Estimation of population growth or decline in genetically monitored populations

This article introduces a new general method for genealogical inference that samples independent genealogical histories using importance sampling (IS) and then samples other parameters with Markov chain Monte Carlo (MCMC). It is then possible to more easily utilize the advantages of importance sampling in a fully Bayesian framework. The method is applied to the problem of estimating recent changes in effective population size from temporally spaced gene frequency data. The method gives the posterior distribution of effective population size at the time of the oldest sample and at the time of the most recent sample, assuming a model of exponential growth or decline during the interval. The effect of changes in number of alleles, number of loci, and sample size on the accuracy of the method is described using test simulations, and it is concluded that these have an approximately equivalent effect. The method is used on three example data sets and problems in interpreting the posterior densities are highlighted and discussed.

Agriculture modifies the seasonal decline of breeding success in a tropical wild bird population

1.Habitat conversion for agriculture is a major driver of biodiversity loss, but our understanding of the demographic processes involved remains poor. We typically investigate the impacts of agriculture in isolation even though populations are likely to experience multiple, concurrent changes in the environment (e.g. land and climate change). Drivers of environmental change may interact to affect demography but the mechanisms have yet to be explored fully in wild populations. 2.Here, we investigate the mechanisms linking agricultural land-use with breeding success using long-term data for the formerly Critically Endangered Mauritius kestrel Falco punctatus; a tropical forest specialist that also occupies agricultural habitats. We specifically focused on the relationship between breeding success, agriculture and the timing of breeding because the latter is sensitive to changes in climatic conditions (spring rainfall), and enables us to explore the interactive effects of different (land and climate) drivers of environmental change. 3.Breeding success, measured as egg survival to fledging, declines seasonally in this population, but we found that the rate of this decline became increasingly rapid as the area of agriculture around a nest site increased. If the relationship between breeding success and agriculture was used in isolation to estimate the demographic impact of agriculture it would significantly under-estimate breeding success in dry (early) springs, and over-estimate breeding success in wet (late) springs. 4.Analysis of prey delivered to nests suggests that the relationship between breeding success and agriculture might be due, in part, to spatial variation in the availability of native, arboreal geckos. 5.Synthesis and applications. Agriculture modifies the seasonal decline in breeding success in this population. As springs are becoming wetter in our study area and since the kestrels breed later in wetter springs, the impact of agriculture on breeding success will become worse over time. Our results suggest that forest restoration designed to reduce the detrimental impacts of agriculture on breeding may also help reduce the detrimental effects of breeding late due to wetter springs. Our results therefore highlight the importance of considering the interactive effects of environmental change when managing wild populations.

Failure to respond to food resource decline has catastrophic consequences for koalas in a high-density population in Southern Australia

Understanding the ability of koalas to respond to changes in their environment is critical for conservation of the species and their habitat. We monitored the behavioural response of koalas to declining food resources in manna gum (Eucalyptus viminalis) woodland at Cape Otway, Victoria, Australia, from September 2011 to November 2013. Over this period, koala population density increased from 10.1 to 18.4 koalas.ha-1. As a result of the high browsing pressure of this population, manna gum canopy condition declined with 71.4% manna gum being completely or highly defoliated in September 2013. Despite declining food resources, radio collared koalas (N = 30) exhibited high fidelity to small ranges (0.4-1.2 ha). When trees became severely defoliated in September 2013, koalas moved relatively short distances from their former ranges (mean predicted change in range centroid = 144 m) and remained in areas of 0.9 to 1.0 ha. This was despite the high connectivity of most manna gum woodland, and close proximity of the study site (< 3 km) to the contiguous mixed forest of the Great Otway National Park. Limited movement had catastrophic consequences for koalas with 71% (15/21) of radio collared koalas dying from starvation or being euthanased due to their poor condition between September and November 2013.

Age-Related Olfactory Decline is Associated with the BDNF Val66met Polymorphism : Evidence from a Population-Based Study

The present study investigates the effect of the brain-derived neurotrophic factor (BDNF) val66met polymorphism on change in olfactory function in a large scale, longitudinal population-based sample (n = 836). The subjects were tested on a 13 item force-choice odor identification test on two test occasions over a 5-year-interval. Sex, education, health-related factors, and semantic ability were controlled for in the statistical analyses. Results showed an interaction effect of age and BDNF val66met on olfactory change, such that the magnitude of olfactory decline in the older age cohort (70–90years old at baseline) was larger for the val homozygote carriers than for the met carriers. The older met carriers did not display larger age-related decline in olfactory function compared to the younger group. The BDNF val66met polymorphism did not affect the rate of decline in the younger age cohort (45–65years). The findings are discussed in the light of the proposed roles of BDNF in neural development and maintenance.

Lifestyle factors associated concurrently and prospectively with co-morbid cardiovascular disease in a population-based cohort of colorectal cancer survivors

Aims To assess self-reported lifetime prevalence of cardiovascular disease (CVD) among colorectal cancer survivors, and examine the cross-sectional and prospective associations of lifestyle factors with co-morbid CVD. Methods Colorectal cancer survivors were recruited (n = 1966). Data were collected at approximately 5, 12, 24 and 36 months post-diagnosis. Cross-sectional findings included six CVD categories (hypercholesterolaemia, hypertension, diabetes, heart failure, kidney disease and ischaemic heart disease (IHD)) at 5 months post-diagnosis. Longitudinal outcomes included the probability of developing (de novo) co-morbid CVD by 36 months post-diagnosis. Lifestyle factors included body mass index, physical activity, television (TV) viewing, alcohol consumption and smoking. Results Co-morbid CVD prevalence at 5 months post-diagnosis was 59%, and 16% of participants with no known CVD at the baseline reported de novo CVD by 36 months. Obesity at the baseline predicted de novo hypertension (odds ratio [OR] = 2.20, 95% confidence intervals [CI] = 1.09, 4.45) and de novo diabetes (OR = 6.55, 95% CI = 2.19, 19.53). Participants watching >4 h of TV/d at the baseline (compared with <2 h/d) were more likely to develop ischaemic heart disease by 36 months (OR = 5.51, 95% CI = 1.86, 16.34). Conclusion Overweight colorectal cancer survivors were more likely to suffer from co-morbid CVD. Interventions focusing on weight management and other modifiable lifestyle factors may reduce functional decline and improve survival.

Marital loss, mental health and the role of perceived social support : findings from six waves of an Australian population based panel study

Objectives: To investigate the impact of transitions out of marriage (separation, widowhood) on the self reported mental health of men and women, and examine whether perceptions of social support play an intervening role. ---------- Methods: The analysis used six waves (2001–06) of an Australian population based panel study, with an analytical sample of 3017 men and 3225 women. Mental health was measured using the MHI-5 scale scored 0–100 (α=0.97), with a higher score indicating better mental health. Perceptions of social support were measured using a 10-item scale ranging from 10 to 70 (α=0.79), with a higher score indicating higher perceived social support. A linear mixed model for longitudinal data was used, with lags for marital status, mental health and social support. ---------- Results: After adjustment for social characteristics there was a decline in mental health for men who separated (−5.79 points) or widowed (−7.63 points), compared to men who remained married. Similar declines in mental health were found for women who separated (−6.65 points) or became widowed (−9.28 points). The inclusion of perceived social support in the models suggested a small mediation effect of social support for mental health with marital loss. Interactions between perceived social support and marital transitions showed a strong moderating effect for men who became widowed. No significant interactions were found for women. ---------- Conclusion: Marital loss significantly decreased mental health. Increasing, or maintaining, high levels of social support has the potential to improve widowed men's mental health immediately after the death of their spouse.

Selenium status of the Australian population : effect of age, gender and cardiovascular disease

Selenium (Se) is an essential trace element and the clinical consequences of Se deficiency have been well-documented. Se is primarily obtained through the diet and recent studies have suggested that the level of Se in Australian foods is declining. Currently there is limited data on the Se status of the Australian population so the aim of this study was to determine the plasma concentration of Se and glutathione peroxidase (GSH-Px), a well-established biomarker of Se status. Furthermore, the effect of gender, age and presence of cardiovascular disease (CVD) was also examined. Blood plasma samples from healthy subjects (140 samples, mean age = 54 years; range, 20-86 years) and CVD patients (112 samples, mean age = 67 years; range, 40-87 years) were analysed for Se concentration and GSH-Px activity. The results revealed that the healthy Australian cohort had a mean plasma Se level of 100.2 +/- 1.3 microg Se/L and a mean GSH-Px activity of 108.8 +/- 1.7 U/L. Although the mean value for plasma Se reached the level required for optimal GSH-Px activity (i.e. 100 microg Se/L), 47% of the healthy individuals tested fell below this level. Further evaluation revealed that certain age groups were more at risk of a lowered Se status, in particular, the oldest age group of over 81 years (females = 97.6 +/- 6.1 microg Se/L; males = 89.4 +/- 3.8 microg Se/L). The difference in Se status between males and females was not found to be significant. The presence of CVD did not appear to influence Se status, with the exception of the over 81 age group, which showed a trend for a further decline in Se status with disease (plasma Se, 93.5 +/- 3.6 microg Se/L for healthy versus 88.2 +/- 5.3 microg Se/L for CVD; plasma GSH-Px, 98.3 +/- 3.9 U/L for healthy versus 87.0 +/- 6.5 U/L for CVD). These findings emphasise the importance of an adequate dietary intake of Se for the maintenance of a healthy ageing population, especially in terms of cardiovascular health.

Population genetics of the frog-killing fungus Batrachochytrium dendrobatidis

Global amphibian decline by chytridiomycosis is a major environmental disaster that has been attributed to either recent fungal spread or environmental change that promotes disease. Here, we present a population genetic comparison of Batrachochytrium dendrobatidis isolates from an intensively studied region of frog decline, the Sierra Nevada of California. In support of a novel pathogen, we find low diversity, no amphibian-host specificity, little correlation between fungal genotype and geography, local frog extirpation by a single fungal genotype, and evidence of human-assisted fungus migration. In support of endemism, at a local scale, we find some diverse, recombining populations. Therefore neither epidemic spread nor endemism alone explains this particular amphibian decline. Recombination raises the possibility of resistant sporangia and a mechanism for rapid spread as well as persistence that could greatly complicate global control of the pathogen.

Impacts of grazing management options on pasture and animal productivity in a Heteropogon contortus (black speargrass) pasture in central Queensland. 2. Population dynamics of Heteropogon contortus and Stylosanthes scabra cv. Seca.

The dynamics of Heteropogon contortus and Stylosanthes scabra cv. Seca populations were studied in a subset of treatments in an extensive grazing study conducted in central Queensland between 1988 and 2001. These treatments were 4 stocking rates in native pasture and 2 of these stocking rates in legume oversown and supplement/spring burning treatments. For the 1999-2000 summer, population data for H. contortus in 5 of these native pasture and supplement/burning treatments were compared with those for an additional burnt treatment. Seasonal rainfall throughout this study was below the long-term mean and mean annual pasture utilisation ranged from 24 to 61%. Increasing stocking rate from 5 to 2 ha/steer in native pasture reduced H. contortus plant density. Increasing stocking rate reduced seedling recruitment as a result of its effect on soil seedbanks. Seedling recruitment was the major determinant of change in plant density, although some individual H. contortus plants did survive throughout the study. Burning in spring 1999, particularly at light stocking rate, promoted seedling recruitment above that in both unburnt native and legume oversown pasture and resulted in increased H. contortus plant density. In the legume oversown treatments, S. scabra cv. Seca density increased rapidly from 15 plants/m2 in 1988 to 140 plants/m2 in 2001 following a lag phase between 1988 and 1993. This increased S. scabra density was associated with an eventual decline in H. contortus plant density through reduced seedling recruitment. It was concluded that H. contortus population density is sustainable at stocking rates of 4 and 5 ha/steer (30% pasture utilisation) and that spring burning at light stocking rate can promote H. contortus populations. Increasing densities of S. scabra need to be managed to prevent its dominance.

Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei

Microsatellite markers were used to examine spatio-temporal genetic variation in the endangered eastern freshwater cod Maccullochella ikei in the Clarence River system, eastern Australia. High levels of population structure were detected. A model-based clustering analysis of multilocus genotypes identified four populations that were highly differentiated by F-statistics (FST = 0· 09 − 0· 49; P < 0· 05), suggesting fragmentation and restricted dispersal particularly among upstream sites. Hatchery breeding programmes were used to re-establish locally extirpated populations and to supplement remnant populations. Bayesian and frequency-based analyses of hatchery fingerling samples provided evidence for population admixture in the hatchery, with the majority of parental stock sourced from distinct upstream sites. Comparison between historical and contemporary wild-caught samples showed a significant loss of heterozygosity (21%) and allelic richness (24%) in the Mann and Nymboida Rivers since the commencement of stocking. Fragmentation may have been a causative factor; however, temporal shifts in allele frequencies suggest swamping with hatchery-produced M. ikei has contributed to the genetic decline in the largest wild population. This study demonstrates the importance of using information on genetic variation and population structure in the management of breeding and stocking programmes, particularly for threatened species.

An evaluation of electrofishing as a control measure for an invasive tilapia (Oreochromis mossambicus) population in northern Australia.

Combating the spread of invasive fish is problematic, with eradication rarely possible and control options varying enormously in their effectiveness. In two small impoundments in north-eastern Australia, an electrofishing removal program was conducted to control an invasive tilapia population. We hypothesised that electrofishing would reduce the population density of Oreochromis mossambicus (Mozambique tilapia), to limit the risk of downstream spread into areas of high conservation value. We sampled by electrofishing monthly for 33 months. Over this period, there was an 87% decline in catch per unit effort (CPUE) of mature fish, coupled with a corresponding increase of 366% in the number of juveniles, suggesting a density-dependent response in the stock-recruitment relationship for the population. Temperature was inversely related to CPUE (r=0.43, lag=10 days), implying greater electrofishing efficiency in cooler months. The reduction in breeding stock is likely to reduce the risk of spread and render the population vulnerable to other control measures such as netting and/or biological control. Importantly, the current study suggests routine electrofishing may be a useful control tool for invasive fish in small impoundments when the use of more destructive techniques, such as piscicides, is untenable.

Population Recovery of Nicobar Long-Tailed Macaque Macaca fascicularis umbrosus following a Tsunami in the Nicobar Islands, India

Natural disasters pose a threat to isolated populations of species with restricted distributions, especially those inhabiting islands. The Nicobar long tailed macaque. Macaca fascicularis umbrosus, is one such species found in the three southernmost islands (viz. Great Nicobar, Little Nicobar and Katchal) of the Andaman and Nicobar archipelago, India. These islands were hit by a massive tsunami (Indian Ocean tsunami, 26 December 2004) after a 9.2 magnitude earthquake. Earlier studies Umapathy et al. 2003; Sivakumar, 2004] reported a sharp decline in the population of M. f. umbrosus after thetsunami. We studied the distribution and population status of M. f. umbrosus on thethree Nicobar Islands and compared our results with those of the previous studies. We carried out trail surveys on existing paths and trails on three islands to get encounter rate as measure of abundance. We also checked the degree of inundation due to tsunami by using Normalized Difference Water Index (NDWI) on landsat imageries of the study area before and after tsunami. Theencounter rate of groups per kilometre of M. f. umbrosus in Great Nicobar, Little Nicobar and Katchal was 0.30, 0.35 and 0.48 respectively with the mean group size of 39 in Great Nicobar and 43 in Katchal following the tsunami. This was higher than that reported in the two earlier studies conducted before and after the tsunami. Post tsunami, there was a significant change in the proportion of adult males, adult females and immatures, but mean group size did not differ as compared to pre tsunami. The results show that population has recovered from a drastic decline caused by tsunami, but it cannot be ascertained whether it has reached stability because of the altered group structure. This study demonstrates the effect of natural disasters on island occurring species.

The decline in the commercially important species of fish and predominance of Clarias lazera in Lake Chad

About 86 species of fish have been recorded in the Lake Chad. Most of the species occurring in the lake are widespread including most of the commercially important species. Fish distribution in the lake was adversely affected by the 1972/73 and 1983/84 droughts. The commercially important species before the 1972/73 drought were; Lates, Labeo distichodus, Heterotis, Gymnarchus, Hydrocynus, Citharinus and Bagrus. Other species which had less commercial value at that time include, Clarias, Gnathanemus, Polypterus, Protopterus, Tilapia and Synodontis. Lates niloticus was the most predominant species of commercial importance comprising 50-60% of the total catches of fishermen between 1962 and 1973. Before the 1972/73 drought, occurrence of Clarias lazera was negligible and restricted to long line catches and had little commercial value. As a result of the drought of 1972/73 which resulted in near drying up to the northern sector of the lake, fish populations were confined to isolated pools and were completely scooped out. The remaining fish populations retreated to the southern basin where enough water always remained to hold the surviving representatives of the population. The effects of the drought resulted in occurrence of the little known C. lazera along with other hardy species like Tilapia and Protopterus to dominate the existing fish species composition. In 1976, C. lazera dominated the total catches of fishermen with 85.6%. An overview of the fish population in the lake, their relative abundance, changes in species composition, the effects of drought on the fauna of the lake based on the available data are discussed in this paper

Decline in condition of northern bluefin tuna (Thunnus thynnus) in the Gulf of Maine

The northern bluefin tuna (Thunnus thynnus) is a highly mobile apex predator in the Gulf of Maine. Despite current stock assessments that indicate historically high abundance of its main prey, Atlantic herring (Clupea harengus), commercial fishermen have observed declines in the somatic condition of northern bluefin tuna during the last decade. We examined this claim by reviewing detailed logbooks of northern bluefin tuna condition from a local fishermen’s cooperative and applying multinomial regression, a robust tool for exploring how a categorical variable may be related to other variables of interest. The data set contained >3082 observations of condition (fat and oil content and fish shape) from fish landed between 1991 and 2004. Energy from stored lipids is used for migration and reproduction; therefore a reduction in energy acquisition on bluefin tuna feeding grounds could diminish allocations to growth and gamete production and have detrimental consequences for rebuilding the western Atlantic population. A decline in northern bluefin tuna somatic condition could indicate substantial changes in the bottom-up transfer of energy in the Gulf of Maine, shifts in their reproductive or migratory patterns, impacts of fishing pressure, or synergistic effects from multiple causes.

New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga)

In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short-and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing.