic histories of two didelphid marsupial species, Gracilinanus microtarsus and Marmosops incanus, from the Atlantic Forest of eastern Brazil to determine how these species responded to environmental changes over time, using mitochondrial and nuclear DNA sequences. We found great intraspecific genetic divergence in both species and a strong geographic structure related to similar and spatially cohesive groups within each species. These groups are consistent with the same topographical barriers, such as mountains and river valleys. Intraspecific clades are very old, dating back to a period of tectonic activities in the Neogene (5.39–8.57 Mya). Changes in the environment over the last 7 million years lead to fairly concordant demographic changes in both marsupial species, including population expansion during the last glacial maximum (ca. 21,000 years ago) or last interglacial (ca. 120,000 years ago) or both. These results do not fit the Pleistocene refuge hypothesis as an explanation of the historical biogeography and diversification of both species in the Atlantic Forest, but are compatible with the Atlantis Forest hypothesis.     

Native and Non‐Native Community Assembly through Edaphic Manipulation: Implications for Habitat Creation and Restoration

Chemical and physical (abiotic) conditions can be determining factors of community assembly and invasibility, but can this observation be used as a practical tool for habitat creation? Serpentine soils, in particular, have three abiotic components thought to confer invasion resistance: a low Ca:Mg ratio, low water‐retention capacity, and high concentrations of heavy metals. Consequently, not only do some serpentine‐adapted native plants persist only on serpentine soils, but also the community members that depend upon those plants become dependent upon serpentine as well. In an effort to provide additional habitat for the threatened and serpentine‐restricted Bay checkerspot butterfly (Euphydryas editha bayensis), we experimentally altered a non‐serpentine site to mimic the abiotic conditions of serpentine. Attempts to lower the Ca:Mg ratio of soils through the addition of MgSO₄ were unsuccessful. We then altered soil depth through the addition of gravel beds to determine the effects of water stress on native and non‐native community composition. We found that shallow soils had lower water content and correspondingly had significantly lower non‐native species richness and cover. The results present promising means, but also cautionary information, for habitat creation efforts and demonstrate the possible utility of edaphic manipulation in abating non‐native plant invasions. None of the experimental plots supported communities capable of sustaining E. editha populations, emphasizing that the manipulation of physical conditions is only likely to be successful in coordination with other restoration techniques.     

Rapid extirpation of a North American frog coincides with an increase in fungal pathogen prevalence: Historical analysis and implications for reintroduction

As extinctions continue across the globe, conservation biologists are turning to species reintroduction programs as one optimistic tool for addressing the biodiversity crisis. For repatriation to become a viable strategy, fundamental prerequisites include determining the causes of declines and assessing whether the causes persist in the environment. Invasive species—especially pathogens—are an increasingly significant factor contributing to biodiversity loss. We hypothesized that Batrachochytrium dendrobatidis (Bd), the causative agent of the deadly amphibian disease chytridiomycosis, was important in the rapid (<10 years) localized extirpation of a North American frog (Rana boylii) and that Bd remains widespread among extant amphibians in the region of extirpation. We used an interdisciplinary approach, combining interviews with herpetological experts, analysis of archived field notes and museum specimen collections, and field sampling of the extant amphibian assemblage to examine (1) historical relative abundance of R. boylii; (2) potential causes of R. boylii declines; and (3) historical and contemporary prevalence of Bd. We found that R. boylii were relatively abundant prior to their rapid extirpation, and an increase in Bd prevalence coincided with R. boylii declines during a time of rapid change in the region, wherein backcountry recreation, urban development, and the amphibian pet trade were all on the rise. In addition, extreme flooding during the winter of 1969 coincided with localized extirpations in R. boylii populations observed by interview respondents. We conclude that Bd likely played an important role in the rapid extirpation of R. boylii from southern California and that multiple natural and anthropogenic factors may have worked in concert to make this possible in a relatively short period of time. This study emphasizes the importance of recognizing historical ecological contexts in making future management and reintroduction decisions.     

Environmental variation shapes genetic variation in Bouteloua gracilis: Implications for restoration management of natural populations and cultivated varieties in the southwestern United States

With the increasing frequency of large‐scale restoration efforts, the need to understand the adaptive genetic structure of natural plant populations and their relation to heavily utilized cultivars is critical. Bouteloua gracilis (blue grama) is a wind‐dispersed, perennial grass consisting of several cytotypes (2n = 2×–6×) with a widespread distribution in western North America. The species is locally dominant and used regularly in restoration treatments. Using amplified fragment length polymorphism (AFLP) and cpDNA analyses, we assessed the genetic variability and adaptive genetic structure of blue grama within and among 44 sampling sites that are representative of the species’ environmental and habitat diversity in the southwestern United States. Five cultivars were also included to investigate genetic diversity and differentiation in natural versus cultivated populations. Three main findings resulted from this study: (a) Ninety‐four polymorphic AFLP markers distinguished two population clusters defined largely by samples on and off the Colorado Plateau; (b) substructure of samples on the Colorado Plateau was indicated by genetic divergence between boundary and interior regions, and was supported by cytotype distribution and cpDNA analysis; and (c) six AFLP markers were identified as “outliers,” consistent with being under selection. These loci were significantly correlated to mean annual temperature, mean annual precipitation, precipitation of driest quarter, and precipitation of wettest quarter in natural populations, but not in cultivated samples. Marker × environment relationships were found to be largely influenced by cytotype and cultivar development. Our results demonstrate that blue grama is genetically variable, and exhibits genetic structure, which is shaped, in part, by environmental variability across the Colorado Plateau. Information from our study can be used to guide the selection of seed source populations for commercial development and long‐term conservation management of B. gracilis, which could include genetic assessments of diversity and the adaptive potential of both natural and cultivated populations for wildland restoration.     

Extreme climatic events drive mammal irruptions: regression analysis of 100‐year trends in desert rainfall and temperature

Extreme climatic events, such as flooding rains, extended decadal droughts and heat waves have been identified increasingly as important regulators of natural populations. Climate models predict that global warming will drive changes in rainfall and increase the frequency and severity of extreme events. Consequently, to anticipate how organisms will respond we need to document how changes in extremes of temperature and rainfall compare to trends in the mean values of these variables and over what spatial scales the patterns are consistent. Using the longest historical weather records available for central Australia – 100 years – and quantile regression methods, we investigate if extreme climate events have changed at similar rates to median events, if annual rainfall has increased in variability, and if the frequency of large rainfall events has increased over this period. Specifically, we compared local (individual weather stations) and regional (Simpson Desert) spatial scales, and quantified trends in median (50th quantile) and extreme weather values (5th, 10th, 90th, and 95th quantiles). We found that median and extreme annual minimum and maximum temperatures have increased at both spatial scales over the past century. Rainfall changes have been inconsistent across the Simpson Desert; individual weather stations showed increases in annual rainfall, increased frequency of large rainfall events or more prolonged droughts, depending on the location. In contrast to our prediction, we found no evidence that intra‐annual rainfall had become more variable over time. Using long‐term live‐trapping records (22 years) of desert small mammals as a case study, we demonstrate that irruptive events are driven by extreme rainfalls (>95th quantile) and that increases in the magnitude and frequency of extreme rainfall events are likely to drive changes in the populations of these species through direct and indirect changes in predation pressure and wildfires.     

Comparison of reproductive parameters for populations of eastern North Pacific common dolphins: Delphinus capensis and D. delphis

Reproductive parameters were estimated and compared for eastern North Pacific populations of common dolphins using specimen and photogrammetric data. Age and length data for Delphinus capensis and D. delphis specimens recovered as bycatch or strandings were used to estimate the postnatal growth rates needed to estimate age for calves measured in aerial photographs. Bayesian methods propagated uncertainty among models and revealed that the 2009 cohort of calves had birth dates centered on 6 March 2009 for D. capensis and 12 December 2008 for D. delphis. The evidence for discrete calving seasons suggests a mechanism of reproductive isolation has evolved between species. Photogrammetric data and Bayesian methods were also used to estimate the average length at which calves swim independently: 145.1 cm (≈ 11.1 mo) in D. capensis and 140.1 cm (≈ 14.0 mo) in D. delphis, and the proportion of calves (calves/dolphins counted): 0.045 in D. capensis and 0.069 in D. delphis. The latter parameter was converted to an index of calf production (calf/female dolphin) that was >50% lower than pregnancy rates suggesting few births occurred during the study year. Comparisons of regional differences in calf production suggest variability in habitat use patterns within the study area.     

Evolutionary structure of Plasmodium falciparum major variant surface antigen genes in South America: Implications for epidemic transmission and surveillance

Strong founder effects resulting from human migration out of Africa have led to geographic variation in single nucleotide polymorphisms (SNPs) and microsatellites (MS) of the malaria parasite, Plasmodium falciparum. This is particularly striking in South America where two major founder populations of P. falciparum have been identified that are presumed to have arisen from the transatlantic slave trade. Given the importance of the major variant surface antigen of the blood stages of P. falciparum as both a virulence factor and target of immunity, we decided to investigate the population genetics of the genes encoding “Plasmodium falciparum Erythrocyte Membrane Protein 1” (PfEMP1) among several countries in South America, in order to evaluate the transmission patterns of malaria in this continent. Deep sequencing of the DBLα domain of var genes from 128 P. falciparum isolates from five locations in South America was completed using a 454 high throughput sequencing protocol. Striking geographic variation in var DBLα sequences, similar to that seen for SNPs and MS markers, was observed. Colombia and French Guiana had distinct var DBLα sequences, whereas Peru and Venezuela showed an admixture. The importance of such geographic variation to herd immunity and malaria vaccination is discussed.     

Factors driving the variability in diving and movement behavior of migrating humpback whales (Megaptera novaeangliae): Implications for anthropogenic disturbance studies

Humpback whales (Megaptera novaeangliae) undertake one of the longest migrations of any animal and while on a broad‐scale this journey appears direct, on a fine‐scale, behaviors associated with socializing and breeding are regularly observed. However, little is known about which social and environmental factors influence behavior during this time. Here we examined the effect of multiple factors on the movement (speed and course) and diving behavior (dive and surfacing duration) of humpback whales during migration off the eastern coast of Australia. Focal data (202 h) were collected on 94 different whale groups with simultaneous social and environmental context data. The environmental factors water depth and wind speed were found to be important predictors of dive and movement behavior, whereas social factors were less influential at this site. Groups tended to dive for longer with increased water depth but traveled more slowly in increasing wind speeds. These baseline studies are crucial when examining the effect of anthropogenic disturbance. Determining which natural factors significantly affect behavior ensures any observed behavioral changes are correctly attributed to the disturbance and are not a result of other factors. In addition, any responses observed can be put into biological context and their relative magnitude determined.     

Growth and fecundity of fertile Miscanthus × giganteus (“PowerCane”) compared to feral and ornamental Miscanthus sinensis in a common garden experiment: Implications for invasion

Perennial grasses are promising candidates for bioenergy crops, but species that can escape cultivation and establish self‐sustaining naturalized populations (feral) may have the potential to become invasive. Fertile Miscanthus × giganteus, known as “PowerCane,” is a new potential biofuel crop. Its parent species are ornamental, non‐native Miscanthus species that establish feral populations and are sometimes invasive in the USA. As a first step toward assessing the potential for “PowerCane” to become invasive, we documented its growth and fecundity relative to one of its parent species (Miscanthus sinensis) in competition with native and invasive grasses in common garden experiments located in Columbus, Ohio and Ames, Iowa, within the targeted range of biofuel cultivation. We conducted a 2‐year experiment to compare growth and reproduction among three Miscanthus biotypes—”PowerCane,” ornamental M. sinensis, and feral M. sinensis—at two locations. Single Miscanthus plants were subjected to competition with a native grass (Panicum virgatum), a weedy grass (Bromus inermis), or no competition. Response variables were aboveground biomass, number of shoots, basal area, and seed set. In Iowa, all Miscanthus plants died after the first winter, which was unusually cold, so no further results are reported from the Iowa site. In Ohio, we found significant differences among biotypes in growth and fecundity, as well as significant effects of competition. Interactions between these treatments were not significant. “PowerCane” performed as well or better than ornamental or feral M. sinensis in vegetative traits, but had much lower seed production, perhaps due to pollen limitation. In general, ornamental M. sinensis performed somewhat better than feral M. sinensis. Our findings suggest that feral populations of “PowerCane” could become established adjacent to biofuel production areas. Fertile Miscanthus × giganteus should be studied further to assess its potential to spread via seed production in large, sexually compatible populations.     

Estimation of calf:cow ratios of Pacific walruses for use in population modeling and monitoring

We report on a method of visually classifying Pacific walruses (Odobenus rosmarus) to sex and age class with the goal of estimating calf:cow ratios. Development of this method began in 1958 by Dr. F. H. Fay and was used during six surveys in the Chukchi Sea between 1981 and 1999. We estimate calf:cow ratios using beta‐binomial models to allow for overdispersion and use Monte Carlo simulations to assess the reliability of prior surveys and quantify sample sizes required for future surveys. Calf:cow ratios did not vary by region, date, or by the number of cows in a group. However, higher ratios were observed in the morning and evening than during the day, indicating haul out behavior of cows varies by reproductive status. Adjusted for solar noon, few calves were observed in 1981 (3:100), 1984 (6:100), and 1998 (5:100), while substantially more were observed in 1982 (15:100) and 1999 (13:100). Classifying between 200 and 300 groups with cows (~1,600–2,300 individual cows) will yield calf:cow ratios with ~20%–30% relative precision. Tagging studies that examine hauling‐out behavior of cows with and without calves relative to time‐of‐day are necessary to better understand how to interpret calf:cow ratios.     

Widespread prevalence but contrasting patterns of intragenomic rRNA polymorphisms in nematodes: Implications for phylogeny,species delimitation and life history inference

Ribosomal RNA genes have long been a favoured locus in phylogenetic and metabarcoding studies. Within a genome, rRNA loci are organized as tandem repeated arrays and the copies are homogenized through the process of concerted evolution. However, some level of rRNA variation (intragenomic polymorphism) is known to persist and be maintained in the genomes of many species. In nematode worms, the extent of rRNA polymorphism (RP) across species and the evolutionary and life history factors that contribute to the maintenance of intragenomic RP is largely unknown. Here, we present an extensive analysis across 30 terrestrial nematode species representing a range of free‐living and parasitic taxa isolated worldwide. Our results indicate that RP is common and widespread, ribosome function appears to be maintained despite mutational changes, and intragenomic variants are stable in the genome and neutrally evolving. However, levels of variation were varied widely across rRNA locus and species, with some taxa observed to lack RP entirely. Higher levels of RP were significantly correlated with shorter generation time and high reproductive rates, and population‐level factors may play a role in the geographic and phylogenetic structuring of rRNA variants observed in genera such as Rotylenchulus and Pratylenchus. Although RP did not dramatically impact the clustering and recovery of taxa in mock metabarcoding analyses, the present study has significant implications for global biodiversity estimates of nematode species derived from environmental rRNA amplicon studies, as well as our understanding of the evolutionary and ecological factors shaping genetic diversity across the nematode Tree of Life.     

Demography of Euterpe precatoria and Mauritia flexuosa in the Amazon: application of integral projection models for their harvest

Non‐Timber Forest Products like palm fruits are fundamental in the livelihood of Amerindian groups. For the last 10 years the fruits of wild palm species, like Euterpe precatoria and Mauritia flexuosa, have been entering into global markets. These species are mostly harvested felling the adults, a practice that may have a disproportionate impact in the conservation of the populations. We studied the demography of E. precatoria and M. flexuosa, two important palms of the Amazon, using integral projection models, to characterize the population dynamics and project impact of different fruit harvest methods: adult felling and direct fruit harvest. We followed over 1400 individuals from populations with low harvest intensities in the Tikuna community of Amacayacu, Amazonas, Colombia from 2011 to 2013, establishing four plots for E. precatoria in seasonally inundated forests and two for M. flexuosa in swamps. The population growth in E. precatoria was slightly declining, whereas M. flexuosa was stable. As expected, the simulations of adult felling diminished λ and the number of available adults under any scenario for either species. On the contrary, the simulations support existing information that climbing and other non‐destructive harvest methods would probably allow a sustainable management, satisfying the demand and preserving wild populations.