Pileated Woodpecker Occupancy and the Occurrence and Recruitment of Key Habitat Attributes in a Managed Forest

Thesis (Master's)--University of Washington, 2016-08

Remarks on the morphology and distribution of some rare centric diatoms in southern Brazilian continental shelf and slope waters

This paper provides information on the morphology and occurrence of extant diatoms of the family Asterolampraceae and Azpeitia species of the southernmost Brazilian continental shelf and slope waters in the Southwestern Atlantic Ocean (28 - 34°S), under the influence of Tropical, Subtropical, Subantarctic Waters, terrestrial discharges from La Plata River and Lagoa dos Patos lagoon. Plankton was sampled (20 µm net; vertical hauls) at the same 27 stations in winter 2005 and summer 2007. Among Asterolampraceae, Asteromphalus flabellatus was the most frequent species (57% of samples) observed mainly in winter samples (92%) in Subtropical Shelf Water but also under the influence of La Plata River plume (salinity <35). Lower frequencies were observed for Asterolampra marylandica, Asteromphalus elegans, Asteromphalus heptactis and Spatangidium arachne. Four species of Azpeitia were observed: A. barronii and A. neocrenulata for the first time in the South Atlantic Ocean while A. africana and A. nodulifer had already been registered in equatorial and southern areas of Brazil. All Azpeitia species were rare (19%) in offshore samples (100-200 m depth. Remarks on the morphology based on light and scanning electron microcopy observations are provided along with their distribution in the study area.

Biogeographical distribution of Rimicaris exoculata resident gut epibiont communities along the Mid-Atlantic Ridge hydrothermal vent sites

Rimicaris exoculata is a deep-sea hydrothermal vent shrimp which enlarged gill chamber houses a complex trophic epibiotic community. Its gut harbours an autochthonous and distinct microbial community. This species dominates hydrothermal ecosystems megafauna along the Mid-Atlantic Ridge, regardless of contrasted geochemical conditions prevailing in them. Here, the resident gut epibiont community at four contrasted hydrothermal vent sites (Rainbow/TAG/Logatchev/Ashadze) was analysed and compiled with previous data to evaluate the possible influence of site location, using 16S rRNA surveys and microscopic observations (TEM, SEM and FISH analyses). Filamentous epibionts inserted between the epithelial cells microvilli were observed on all examined samples. Results confirmed resident gut community affiliation to Deferribacteres, Mollicutes, Epsilonproteobacteria and to a lesser extent Gammaproteobacteria lineages. Still a single Deferribacteres phylotype was retrieved at all sites. Four Mollicutes-related OTUs were distinguished, one being only identified on Rainbow specimens. The topology of ribotypes median-joining networks illustrated a community diversification possibly following demographic expansions, suggesting a more ancient evolutionary history and/or a larger effective population size at Rainbow. Finally, the gill chamber community distribution was also analysed through ribotypes networks based on sequences from R. exoculata collected at Rainbow/Snake Pit/TAG/Logatchev/Ashadze sites. Results allow refining hypotheses on the epibiont role and transmission pathways.

Bioecology and conservation of Duck Mussel Species (Anodonta anatina L., 1758) in Northeastern Portugal

Freshwater mussel (Mollusca, Bivalvia, Unionoida) populations are one of the most endangered faunistic groups. Mussels play an important role in the functioning of aquatic ecosystems, because they are responsible for the filtration and purification of water. They have a complex life cycle, with a parasitic larvae and usually limited host fish species. The real status of these populations is still poorly understood worldwide. The objectives of the present work were the study of bioecology of duck mussel (Anodonta anatina L.) populations of Tua Basin (NE Portugal). It was made the characterization of the ecological status of Rabaçal, Tuela and Tua Rivers, selecting 15 sampling sites, equally distributed by the three rivers. Samplings were made in the winter of 2016, and several physico-chemical water parameters measured and two habitat quality indexes calculated (GQC and QBR indexes). Benthic macroinvertebrate communities were sampled based on the protocols established by the Water Framework Directive. Host fish populations for duck mussel were determined in laboratorial conditions, testing several native and exotic fish species. The results showed that several water quality variables (e.g. dissolved oxygen, conductivity, pH, total dissolved solids, and nutrients) can be used for the classification of river typology. Other responsive metrics were also determined to identify environmental degradation. For instances, hydromorphological conditions (GQC and QBR indexes) and biota related metrics (e.g. composition, distribution, abundance, diversity of invertebrate communities) contributed to the evaluation of the ecological integrity. The upper zones of Rabaçal and Tuela rivers were classified with excellent and good ecological integrity, while less quality was found in downstream zones. The host fish tests showed that only native species are effective hosts, essential for the conservation purposes of this mussel species. Threats, like pollution, sedimentation and river regularization (3 big dams are in construction or in filling phase), are the main cause of habitat loss for native mussel and fish populations in the future. Rehabilitation and mitigation measures are essential for these lotic ecosystems in order to preserve the prioritary habitats and the native species heavily threatened.

Sea otter predation and the distribution of bivalve prey in the Elkhorn Slough National Estuarine Research Reserve

The California sea otter population is gradually expanding in size and geographic range and is consequently invading new feeding grounds, including bays and estuaries that are home to extensive populations of bivalve prey. One such area is the Elkhorn Slough, where otters have apparently established a spring and summer communal feeding and resting area. In anticipation of future otter foraging in the slough, an extensive baseline database on bivalve densities, size distributions, biomasses, and burrow depths has been established for three potential bivalve prey species, Saxidomus nuttalli, Tresus nutallii, and Zirphaea pilsbryi. In 1986, the Elkhorn Slough otters were foraging predominately at two areas immediately east and west of the Highway 1 bridge (Skipper's and the PG&E Outfall). Extensive subtidal populations of Saxidomus nuttalli and Tresus nuttallii occur in these areas. Shell records collected at these study areas indicated that sea otters were foraging selectively on Saxidomus over Tresus. The reason for this apparent preference was not clear. At the Skipper's study site, 51% of the shell record was composed of Saxidomus, yet this species accounted for only 16% of the in situ biomass, and only 39% of the available clams. Tresus represented 49% of the shell record at Skipper's, yet this species accounted for 84% of the in situ biomass and 61% of the available clams. There was no difference in mean burrow depth between the two species at this site so availability does not explain the disparity in consumption. At the PG&E Outfall, Saxidomus represents 66% of the in situ biomass and 81% of the available clams, while Tresus accounts for 34% of the in situ biomass and 19% of the available clams. Saxidomus accounts for 96% of the shell record at this site vs. 4% for Tresus, again indicating that the otters were preying on Saxidomus out of proportion to their density or biomass. High densities and biomasses of a third species, Zirphaea pilsbryi, occur in areas where sea otters were observed to be foraging, yet no cast-off Zirphaea shells were found. Although it is possible this species was not represented in the shell record because the otters were simply chewing up the shells, it is more likely this species is avoided by sea otters. There were relatively few sea otters in the Elkhorn Slough in 1986 compared to the previous two years. This, coupled with high bivalve densities, precluded any quantitative comparison of bivalve densities before and after the 1986 sea otter occupation. Qualitative observations made during the course of this study, and quantitative observations from previous studies indicate that, after 3 years, sea otters are not yet significantly affecting bivalve densities in the Elkhorn Slough.

Effect of Cocoa ( Theobroma cacao ) Plantation Types on the Distribution of Anuran Communities in Ore, Ondo State, Nigeria

Anuran species diversity and abundance were evaluated in different farming status of cocoa plantation in Ore, Ondo State, Nigeria. Applying the combination of visual encounter survey (VES) and acoustical survey (AES), the different farms surveyed were categorized as; 1) pure cocoa farms with pesticides applied (PCWP); 2) pure cocoa farms without pesticides application; 3) intercropped cocoa farms with pesticides applied (ICWP); and 4) intercropped cocoa farms without pesticides application (ICNP). The surrounding primary/secondary forest (PSFV) was sampled applying the transect method. A mean total of 690±2.6 anurans belonging to 28 species, 14 genera and 9 families were recorded during the study. Out of these, 10, 19, 17, 22 and 26 species were recorded respectively from PCWP, PCNP, ICWP, ICNP and PSFV. The anuran species richness was significantly different between the different cocoa plantation status and the forest sites (F4, 10 = 20.55, P< 0.01). The highest mean number of individuals (190±9.5) was observed at ICNP followed by PSFV (183±5.7), while the least was at PCWP (77±8.0). There was also significant difference (F4, 10 = 150.48, P< 0.01) between the abundance of anuran species at the various sites. Diversity indices (Shannon and Margalef) showed that the forest sites had the greatest (3.204 and 4.799) respectively while the pesticide using pure cocoa farms had the least (1.853 and 2.072). Generally, the result of the study clearly indicated that pesticide use cocoa farms were significantly lower compared to other sites. Farmers are encouraged to engage in intercropping (polyculture) especially with food and economic crops in a biodiversity friendly manner which could have similar characteristics of a natural ecosystem, thereby enhancing the biological diversity of agro-ecosystems.

Spatial distribution of triatomines in domiciles of an urban area of the Brazilian Southeast Region

Reports of triatomine infestation in urban areas have increased. We analysed the spatial distribution of infestation by triatomines in the urban area of Diamantina, in the state of Minas Gerais, Brazil. Triatomines were obtained by community-based entomological surveillance. Spatial patterns of infestation were analysed by Ripley’s K function and Kernel density estimator. Normalised difference vegetation index (NDVI) and land cover derived from satellite imagery were compared between infested and uninfested areas. A total of 140 adults of four species were captured (100 Triatoma vitticeps, 25 Panstrongylus geniculatus, 8 Panstrongylus megistus, and 7 Triatoma arthurneivai specimens). In total, 87.9% were captured within domiciles. Infection by trypanosomes was observed in 19.6% of 107 examined insects. The spatial distributions of T. vitticeps, P. geniculatus, T. arthurneivai, and trypanosome-positive triatomines were clustered, occurring mainly in peripheral areas. NDVI values were statistically higher in areas infested by T. vitticeps and P. geniculatus. Buildings infested by these species were located closer to open fields, whereas infestations of P. megistus and T. arthurneivai were closer to bare soil. Human occupation and modification of natural areas may be involved in triatomine invasion, exposing the population to these vectors.

Recruitment patterns and processes of coastal fish species in a temperate rocky reef

Tese de Doutoramento, Ciências do Mar, da Terra e do Ambiente, Ramo: Ciências do Mar, Especialização em Ecologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2016

Depth distribution of the velvet belly, Etmopterus spinax, in relation to growth and reproductive cycle: The case study of a deep-water lantern shark with a wide-ranging critical habitat

The velvet belly lantern shark, Etmopterus spinax (Squaliformes: Etmopteridae), is a small-sized squalid shark commonly found in deep waters off the Portuguese coast, mainly on soft bottoms. In this study, 67 research cruise bottom trawl tows (with 1-hour duration) were carried out at depths that ranged from 84 to 786 m. A total of 396 specimens (192 males and 204 females) were caught, with total lengths and ages ranging, respectively, from 10.2 to 32.9 cm and 0 to 7 years for males and from 9.8 to 41.1 cm and 0 to 10 years for females. Size, age, sex and maturity stages were found to be correlated with depth, with the larger, older and mostly mature specimens occurring predominantly at greater depths. There seems to be a depth-related migration, where the pregnant females migrate from deeper mating grounds to shallower nursery grounds. The sex ratios were relatively similar in the shallower strata, but females dominated at more than 600 m and were exclusive at more than 700 m. Fishing-related mortality may have complex and significant repercussions on this species, given that commercial fisheries are impacting different segments of this population differently.

Use of different intertidal habitats by faunal communities in a temperate coastal lagoon

The faunal communities of four intertidal habitats namely sand, mud, seagrass (Zostera noltii) and seagrass patches (mixSM) of a temperate coastal lagoon, Ria Formosa (southern Portugal), were sampled. A total of 47 species were taken in 428 bottomless drop sampler samples, with the highest number of species and the more commonly occurring species belonging to the Mollusca phylum. The dominance of these gastropod species underlines the importance of the grazing food chain in these habitats. Bittium reticulatum was the most abundant species, being especially abundant in the seagrass habitat. The most frequent and highest biomass species in the community was Carcinus maenas, a predator that makes use of the available resources and that is adapted to the highly variable intertidal environment. Pomatoschistus microps was the most abundant fish species, with highest densities in the mud habitat, which demonstrates an ability to occupy a low depth area. The seagrass; habitat had the highest diversity, abundance and biomass, followed by the mixSM habitat and was different from all the others. Assemblages were highly influenced by the presence of vegetation, providing forage and refuge from predation. A well defined summer group was identified in all habitats. These results highlight the importance of seagrass beds and the idea that their decrease implies the decrease of lagoon production through the impoverishment of the trophic structure of the lagoon. (C) 2008 Elsevier Ltd. All rights reserved.

Conservation biogeography of ecologically interacting species: The case of the Iberian lynx and the European rabbit

Aim To relate the recent Iberian lynx decline to changes in the distribution of the European rabbit after the haemorrhagic disease outbreak of 1989. As Iberian rabbits evolved in two geographically separated lineages, being the recent lynx range practically restricted to the southwestern lineage, we also test if differential range dynamics exists for these lineages, with the consequent implications for lynx conservation and reintroduction planning.

Modelling the distribution of Bonelli's eagle in Spain: Implications for conservation planning

Bonelli’s eagle, Hieraaetus fasciatus , has recently suffered a severe population decline and is currently endangered. Spain supports about 70% of the European population. We used stepwise logistic regression on a set of environmental, spatial and human variables to model Bonelli’s eagle distribution in the 5167 UTM 10 × 10 km quadrats of peninsular Spain. We obtained a model based on 16 variables, which allowed us to identify favourable and unfavourable areas for this species in Spain, as well as intermediate favourability areas. We assessed the stepwise progression of the model by comparing the model’s predictions in each step with those of the final model, and selected a parsimonious explanatory model based on three variables — slope, July temperature and precipitation — comprising 76% of the predictive capacity of the

Relative importance of environment, human activity and spatial situation in determining the distribution of terrestrial mammal diversity in Argentina

We recorded the number of terrestrial mammal species in each Argentinian province, and the number of species belonging to particular groups (Marsupialia, Placentaria, and among the latter, Xenarthra, Carnivora, Ungulates and Rodentia). We performed multiple regressions of each group’s SR on environmental, human and spatial variables, to determine the amounts of variation explained by these factors. We then used a variance partitioning procedure to specify which proportion of the variation in SR is explained by each of the three factors exclusively and which proportions are attributable to interactions between factors.

Spatial, environmental and human influences on the distribution of otter (Lutra lutra) in the Spanish provinces

In a previous survey of otters ( Lutra lutra L. 1758) in Spain, different causes were invoked to explain the frequency of the species in each province. To find common causes of the distribution of the otter in Spain, we recorded a number of spatial, environmental and human variables in each Spanish province. We then performed a stepwise linear multiple regression of the proportion of positive sites of otter in the Spanish provinces separately on each of the three groups of variables. Geographic longitude, January air humidity, soil permeability and highway density were the variables selected. A linear regression of the proportion of otter presence on these variables explained 62.4% of the variance. We then used the selected variables in a partial regression analysis to specify which proportions of the variation are explained exclusively by spatial, environmental and human factors, and which proportions are attributable to interactions between these components. Pure environmental effects accounted for only 5.5% of the variation, while pure spatial and pure human effects explained 18% and 9.7%, respectively. Shared variation among the components totalled 29.2%, of which 10.9% was explained by the interaction between environmental and spatial factors. Human factors explained globally less variance than spatial and environmental ones, but the pure human influence was higher than the pure environmental one. We concluded that most of the variation in the proportion of occurrences of otter in Spanish provinces is spatially structured, and that environmental factors have more influence on otter presence than human ones; however, the human influence on otter distribution is less structured in space, and thus can be more disruptive. This effect of large infrastructures on wild populations must be taken into account when planning large-scale conservation policies

Co-Infestation and Spatial Distribution of Bactrocera carambolae and Anastrepha spp. (Diptera: Tephritidae) in Common Guava in the Eastern Amazon.

Field infestation and spatial distribution of introduced Bactrocera carambolae Drew and Hancock and native species of Anastrepha in common guavas [Psidium guajava (L.)] were investigated in the eastern Amazon. Fruit sampling was carried out in the municipalities of Calc¸oene and Oiapoque in the state of Amapa, Brazil. The frequency distribution of larvae in fruit was fitted to the negative binomial distribution. Anastrepha striata was more abundant in both sampled areas in comparison to Anastrepha fraterculus (Wiedemann) and B. carambolae. The frequency distribution analysis of adults revealed an aggregated pattern for B. carambolae as well as for A. fraterculus and Anastrepha striata Schiner, described by the negative binomial distribution. Although the populations of Anastrepha spp. may have suffered some impact due to the presence of B. carambolae, the results are still not robust enough to indicate effective reduction in the abundance of Anastrepha spp. caused by B. carambolae in a general sense. The high degree of aggregation observed for both species suggests interspecific co-occurrence with the simultaneous presence of both species in the analysed fruit. Moreover, a significant fraction of uninfested guavas also indicated absence of competitive displacement.