Additional file 1: of Huntingtin-associated protein 1: Eutherian adaptation from a TRAK-like protein, conserved gene promoter elements, and localization in the human intestine

Identity matrix showing pairwise percentage amino acid sequence identity between HAP1 family proteins: TRAK1 and TRAK2 (human, opossum, zebrafish, Xenopus, anole lizard, chicken), HAP1 (species as above, plus rat, dog, and Tasmanian devil), Drosophila (fruitfly) Milton, and C. elegans (nematode) T27A3.1. Sequence identifiers are as indicated in Materials and methods. (JPG 1967 kb

‘Time Period’ categorical variable with eight levels used as a proxy to account for intra- and inter-annual changes in water level and resultant productivity, fish growth, and biomass density.

<p>Variables used to categorise months into groups. Months marked with an asterisk are those in which data were collected in both years (2009 and 2010). Water level categories reflect the average range of values above the mean lowest water level: Highest = +1.6m to +2.0m; High = +0.9m to +1.69m; Medium = +0.2m to +0.89m; Low = 0m to +0.19m. Mean rainfall: High >150mm; Medium = 30mm to 149mm; Low = 10mm to 29mm; Very low <10mm.</p

Variables used in each linear mixed effects model.

<p>List, type, and description of variables used to predict catch weight in two separate LMMs for trap and gill net fishers.</p

Averaged model results for each gear type.

<p>Averaged model parameters explaining catch weight for trap and gill net fishers. The coefficients, standard error, and lower and upper confidence intervals for each variable are provided for each averaged set of models. Baseline levels for restricted, time period, and habitat variables for both models are ‘non-restricted’, ‘Time period May-Jun '09’, and ‘edge’, respectively.</p

Coefficients for factors affecting catch weight for fishers using traps in the 16 top models used in model averaging.

<p>Coefficients for the fixed effects of the 16 most parsimonious models that were used in model averaging to identify factors influencing catch weight for fishers using traps. A ‘+’ indicates that a factor variable was included in the model, whereas a blank field means that the variable was not included. Coefficients cannot be presented for factor variables (see Table S5 in the Supporting Information for averaged model parameters). The number of parameters in the model (k), the AIC and AIC difference (ΔAIC), and weight (Wi) is given for each model. Individual variable weights (wi) are also provided.</p

Coefficients for factors affecting catch weight for fishers using gill nets in the 14 top models used in model averaging.

<p>Coefficients for the fixed effects of the 14 most parsimonious models that were used in model averaging to identify factors influencing catch weight for fishers using gill nets. A ‘+’ indicates that a factor variable was included in the model, whereas a blank field means that the variable was not included. Coefficients cannot be presented for factor variables (see Table S5 in the Supporting Information for averaged model parameters). The number of parameters in the model (k), the AIC and AIC difference (ΔAIC), and weight (Wi) is given for each model. Individual variable weights (wi) are also provided.</p

Short-term costs of conservation interventions for fishers at Lake Alaotra, Madagascar

<p><strong>Table S1.</strong> ‘Time Period’ categorical variable with eight levels used as a proxy to account for intra- and inter-annual changes in water level and resultant productivity, fish growth, and biomass density. Variables used to categorise months into groups. Months marked with an asterisk are those in which data were collected in both years (2009 and 2010). Water level categories reflect the average range of values above the mean lowest water level: Highest = +1.6m to +2.0m; High = +0.9m to +1.69m; Medium = +0.2m to +0.89m; Low = 0m to +0.19m. Mean rainfall: High >150mm; Medium = 30mm to 149mm; Low = 10mm to 29mm; Very low <10mm.</p> <p><strong>Table S2.</strong> Variables used in each linear mixed effects model. List, type, and description of variables used to predict catch weight in two separate LMMs for trap and gill net fishers.</p> <p><strong>Table S3.</strong> Coefficients for factors affecting catch weight for fishers using traps in the 16 top models used in model averaging. Coefficients for the fixed effects of the 16 most parsimonious models that were used in model averaging to identify factors influencing catch weight for fishers using traps. A ‘+’ indicates that a factor variable was included in the model, whereas a blank field means that the variable was not included. Coefficients cannot be presented for factor variables (see Table S5 in the Supporting Information for averaged model parameters). The number of parameters in the model (k), the AIC and AIC difference (ΔAIC), and weight (Wi) is given for each model. Individual variable weights (wi) are also provided.</p> <p><strong>Table S4.</strong> Coefficients for factors affecting catch weight for fishers using gill nets in the 14 top models used in model averaging. Coefficients for the fixed effects of the 14 most parsimonious models that were used in model averaging to identify factors influencing catch weight for fishers using gill nets. A ‘+’ indicates that a factor variable was included in the model, whereas a blank field means that the variable was not included. Coefficients cannot be presented for factor variables (see Table S5 in the Supporting Information for averaged model parameters). The number of parameters in the model (k), the AIC and AIC difference (ΔAIC), and weight (Wi) is given for each model. Individual variable weights (wi) are also provided.</p> <p><strong>Table S5.</strong> Averaged model results for each gear type. Averaged model parameters explaining catch weight for trap and gill net fishers. The coefficients, standard error, and lower and upper confidence intervals for each variable are provided for each averaged set of models. Baseline levels for restricted, time period, and habitat variables for both models are ‘non-restricted’, ‘Time period May-Jun '09’, and ‘edge’, respectively.</p

Impacts of spatial and temporal restrictions by gear type.

<p>Mean catch weight per trip for all catches and under spatial and temporal restrictions for each gear type. 'Current overall' shows the mean catch averaged over all locations and times of year. 'Spatial closure' compares catches in restricted areas with catches in non-restricted fishing locations. 'Temporal closure' compares catches during an October-November closed period with catches over the remainder of the year. Mean catches in non-restricted areas and not in the closed period comprise ‘both closures’. Catch weight is in kilograms (kg) with lower and upper values given for the 95% confidence interval (CI).</p><p>^a Median price paid for catches by trap fishers was US0.83 per kilogram [15].

^b Median price paid for catches by gill net fishers was US0.91 per kilogram [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129440#pone.0129440.ref015" target="_blank">15</a>].</p><p>Impacts of spatial and temporal restrictions by gear type.</p

Temporal variation in catch weight.

<p>Fitted catch weight for the top model based on lowest AIC for each gear type. Box and whisker plot of modelled catch weight per trip in kilograms for a) trap fishers and b) gill net fishers over the study period; the horizontal bar represents the 50th percentile, the top of the box the 75th percentile, and the base of the box the 25th percentile. Whiskers represent the range of data, and open circles are outliers. Catch weights are largest in Jan-Feb for trap fishers and in Oct-Nov for gill net fishers. Time periods with smallest catch weight are May-Jun and Jul-Sep for trap fishers and Jan-Feb for gill net fishers. Grey shading refers to the proposed earlier closed period; the current closed period is not represented in the data.</p

Lake Alaotra management zones.

<p>Map of Lake Alaotra showing management zones within the lake and adjacent marsh, and the centroids of fishing locations used by local fishers as recorded in the catch interview data. Restricted areas where fishing is prohibited are the strict conservation zone in the centre of the marsh and no-take zones around the lake edge.</p