A note on the accuracy of PAC-likelihood inference with microsatellite data

Stephens and Donnelly have introduced a simple yet powerful importance sampling scheme for computing the likelihood in population genetic models. Fundamental to the method is an approximation to the conditional probability of the allelic type of an additional gene, given those currently in the sample. As noted by Li and Stephens, the product of these conditional probabilities for a sequence of draws that gives the frequency of allelic types in a sample is an approximation to the likelihood, and can be used directly in inference. The aim of this note is to demonstrate the high level of accuracy of "product of approximate conditionals" (PAC) likelihood when used with microsatellite data. Results obtained on simulated microsatellite data show that this strategy leads to a negligible bias over a wide range of the scaled mutation parameter theta. Furthermore, the sampling variance of likelihood estimates as well as the computation time are lower than that obtained with importance sampling on the whole range of theta. It follows that this approach represents an efficient substitute to IS algorithms in computer intensive (e.g. MCMC) inference methods in population genetics. (c) 2006 Elsevier Inc. All rights reserved.

Inference on microsatellite mutation processes in the invasive mite, Varroa destructor, using reversible jump Markov chain Monte Carlo

Varroa destructor is a parasitic mite of the Eastern honeybee Apis cerana. Fifty years ago, two distinct evolutionary lineages (Korean and Japanese) invaded the Western honeybee Apis mellifera. This haplo-diploid parasite species reproduces mainly through brother sister matings, a system which largely favors the fixation of new mutations. In a worldwide sample of 225 individuals from 21 locations collected on Western honeybees and analyzed at 19 microsatellite loci, a series of de novo mutations was observed. Using historical data concerning the invasion, this original biological system has been exploited to compare three mutation models with allele size constraints for microsatellite markers: stepwise (SMM) and generalized (GSM) mutation models, and a model with mutation rate increasing exponentially with microsatellite length (ESM). Posterior probabilities of the three models have been estimated for each locus individually using reversible jump Markov Chain Monte Carlo. The relative support of each model varies widely among loci, but the GSM is the only model that always receives at least 9% support, whatever the locus. The analysis also provides robust estimates of mutation parameters for each locus and of the divergence time of the two invasive lineages (67,000 generations with a 90% credibility interval of 35,000-174,000). With an average of 10 generations per year, this divergence time fits with the last post-glacial Korea Japan land separation. (c) 2005 Elsevier Inc. All rights reserved.

On the structural differences between markers and genomic AC microsatellites

AC microsatellites have proved particularly useful as genetic markers. For some purposes, such as in population biology, the inferences drawn depend on the quantitative values of their mutation rates. This, together with intrinsic biological interest, has led to widespread study of microsatellite mutational mechanisms. Now, however, inconsistencies are appearing in the results of marker-based versus non-marker-based studies of mutational mechanisms. The reasons for this have not been investigated, but one possibility, pursued here, is that the differences result from structural differences between markers and genomic microsatellites. Here we report a comparison between the CEPH AC marker microsatellites and the global population of AC microsatellites in the human genome. AC marker microsatellites are longer than the global average. Controlling for length, marker microsatellites contain on average fewer interruptions, and have longer segments, than their genomic counterparts. Related to this, marker microsatellites show a greater tendency to concentrate the majority of their repeats into one segment. These differences plausibly result from scientists selecting markers for their high polymorphism. In addition to the structural differences, there are differences in the base composition of flanking sequences, marker flanking regions being richer in C and G and poorer in A and T. Our results indicate that there are profound differences between marker and genomic microsatellites that almost certainly affect their mutation rates. There is a need for a unified model of mutational mechanisms that accounts for both marker-derived and genomic observations. A suggestion is made as to how this might be done.

The coevolution of two phytoplankton species on a single resource: allelopathy as a pseudo-mixotrophy

Without the top-down effects and the external/physical forcing, a stable coexistence of two phytoplankton species under a single resource is impossible — a result well known from the principle of competitive exclusion. Here I demonstrate by analysis of a mathematical model that such a stable coexistence in a homogeneous media without any external factor would be possible, at least theoretically, provided (i) one of the two species is toxin producing thereby has an allelopathic effect on the other, and (ii) the allelopathic effect exceeds a critical level. The threshold level of allelopathy required for the coexistence has been derived analytically in terms of the parameters associated with the resource competition and the nutrient recycling. That the extra mortality of a competitor driven by allelopathy of a toxic species gives a positive feed back to the algal growth process through the recycling is explained. And that this positive feed back plays a pivotal role in reducing competition pressures and helping species succession in the two-species model is demonstrated. Based on these specific coexistence results, I introduce and explain theoretically the allelopathic effect of a toxic species as a ‘pseudo-mixotrophy’—a mechanism of ‘if you cannot beat them or eat them, just kill them by chemical weapons’. The impact of this mechanism of species succession by pseudo-mixotrophy in the form of alleopathy is discussed in the context of current understanding on straight mixotrophy and resource-species relationship among phytoplankton species.

Social organization of marine Tucuxi dolphins, Sotalia guianensis, in the Cananeia Estuary of southeastern Brazil

Social organization is an important component of the population biology of a species that influences gene flow, the spatial pattern and scale of movements, and the effects of predation or exploitation by humans. An important element of social structure in mammals is group fidelity, which can be quantified through association indices. To describe the social organization of marine tucuxi dolphins (Sotalia guianensis) found in the Cananeia estuary, southeastern Brazil, association indices were applied to photo-identification data to characterize the temporal stability of relationships among members of this population. Eighty-seven days of fieldwork were conducted from May 2000 to July 2003, resulting in direct observations of 374 distinct groups. A total of 138 dolphins were identified on 1-38 distinct field days. Lone dolphins were rarely seen, whereas groups were composed of up to 60 individuals (mean +/- 1 SD = 12.4 +/- 11.4 individuals per group). A total of 29,327 photographs were analyzed, of which 6,312 (21.5%) were considered useful for identifying individuals. Half-weight and simple ratio indices were used to investigate associations among S. guianensis as revealed by the entire data set, data from the core study site, and data from groups composed of <= 10 individuals. Monte Carlo methods indicated that only 3 (9.3%) of 32 association matrices differed significantly from expectations based on random association. Thus, our study suggests that stable associations are not characteristic of S. guianensis in the Cananeia estuary.

Climate Change and its Effects on Polar Bears

Polar bears are key indicators of the effects of climate change on the arctic ecosystem, because their existence is directly related to the sea ice habitat, where they hunt. As the Arctic continues to warm, their habitat will be reduced further and local extinction is likely to occur, especially in southern populations.

Aspects of the interaction between Xanthorrhoea australis and Phytophthora cinnamomi in south-western Victoria, Australia

Diseases in natural ecosystems are often assumed to be less severe than those observed in domestic cropping systems due to the extensive biodiversity exhibited in wild vegetation communities. In Australia, it is this natural biodiversity that is now under threat from Phytophthora cinnamomi. The soilborne Oomycete causes severe decline of native vegetation communities in south-western Victoria, Australia, disrupting the ecological balance of native forest and heathland communities. While the effect of disease caused by P. cinnamomi on native vegetation communities in Victoria has been extensively investigated, little work has focused on the Anglesea healthlands in south-western Victoria. Nothing is known about the population structure of P. cinnamomi at Anglesea. This project was divided into two main components to investigate fundamental issues affecting the management of P. cinnamomi in the Anglesea heathlands. The first component examined the phenotypic characteristics of P. cinnamomi isolates sampled from the population at Anglesea, and compared these with isolates from other regions in Victoria, and also from Western Australia. The second component of the project investigated the effect of the fungicide phosphonate on the host response following infection by P. cinnamomi. Following soil sampling in the Anglesea heathlands, a collection of P, cinnamomi isolates was established. Morphological and physiological traits of each isolate were examined. All isolates were found to be of the A2 mating type. Variation was demonstrated among isolates in the following characteristics: radial growth rate on various nutrient media, sporangial production, and sporangial dimensions. Oogonial dimensions did not differ significantly between isolates. Morphological and physiological variation was rarely dependant on isolate origin. To examine the genetic diversity among isolates and to determine whether phenotypic variation observed was genetically based, Random Amplified Polymorphic DNA (RAPD) analyses were conducted. No significant variation was observed among isolates based on an analysis of molecular variance (AMQVA). The results are discussed in relation to population biology, and the effect of genetic variation on population structure and population dynamics. X australis, an arborescent monocotyledon indigenous to Australia, is highly susceptible to infection by P. cinnamomi. It forms an important component of the heathland vegetation community, providing habitat for native flora and fauna, A cell suspension culture system was developed to investigate the effect of the fungicide phosphonate on the host-pathogen interaction between X. australis and P. cinnamomi. This allowed the interaction between the host and the pathogen to be examined at a cellular level. Subsequently, histological studies using X. australis seedlings were undertaken to support the cellular study. Observations in the cell culture system correlated well with those in the plant. The anatomical structure of X australis roots was examined to assist in the interpretation of results of histopathological studies. The infection of single cells and roots of X. australis, and the effect of phosphonate on the interaction are described. Phosphonate application prior to inoculation with P. cinnamomi reduced the infection of cells in culture and of cells in planta. In particular, phosphonate was found to stimulate the production of phenolic material in roots of X australis seedlings and in cells in suspension cultures. In phosphonate-treated roots of X australis seedlings, the deposition of electron dense material, possibly lignin or cellulose, was observed following infection with P. cinnamomi. It is proposed that this is a significant consequence of the stimulation of plant defence pathways by the fungicide. Results of the study are discussed in terms of the implications of the findings on management of the Anglesea heathlands in Victoria, taking into account variation in pathogen morphology, pathogenicity and genotype. The mode of action of phosphonate in the plant is discussed in relation to plant physiology and biochemistry.

Mortality Risk in Insects

Understanding how and why insect numbers fluctuate through time and space has been a central theme in ecological research for more than a century. Life tables have been used to understand temporal and spatial patterns in insect numbers. In this study, we estimated cause-of-death probabilities for phytophagous insects using multiple decrement life tables and the irreplaceable mortality analytic technique. Multiple decrement life tables were created from 73 insect life tables published from 1954 to 2004. Irreplaceable mortality (the portion of mortality that cannot be replaced by another cause) from pathogens, predators, and parasitoids was 8.6 +/- 7.2, 7.8 +/- 4.9, and 6.2 +/- 1.6%, respectively. In contrast, the mean irreplaceable mortality from all non-natural enemy mortality factors (mortality from factors other than natural enemies) was 35.1 +/- 4.4%. Irreplaceable mortality from natural enemies was significantly lower compared with non-natural enemy factors. Our results may partially explain cases of unsuccessful efficacy in classical biological control, after successful establishment, by showing low irreplaceable mortality for natural enemies, including 5.2 +/- 1.6% for introduced natural enemies. We suggest that the environment (i.e., the degree of environmental stability) influences the magnitude of the irreplaceable mortality from natural enemies. Our results lead to several testable hypotheses and emphasize that it is not possible to estimate the effect of any mortality factor without considering its interaction with competing mortality factors, which has far-reaching consequences for population biology and applied ecology.

Estimativa populacional e uso do hábitat do boto-cinza (Sotalia guianensis) no litoral sul do Rio Grande do Norte

Four areas are known as of frequent usage by Guiana dolphins (Sotalia guianensis) in the south coast of Rio Grande do Norte state, northeast Brazil: Tabatinga, Pipa, Lagoa de Guaraíras and Baia Formosa. This extension of 40 km of shoreline is under increasing anthropogenic impacts due to continuous development of the coastal areas and vessel traffic. The objective of this study was to investigate aspects of population biology and habitat use of the population of Sotalia guianensis in the south coast of Rio Grande do Norte. It was applied the photo-identification technique and posterior methods of capture-recapture for population estimation (POPAN extension in MARK). The distribution, movement and site fidelity of the dolphins were analyzed trough the geographic information system (GIS) and group characteristics and behavior trough non-parametric statistics. Field work was conducted on board a 10m motor vessel from March 2008 to March 2009. Photo-identification effort was 329h with 113h of direct observation of the dolphins. The population estimatives for each area: Tabatinga: 75 (63-92); Pipa 105 (88-129); Lagoa de Guaraíras: 27 (18-54) e Baia Formosa: 112 (89-129) individuals. Total population estimative was: 223 (192 a 297). High site fidelity was detected for only part of the population (<15%) as low site fidelity and transients individuals were also detected (>20%). It was observed frequent movements between Tabatinga, Lagoa de Guaraíras and Pipa, but not Baía Formosa. This suggests a division in two communities along this shore extension: one in Pipa and other in Baía Formosa. Group size was small, most groups with up to 10 dolphins. The areas were use intensively, only in Lagoa de Guaraíras dolphins were not seen in all field trips. Lagoa de Guaraíras is an area used by small groups exclusively for foraging. In Tabatinga and Pipa dolphins concentrated close to the shore, in the inner sector of the area and the main activity is also foraging. Significant larger groups were seen in socializing behavior but there was no difference in group size between the inner and external sectors of the area. The presence of calves and juveniles were significant greater in the inner areas of Tabatinga and Pipa, confirming the hypothesis that these beaches are also used for parental care. In Baia Formosa dolphins concentrated in the outer sector and foraging was also predominant. Significant larger groups were seen in the outer sector, mainly engaged in mixed behaviors of travel/foraging, possibly in some kind of group foraging. Calves and juveniles were significant more present in the outer sector where group size was also larger. In general there was no difference in area usage and period of the day. Sotalia guianensis has characteristics that make the species vulnerable to human activities such as small population concentrated in patches of suitable habitats restrict to coastal areas. We hope that this study bring new information for the species and help for the adequate management of the area in order to assure the presence of the dolphins as well as its behavior pattern and gene flow betweencommunities.

Social organization of marine Tucuxi dolphins, Sotalia guianensis, in the Cananeia Estuary of southeastern Brazil

Social organization is an important component of the population biology of a species that influences gene flow, the spatial pattern and scale of movements, and the effects of predation or exploitation by humans. An important element of social structure in mammals is group fidelity, which can be quantified through association indices. To describe the social organization of marine tucuxi dolphins (Sotalia guianensis) found in the Cananeia estuary, southeastern Brazil, association indices were applied to photo-identification data to characterize the temporal stability of relationships among members of this population. Eighty-seven days of fieldwork were conducted from May 2000 to July 2003, resulting in direct observations of 374 distinct groups. A total of 138 dolphins were identified on 1-38 distinct field days. Lone dolphins were rarely seen, whereas groups were composed of up to 60 individuals (mean +/- 1 SD = 12.4 +/- 11.4 individuals per group). A total of 29,327 photographs were analyzed, of which 6,312 (21.5%) were considered useful for identifying individuals. Half-weight and simple ratio indices were used to investigate associations among S. guianensis as revealed by the entire data set, data from the core study site, and data from groups composed of <= 10 individuals. Monte Carlo methods indicated that only 3 (9.3%) of 32 association matrices differed significantly from expectations based on random association. Thus, our study suggests that stable associations are not characteristic of S. guianensis in the Cananeia estuary.

Estrutura populacional de Callinectes ornatus Ordway (Crustacea, Portunidae) no Balneário Shangri-Lá, Pontal do Paraná, Paraná, Brasil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Biologia populacional e reprodutiva de Callinectes danae Smith (Crustacea, Portunidae), no Balneário Shangri-lá, Pontal do Paraná, Paraná, Brasil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Size and sex compositions, length-weight relationship, and occurrence of the Brazilian sharpnose shark, Rhizoprionodon lalandii, caught by artisanal fishery from southeastern Brazil

Although the Brazilian sharpnose shark, Rhizoprionodon lalandii (Muller and Henle, 1839), is an inshore species widely distributed in the Western Atlantic from Panama to Uruguay, there is little available information on its biology. During a long-term study of small coastal sharks caught by gill net fisheries in southeastern Brazil (PROJETO CACAO), 3643 specimens of R. lalandii were examined, comprising 61.3% of the total sharks,and including all sizes classes, from 30 to 78,5 cm TL., and weights from 100 to 2950 g. The length-weight relationships were not significantly different between sexes, Overall sex ratio favoured the males slightly at the rate of 1.3: 1. Sex ratios, however, did differ significantly between season and size classes. This species occurred in this area all year long. Three seasonal size-class Occurrence patterns were recognized: (1) between October and March, the juveniles were more frequents (2) from April to July, adults were most common, and (3) from August to September, neonates were most numerically abundant. Such patterns we to associated with reproductive tactics that may reduce intra-specific and inter-specific competition with hammerhead shark neonates (Sphyrna lewini). probably result in reduced natural mortality of the offspring during their first few months. (C) 2005 Elsevier B.V. All rights reserved.

Larval aggregation and competition for food in experimental populations of Chrysomya putoria (Wied.) and Cochliomyia macellaria (F.) (Dipt., Calliphoridae)

In blowflies, larval aggregation in patches of food can be both intra- and interspecific, depending upon the degree to which competitors are clumped among the patches. In the present study, the implications of spatial aggregation for larval competition was investigated in experimental populations of the introduced blowfly Chrysomya putoria and the native Cochliomyia macellaria, using data from survival to adulthood in a range of single- and double-species larval cultures. The reduction in C. macellaria survival rate in the presence of C. putoria suggests that the former species is the inferior competitor. The results on survival to adulthood for both species in single- and double-species cultures can be explained in the light of the relationship between the level of intra- and interspecific aggregation and the efficiency of the larval feeding process. The possible implications of these results for the population biology of both species in natural environments are discussed.

Reproductive ecology of the freshwater red alga Batrachospermum delicatulum (Batrachospermales, Rhodophyta) in three tropical streams

Batrachospermum delicatulum specimens from three stream segments were analyzed from a tropical region in south-eastern Brazil (20°18′- 20°49′S, 49°13′-49°46′W). Physical and chemical parameters and the spatial placement of thalli were investigated along with the reproductive characteristics of the gametophytic phase. Sequence data of the cox 2-3 spacer region was also utilized to evaluate genetic variation in individuals within and among stream segments. Gametophyte occurred under relatively diverse environmental conditions, whereas thalli abundance was weakly or not correlated to environmental variables within the stream segments. All specimens examined were dioecious. The ratio of male/female plants was relatively low (0.5 to 1.3) and male plants tended to occur as clumps (two or three plants together). High reproductive success was observed, as indicated by the occurrence of 100% fertilized (carposporophytic) female plants. This is similar to previous reports for this and other dioecious species, which is remarkable considering the relatively low proportion of male/female plants. Results support the two hypotheses to explain the high reproductive success in dioecious species. The occurrence of male plants in clumps was evidence for a strict spatial relationship (i.e. male plants located in upstream position of female plants in order to release spermatia, which would be carried by eddies through female plants). In contrast, the occurrence of male and female plants adjacent to each other allowed outcrossing among neighboring plants with intermingled male and female branches, which seemed more applicable to some situations (low turbulence habitats). The cox 2-3 spacer region from the 18 individuals sequenced was 376 bp and the DNA sequence was identical with no base pair substitutions. Likewise, a previous study of another Batrachospermum species showed that the same haplotypes were present in all stream segments from the same drainage basin, even though the stream segments were a considerable distance apart. Short distance dispersal either by small birds or waterway connectivity might explain these findings.