Isolation of DNA from small amounts of elephant ivory

This protocol describes a method for the extraction of DNA from elephant ivory. These techniques are being used to assign geographic origin to poached ivory by comparing the ivory genotype to a geographic-based gene frequency map, developed separately. The method has three components: ivory pulverization, decalcification and DNA extraction. Pulverization occurs in a freezer mill while the sample is deep frozen in liquid nitrogen, preventing degradation of DNA during the process. Decalcification involves repeated agitation of the sample in 0.5 M ethylenediaminetetraacetic acid over a 4-d period. Extraction follows a modified Qiagen protocol for the extraction of DNA from animal tissue. This method can be used on all forms of ivory. However, DNA recovery is highest when the outermost layer of the tusk, the cementum, is used. When applied to extract DNA from 11 samples, in duplicate, the entire protocol can be completed in 6 d, although much of this time consists of pause points that do not require effort. The protocol provides 0.8 +/- 0.11 ng microl(-1) (mean +/- s.e., n = 48) of DNA per sample.     

Maximum sustainable yield of populations with continuous age-structure.

We address the problem of finding the harvesting policy that will maximize the yield and maintain a population in a steady state. The population is characterized by continuous age classes and therefore follows differential equations. Here, we assume that the equations are linear (no density dependence). Two possible constraints are considered: either recruitment or total population are fixed to a constant. Under these conditions, the optimal policy is to harvest the fraction theta of a younger age class ? and to harvest totally an older age class b. The optimal solution (theta, ?, b) can be calculated explicitly if the fecundity and mortality schedules are given. The solution is compared to the simpler strategy of harvesting all individuals beyond a single age class a. It is shown that the latter strategy can be much less profitable than harvesting two age classes because it cannot take account of the different values of individuals according to their age.     

Patterns of molecular genetic variation among African elephant populations

The highly threatened African elephants have recently been subdivided into two species, Loxodonta africana (savannah or bush elephant) and L. cyclotis (forest elephant) based on morphological and molecular studies. A molecular genetic assessment of 16 microsatellite loci across 20 populations (189 individuals) affirms species level genetic differentiation and provides robust genotypic assessment of species affiliation. Savannah elephant populations show modest levels of phylogeographic subdivision based on composite microsatellite genotype, an indication of recent population isolation and restricted gene flow between locales. The savannah elephants show significantly lower genetic diversity than forest elephants, probably reflecting a founder effect in the recent history of the savannah species.     

Stable isotope series from elephant ivory reveal lifetime histories of a true dietary generalist

Longitudinal studies have revealed how variation in resource use within consumer populations can impact their dynamics and functional significance in communities. Here, we investigate multi-decadal diet variations within individuals of a keystone megaherbivore species, the African elephant (Loxodonta africana), using serial stable isotope analysis of tusks from the Kruger National Park, South Africa. These records, representing the longest continuous diet histories documented for any extant species, reveal extensive seasonal and annual variations in isotopic--and hence dietary--niches of individuals, but little variation between them. Lack of niche distinction across individuals contrasts several recent studies, which found relatively high levels of individual niche specialization in various taxa. Our result is consistent with theory that individual mammal herbivores are nutritionally constrained to maintain broad diet niches. Individual diet specialization would also be a costly strategy for large-bodied taxa foraging over wide areas in spatio-temporally heterogeneous environments. High levels of within-individual diet variability occurred within and across seasons, and persisted despite an overall increase in inferred C(4) grass consumption through the twentieth century. We suggest that switching between C(3) browsing and C(4) grazing over extended time scales facilitates elephant survival through environmental change, and could even allow recovery of overused resources.     

Redefining the maximum sustainable yield for the Schaefer population model including multiplicative environmental noise

The focus of this article is to investigate the biological reference points, such as the maximum sustainable yield (MSY), in a common Schaefer (logistic) surplus production model in the presence of a multiplicative environmental noise. This type of model is used in fisheries stock assessment as a first-hand tool for biomass modelling. Under the assumption that catches are proportional to the biomass, we derive new conditions on the environmental noise distribution such that stationarity exists and extinction is avoided. We then get new explicit results about the stationary behavior of the biomass distribution for a particular specification of the noise, namely the biomass distribution itself and a redefinition of the MSY and related quantities that now depend on the value of the variance of the noise. Consequently, we obtain a more precise vision of how less optimistic the stochastic version of the MSY can be than the traditionally used (deterministic) MSY. In addition, we give empirical conditions on the error variance to approximate our specific noise by a lognormal noise, the latter being more natural and leading to easier inference in this context. These conditions are mild enough to make the explicit results of this paper valid in a number of practical applications. The outcomes of two case-studies about northwest Atlantic haddock [Spencer, P.D., Collie, J.S., 1997. Effect of nonlinear predation rates on rebuilding the Georges Bank haddock (Melanogrammus aeglefinus) stock. Can. J. Fish. Aquat. Sci. 54, 2920-2929] and South Atlantic albacore tuna [Millar, R.B., Meyer, R., 2000. Non-linear state space modelling of fisheries biomass dynamics by using Metropolis-Hastings within-Gibbs sampling. Appl. Stat. 49, 327-342] are used to illustrate the impact of our results in bioeconomic terms.     

Notes on the adrenal of the African elephant

Sections of the adrenals of two male specimens of Loxodonta africana were examined. Apart from the dimensions of the gland and the amount and disposition of connective tissue in it, the most characteristic features were the very high lipid content of the cortical secretory cells, the large size of these cells, and the occurrence of dark cells in the zona fasciculata.     

African elephant age determination from teeth: validation from known individuals

We assess tooth‐based age criteria for African elephants developed by Laws in relation to known‐aged individuals in the Amboseli elephant population. Laws’s technique remains a robust and useful mechanism for age determination, although we suggest revisions to the oldest age categories. Blind age assignment to jaws of unknown sex using the Laws criteria resulted in misclassification of M4 and M5; measures overlapped too much to differentiate these teeth by sex. Sexes could be reliably distinguished after age 30 or XIX in tooth category by two measures: mandible thickness and width of the ascending ramus, but individuals of the same known age differed in tooth wear and progression rates. Such variation needs to be incorporated in the error assigned to tooth age categories. Ages at death of found jaws (n = 266) were similar to results of survival analysis from all demographic data (n = 2455), excluding calves whose jaws decompose because of weathering and scavengers. Jaw‐based models of age at death need correction for the inability to detect this early mortality, which artificially extends mean longevity by up to 6 years.     

Bioenergy from plants and the sustainable yield challenge

Bioenergy from plants, particularly from perennial grasses and trees, could make a substantial contribution to alleviation of global problems in climate change and energy security if high yields can be sustained. Here, yield traits in a range of key bioenergy crops are reviewed, from which several targets for future improvement can be identified. Some are already the focus of genetically modified (GM) and non-GM approaches. However, the efficient growth strategies of perennial bioenergy crops rely on newly assimilated and recycled carbon and remobilized nitrogen in a continually shifting balance between sources and sinks. This balance is affected by biotic (e.g. pest, disease) and abiotic (e.g. drought) stresses. Future research should focus on three main challenges: changing (photo)thermal time sensitivity to lengthen the growing season without risking frost damage or limiting remobilization of nutritional elements following senescence; increasing aboveground biomass without depleting belowground reserves required for next year's growth and thus without increasing the requirement for nutrient applications; and increasing aboveground biomass without increasing water use.     

Is maximum sustainable yield independent of body size for mammals (and others)?

Summary Provided carrying capacity (K) for non-primate mammals scales with the –0.75 power of adult body weight (W), MSY (in weight) should be approximately one-sixth ofC, whereC is defined byK =CW ^–0.75.     

Genetic assessment of captive elephant (Elephas maximus) populations in Thailand

The genetic diversity and population structure of 136 captive Thai elephants (Elephas maximus) with known region of origin were investigated by analysis of 14 highly polymorphic microsatellite loci. We did not detect significant indications of inbreeding and only a low differentiation of elephants from different regions. This is probably explained by the combined effects of isolation by distance and exchange between different regions or between captive and wild elephant populations. Estimates of effective population sizes were in the range of 90–240 individuals, which emphasizes the necessity to guard against inbreeding as caused by the current use of a restricted number of breeding bulls.     

Molecular phylogeny of Elephantidae. Extreme divergence of the extant forest African elephant.

A phylogenetic study of the Elephantidae (Proboscidea, Mammalia) is based on the cytochrome b mitochondrial gene: 31 terminals, that is, all known sequences, one non-elephantid proboscidean, the extinct American mastodon, and four outgroups. The data set includes 11 new sequences with the first published sequence of the forest African elephant, L. a. cyclotis. The analyses of extant taxa only and of both extant and extinct taxa show that L. a. cyclotis is highly divergent from L. a. africana. It is as divergent from L. a. africana as Loxodonta is divergent from Elephas. Southern L. a. africana form a clade. The continental subspecies E. m. indicus is paraphyletic with individuals from India and Thailand closer to E. m. maximus (Sri-Lanka). Members of Mammuthus primigenius are more closely related to Loxodonta although they do not form a clade; two specimens of M. primigenius are closer to L. a. africana making the genus Loxodonta paraphyletic. The latter conclusion may be partly due to unequal length of the various polymorphic mammoth sequences.     

Growth of the African elephant (Loxodonta africana)

The three-stage desk calculation of the von Bertalanffy equation to describe growth in height and weight with age in the elephant is compared with a new approach to calculating the three coefficients in the function by a computer. The two methods give different results with respect to the weight/age calculations. Theoretical von Bertalanffy equations calculated by both methods to describe growth in height and weight with age in the African elephant in Zambia are compared with previously published equations for the elephant in East Africa. Details are given of growth in height in two known-age African elephants, a female ‘Diksie’ and a male ‘Kartoum’. Theoretical growth in height curves for the female African and Asiatic elephant are compared. The coefficients K and / for growth in height are not transferable to the growth in weight equations. Inherent inaccuracies in the calculation of the coefficients in the von Bertalanffy equation are discussed, and it is concluded that in animals which have a long life-span such as the elephant, the equation serves as a purely empirical representation of weight-at-age data and that there is little biological significance in the parameters it contains. The computer-calculated curves give the best fit to the data. The regression of log age on log shoulder height from 2–20 years of age provides a more realistic approach to comparative growth studies. The increase in adrenal weight with age is linear. Tusk growth in relation to age and sex in Zambia is compared with East Africa. It is concluded that the tusks in Zambia are smaller and are more difficult to sex correctly than their East African counterparts, possibly a consequence of the Zambian elephant having a greater degree of tusk wear. Allometric growth is described with emphasis on the estimation of body weight from shoulder height. The most reliable estimates are obtained from a purely empirical representation of the data, a semilog plot of log body weight on shoulder height.     

An empirical genetic assessment of the severity of the northern elephant seal population bottleneck

A bottleneck in population size of a species is often correlated with a sharp reduction in genetic variation. The northern elephant seal (Mirounga angustirostris) has undergone at least one extreme bottleneck, having rebounded from 20-100 individuals a century ago to over 175,000 individuals today. The relative lack of molecular-genetic variation in contemporary populations has been documented, but the extent of variation before the late 19th century remains unknown. We have determined the nucleotide sequence of a 179 base-pair segment of the mitochondrial DNA (mtDNA) control region from seals that lived before, during and after a bottleneck low in 1892. A 'primerless' PCR was used to improve the recovery of information from older samples. Only two mtDNA genotypes were present in all 150+ seals from the 1892 bottleneck on, but we discovered four genotypes in five pre-bottleneck seals. This suggests a much greater amount of mtDNA genotypic variation before this bottleneck, and that the persistence of two genotypes today is a consequence of random lineage sampling. We cannot correlate the loss of mtDNA genotypes with a lowered mean fitness of individuals in the species today. However, we show that the species historically possessed additional genotypes to those present now, and that sampling of ancient DNA could elucidate the genetic consequences of severe reductions in population size.     

Estimating the maximum sustainable yield of snow crab (Chionoecetes opilio) off Tohoku,Japan via a state-space stock assessment model with time-varying natural mortality

A maximum sustainable yield (MSY) obtained by maintaining or restoring fish stock levels is a tangible benefit of ecosystem services. Snow crab (Chionoecetes opilio) off Tohoku, Japan has been managed by a total allowable catch since 1996, although the abundance has not increased. Surprisingly, there was no increase after 2011, when fishing pressure was greatly reduced because of the Great East Japan earthquake. This implies that some of the crab's biological characteristics, such as recruits, natural mortality coefficient (M) and terminal molting probabilities (p), might have changed. We developed “just another state-space stock assessment model” to estimate the MSY of the snow crab off Tohoku considering interannual variations in M and p. The multimodel inference revealed that M increased from 0.2 in 1997 to 0.59 in 2018, although it did not vary according to instars, sex or terminal molt. The parameter p also increased by 1.34–2.46 times depending on the instar growth stages from 1997 to 2018. We estimated the MSYs in three scenarios, which changed drastically if M and p were set as they were in the past or at the current values estimated from this study. This result indicated that the MSY of snow crab would also vary with time based on their time-varying biological characteristics.     

Landscape-scale feeding patterns of African elephant inferred from carbon isotope analysis of feces

The African elephant (Loxodonta africana) is a large-bodied, generalist herbivore that eats both browse and grass. The proportions of browse and grass consumed are largely expected to reflect the relative availability of these resources. We investigated variations in browse (C(3) biomass) and grass (C(4)) intake of the African elephant across seasons and habitats by stable carbon isotope analysis of elephant feces collected from Kruger National Park, South Africa. The results reflect a shift in diet from higher C(4) grass intake during wet season months to more C(3) browse-dominated diets in the dry season. Seasonal trends were correlated with changes in rainfall and with nitrogen (%N) content of available grasses, supporting predictions that grass is favored when its availability and nutritional value increase. However, switches to dry season browsing were significantly smaller in woodland and grassland habitats where tree communities are dominated by mopane (Colophospermum mopane), suggesting that grasses were favored here even in the dry season. Regional differences in diet did not reflect differences in grass biomass, tree density, or canopy cover. There was a consistent relationship between %C(4) intake and tree species diversity, implying that extensive browsing is avoided in habitats characterized by low tree species diversity and strong dominance patterns, i.e., mopane-dominated habitats. Although mopane is known to be a preferred species, maintaining dietary diversity appears to be a constraint to elephants, which they can overcome by supplementing their diets with less abundant resources (dry season grass). Such variations in feeding behavior likely influence the degree of impact on plant communities and can therefore provide key information for managing elephants over large, spatially diverse, areas.     

Six new polymorphic microsatellite loci isolated and characterized from the African savannah elephant genome

The African savannah elephant (Loxodonta africana) is a ‘keystone’ species that plays a vital role in regulating the dynamics of both plant and animal communities and yet it is endangered and its numbers have been reduced to approximately 500 000 across their entire continental range. Molecular genetic markers are important tools for providing genetic information useful in formulating effective management and conservation strategies for the surviving elephant populations. We describe the isolation and characterization of six new polymorphic microsatellite markers in the African savannah elephant and demonstrate that these loci can be PCR (polymerase chain reaction)‐multiplexed, a desirable attribute that saves costs in large‐scale microsatellite screening.