Non‐timber Forest Product Harvest does not Affect the Genetic Diversity of a Tropical Tree Despite Negative Effects on Population Fitness

The level of genetic diversity in a population can affect ecological processes and plant responses to disturbance. In turn, disturbance can alter population genetic diversity and structure. Populations in fragmented and logged habitats often show reduced genetic diversity and increased inbreeding and differentiation. Long‐term harvesting of wild plants (for foliage, bark, and roots), can affect population genetic diversity by altering individual fitness and genetic contribution. Our understanding of these changes in genetic diversity due to the harvesting of plant organs is still limited. We used nine microsatellite markers to study the effect of long‐term bark and foliage harvest by Fulani people on the genetic diversity and structure of 12 populations of African mahogany (Khaya senegalensis) in Benin. We sampled 20 individuals in each population to test the effect of harvesting. For each population, we divided the samples equally between seedling and adults to test if the effects are stronger in seedlings. We found moderate genetic diversity (H_e = 0.53 ± 0.04) and weak but significant differentiation among local populations (F_ST = 0.043, P < 0.001). There was no significant effect of harvest on genetic diversity or structure, although previous work found significant negative effects of harvest on the reproduction of adults, offspring density, and population fitness. Our results suggest that demographic responses to disturbance precede a detectable genetic response. Future studies should focus on using parentage analysis to test if genotypes of harvested parents are directly represented in the offspring populations.     

Effects of size‐ and sex‐selective harvesting: An integral projection model approach

Harvesting is often size‐selective, and in species with sexual size dimorphism, it may also be sex‐selective. A powerful approach to investigate potential consequences of size‐ and/or sex‐selective harvesting is to simulate it in a demographic population model. We developed a population‐based integral projection model for a size‐ and sex‐structured species, the commonly exploited pike (Esox lucius). The model allows reproductive success to be proportional to body size and potentially limited by both sexes. We ran all harvest simulations with both lower size limits and slot limits, and to quantify the effects of selective harvesting, we calculated sex ratios and the long‐term population growth rate (λ). In addition, we quantified to what degree purely size‐selective harvesting was sex‐selective, and determined when λ shifted from being female to male limited under size‐ and sex‐selective harvesting. We found that purely size‐selective harvest can be sex‐selective, and that it depends on the harvest limits and the size distributions of the sexes. For the size‐ and sex‐selective harvest simulations, λ increased with harvest intensity up to a threshold as females limited reproduction. Beyond this threshold, males became the limiting sex, and λ decreased as more males were harvested. The peak in λ, and the corresponding sex ratio in harvest, varied with both the selectivity and the intensity of the harvest simulation. Our model represents a useful extension of size‐structured population models as it includes both sexes, relaxes the assumption of female dominance, and accounts for size‐dependent fecundity. The consequences of selective harvesting presented here are especially relevant for size‐ and sex‐structured exploited species, such as commercial fisheries. Thus, our model provides a useful contribution toward the development of more sustainable harvesting regimes.     

Matrix population models indicate that bark harvest of two medicinal plants in Uganda's Bwindi Impenetrable National Park is sustainable

Balancing forest conservation with resource extraction by local people is challenging. In the mountain forests of Bwindi Impenetrable National Park in Uganda, this was addressed by permitting regulated access to certain forest products in specific areas by authorized local people. However, it remained unclear whether harvest levels were biologically sustainable. Here, we used matrix population models and long‐term data to examine the impacts of bark harvesting on population dynamics of two important medicinal plants, Rytigynia kigeziensis and Ocotea usambarensis, in Bwindi. Only 4% of R. kigeziensis and 3% of O. usambarensis stems (>1.3 m height) showed signs of bark harvest, mostly mild harvesting. We found that the harvested populations of both species appeared stable or will moderately grow in the long run. Modelled population growth rates were mostly determined by survival probabilities. Similarity between the stable stage distributions predicted by the model and observed population structures suggests that our estimated vital rates (growth, recruitment and survival rates) are a reasonable representation of actual values in these populations. Thus, recent harvest levels of R. kigeziensis and O. usambarensis appear sustainable. Nonetheless, monitoring of harvested and unharvested populations by tagging, marking and remeasuring individuals should continue for both species.     

Modelling Recolonization of Second-Growth Forest Stands by the North American Red Squirrel Tamiasciurus hudsonicus

In this paper, we present a model for source–sink population dynamics where the locations of source and sink habitats change over time. We do this in the context of the population dynamics of the North American red squirrel, Tamiasciurus hudsonicus, within a forest environment subject to harvesting and regrowth. Harvested patches of forest are initially sinks, then eventually become source habitat again as the forest regrows. At the same time, each harvested patch is gradually recolonized by squirrels from other forest patches. We are interested in the interaction of forest harvesting dynamics with squirrel population dynamics. This depends on the harvesting schedule, and on the choices squirrels make when deciding whether to settle in a mature forest patch or in a recently harvested patch. We find that the time it takes for a second-growth forest patch to be recolonized at the mature forest level is longer than the time required for the habitat quality to be restored to the mature forest level. We also notice that recolonization pressure decreases squirrel populations in neighbouring patches. The connectivity between forest patches and the cutting schedule used also affect the time course of recolonization and steady-state population levels.     

广义Logistic模型的捕获优化问题

以王寿松所提出的广义Ｌｏｇｉｓｔｉｃ模型为基础,讨论单种群生物资源的捕获优化问题,分析了被开发生物种群的动力学性质。在单位捕获努力量假定下,以最大可持续捕获量为管理目标,确定了线性捕获下的最优捕获策略,得到了最优捕获努力量,最大可持续收获及相应的最优种群水平的显式表达式,包括著名的Ｓｃｈａｅｆｅｒ模型作为特例,推广了相应的结果。     

Modeling Harvest Intensity of Sooty Shearwater Chicks by Rakiura Māori in New Zealand

Abstract: Cultural evidence suggests that sooty shearwater (Puffinus griseus) chicks have been harvested by Rakiura Māori on islands in southern New Zealand since prehistoric times. Concerns exist that modern harvests may be impacting sooty shearwater abundance. We modeled human-related and ecological determinants of harvest (total no. of individuals harvested) of sooty shearwater chicks on 11 islands and examined the relationship between shearwater abundance and harvesting rates (chicks/hr) and harvester behavior throughout the harvesting season. Models best explaining variation in harvest between harvesting areas (manu), for both the early and late parts of the harvesting season, included harvester-days (included in all models with change in deviance information criteria [ΔDIC], ΔDIC < 8.36 and ΔDIC < 11.5, for the early and late periods, respectively). Other harvest determinants included shearwater density, size of the manu, and number of people helping harvesters (all included in the top 5 models within ΔDIC = 2.25 for the late period). Areas harvested by several families under a common-property harvesting system had higher harvest intensity for their size (24% points higher, 95% credible interval 11–36%) than those managed as an exclusive resource for one family. The slowest harvesters spent more time harvesting but on average only harvested 36% (95% credible interval 15–65%) and 34% (95% credible interval 12–63%) of the harvest taken by the fastest harvesters during the early and late periods, respectively. Our results highlight the possibility of elevated harvest intensity as the population of harvesters increases. However, our models suggested that a corresponding reduction in harvesting rate at low prey densities during the most productive period could potentially regulate harvest intensity. Future research will integrate these results into prospective shearwater demographic models to assess the utility of a range of harvesting strategies in ensuring harvest sustainability.     

Harvest-induced maturation evolution under different life-history trade-offs and harvesting regimes

The potential of harvesting to induce adaptive changes in exploited populations is now increasingly recognized. While early studies predicted that elevated mortalities among larger individuals select for reduced maturation size, recent theoretical studies have shown conditions under which other, more complex evolutionary responses to size-selective mortality are expected. These new predictions are based on the assumption that, owing to the trade-off between growth and reproduction, early maturation implies reduced growth. Here we extend these findings by analyzing a model of a harvested size-structured population in continuous time, and by systematically exploring maturation evolution under all three traditionally acknowledged costs of early maturation: reduced fecundity, reduced growth, and/or increased natural mortality. We further extend this analysis to the two main types of harvest selectivity, with an individual's chance of getting harvested depending on its size and/or maturity stage. Surprisingly, we find that harvesting mature individuals not only favors late maturation when the costs of early maturation are low, but promotes early maturation when the costs of early maturation are high. To our knowledge, this study therefore is the first to show that harvesting mature individuals can induce early maturation.     

Are Protea populations seed limited? Implications for wildflower harvesting in Cape fynbos

Abstract Little is known about the extent to which plant population growth is limited by seed production. We studied two non-sprouting Protea species, both entirely dependent on seeds for recruitment after fire, to determine how flower harvesting would affect the size of the next generation after burning. Five harvesting treatments (0, 25, 50, 75 and 100% inflorescence removal) were applied, each replicated four times in 10 × 10m plots. Seedbanks were censused before a late-summer burn for each species and each replicate. The mean proportion of seeds surviving the burn until germination the following spring was 0.46 for Protea repens and 0.57 for Protea neriifolia. Of the seedlings that emerged, 90% and 55%, respectively, survived the first summer drought. Flower production in the 9 year old stand was strongly related to population density. Optimal plant densities for maximum flower production were estimated as 150 for P. repens and 70 for P. neriifolia. These target densities were greatly exceeded by seedling populations surviving the first summer drought in unharvested stands. If future density-independent mortality is negligible, the excess represents that part of the seedbank that could have been harvested before the burn without influencing future flower production. We developed a simple static model for setting flower harvesting levels in these seed-saturated populations. The predicted harvesting levels (50% of inflorescences in P. repens and 85% in P. neriifolia) were validated against the experimental harvests. We discuss the sensitivity of harvesting levels to variation in fecundity/density relationships, seed survival through a burn and seedling survival until flowering, and the implications for flower harvesting.     

Effects of Commercial Harvesting on Population Characteristics and Rhizome Yield of Anemone altaica

Effects of Commercial Harvesting on Population Characteristics and Rhizome Yield of Anemone altaica. Commercial harvesting constitutes a direct threat to numerous non–timber forest products (NTFPs), but its ecological effects have not been well documented. Anemone altaica Fisch. ex C. A. Mey, a spring ephemeral plant found in temperate forests of Eurasia, is a traditional Chinese herb. Owing to medicinal value, its rhizomes have been harvested for commercial purposes in northwestern China for many years. This paper addresses the ecological effects of commercial harvesting on A. altaica populations under different harvest intensities. The results show that size–selective harvesting of rhizomes can increase population densities by asexual propagation. Currently, two– to three–year–old individuals derived from asexual propagation are the main targets of commercial harvesting. The increased demand in recent years has resulted in earlier and more intensive harvesting activities largely impacting the natural recovery of the harvested populations. For sustainable use of this traditional medicinal species, we recommend that a periodic harvest strategy of three to four years be adopted.     

Population Genetics of Y-Chromosome Short Tandem Repeats in Humans

Eight human short tandem repeat polymorphisms (STRs) also known as microsatellites—DYS19, DYS388, DYS390, DYS391, DYS392, DYS393, DYS389I, and DYS389II, mapping in the Y chromosome—were analyzed in two Iberian samples (Basques and Catalans). Allele frequency distributions showed significant differences only for DYS392. Fst and gene diversity index (D) were estimated for the Y STRs. The values obtained are comparable to those of autosomal STR if corrections for the smaller effective population size on the Y chromosome are taken into account. This suggests that Y-chromosome microsatellites might be as useful as their autosomal counterparts to both human population genetics and forensics. Our results also reinforce the hypothesis that selective sweeps in the Y chromosome in recent times are unlikely. Haplotypes combining five of the loci were constructed for 71 individuals, showing 29 different haplotypes. A haplotype tree was constructed, from which an estimate of 7,000 to 60,000 years for the age of the Y-chromosome variation in Iberia was derived, in accordance with previous estimates obtained with mtDNA sequences and nuclear markers. Received: 3 January 1997 / Accepted: 25 April 1997     

Testing sustainable management in Northern Chile: harvesting Macrocystis pyrifera (Phaeophyceae, Laminariales). A case study

Kelp harvesting in northern Chile is managed by local fishermen and is part of an organized industry. However, the lack of standardized harvesting protocols has made regulation difficult. This, in combination with the impacts of oceanographic disturbances has resulted in some kelp populations being considerably reduced during the last decade. Consequently, harvest methods that maintain kelp resources are sorely needed if harvesting is to remain a viable industry in Chile. Here, experiments were done to identify sustainable methods for harvesting Macrocystis pyrifera along the coast of northern Chile. Three methods were compared with regard to their impacts on kelp populations; one that involves extracting half of the fronds from each individual in a population, one that involves extracting all the fronds from half of the individuals in a population, and a third that involves extracting all the fronds from all of the individuals in a population (i.e., the method currently used). Following this, populations were evaluated over a 2-month period to monitor re-growth of the remaining individuals and recruitment of new individuals, as well as changes in understory algal diversity and herbivore abundance. Our results indicate that removing half of the fronds from each individual in a population was the best method for maintaining the resource for future harvest because, it (1) maintains rapid growth of new fronds on the harvested individuals, (2) promotes recruitment of new individuals, and (3) reduces herbivore densities through physical abrasion. Consequently, this method is recommended for future harvesting of M. pyrifera in Northern Chile.     

An adaptive management approach to an octocoral fishery based on the Beverton-Holt model

Coral reef species are frequently the focus of bio-prospecting, and when promising bioactive compounds are identified there is often a need for the development of responsible harvesting based on relatively limited data. The Caribbean gorgonian Pseudopterogorgia elisabethae has been harvested in the Bahamas for over a decade. Data on population age structure and growth rates in conjunction with harvest data provide an opportunity to compare fishery practices and outcomes to those suggested by a Beverton-Holt fishery model. The model suggests a minimum colony size limit of 7–9 years of age (21–28 cm height), which would allow each colony 2–4 years of reproduction prior to harvesting. The Beverton-Holt model assumes that colonies at or above the minimum size limit are completely removed. In the P. elisabethae fishery, colonies are partially clipped and can be repeatedly harvested. Linear growth of surviving colonies was up to 3 times that predicted for colonies that were not harvested and biomass increase was up to 9 times greater than that predicted for undisturbed colonies. The survival of harvested colonies and compensatory growth increases yield, and yields at sites that had previously been harvested were generally greater than predicted by the Beverton-Holt model. The model also assumes recruitment is independent of fishing intensity, but lower numbers of young colonies in the fished populations, compared to unfished populations, suggest possible negative effects of the harvest on reproduction. This suggests the need for longer intervals between harvests. Because it can be developed from data that can be collected at a single time, the Beverton-Holt model provides a rational starting point for regulating new fisheries where long-term characterizations of population dynamics are rarely available. However, an adaptive approach to the fishery requires the incorporation of reproductive data.     

Multiple Origins of Cyclodiene Insecticide Resistance in Tribolium castaneum (Coleoptera: Tenebrionidae)

The number of origins of pesticide resistance-associated mutations is important not only to our understanding of the evolution of resistance but also in modeling its spread. Previous studies of amplified esterase genes in a highly dispersive Culex mosquito have suggested that insecticide resistance-associated mutations (specifically a single-gene duplication event) can occur a single time and then spread throughout global populations. In order to provide data for resistance-associated point mutations, which are more typical of pesticide mechanisms as a whole, we studied the number of independent origins of cyclodiene insecticide resistance in the red flour beetle Tribolium castaneum. Target-site insensitivity to cyclodienes is conferred by single point mutations in the gene Resistance to dieldrin (Rdl), which codes for a subunit of a γ-aminobutyric acid (GABA) receptor. These point mutations are associated with replacements of alanine 302 which render the receptor insensitive to block by the insecticide. We collected 141 strains of Tribolium worldwide and screened them for resistance. Twenty-four strains contained resistant individuals. After homozygosing 23 of these resistance alleles we derived a nucleotide sequence phylogeny of the resistant strains from a 694-bp section of Rdl, encompassing exon 7 (which contains the resistance-associated mutation) and part of a flanking intron. The phylogeny also included six susceptible alleles chosen at random from a range of geographical locations. Resistance alleles fell into six clades and three clades contained both resistant and susceptible alleles. Although statistical analysis provided support at only the 5–6% level, the pattern of variation in resistance alleles is more readily explained by multiple independent origins of resistance than by spread of a single resistance-associated mutation. For example, two resistance alleles differed from two susceptible alleles only by the resistance-associated mutation itself, suggesting that they form the susceptible ancestors and that resistance arose independently in several susceptible backgrounds. This suggests that in Tribolium Rdl, de novo mutations for resistance have arisen independently in several populations. Identical alleles were found in geographically distant regions as well, also implying that some Rdl alleles have been exported in stored grain. These differences from the Culex study may stem both from differences in the population genetics of Tribolium versus that of mosquitoes and differences in mutation rates associated with point mutations versus gene duplication events. The Tribolium data therefore suggest that multiple origins of insecticide resistance (associated with specific point mutations) may be more common than the spread of single events. These findings have implications for the way in which we model the evolution and spread of insecticide resistance genes and also suggest that parallel adaptive substitutions may not be uncommon in phyletic evolution. Received: 14 October 1998 / Accepted: 4 January 1999     

Gelidium pristoides in South Africa

Gelidium pristoides has been harvested commercially from the eastern Cape, South Africa, since 1951, with 40–80 t y^–1 (dry wt) collected in recent years. This species has been intensively studied since 1983, and we briefly review knowledge of its biology in relation to harvesting. We describe a new study of intertidal epiphytic animals, showing that none is specific to G. pristoides, and that only 2.8% of these animals (numbers) inhabit this agarophyte, while the rest are found in other intertidal algal communities: harvesting is considered to have negligible effects on epifauna. Over the past 3 y, we have monitored, at two sites, the effects of the harvesting of G. pristoides on other benthic algae and animals. In only two of the seven main components analysed, did we find any difference between harvested and control plots. At one site only, the number of limpets and percentage cover of Gelidium was higher in harvested plots. These results show that harvesting has no significant biological effect. Regulations governing seaweed exploitation in South Africa were amended in 1988, to encourage local processing of products, and these changes are discussed in relation to the local Gelidium industry. Despite experimental results predicting a higher yield per unit effort if harvesting is limited to summer, harvesting continues throughout the year for practical reasons.     

Plucking or cutting Gelidium sesquipedale? A demographic simulation of harvest impact using a population projection matrix model.

A matrix model describes the annual dynamics of a commercial (harvested by plucking) Gelidium sesquipedale population off Cape Espichel, Portugal. Vital rates were measured from a frond population divided into size classes; annual transition probabilities among them were calculated. Transition probabilities under harvest by cutting are derived by assuming that all harvested fronds are cut to the first size class, and none are plucked. Simulations of the annual population dynamics for harvest by both plucking and cutting are used to assess which harvest strategy will optimize yields. Assuming the same efficiency for both strategies, cutting fronds to 7 cm (as mechanical harvesters do) results in a higher population growth rate ( = 1.08 to 1.35) than occurs with the plucking technique ( = 0.85). Simulations of population recovery show the number of fronds in each size class available the next harvest season will be higher when cut than plucked. This model can also optimize yields by predicting the more efficient season opening, and harvesting cutting height.     

Substitution Model of Sequence Evolution for the Human Immunodeficiency Virus Type 1 Subtype B gp120 Gene over the C2-V5 Region

Phylogenetic analyses frequently rely on models of sequence evolution that detail nucleotide substitution rates, nucleotide frequencies, and site-to-site rate heterogeneity. These models can influence hypothesis testing and can affect the accuracy of phylogenetic inferences. Maximum likelihood methods of simultaneously constructing phylogenetic tree topologies and estimating model parameters are computationally intensive, and are not feasible for sample sizes of 25 or greater using personal computers. Techniques that initially construct a tree topology and then use this non-maximized topology to estimate ML substitution rates, however, can quickly arrive at a model of sequence evolution. The accuracy of this two-step estimation technique was tested using simulated data sets with known model parameters. The results showed that for a star-like topology, as is often seen in human immunodeficiency virus type 1 (HIV-1) subtype B sequences, a random starting topology could produce nucleotide substitution rates that were not statistically different than the true rates. Samples were isolated from 100 HIV-1 subtype B infected individuals from the United States and a 620 nt region of the env gene was sequenced for each sample. The sequence data were used to obtain a substitution model of sequence evolution specific for HIV-1 subtype B env by estimating nucleotide substitution rates and the site-to-site heterogeneity in 100 individuals from the United States. The method of estimating the model should provide users of large data sets with a way to quickly compute a model of sequence evolution, while the nucleotide substitution model we identified should prove useful in the phylogenetic analysis of HIV-1 subtype B env sequences. Received: 4 October 2000 / Accepted: 1 March 2001     

Wild boar (Sus scrofa) harvesting using the espera hunting method: side effects and management implications

Harvesting of wildlife by man has been linked to demographic and evolutionary impacts in many populations. We investigated the sex ratio and age class structure in hunting bags of wild boar harvested by espera—nocturnal single hunt at bait—during four hunting seasons in Alentejo (Portugal). In addition, we assessed whether the hunting method is a significant predictor of the probability of harvesting an animal of a particular gender, of particular age class or of a particular combination of these two attributes. We found that the espera hunting method allows very selective harvesting regimes, and thus, it seems a highly effective population management tool. Removing a large proportion of adult males, however, may bias the population sex ratio towards females, reduce male life expectancy and raise the degree of polygyny. Our results suggest that recruitment rates are resilient to this skewed sex ratio, and possibly the higher proportion of females in the adult population may even increase productivity.

     

Genetic variation within maize population GT-MAS:gk and the relationship with resistance to Aspergillus flavus and aflatoxin production

Aspergillus flavus (Link:Fr.) infection and aflatoxin contamination of maize (Zea mays L.) grain are an extremely serious problem. Maize genotypes resistant to A. flavus attack are needed. Maize breeders and plant pathologists must identify resistance sources and incorporate resistance into adapted breeding material. Maize population GT-MAS:gk has been released for use as a resistance source. In this study, we surveyed the genetic variation in this population and made the breeders/plant pathologists aware of the heterogeneous nature in this maize population by using RAPD analysis and correlated the RAPD marker association with the resistance to A. flavus and aflatoxin production. Of 40 RAPD primers, only 15 gave sufficient numbers of reproducible and readily scored polymorphic bands suggesting that this population was highly homogeneous. However, genetic distances, ranging from 0.08 to 0.28 and averaging 0.17, suggest that there is variation within the population. Cluster analysis distinguished three major polymorphic groups. Laboratory bioassay revealed that group I contained the most resistant individuals, i.e., those with less aflatoxin production. Group II had the least resistance, and group III was intermediate. This study showed that the maize population GT-MAS:gk is heterogeneous and individuals are different in resistance to A. flavus and aflatoxin production. Resistance should be confirmed through progeny testing before further development. The RAPD marker OPX-04, which may be associated with the resistance trait, has been cloned and further characterization will be pursued. Received: 10 May 2000 / Accepted: 12 January 2001     

The Evolution of Codon Preferences in Drosophila: A Maximum-Likelihood Approach to Parameter Estimation and Hypothesis Testing

Synonymous codon usage in related species may differ as a result of variation in mutation biases, differences in the overall strength and efficiency of selection, and shifts in codon preference—the selective hierarchy of codons within and between amino acids. We have developed a maximum-likelihood method to employ explicit population genetic models to analyze the evolution of parameters determining codon usage. The method is applied to twofold degenerate amino acids in 50 orthologous genes from D. melanogaster and D. virilis. We find that D. virilis has significantly reduced selection on codon usage for all amino acids, but the data are incompatible with a simple model in which there is a single difference in the long-term N _e, or overall strength of selection, between the two species, indicating shifts in codon preference. The strength of selection acting on codon usage in D. melanogaster is estimated to be |N _e s|≈ 0.4 for most CT-ending twofold degenerate amino acids, but 1.7 times greater for cysteine and 1.4 times greater for AG-ending codons. In D. virilis, the strength of selection acting on codon usage for most amino acids is only half that acting in D. melanogaster but is considerably greater than half for cysteine, perhaps indicating the dual selection pressures of translational efficiency and accuracy. Selection coefficients in orthologues are highly correlated (ρ= 0.46), but a number of genes deviate significantly from this relationship. Received: 20 December 1998 / Accepted: 17 February 1999