Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus

Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed.     

Antiquity and diversity of aboriginal Australian Y‐chromosomes

Humans are limited in their capacity to convert protein into energy. We present a hypothesis that a “bell” shaped thorax and a wide pelvis evolved in Neandertals, at least in part, as an adaptation to a high protein diet. A high protein diet created a need to house an enlarged liver and urinary system in a wider lower trunk. To test the hypothesis, we applied a model developed to identify points of nutritional stress. A ratio of obligatory dietary fat to total animal fat and protein sourced calories is calculated based on various known and estimated parameters. Stress is identified when the obligatory dietary fat ratio is higher than fat content ratios in available prey. The model predicts that during glacial winters, when carbohydrates weren't available, 74%?85% of Neandertals' caloric intake would have had to come from animal fat. Large animals contain around 50% fat calories, and their fat content is diminished during winter, so a significant stressful dietary fat deficit was identified by the model. This deficit could potentially be ameliorated by an increased capability to convert protein into energy. Given that high protein consumption is associated with larger liver and kidneys in animal models, it appears likely that the enlarged inferior section of the Neandertals thorax and possibly, in part, also his wide pelvis, represented an adaptation to provide encasement for those enlarged organs. Behavioral and evolutionary implications of the hypothesis are also discussed. Am J Phys Anthropol 160:367–378, 2016. © 2016 Wiley Periodicals, Inc.     

Genetic Variability and Structuring of Arctic Charr (Salvelinus alpinus) Populations in Northern Fennoscandia

Variation in presumably neutral genetic markers can inform us about evolvability, historical effective population sizes and phylogeographic history of contemporary populations. We studied genetic variability in 15 microsatellite loci in six native landlocked Arctic charr (Salvelinus alpinus) populations in northern Fennoscandia, where this species is considered near threatened. We discovered that all populations were genetically highly (mean F _ST ≈ 0.26) differentiated and isolated from each other. Evidence was found for historical, but not for recent population size bottlenecks. Estimates of contemporary effective population size (N _e) ranged from seven to 228 and were significantly correlated with those of historical N _e but not with lake size. A census size (N _C) was estimated to be approximately 300 individuals in a pond (0.14 ha), which exhibited the smallest N _e (i.e. N _e/N _C = 0.02). Genetic variability in this pond and a connected lake is severely reduced, and both genetic and empirical estimates of migration rates indicate a lack of gene flow between them. Hence, albeit currently thriving, some northern Fennoscandian populations appear to be vulnerable to further loss of genetic variability and are likely to have limited capacity to adapt if selection pressures change.     

The Abundance of Protein in Amazonia: A Reply to Gross

A critical examination of Gross's hypothesis that aboriginal Amazonian populations were limited to low levels by lack of adequate protein resources concludes that (1) evidence either for or against the hypothesis is still in short supply; (2) the role of vegetable protein in aboriginal diets needs much more attention and may ultimately overthrow the protein-limitation hypothesis; (3) the abundance of animal protein in the tropical forest has likely also been underestimated; (4) the abundance of people in precontact Amazonia may well have been underestimated as well. [Amazonia, protein, cultural ecology, limiting factors, population].     

Signatures of Demography and Recombination at Coding Genes in Naturally-Distributed Populations of Arabidopsis Lyrata Subsp. Petraea

Demography impacts the observed standing level of genetic diversity present in populations. Distinguishing the relative impacts of demography from selection requires a baseline of expressed gene variation in naturally occurring populations. Six nuclear genes were sequenced to estimate the patterns and levels of genetic diversity in natural Arabidopsis lyrata subsp. petraea populations that differ in demographic histories since the Pleistocene. As expected, northern European populations have genetic signatures of a strong population bottleneck likely due to glaciation during the Pleistocene. Levels of diversity in the northern populations are about half of that in central European populations. Bayesian estimates of historical population size changes indicate that central European populations also have signatures of population size change since the last glacial maxima, suggesting that these populations are not as stable as previously thought. Time since divergence amongst northern European populations is higher than amongst central European populations, suggesting that the northern European populations were established before the Pleistocene and survived glaciation in small separated refugia. Estimates of demography based on expressed genes are complementary to estimates based on microsatellites and transposable elements, elucidating temporal shifts in population dynamics and confirming the importance of marker selection for tests of demography.     

Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers

The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, with high levels of adaptive evolution in Drosophila, bacteria, and viruses but very little evidence of widespread adaptive evolution in hominids. Although estimates in plants are more limited, some recent work has suggested that rates of adaptive evolution in a range of plant taxa are surprisingly low and that there is little association between adaptive evolution and effective population size in contrast to patterns seen in other taxa. Here, we analyze data from 35 loci for six sunflower species that vary dramatically in effective population size. We find that rates of adaptive evolution are positively correlated with effective population size in these species, with a significant fraction of amino acid substitutions driven by positive selection in the species with the largest effective population sizes but little or no evidence of adaptive evolution in species with smaller effective population sizes. Although other factors likely contribute as well, in sunflowers effective population size appears to be an important determinant of rates of adaptive evolution.     

Genome-Wide Estimates of Coancestry,Inbreeding and Effective Population Size in the Spanish Holstein Population

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.     

Rates of euthanasia and adoption for dogs and cats in Michigan animal shelters

Estimates of canine and feline euthanasia at U.S. animal shelters—largely based on voluntary surveys with low response rates—make it difficult to estimate the population from which the euthanized animals derive. Estimates of euthanasia rates (animals euthanized per unit of population) have varied widely and been available only sporadically. This study used requirements of Michigan state law (Pet Shops, Dog Pounds, and Animal Shelters Act, 1969) for animal shelters to collect admission and discharge data for all 176 Michigan-licensed animal shelters. In 2003, Michigan shelters discharged 140,653 dogs: Of these, 56,972 (40%) were euthanized; 40,005 (28%) were adopted. This annual euthanasia rate is 2.6% of the estimated 2003 Michigan dog population. Michigan shelters discharged 134,405 cats in 2003: 76,321 (57%) by euthanasia and (24%) by adoption. The estimated ratio of euthanized cats to cats who had owners was 3.1%. Small shelters and privately owned shelters were associated with higher adoption rates. Comparison with historical information from the past 10 to 20 years suggests the number of companion animals being euthanized in shelters has decreased and that progress has been made in reducing the companion animal overpopulation problem.     

The Genetic Structure of Natural Populations of DROSOPHILA MELANOGASTER. Xviii. Clinal and Uniform Genetic Variation over Populations

It has been reported in the previous papers of this series that in the eastern United States and Japan there is a north-to-south cline of additive genetic variance of viability and that the amount of the additive genetic variance in the northern population can be explained by mutation-selection balance. To determine whether or not the difference in the genetic variation in northern and southern populations can be explained by the differences in mutation rate and/or effective population size, numerical calculations were made using population genetic parameters. In addition, the average heterozygosities of the northern and southern populations at ten of 19 polymorphic structural loci surveyed were estimated in relation to the cline of additive genetic variance of viability, and the following findings were obtained. (1) The changes in mutation rate and population size cannot simultaneously explain the difference in additive genetic variance and inbreeding decline between the northern and southern populations. Thus, the operation of some kind of balancing selection, most likely diversifying selection, was suggested to explain the observed excess of additive genetic variance. (2) Estimates of the average heterozygosities of the southern population were not significantly different from those of the northern population. Thus, it was strongly suggested that the excess of additive genetic variance in the southern population cannot be caused by structural loci, but by factors outside the structural loci, and that protein polymorphisms are selectively neutral or nearly neutral.     

Development of mitochondrial and contractile components of the flight muscle in adult tsetse flies, Glossina morsitans

Estimates have been made of the phospholipid, the water, and the cytochrome-c content of the dorsal longitudinal flight muscles of the tsetse fly, and of the total non-fatty dry weight of the thorax, at different stages of adult development. The results have served as a basis for the partitioning of the dry weight of flight muscle into its three main components—contractile protein, mitochondrial protein, and phospholipid. Development is shown to involve a twofold increase in the amount of contractile protein, and a threefold increase in the amount of mitochondrial protein. These changes are discussed in relation to associated changes in wingbeat frequency.     

Density-dependent dispersal and spatial distribution of a population

Many models have been proposed to suggest that animal dispersal enhances stability of an ecological system. However, little attention has been paid on the property of a boundary and on the size of a region. In this paper, we will consider the models proposed by Gurney & Nisbet (1975), from those points of view. We will show that, if a population is dispersing in a highly density-dependent manner, a stationary distribution which does not depend on boundary conditions is established in a finite region by interactions between the population and a heterogeneous environment. We will also show that, even when a population is confined in a habitat with a limited size a population dispersing density-dependently can establish a stationary distribution, whereas a population dispersing randomly either goes to extinction or grows explosively.     

A Global Assessment of the Water Footprint of Farm Animal Products

The increase in the consumption of animal products is likely to put further pressure on the world’s freshwater resources. This paper provides a comprehensive account of the water footprint of animal products, considering different production systems and feed composition per animal type and country. Nearly one-third of the total water footprint of agriculture in the world is related to the production of animal products. The water footprint of any animal product is larger than the water footprint of crop products with equivalent nutritional value. The average water footprint per calorie for beef is 20 times larger than for cereals and starchy roots. The water footprint per gram of protein for milk, eggs and chicken meat is 1.5 times larger than for pulses. The unfavorable feed conversion efficiency for animal products is largely responsible for the relatively large water footprint of animal products compared to the crop products. Animal products from industrial systems generally consume and pollute more ground- and surface-water resources than animal products from grazing or mixed systems. The rising global meat consumption and the intensification of animal production systems will put further pressure on the global freshwater resources in the coming decades. The study shows that from a freshwater perspective, animal products from grazing systems have a smaller blue and grey water footprint than products from industrial systems, and that it is more water-efficient to obtain calories, protein and fat through crop products than animal products.     

Dietary fat and weight gain among women in the Nurses' Health Study

Objective: To assess the association of dietary fat and weight gain among adult women and to investigate whether offspring of overweight parents have a greater predisposition to weight gain due to intake of dietary fat. Research Methods and Procedures: This was an 8‐year follow‐up of 41,518 women in the Nurses’ Health Study (NHS), a population‐based, prospective cohort. The women were 41 to 68 years of age, free of cardiovascular disease, cancer, and diabetes in 1986 when “baseline” weight and diet were assessed. Eight years later (1994), changes in weight and dietary intake were assessed. Linear regression models were used to relate change in weight to fat intake and change in fat intake, using the percentage of energy from carbohydrate as the comparison, adjusted for age, BMI in 1986, leisure time physical activity, time spent sitting, percent of calories from protein, and change in percentage of calories from protein. Results: Overall, there was a weak positive association between total fat intake (β = 0.11) and weight gain. Increases in monosaturated and polyunsaturated fat were not associated with weight gain, but increases in animal fat, saturated fat, and trans fat had a positive association with weight change. There was not strong evidence of effect modification by parental weight status (p = 0.7 to 0.8 for percentage of calories from total fat, animal fat, and vegetable fat); however, the associations were stronger among the overweight compared with leaner women (p < 0.05 for percentage of calories from each type of fat). Among overweight women, for every one percentage increase in percentage of calories from trans fat, women gained an additional 2.3 lb (95% confidence interval, 1.80 to 2.86). Conclusion: Our results show that, overall, percent of calories from fat has only a weak positive association with weight gain; however, percentage of calories from animal, saturated, and trans fat has stronger associations. There was no clear evidence that the diet‐weight gain association was stronger among offspring of overweight parents, but dietary fat was associated with greater weight gain among overweight women.     

How much cytoplasm can a bacterial genome control?

In this perspective we discuss that bacterial genomes have optimized during evolution to control a range of cytoplasm, from immediately after cell division to a maximum amount/volume present just prior to DNA replication and subsequent cell division. The genetic expansion of bacteria via evolution may be limited to a genome size:cytoplasm amount/volume ratios and energetics that have been selected for during 3.6-4 billion years of evolution on the Earth. The optimal genome size is one that is relatively constant, but also has some plasticity for evolutionary change (via gene transfer) and mutational events, and can control a range of cytoplasm during the cell cycle.     

Assessing consistency of fish survey data: uncertainties in the estimation of mackerel icefish (<Emphasis Type="Italic">Champsocephalus gunnari</Emphasis>) abundance at South Georgia

Mackerel icefish (Champsocephalus gunnari) is a semi-pelagic finfish species inhabiting shelf areas in the Southern Ocean. The population at South Georgia is currently exploited by pelagic trawlers fishing close to the seabed. Annual catches peaked at 150,000 t in 1983 and have declined since the mid-to-late 1980s. Bottom-trawl surveys have been conducted since 1987, providing a time series of abundance and size distribution for use in assessing the status of the stock and setting quotas. Food web models suggest that estimates of the biomass from survey data are substantially lower than the amount of icefish required by the local ecosystem. The aim of this study was to assess the uncertainty around current estimates of density and variance, using alternative nonparametric stratified bootstrapping methods. The stratified rescaling bootstrap estimator was identified as the most appropriate method of those tested: in comparison with the existing method, confidence intervals and the inter-annual variability of the estimates were reduced. Numbers-at-age were estimated from mixture distribution models fitted to length-disaggregated density data in order to determine whether individual cohorts were consistently detected by the surveys. Estimates of numbers-at-age could not consistently delineate cohorts in successive years indicating that survey-based estimates of density were biased. These biases may have arisen because the trawl gear did not select individuals of all sizes equally, or because sampling was restricted to the demersal component of the stock. Estimates of abundance of the pelagic component of the stock should be derived from acoustic data to improve the assessment.     

Isolation of Murine Valve Endothelial Cells

Normal valve structures consist of stratified layers of specialized extracellular matrix (ECM) interspersed with valve interstitial cells (VICs) and surrounded by a monolayer of valve endothelial cells (VECs). VECs play essential roles in establishing the valve structures during embryonic development, and are important for maintaining life-long valve integrity and function. In contrast to a continuous endothelium over the surface of healthy valve leaflets, VEC disruption is commonly observed in malfunctioning valves and is associated with pathological processes that promote valve disease and dysfunction. Despite the clinical relevance, focused studies determining the contribution of VECs to development and disease processes are limited. The isolation of VECs from animal models would allow for cell-specific experimentation. VECs have been isolated from large animal adult models but due to their small population size, fragileness, and lack of specific markers, no reports of VEC isolations in embryos or adult small animal models have been reported. Here we describe a novel method that allows for the direct isolation of VECs from mice at embryonic and adult stages. Utilizing the Tie2-GFP reporter model that labels all endothelial cells with Green Fluorescent Protein (GFP), we have been successful in isolating GFP-positive (and negative) cells from the semilunar and atrioventricular valve regions using fluorescence activated cell sorting (FACS). Isolated GFP-positive VECs are enriched for endothelial markers, including CD31 and von Willebrand Factor (vWF), and retain endothelial cell expression when cultured; while, GFP-negative cells exhibit molecular profiles and cell shapes consistent with VIC phenotypes. The ability to isolate embryonic and adult murine VECs allows for previously unattainable molecular and functional studies to be carried out on a specific valve cell population, which will greatly improve our understanding of valve development and disease mechanisms.     

Conservation genetics of Boelen’s python (Morelia boeleni) from New Guinea: reduced genetic diversity and divergence of captive and wild animals

Boelen’s python (Morelia boeleni) is a montane New Guinea endemic found in highlands above 1000 m and below the tree line. The ecology, natural history, distribution, population size, and conservation status of this species are largely unknown. It has a protected status in Papua New Guinea but not in Indonesian Papua and several US and European zoos have active captive breeding programs that have been largely unsuccessful. To understand the degree of genetic diversity in wild and captive animals we undertook a genetic analysis of 90 M. boeleni for which we sequenced two mtDNA loci and one nuclear locus for a total of 1,418 bp of sequence data per individual. All 16 wild-caught M. boeleni from Indonesia and all captive M. boeleni are genetically uniform for all three loci. The single wild-caught animal from Papua New Guinea showed extremely low levels of genetic divergence and diversity from the Indonesian and captive samples. Data from two congeners, M. amethistina and M. viridis, suggests that M. boeleni have reduced genetic variation with a small effective population size possibly due to historical bottlenecks. These data demonstrate the need for further studies of genetic diversity of M. boeleni from across its range and raise particular concern for the limited genetic diversity of M. boeleni used captive breeding programs in zoological parks.     

Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites

Adaptation in eukaryotes is generally assumed to be mutation-limited because of small effective population sizes. This view is difficult to reconcile, however, with the observation that adaptation to anthropogenic changes, such as the introduction of pesticides, can occur very rapidly. Here we investigate adaptation at a key insecticide resistance locus (Ace) in Drosophila melanogaster and show that multiple simple and complex resistance alleles evolved quickly and repeatedly within individual populations. Our results imply that the current effective population size of modern D. melanogaster populations is likely to be substantially larger (≥100-fold) than commonly believed. This discrepancy arises because estimates of the effective population size are generally derived from levels of standing variation and thus reveal long-term population dynamics dominated by sharp—even if infrequent—bottlenecks. The short-term effective population sizes relevant for strong adaptation, on the other hand, might be much closer to census population sizes. Adaptation in Drosophila may therefore not be limited by waiting for mutations at single sites, and complex adaptive alleles can be generated quickly without fixation of intermediate states. Adaptive events should also commonly involve the simultaneous rise in frequency of independently generated adaptive mutations. These so-called soft sweeps have very distinct effects on the linked neutral polymorphisms compared to the standard hard sweeps in mutation-limited scenarios. Methods for the mapping of adaptive mutations or association mapping of evolutionarily relevant mutations may thus need to be reconsidered.     

Level,content, and caloric equivalents of the lipid,carbohydrate, and protein in the body components of Luidia clathrata (echinodermata: asteroidea: platyasterida) in Tampa bay

The body components of the primitive platyasterid starfish, Luidia clathrata (Say) have been characterized according to season, reproductive, and nutritional condition. The animal has been ‘reconstructed’ in terms of the wet and dry weights, the weight of organic matter, and the caloric equivalents of the body components in early summer (when there are no gonads and the pyloric caeca are small), in autumn (just prior to initiation of gonadal development and at maximal caeca size), and in early spring (at maximal gonad size). The body wall is always the most significant component in terms of wet and dry weights. In terms of organic matter and calories, the pyloric caeca are the most significant compartment in the fall and, together with the gonads, in the spring. On starvation for one month, the decrease in the size of the pyloric caeca is calculated to have produced 2.048 kcal. The energy requirement over the period, calculated from Q_o2 values, is 2.112 kcal. There was no change in biochemical composition of the pyloric caeca with starvation, suggesting that energy production came about through cell destruction rather than preferential utilization of cellular nutrient stores. Lack of extreme change in the composition of the pyloric caeca with size through the year also suggests that energy deposition in the organ is primarily by change in cell number and not by cell size.