Using genetic evaluation to guide conservation of remnant Juniperus communis (Cupressaceae) populations

• Many critically endangered plant species exist in small, genetically depauperate or inbred populations, making assisted gene flow interventions necessary for long‐term population viability. However, before such interventions are implemented, conservation practitioners must consider the genetic and demographic status of extant populations, which are strongly affected by species’ life‐history traits. In northwestern Europe, Juniperus communis, a dioecious, wind‐pollinated and bird‐dispersed gymnosperm, has been declining for the past century and largely exists in small, isolated and senescent populations.
• To provide useful recommendations for a recovery plan involving translocation of plants, we investigated genetic diversity and structure of populations in Belgium using four microsatellite and five plastid single‐nucleotide polymorphism (SNP) markers.
• We detected no clonality in the populations, suggesting predominantly sexual reproduction. Populations exhibited high genetic diversity (H_e = 0.367–0.563) and low to moderate genetic differentiation (F_ST ≤ 0.133), with no clear geographic structure. Highly positive inbreeding coefficients (F_IS = 0.221–0.507) were explained by null alleles, population substructuring and biparental inbreeding. No isolation by distance was observed among distant populations, but isolation at close geographic proximity was found. Patterns were consistent with high historical gene flow through pollen and seed dispersal at both short and long distances. We also tested four pre‐germination treatments among populations to improve germination rates; however, germination rates remained low and only cold‐stratification treatments induced germination in some populations.
• To bolster population regeneration, introductions of cuttings from several source populations are recommended, in combination with in situ management practices that improve seedling survival and with ex situ propagation.

     

Removal of chronic Mycoplasma ovipneumoniae carrier ewes eliminates pneumonia in a bighorn sheep population

1. Chronic pathogen carriage is one mechanism that allows diseases to persist in populations. We hypothesized that persistent or recurrent pneumonia in bighorn sheep (Ovis canadensis) populations may be caused by chronic carriers of Mycoplasma ovipneumoniae (Mo). Our experimental approach allowed us to address a conservation need while investigating the role of chronic carriage in disease persistence.
2. We tested our hypothesis in two bighorn sheep populations in South Dakota, USA. We identified and removed Mo chronic carriers from the Custer State Park (treatment) population. Simultaneously, we identified carriers but did not remove them from the Rapid City population (control). We predicted removal would result in decreased pneumonia, mortality, and Mo prevalence. Both population ranges had similar habitat and predator communities but were sufficiently isolated to preclude intermixing.
3. We classified chronic carriers as adults that consistently tested positive for Mo carriage over a 20‐month sampling period (n = 2 in the treatment population; n = 2 in control population).
4. We failed to detect Mo or pneumonia in the treatment population after chronic carrier removal, while both remained in the control. Mortality hazard for lambs was reduced by 72% in the treatment population relative to the control (CI = 36%, 91%). There was also a 41% reduction in adult mortality hazard attributable to the treatment, although this was not statistically significant (CI = 82% reduction, 34% increase).
5. Synthesis and Applications: These results support the hypothesis that Mo is a primary causative agent of persistent or recurrent respiratory disease in bighorn sheep populations and can be maintained by a few chronic carriers. Our findings provide direction for future research and management actions aimed at controlling pneumonia in wild sheep and may apply to other diseases.

     

Low‐temperature physiology of climatically distinct south African populations of the biological control agent Neochetina eichhorniae

1. Neochetina eichhorniae is the most widely established biocontrol agent on water hyacinth populations around South Africa. However, some N. eichhorniae populations have failed to adequately control their host population, specifically those exposed to cold conditions.
2. The aim of this study was to determine whether two climatically distinct populations of N. eichhorniae in South Africa differ in their low‐temperature physiology, which tests whether local‐climate adaptation has occurred.
3. We estimated weevil CT_min, LLT₅₀, SCP, and SCP mortality using standard approaches. Contrary to expectation based on climatic thermal profiles at the two sites, weevils from the warm locality ((mean ± SE) CT_min = 5.0 °C ± 0.2, LLT₅₀ = ?11.3 °C ± 0.03, SCP = ?15.8 °C ± 0.6) were able to maintain activity and tolerate colder temperatures than the weevils from the colder site (CT_min = 6.0 °C ± 0.5, LLT₅₀ = ?10.1 °C ± 0.1, SCP = ?12.9 °C ± 0.8).
4. These contradictory outcomes are likely explained by the poor nutrient quality of the plants at the cold site, driving low‐temperature performance variation that overrode any macroclimate variation among sites. The cold site weevils may also have adapted to survive wide‐temperature variability, rather than perform well under very cold conditions. In contrast, the mass‐reared population of insects from the warm site has likely adapted to the consistent conditions that they experience over many years in confinement.

     

Assessment of spatial genetic structure to identify populations at risk for infection of an emerging epizootic disease

1. Understanding the geographic extent and connectivity of wildlife populations can provide important insights into the management of disease outbreaks but defining patterns of population structure is difficult for widely distributed species. Landscape genetic analyses are powerful methods for identifying cryptic structure and movement patterns that may be associated with spatial epizootic patterns in such cases.
2. We characterized patterns of population substructure and connectivity using microsatellite genotypes from 2,222 white‐tailed deer (Odocoileus virginianus) in the Mid‐Atlantic region of the United States, a region where chronic wasting disease was first detected in 2009. The goal of this study was to evaluate the juxtaposition between population structure, landscape features that influence gene flow, and current disease management units.
3. Clustering analyses identified four to five subpopulations in this region, the edges of which corresponded to ecophysiographic provinces. Subpopulations were further partitioned into 11 clusters with subtle (F_ST ≤ 0.041), but significant genetic differentiation. Genetic differentiation was lower and migration rates were higher among neighboring genetic clusters, indicating an underlying genetic cline. Genetic discontinuities were associated with topographic barriers, however.
4. Resistance surface modeling indicated that gene flow was diffuse in homogenous landscapes, but the direction and extent of gene flow were influenced by forest cover, traffic volume, and elevational relief in subregions heterogeneous for these landscape features. Chronic wasting disease primarily occurred among genetic clusters within a single subpopulation and along corridors of high landscape connectivity.
5. These results may suggest a possible correlation between population substructure, landscape connectivity, and the occurrence of diseases for widespread species. Considering these factors may be useful in delineating effective management units, although only the largest features produced appreciable differences in subpopulation structure. Disease mitigation strategies implemented at the scale of ecophysiographic provinces are likely to be more effective than those implemented at finer scales.

     

Population dynamics of brown trout (Salmo trutta) in Spruce Creek Pennsylvania: A quarter‐century perspective

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Evaluating intraspecific variation in insect trait analysis

1. Intraspecific variation plays important roles in ecology and evolution. Yet, information on how species and populations vary remains scarce, particularly for insects and regarding functional traits. This lack of knowledge can be problematic in trait‐based ecology because traditional approaches assume negligible intraspecific variation, even for analyses that assess highly variable taxa.
2. We measured 291 Arctic fritillary butterflies (Boloria chariclea) to assess the intraspecific variation in one population of this species, evaluating (i) how wingspan of Arctic fritillaries varies in relation to the other species of its community, and (ii) how well wingspan, a measure of body size, predicts weight, a measure of body mass.
3. Wingspan of Arctic fritillaries varied between 2.62 and 4.07 cm, with the 95% interval range, including ～33% (14/42) of the species in the community, and ～30% (84/279) of the butterflies of Canada. The relationship between wingspan and weight was significant (β_wingspan = 0.002, SE = 0.0008, P < 0.001), but relatively weak (R²_adj = 0.31, F_2,288 = 67.82, P < 0.001).
4. We discuss our findings in relation to the assumption of species homogeneity and the use of proxies in the analysis of species traits, complementing our case study with simulations to illustrate how intraspecific and interspecific variation interact in determining when traditional trait analyses are robust. We suggest entomologists interested in trait analyses should critically evaluate how intraspecific variation could affect their inference, especially when evaluating species that are highly sexually dimorphic, phenotypically plastic, and/or distributed across broad environmental and spatial clines.

     

Influence of body mass and environmental conditions on winter mortality risk of a northern ungulate: Evidence for a late‐winter survival bottleneck

1. A relationship between winter weather and survival of northern ungulates has long been established, yet the possible roles of biological (e.g., nutritional status) and environmental (e.g., weather) conditions make it important to determine which potential limiting factors are most influential.
2. Our objective was to examine the potential effects of individual (body mass and age) and extrinsic (winter severity and snowmelt conditions) factors on the magnitude and timing of mortality for adult (>2.5 years old) female white‐tailed deer (Odocoileus virginianus [Zimmerman, 1780]) during February–May in the Upper Peninsula of Michigan, USA.
3. One hundred and fifty deer were captured and monitored during 2009–2015 in two areas with varying snowfall. February–May survival ranged from 0.24 to 0.89 (mean = 0.69) across years. Mortality risk increased 1.9% with each unit increase in cumulative winter severity index, decreased 8.2% with each cumulative snow‐free day, and decreased 4.3% with each kg increase in body mass. Age and weekly snow depth did not influence weekly deer survival. Predation, primarily from coyote (Canis latrans [Say, 1823]) and wolves (Canis lupus [L., 1758]), accounted for 78% of known‐cause mortalities.
4. Our results suggest that cumulative winter severity, and possibly to a lesser degree deer condition entering winter, impacted deer winter survival. However, the timing of spring snowmelt appeared to be the most influential factor determining late‐winter mortality of deer in our study. This supports the hypothesis that nutrition and energetic demands from weather conditions are both important to northern ungulate winter ecology. Under this model, a delay of several weeks in the timing of spring snowmelt could exert a large influence on deer survival, resulting in a survival bottleneck.

     

Pupae survival following fire in the frosted elfin (Callophrys irus)

1. The frosted elfin (Callophrys irus) butterfly inhabits landscapes that may be subject to frequent fire to be sustained. Frosted elfins pupate primarily in leaf litter, at the soil surface, or just below it, and may suffer high mortality rates when fires occur. Gathering better information on this source of mortality is critical to planning prescribed fire operations in a manner conducive to the long-term survival of the species.
2. We buried lab-reared frosted elfin pupae (n = 61) at 0.75 cm (n = 31) or 1.75 cm (n = 30) below the ground and conducted two experimental fires that mimicked typical prescribed fires.
3. Eighteen of 30 (60%) buried at 1.75 cm survived 4 weeks postburn; no pupae buried at 0.75 cm survived. Most (n = 17) of the pupae that survived successfully enclosed the following year. Surviving pupae encountered lower maximum temperatures and were exposed to shorter durations of above-lethal temperatures compared to those that died.
4. Our data demonstrate that high mortality rates can be expected due to fire, yet fire remains a critical tool for maintaining the habitat. Fire practitioners should mitigate losses by using ignition patterns and suboptimal burn conditions to reduce fire intensity, or burn in a mosaic pattern across the landscape to ensure enough survival to perpetuate frosted elfin populations.

     

Predation yields greater population performance: what are the contributions of density‐ and trait‐mediated effects?

1. Population responses to extrinsic mortality can yield no change in the number of survivors (compensation) or an increase in the number of survivors (overcompensation) when the population is regulated by negative density‐dependence. This intriguing response has been the subject of theoretical studies, but few experiments have explored how the source of extrinsic mortality affects the response.
2. This study tests abilities of three functionally diverse predators, alone and combined, to induce (over)compensation of a prey population. Larval Aedes aegypti (Diptera: Culicidae) were exposed to predation by Mesocyclops longisetus (Crustacea: Copepoda), Anopheles barberi (Diptera: Culicidae), Corethrella appendiculata (Diptera: Corethrellidae), all three in a substitutive design, or no predation.
3. Predator treatment had no significant effect on the total number of adult survivors, nor on numbers of surviving males or females. The female development rate and a composite index of performance (r′) were greater with predation relative to no‐predator control. No differences were detected between diverse and single‐species predator treatments.
4. Sensitivity analyses indicated predation effects on the number of female adults produced, despite not being affected significantly, was the largest contributing factor to significant treatment effects on the demographic index r′. While predation did not significantly increase the production of adults, it did release survivors from density‐dependent effects sufficiently to increase population performance. This study provides an empirical test of mechanisms by which predation may yield positive mortality effects on victim populations, a phenomenon predicted to occur across many taxa and food webs.

     

Assessing the short‐term effects of capture,handling and tagging of sandgrouse

Capturing and marking free‐living birds permits the study of important aspects of their biology but may have undesirable effects. Bird welfare should be a primary concern, so it is necessary to evaluate and minimize any adverse effects of procedures used. We assess short‐term effects associated with the capture, handling and tagging with backpack‐mounted transmitters of Pin‐tailed Pterocles alchata and Black‐bellied Pterocles orientalis Sandgrouse, steppe birds of conservation concern. There was a significantly higher mortality (15%) during the first week after capture than during the following weeks (< 2.5%) in Pin‐tailed Sandgrouse, but no significant temporal mortality pattern in Black‐bellied Sandgrouse. In Pin‐tailed Sandgrouse, mortality rate during the first week increased with increasing relative transmitter and harness weight regardless of season, and with increasing handling time during the breeding season. There were no significant differences in mortality rate between study areas, type of tag, sex or age or an effect of restraint time. These results suggest the use of lighter transmitters (< 3% of the bird's weight) and a reduction of handling time (< 20 min), particularly during the breeding season, as essential improvements in procedure to reduce the mortality risk associated with the capture, handling and tagging of these vulnerable species.     

A metabolome‐based core hybridisation strategy for the prediction of rice grain weight across environments

Marker‐based prediction holds great promise for improving current plant and animal breeding efficiencies. However, the predictabilities of complex traits are always severely affected by negative factors, including distant relatedness, environmental discrepancies, unknown population structures, and indeterminate numbers of predictive variables. In this study, we utilised two independent F₁ hybrid populations in the years 2012 and 2015 to predict rice thousand grain weight (TGW) using parental untargeted metabolite profiles with a partial least squares regression method. A stable predictive model for TGW was built based on hybrids from the population in 2012 (r = 0.75) but failed to properly predict TGW for hybrids from the population in 2015 (r = 0.27). After integrating hybrids from both populations into the training set, the TGW of hybrids could be predicted but was largely dependent on population structures. Then, core hybrids from each population were determined by principal component analysis and the TGW of hybrids in both environments were successfully predicted (r > 0.60). Moreover, adjusting the population structures and numbers of predictive analytes increased TGW predictability for hybrids in 2015 (r = 0.72). Our study demonstrates that the TGW of F₁ hybrids across environments can be accurately predicted based on parental untargeted metabolite profiles with a core hybridisation strategy in rice. Metabolic biomarkers identified from early developmental stage tissues, which are grown under experimental conditions, may represent a workable approach towards the robust prediction of major agronomic traits for climate‐adaptive varieties.     

Population ecology and the management of whale watching operations on a data‐deficient dolphin population

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High‐resolution distribution modeling of a threatened short‐range endemic plant informed by edaphic factors

1. Short‐range endemic plants often have edaphic specializations that, with their restricted distributions, expose them to increased risk of anthropogenic extinction.
2. Here, we present a modeling approach to understand habitat suitability for Ricinocarpos brevis R.J.F.Hend. & Mollemans (Euphorbiaceae), a threatened shrub confined to three isolated populations in the semi‐arid south‐west of Western Australia. The model is a maximum entropy species distribution projection constructed on the basis of physical soil characteristics and geomorphology data at approximately 25 m² (1 arc‐second) resolution.
3. The model predicts the species to occur on shallow, low bulk density soils that are located high in the landscape. The model shows high affinity (72.1% average likelihood of occurrence) for the known populations of R. brevis, as well as identifying likely locations that are not currently known to support the species. There was a strong relationship between the likelihood of R. brevis occurrence and soil moisture content that the model estimated at a depth of 20 cm.
4. We advocate that our approach should be standardized using publicly available data to generate testable hypotheses for the distribution and conservation management of short‐range endemic plant species for all of continental Australia.

     

Survivorship of geographic Pomacea canaliculata populations in responses to cold acclimation

1. Pomacea canaliculata, a freshwater snail from South America, has rapidly established natural populations from south to north subtropical region in China, since its original introductions in the 1980s. Low temperature in winter is a limiting factor in the geographic expansion and successfully establishment for apple snail populations. There have been some studies on population level of low temperature tolerance for P. canaliculata, yet little is quantified about its life‐history traits in responses to cold temperatures. Whether these responses vary with the acclimation location is also unclear. We investigated the survivorship and longevity of P. canaliculata in responses to cold temperatures and examine whether these responses vary with the location and snail size. We hypothesized that survival of the snails depends on their shell height and the level of low temperature, and P. canaliculata population from the mid-subtropical zone may exhibit the highest viability over the cold thermal range.
2. We sampled P. canaliculata populations from five latitude and longitude ranges of subtropical China: Guangzhou population in southernmost (SM‐GZ), three populations of Yingtan (MR‐YT), Ningbo (MR‐NB), Ya'an (MR‐YA) in midrange, and Huanggang population in northernmost (NM‐HG) subtropical zone. For each P. canaliculata population, survival and longevity at six cold acclimation temperature levels (12, 9, 6, 3, 0, and ?3°C) were quantified, and the effects of location and shell height were examined.
3. The MR‐YA population from mid-subtropical zone of China exhibited the highest survival rate and prolonged survival time regardless of the temperature acclimation treatments, whereas the SM‐GZ population from southern subtropical was the most sensitive to cold temperatures, particular temperatures below 9°C. No individuals of the SM‐GZ population could survive after stressed for 30 days (3°C), 5 days (0°C) and 2 days (?3°C), respectively. For each experimental P. canaliculata population held at 3, 0, and ?3°C, individuals with intermediate shell height of 15.0–25.0 mm had significantly higher survivals.
4. The results highlight a request of a more thorough investigation on acclimation responses in each of the life table demographic parameters for P. canaliculata, and pose the question of whether natural selection or some genetic changes may have facilitated adaptation in invasive locations.

     

The FoxO3 gene and cause‐specific mortality

The G allele of the FOXO3 single nucleotide polymorphism (SNP) rs2802292 exhibits a consistently replicated genetic association with longevity in multiple populations worldwide. The aims of this study were to quantify the mortality risk for the longevity‐associated genotype and to discover the particular cause(s) of death associated with this allele in older Americans of diverse ancestry. It involved a 17‐year prospective cohort study of 3584 older American men of Japanese ancestry from the Honolulu Heart Program cohort, followed by a 17‐year prospective replication study of 1595 white and 1056 black elderly individuals from the Health Aging and Body Composition cohort. The relation between FOXO3 genotype and cause‐specific mortality was ascertained for major causes of death including coronary heart disease (CHD), cancer, and stroke. Age‐adjusted and multivariable Cox proportional hazards models were used to compute hazard ratios (HRs) for all‐cause and cause‐specific mortality. We found G allele carriers had a combined (Japanese, white, and black populations) risk reduction of 10% for total (all‐cause) mortality (HR = 0.90; 95% CI, 0.84–0.95; P = 0.001). This effect size was consistent across populations and mostly contributed by 26% lower risk for CHD death (HR = 0.74; 95% CI, 0.64–0.86; P = 0.00004). No other causes of death made a significant contribution to the survival advantage for G allele carriers. In conclusion, at older age, there is a large risk reduction in mortality for G allele carriers, mostly due to lower CHD mortality. The findings support further research on FOXO3 and FoxO3 protein as potential targets for therapeutic intervention in aging‐related diseases, particularly cardiovascular disease.     

Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

Rufiji tilapia (Oreochromis urolepis urolepis) is an endemic cichlid in Tanzania. In addition to its importance for biodiversity conservation, Rufiji tilapia is also attractive for farming due to its high growth rate, salinity tolerance, and the production of all‐male hybrids when crossed with Nile tilapia (Oreochromis niloticus). The aim of the current study was to assess the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations in order to inform conservation and aquaculture practices. Double‐digest restriction‐site‐associated DNA (ddRAD) libraries were constructed from 195 animals originating from eight wild (Nyamisati, Utete, Mansi, Mindu, Wami, Ruaha, Kibasira, and Kilola) and two farmed (Bwawani and Chemchem) populations. The identified single nucleotide polymorphisms (SNPs; n = 2,182) were used to investigate the genetic variation within and among the studied populations. Genetic distance estimates (F_st) were low among populations from neighboring locations, with the exception of Utete and Chemchem populations (F_st = 0.34). Isolation‐by‐distance (IBD) analysis among the wild populations did not detect any significant correlation signal (r = .05; p‐value = .4) between the genetic distance and the sampling (Euclidean distance) locations. Population structure and putative ancestry were further investigated using both Bayesian (Structure) and multivariate approaches (discriminant analysis of principal components). Both analysis indicated the existence of three distinct genetic clusters. Two cross‐validation scenarios were conducted in order to test the efficiency of the SNP dataset for discriminating between farmed and wild animals or predicting the population of origin. Approximately 95% of the test dataset was correctly classified in the first scenario, while in the case of predicting for the population of origin 68% of the test dataset was correctly classified. Overall, our results provide novel insights regarding the population structure of Rufiji tilapia and a new database of informative SNP markers for both conservation management and aquaculture activities.     

Ecological genetics of Italian peach‐potato aphid (Myzus persicae) populations in relation to geography,dispersal and insecticide resistance as studied using microsatellite and resistance markers

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Temperature elevation reduces the sensitivity of invasive cladoceran Daphnia lumholtzi to filamentous cyanobacterium Raphidiopsis raciborskii

1. Exotic cladoceran Daphnia lumholtzi is a highly invasive species in the north and south American continents and can potentially also invade European freshwaters and outcompete native Daphnia populations. However, European waterbodies are frequently dominated by less edible filamentous cyanobacteria including also invaders such as Raphidiopsis raciborskii, which might affect the fitness of D. lumholtzi. Furthermore, temperature may influence the sensitivity of D. lumholtzi to R. raciborskii filaments.
2. In this study, we determined whether the presence of R. raciborskii could obstruct the invasion of Europe by D. lumholtzi, through reducing its fitness, and whether this depends on temperature. We compared the population growth rate (r) and the somatic growth rate of D. lumholtzi maintained at two temperatures (20 or 26°C) and fed with two diets: green microalgae alone or green microalgae mixed with filaments of R. raciborskii. Three clones of D. lumholtzi were used to evaluate potential variation in response to the treatments among different clones.
3. At 20°C, the population growth rate of D. lumholtzi fed with cyanobacterial filaments declined sharply. This reduction was caused by increased egg abortion, egg degeneration, and mortality of newborn daphnids. At 26°C, R. raciborskii lost its harmful effect on the population growth of D. lumholtzi. The presence of cyanobacteria did reduce the somatic growth rate of D. lumholtzi at both temperatures and in all three clones except for one that had a similar somatic growth rate on both diets at 26°C.
4. The presence of filamentous cyanobacteria does affect growth in D. lumholtzi and may thereby substantially reduce its invasive potential, but only at lower temperatures. Therefore, the presence of filamentous cyanobacteria may not present an obstacle to the invasion of Europe by D. lumholtzi in a warmer future climate.

     

A review of the population dynamics of mule deer and black‐tailed deer Odocoileus hemionus in North America

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