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Athearn N.D.,U.S. Geological Survey | Athearn N.D.,U.S. Fish and Wildlife Service | Athearn N.D.,University of California at Davis | Takekawa J.Y.,U.S. Geological Survey | And 5 more authors.
Hydrobiologia | Year: 2012

Salt evaporation ponds are used in place of lost natural estuarine habitats for foraging and roosting by waterbirds around the world, but have started to be decommissioned in some areas due to low profitability. In San Francisco Bay, three former salt pond complexes (Alviso, Eden Landing, and Ravenswood) have been decommissioned, i. e., taken out of commission, and are planned for marsh restoration. We compared total and foraging abundance and densities of ducks, shorebirds, and piscivores, as well as eared grebes (Podiceps nigricollis) among decommissioned and commercial pond complexes. Complex use was consistent within groups and variable among groups, with most use occurring in decommissioned ponds: 73% of ducks were observed in the Alviso complex and 9% in the commercial ponds; 51% of shorebirds were in the Eden Landing complex and only 17% in commercial ponds; and 56% of piscivores were in the Alviso complex and <18% in commercial ponds. Only eared grebes were more abundant (59%) in commercial ponds. Differences among groups in within-complex and within-pond abundance were likely related to pond salinity and topography, respectively. Our results suggest that the effects of pond conversion on waterbird groups may be disproportionate to pond area depending on the characteristics of the converted ponds. © 2012 Springer Science+Business Media B.V. (outside the USA).


Chapman H.,University of Canterbury | Cordeiro N.J.,Roosevelt University | Dutton P.,University of Canterbury | Wenny D.,San Francisco Bay Bird Observatory | And 4 more authors.
Journal of Tropical Ecology | Year: 2016

Seed-dispersal ecology in tropical montane forests (TMF) differs in some predictable ways from tropical lowland forests (TLF). Environmental, biogeographic and biotic factors together shape dispersal syndromes which in turn influence forest structure and community composition. Data on diaspore traits along five elevational gradients from forests in Thailand, the Philippines, Tanzania, Malawi and Nigeria showed that diaspore size decreases with increasing altitude, fleshy fruits remain the most common fruit type but the relative proportion of wind-dispersed diaspores increases with altitude. Probably corresponding to diaspore size decreasing with increasing elevation, we also provide evidence that avian body size and gape width decrease with increasing altitude. Among other notable changes in the frugivorous fauna across elevational gradients, we found quantitative evidence illustrating that the proportion of bird versus mammalian frugivores increases with altitude, while TMF primates decrease in diversity and density, and switch diets to include less fruit and more leaf proportionately. A paucity of studies on dispersal distance and seed shadows, the dispersal/predation balance and density-dependent mortality thwart much-needed conclusive comparisons of seed dispersal ecology between TMF and TLF, especially from understudied Asian forests. We examine the available evidence, reveal knowledge gaps and recommend research to enhance our understanding of seed dispersal ecology in tropical forests. This review demonstrates that seed dispersal is a more deterministic and important process in tropical montane forests than has been previously appreciated. Copyright © Cambridge University Press 2016


Kirkman K.P.,University of KwaZulu - Natal | Collins S.L.,University of New Mexico | Smith M.D.,Colorado State University | Knapp A.K.,Colorado State University | And 11 more authors.
Journal of Vegetation Science | Year: 2014

Question: Does fire frequency affect mesic grassland plant community structure and composition similarly in North America and South Africa? Location: Konza Prairie Biological Station (KNZ), Kansas, USA, and Ukulinga Research Farm (URF), KwaZulu-Natal, South Africa. Methods: Plant community structure and composition were compared among annually burned, unburned and intermediate treatments within two long-term fire frequency manipulation experiments in native grasslands in North America and South Africa using comparable methodology over a 5-yr period. Because fire may reduce soil nitrogen (N) availability and thus affect plant community structure, N additions were superimposed on the fire treatments as a means of assessing direct vs indirect mechanisms driving responses to fire. Results: The total number of species was higher at URF (183) than at KNZ (57). Overall divergence in plant community response to fire frequency occurred despite similar responses to nutrient additions. At KNZ, more frequent fire resulted in dominance by a few, tall, deep-rooted rhizomatous grasses (e.g. Andropogon gerardii). On unburned sites, shorter, more shade-tolerant species such as Poa pratensis increased in abundance, although A. gerardii remained dominant. Species richness increased with decreasing fire frequency at KNZ. At URF, frequent fire resulted in short, diverse grassland weakly dominated by a range of grass species, including Themeda triandra, Tristachya leucothrix and Hyparrhenia hirta. Decreasing fire frequency reduced species richness and resulted in dominance by a few, relatively tall caespitose grasses such as Aristida junciformis. There was a complete turnover of dominant species between annually burned and unburned treatments at URF, while at KNZ A. gerardii and Sorghastrum nutans occurred across the range of treatments. N addition reduced species richness in both sites. Conclusions: Different responses to fire frequency between KNZ and URF are likely linked to the dominant species and their characteristic traits, including height and method of clonal reproduction, with the rhizomatous growth form of A. gerardii dominating the North American grassland. South Africa does not have an equivalent grass species; instead, a range of tufted, non-rhizomatous species dominate across the fire frequency treatments at URF. Reductions in soil N due to frequent fire did not appear to be a common mechanism driving responses in community composition in these two grasslands. © 2013 International Association for Vegetation Science.


Harrison P.,Swingates | Sallaberry M.,University of Chile | Gaskin C.P.,400 Leigh Road | Baird K.A.,Forest and Bird | And 9 more authors.
Auk | Year: 2013

We describe a new species of storm-petrel, Oceanites pincoyae (Pincoya Storm-Petrel), from the Puerto Montt and Chacao channel area, Chile. The description is based on 1 specimen collected at sea in Seno Reloncavi on 19 February 2011 and 11 other individuals that were caught, examined, and released. The new taxon's foraging ecology and behavioral habits are unique among the southern Oceanitinae, including "mouse-runs" and repeated diving beneath the surface to retrieve food items. Its distinctive appearance includes bold white ulnar bars, extensive white panels to the underwing, and white to the lower belly and vent. Among species of Oceanites, it is unique in showing white outer vanes to the outer two pairs of rectrices. It further differs from all other storm-petrels in having a distinctive juvenile plumage. Morphometrically it is distinct from Oceanites gracilis gracilis (Elliot's Storm-Petrel) and smaller than O. oceananicus chilensis (the Fuegian form of Wilson's Storm-Petrel), having a shorter tarsus and longer middle toe. There also appear to be differences in the timing of breeding and molt between the new taxon and both O. o. chilensis and O. g. gracilis. We estimate the population size of the new species as ~3,000 individuals. Copyright © 2013 by The American Ornithologists' Union.


Eby S.,Colorado State University | Burkepile D.E.,Florida International University | Fynn R.W.S.,Okavango Research Institute | Burns C.E.,San Francisco Bay Bird Observatory | And 11 more authors.
Oecologia | Year: 2014

Large herbivore grazing is a widespread disturbance in mesic savanna grasslands which increases herbaceous plant community richness and diversity. However, humans are modifying the impacts of grazing on these ecosystems by removing grazers. A more general understanding of how grazer loss will impact these ecosystems is hampered by differences in the diversity of large herbivore assemblages among savanna grasslands, which can affect the way that grazing influences plant communities. To avoid this we used two unique enclosures each containing a single, functionally similar large herbivore species. Specifically, we studied a bison (Bos bison) enclosure at Konza Prairie Biological Station, USA and an African buffalo (Syncerus caffer) enclosure in Kruger National Park, South Africa. Within these enclosures we erected exclosures in annually burned and unburned sites to determine how grazer loss would impact herbaceous plant communities, while controlling for potential fire-grazing interactions. At both sites, removal of the only grazer decreased grass and forb richness, evenness and diversity, over time. However, in Kruger these changes only occurred with burning. At both sites, changes in plant communities were driven by increased dominance with herbivore exclusion. At Konza, this was caused by increased abundance of one grass species, Andropogon gerardii, while at Kruger, three grasses, Themeda triandra, Panicum coloratum, and Digitaria eriantha increased in abundance. © 2014 Springer-Verlag Berlin Heidelberg.


Carmi O.,San Francisco State University | Carmi O.,California Academy of Sciences | Witt C.C.,University of New Mexico | Jaramillo A.,San Francisco Bay Bird Observatory | And 2 more authors.
Molecular Phylogenetics and Evolution | Year: 2016

The Vermilion Flycatcher (Pyrocephalus rubinus) is a widespread species found in North and South America and the Galápagos. Its 12 recognized subspecies vary in degree of geographic isolation, phenotypic distinctness, and migratory status. Some authors suggest that Galápagos subspecies nanus and dubius constitute one or more separate species. Observational reports of distinct differences in song also suggest separate species status for the austral migrant subspecies rubinus. To evaluate geographical patterns of diversification and taxonomic limits within this species complex, we carried out a molecular phylogenetic analysis encompassing 10 subspecies and three outgroup taxa using mitochondrial (ND2, Cyt b) and nuclear loci (ODC introns 6 through 7, FGB intron 5). We used samples of preserved tissues from museum collections as well as toe pad samples from museum skins. Galápagos and continental clades were recovered as sister groups, with initial divergence at ~1 mya. Within the continental clade, North and South American populations were sister groups. Three geographically distinct clades were recovered within South America. We detected no genetic differences between two broadly intergrading North American subspecies, mexicanus and flammeus, suggesting they should not be recognized as separate taxa. Four western South American subspecies were also indistinguishable on the basis of loci that we sampled, but occur in a region with patchy habitat, and may represent recently isolated populations. The austral migrant subspecies, rubinus, comprised a monophyletic mitochondrial clade and had many unique nuclear DNA alleles. In combination with its distinct song, exclusive song recognition behavior, different phenology, and an isolated breeding range, our data suggests that this taxon represents a separate species from other continental populations. Mitochondrial and nuclear genetic data, morphology, and behavior suggest that Galápagos forms should be elevated to two full species corresponding to the two currently recognized subspecies, nanus and dubius. The population of dubius is presumed to be extinct, and thus would represent the first documented extinction of a Galápagos-endemic bird species. Two strongly supported mitochondrial clades divide Galápagos subspecies nanus in a geographic pattern that conflicts with previous hypotheses that were based on plumage color. Several populations of nanus have recently become extinct or are in serious decline. Urgent conservation measures should seek to preserve the deep mitochondrial DNA diversity within nanus, and further work should explore whether additional forms should be recognized within nanus. Ancestral states analysis based on our phylogeny revealed that the most recent common ancestor of extant Vermilion Flycatcher populations was migratory, and that migratory behavior was lost more often than gained within Pyrocephalus and close relatives, as has been shown to be the case within Tyrannidae as a whole. © 2016 Elsevier Inc.


Bluso-Demers J.D.,U.S. Geological Survey | Bluso-Demers J.D.,San Francisco Bay Bird Observatory | Ackerman J.T.,U.S. Geological Survey | Takekawa J.Y.,U.S. Geological Survey
Ardea | Year: 2010

In order to examine 24-hour colony attendance patterns by mated Forster's Terns Sterna forsteri in South San Francisco Bay, California, during incubation and chick-rearing stages, we radio-marked 10 individuals consisting of five pairs and recorded colony attendance using an automated data-logging receiver system. We calculated and analyzed five variables: the total attendance time by pairs and individuals, the duration of individual attendance bouts, and the duration both members of a pair either overlapped in colony attendance or were both absent from the colony. The percentage of time spent on the colony by at least one individual of a pair was highest during incubation and declined during chick rearing. Overall, male terns spent a greater proportion of time diurnally attending the colony than females. Females spent a greater proportion of time on colony at night, and without these nocturnal records, we would have reported overall female colony attendance rates as being much lower. Despite sex-specific differences in attendance rates, the length of attendance bouts did not differ between the sexes. Simultaneous colony attendance by both members of a pair was high at night, but during the day, pairs infrequently overlapped in their colony attendance and both members were frequently absent. Our datalogging system functioned well, and our data illustrates the importance of collecting 24-hour records when considering attendance rates.


Goodman R.E.,San Francisco State University | Lebuhn G.,San Francisco State University | Seavy N.E.,PRBO Conservation Science | Gardali T.,PRBO Conservation Science | Bluso-Demers J.D.,San Francisco Bay Bird Observatory
Global Change Biology | Year: 2012

There has been a growing interest in whether established ecogeographical patterns, such as Bergmann's rule, explain changes in animal morphology related to climate change. Bergmann's rule has often been used to predict that body size will decrease as the climate warms, but the predictions about how body size will change are critically dependent on the mechanistic explanation behind the rule. To investigate change in avian body size in western North America, we used two long-term banding data sets from central California, USA; the data spanned 40 years (1971-2010) at one site and 27 years (1983-2009) at the other. We found that wing length of birds captured at both sites has been steadily increasing at a rate of 0.024-0.084% per year. Although changes in body mass were not always significant, when they were, the trend was positive and the magnitudes of significant trends were similar to those for wing length (0.040-0.112% per year). There was no clear difference between the rates of change of long-distance vs. short-distance migrants or between birds that bred locally compared to those that bred to the north of the sites. Previous studies from other regions of the world have documented decreases in avian body size and have used Bergmann's rule and increases in mean temperature to explain these shifts. Because our results do not support this pattern, we propose that rather than responding to increasing mean temperatures, avian body size in central California may be influenced by changing climatic variability or changes in primary productivity. More information on regional variation in the rates of avian body size change will be needed to test these hypotheses. © 2011 Blackwell Publishing Ltd.


Spotswood E.N.,University of California at Berkeley | Goodman K.R.,University of California at Berkeley | Carlisle J.,Boise State University | Cormier R.L.,PRBO Conservation Science | And 4 more authors.
Methods in Ecology and Evolution | Year: 2012

The capture of birds using mist nets is a widely utilized technique for monitoring avian populations. While the method is assumed to be safe, very few studies have addressed how frequently injuries and mortalities occur and the associated risks have not been formally evaluated. We quantified the rates of mortality and injury at 22 banding organizations in the United States and Canada and used capture data from five organizations to determine what kinds of incidents occur most frequently. Analyses focused on passerines and near-passerines, but other groups were included. We evaluated whether body mass, age, sex, mist net mesh size, month and time of day or frequency of capture are related to the risk or type of incident. We also compared the recapture histories over time between birds that were injured and those that were never injured for 16 species. The average rate of injury was 0·59%, while mortality was 0·23%. Birds captured frequently were less at risk to incident. Body mass was positively correlated with incident and larger birds were at greater risk to predation, leg injuries, broken legs, internal bleeding and cuts, while smaller birds were more prone to stress, tangling-related injuries and wing strain. Rates of incident varied among species, with some at greater risk than others. We found no evidence for increased mortality over time of injured birds compared with uninjured birds. We provide the first comprehensive evaluation of the risks associated with mist netting. Our results indicate that (1) injury and mortality rates below one percent can be achieved during mist netting and (2) injured birds are likely to survive in comparable numbers to uninjured birds after release. While overall risks are low, this study identified vulnerable species and traits that may increase a bird's susceptibility to incident that should be considered in banding protocols aimed at minimizing injury and mortality. Projects using mist nets should monitor their performance and compare their results to those of other organizations. © 2011 The Authors. Methods in Ecology and Evolution © 2011 British Ecological Society.


PubMed | San Francisco State University, University of New Mexico and San Francisco Bay Bird Observatory
Type: | Journal: Molecular phylogenetics and evolution | Year: 2016

The Vermilion Flycatcher (Pyrocephalus rubinus) is a widespread species found in North and South America and the Galpagos. Its 12 recognized subspecies vary in degree of geographic isolation, phenotypic distinctness, and migratory status. Some authors suggest that Galpagos subspecies nanus and dubius constitute one or more separate species. Observational reports of distinct differences in song also suggest separate species status for the austral migrant subspecies rubinus. To evaluate geographical patterns of diversification and taxonomic limits within this species complex, we carried out a molecular phylogenetic analysis encompassing 10 subspecies and three outgroup taxa using mitochondrial (ND2, Cyt b) and nuclear loci (ODC introns 6 through 7, FGB intron 5). We used samples of preserved tissues from museum collections as well as toe pad samples from museum skins. Galpagos and continental clades were recovered as sister groups, with initial divergence at 1mya. Within the continental clade, North and South American populations were sister groups. Three geographically distinct clades were recovered within South America. We detected no genetic differences between two broadly intergrading North American subspecies, mexicanus and flammeus, suggesting they should not be recognized as separate taxa. Four western South American subspecies were also indistinguishable on the basis of loci that we sampled, but occur in a region with patchy habitat, and may represent recently isolated populations. The austral migrant subspecies, rubinus, comprised a monophyletic mitochondrial clade and had many unique nuclear DNA alleles. In combination with its distinct song, exclusive song recognition behavior, different phenology, and an isolated breeding range, our data suggests that this taxon represents a separate species from other continental populations. Mitochondrial and nuclear genetic data, morphology, and behavior suggest that Galpagos forms should be elevated to two full species corresponding to the two currently recognized subspecies, nanus and dubius. The population of dubius is presumed to be extinct, and thus would represent the first documented extinction of a Galpagos-endemic bird species. Two strongly supported mitochondrial clades divide Galpagos subspecies nanus in a geographic pattern that conflicts with previous hypotheses that were based on plumage color. Several populations of nanus have recently become extinct or are in serious decline. Urgent conservation measures should seek to preserve the deep mitochondrial DNA diversity within nanus, and further work should explore whether additional forms should be recognized within nanus. Ancestral states analysis based on our phylogeny revealed that the most recent common ancestor of extant Vermilion Flycatcher populations was migratory, and that migratory behavior was lost more often than gained within Pyrocephalus and close relatives, as has been shown to be the case within Tyrannidae as a whole.

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