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Geology topics

S. M. Haig

Publications and source records attributed to S. M. Haig.

At least 19 recordsLinked to original sources
USGS2011

Multiplexed microsatellite recovery using massively parallel sequencing

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

Molecular Ecology Resources↗
USGS2010

Multiscale habitat use and selection in cooperatively breeding Micronesian kingfishers

Information about the interaction between behavior and landscape resources is key to directing conservation management for endangered species. We studied multi-scale occurrence, habitat use, and selection in a cooperatively breeding population of Micronesian kingfishers (Todiramphus cinnamominus) on the island of Pohnpei, Federated States of Micronesia. At the landscape level, point-transect surveys resulted in kingfisher detection frequencies that were higher than those reported in 1994, although they remained 15-40% lower than 1983 indices. Integration of spatially explicit vegetation information with survey results indicated that kingfisher detections were positively associated with the amount of wet forest and grass-urban vegetative cover, and they were negatively associated with agricultural forest, secondary vegetation, and upland forest cover types. We used radiotelemetry and remote sensing to evaluate habitat use by individual kingfishers at the home-range scale. A comparison of habitats in Micronesian kingfisher home ranges with those in randomly placed polygons illustrated that birds used more forested areas than were randomly available in the immediate surrounding area. Further, members of cooperatively breeding groups included more forest in their home ranges than birds in pair-breeding territories, and forested portions of study areas appeared to be saturated with territories. Together, these results suggested that forest habitats were limited for Micronesian kingfishers. Thus, protecting and managing forests is important for the restoration of Micronesian kingfishers to the island of Guam (United States Territory), where they are currently extirpated, as well as to maintaining kingfisher populations on the islands of Pohnpei and Palau. Results further indicated that limited forest resources may restrict dispersal opportunities and, therefore, play a role in delayed dispersal and cooperative behaviors in Micronesian kingfishers.

Journal of Wildlife Management↗
USGS2010

Subspecies status and population genetic structure in Piping Plover ( Charadrius melodus )

Piping Plover (Charadrius melodus) is a migratory shorebird that is listed as endangered in Canada and the U.S. Great Lakes and as threatened throughout the rest of its breeding and winter range. We undertook a comprehensive molecular-genetic investigation to (1) address subspecific taxonomy, (2) characterize population genetic structure, and (3) infer past bottlenecks and demographic processes in this species. Analyses included individuals from 23 U.S. states and Canadian provinces and were based on mitochondrial DNA sequences (580 base pairs, n = 245) and 8 nuclear microsatellite loci (n = 229). Our findings provide support for separate Atlantic and Interior subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies and should be referred to as C. m. circumcinctus. Population genetic analyses illustrated stronger genetic structure among Atlantic than among Interior birds, which may reflect reduced natal- and breeding-site fidelity of Interior individuals. Furthermore, analyses suggested that Interior birds previously experienced genetic bottlenecks, whereas there was no evidence of such patterns in the Atlantic subspecies. We interpret these results in light of 25 years of range-wide census data. Overall, differences between Interior and Atlantic Piping Plovers may reflect differences in spatiotemporal stability of nesting habitat between regions. ?? 2010 The American Ornithologists' Union.

The Auk↗
USGS2010

Seasonal movements, winter range use, and migratory connectivity of the Black Oystercatcher

The Black Oystercatcher (Haematopus bachmani) is an intertidal obligate along North America's Pacific coast and a species of high conservation concern (population size 8900-11 000 individuals). Understanding birds' movements and space use throughout the annual cycle has become paramount in the face of changing environmental conditions, and intertidal species may be particularly vulnerable to habitat change due to anticipated sea-level rise associated with climate change and increasing coastal development. Conservation of the Black Oystercatcher is hindered by a lack of information on the species' nonbreeding distribution, seasonal movements, and habitat connectivity. Using satellite (n = 19) and VHF (n = 19) radio transmitters, we tracked Black Oystercatchers from five breeding sites (Vancouver Island, British Columbia; Kodiak Island, Prince William Sound, Middleton Island, and Juneau, Alaska) through one and one half annual cycles (May 2007-Dec 2008). We documented medium- to long-distance migration (range of migration distance 130-1667 km) in three populations (Prince William Sound, Middleton Island, and Juneau) and year-round residency in two others (Kodiak and Vancouver Island). We observed variation in the timing and length of migration by study site, and individual birds demonstrated fidelity to breeding and nonbreeding sites. We did not observe strong migratory connectivity. Migratory oystercatchers distributed themselves widely along the coasts of British Columbia and southeast Alaska during winter. Results provide baseline information on the Black Oystercatcher's movements and space use throughout the annual cycle. ?? 2010 The Cooper Ornithological Society.

Condor↗
USGS2010

Genetic characterization of Neotropical Jabiru Storks: Insights for conservation

Jabiru Stork (Jabiru mycteria is listed under Appendix I of CITES and considered threatened in Central America. The first population genetic analysis of Jabiru Storks was carried out using mitochondrial DNA (mtDNA) control region sequences (520 bp) and five heterologous microsatellite loci. Samples were collected from the field (N = 49) and museum skins (N = 22) in Central (mainly Belize, Nicaragua and Costa Rica) and South America (Colombia, Venezuela, Peru and Brazil). A decline of mtDNA diversity was observed in comparisons between past (N = 20) and present (N = 40) samples collected in Central America and northern South America. Similar levels of microsatellite loci diversity were observed among contemporary samples. Lower levels of mtDNA variability were observed in samples from Central America and northern South America when compared to the Brazilian Pantanal region. Significant levels of genetic differentiation were found between contemporary locations sampled, whereas non-significant results were observed for historic samples. The non-geographic association of haplotypes observed at the cladograms and the recent divergence times estimated between locations are indicative of an evolutionary history of a large population size with limited population structure. Reconnection of populations via increased gene flow, particularly in Central America, is recommended if genetic structure and status are to be restored.

Waterbirds↗
USGS2009

Behavior and reproductive success of rock sandpipers breeding on the Yukon-Kuskokwim river delta, Alaska

We studied Rock Sandpiper ( Calidris ptilocnemis ) breeding behavior and monitored reproductive success from 1998 to 2005 on the Yukon-Kuskokwim River Delta, Alaska, USA. We banded 24 adults and monitored 45 nests. Annual return rate of adults ranged between 67 and 100%. Six pairs of Rock Sandpipers bred at our study site for ≥2 years, and among these we did not observe mate change (i.e., when both members of a pair returned and each mated with a new individual). Nests were typically initiated by mid-May and 53% of females laid second clutches if first clutches were lost through mid-June. Males regularly incubated clutches during the morning (0800–1259 hrs AKDT) and afternoon (1300–1759 hrs) and rarely during the evening (1800– 2300 hrs), whereas female incubation was relatively consistent throughout the day. Apparent nest success (percent of known nests successfully hatching >1 chick) among first and second nests was 19 and 44%, respectively ( n = 45). A minimum of 44% of hatching nests fledged at least one young. Males cared for young but half of females deserted mate and brood 1–7 days post-hatch. This first description of North American Rock Sandpiper breeding behavior from a color-marked population complements previous work on this species on the Chukotsky Peninsula, Russia.

Wilson Journal of Ornithology↗
USGS2008

Movements of wintering Dunlin Calidris alpina and changing habitat availability in an agricultural wetland landscape

Few studies have assessed how the dynamics of wetland bird movements relate to changing resource availability, particularly at more than one spatial scale. Within western Oregon's Williamette Valley, we examined winter resident Dunlin Calidris alpina movements in relation to a decrease in availability of preferred shorebird foraging habitat from early to late winter of 1999-2000. By tracking movements of 15 (early winter) and 12 (late winter) radiomarked individuals, we calculated home ranges and characterized presence/absence of a preference for shorebird foraging habitat during each winter period. Between periods, we compared: (1) percentage of shorebird habitat in home ranges to its availability in the landscape (regional preference), (2) percentage of radio locations in shorebird habitat to its availability within home ranges (local preference) and (3) relative use of roost sites. Concurrent with a 75% decrease in available shorebird habitat from early to late winter, average home range sizes increased by a factor of 3.8. At a regional scale, home ranges in early winter included a significantly greater percentage of shorebird foraging habitat than was available in the wider landscape. However, by late winter, the percent of shorebird habitat in home ranges did not match availability in the landscape. At the local scale, for both winter periods Dunlin were located in shorebird foraging habitat more often than expected given availability of habitat within home ranges [Correction added after online pub-lication 23 May 2008: sentence amended]. An increase in the number of roosts used from early to late winter implies possible reliance on additional sites in late winter for foraging opportunities. Results suggest that wet, unvegetated habitat is sought by Dunlin throughout winter, but individuals could not select home ranges in late winter that fully compensated for seasonal loss of habitat. ?? 2008 The Authors.

Ibis↗
USGS2008

Blood parasites in Owls with conservation implications for the Spotted Owl (Strix occidentalis)

The three subspecies of Spotted Owl (Northern, Strix occidentalis courina; California, S. o. occidentalis; and Mexican, S. o. lucida) are all threatened by habitat loss and range expansion of the Barred Owl (S. varia). An unaddressed threat is whether Barred Owls could be a source of novel strains of disease such as avian malaria (Plasmodium spp.) or other blood parasites potentially harmful for Spotted Owls. Although Barred Owls commonly harbor Plasmodium infections, these parasites have not been documented in the Spotted Owl. We screened 111 Spotted Owls, 44 Barred Owls, and 387 owls of nine other species for haemosporidian parasites (Leucocytozoon, Plasmodium, and Haemoproteus spp.). California Spotted Owls had the greatest number of simultaneous multi-species infections (44%). Additionally, sequencing results revealed that the Northern and California Spotted Owl subspecies together had the highest number of Leucocytozoon parasite lineages (n=17) and unique lineages (n=12). This high level of sequence diversity is significant because only one leucocytozoon species (L. danilewskyi) has been accepted as valid among all owls, suggesting that L. danilewskyi is a cryptic species. Furthermore, a Plasmodium parasite was documented in a Northern Spotted Owl for the first time. West Coast Barred Owls had a lower prevalence of infection (15%) when compared to sympatric Spotted Owls (S. o. caurina 52%, S. o. occidentalis 79%) and Barred Owls from the historic range (61%). Consequently, Barred Owls on the West Coast may have a competitive advantage over the potentially immune compromised Spotted Owls. ?? 2008 Ishak et al.

PLoS ONE↗
USGS2008

Range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) in northwestern North America

The dynamic geological and climatic history of northwestern North America has made it a focal region for phylogeography. We conducted a range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) across its range in northwestern North America to understand its evolutionary history and the distribution of clades to inform conservation of R. pretiosa and Great Basin R. luteiventris, candidates for listing under the US Endangered Species Act. Mitochondrial DNA sequence data from a segment of the cytochrome b gene were obtained from 308 R. luteiventris and R. pretiosa from 96 sites. Phylogenetic analysis revealed one main R. pretiosa clade and three main R. luteiventris clades, two of which overlapped in southeastern Oregon. The three R. luteiventris clades were separated from each other by high levels of sequence divergence (average of 4.75-4.97%). Two divergent clades were also uncovered within the Great Basin. Low genetic variation in R. pretiosa and the southeastern Oregon clade of R. luteiventris suggests concern about their vulnerability to extinction. ?? 2008 Elsevier Inc.

Molecular Phylogenetics and Evolution↗
USGS2007

Conservation genetics of snowy plovers (Charadrius alexandrinus) in the Western Hemisphere: Population genetic structure and delineation of subspecies

We examined the genetic structure of snowy plovers (Charadrius alexandrinus) in North America, the Caribbean, and the west coast of South America to quantify variation within and among breeding areas and to test the validity of three previously recognized subspecies. Sequences (676 bp) from domains I and II of the mitochondrial control region were analyzed for 166 snowy plovers from 20 breeding areas. Variation was also examined at 10 microsatellite loci for 144 snowy plovers from 14 breeding areas. The mtDNA and microsatellite data provided strong evidence that the Puerto Rican breeding group is genetically divergent from sites in the continental U.S. (net sequence divergence = 0.38%; F ST for microsatellites = 0.190). Our data also revealed high levels of differentiation between sites from South America and North America (net sequence divergence = 0.81%; F ST for microsatellites = 0.253). In contrast, there was little genetic structure among breeding sites within the continental U.S. Our results suggest that snowy plovers in Florida should be considered part of C. a. nivosus (rather than part of C. a. tenuirostris, where they are currently placed), whereas snowy plovers from Puerto Rico should be considered part of C. a. tenuirostris. Snowy plovers in South America should remain a separate subspecies (C. a. occidentalis). Although U.S. Pacific and Gulf Coast breeding areas were not genetically distinct from other continental U.S. sites, demographic isolation, unique coastal habitats, and recent population declines suggest they warrant special concern. ?? 2007 Springer Science+Business Media, Inc.

Conservation Genetics↗
USGS2007

Conservation biology for suites of species: Demographic modeling for Pacific island kingfishers

Conservation practitioners frequently extrapolate data from single-species investigations when managing critically endangered populations. However, few researchers initiate work with the intent of making findings useful to conservation efforts for other species. We presented and explored the concept of conducting conservation-oriented research for suites of geographically separated populations with similar natural histories, resource needs, and extinction threats. An example was provided in the form of an investigation into the population demography of endangered Micronesian kingfishers (Todiramphus cinnamominus). We provided the first demographic parameter estimates for any of the 12 endangered Pacific Todiramphus species, and used results to develop a population projection matrix model for management throughout the insular Pacific. Further, we used the model for elasticity and simulation analyses with demographic values that randomly varied across ranges that might characterize congener populations. Results from elasticity and simulation analyses indicated that changes in breeding adult survival exerted the greatest magnitude of influence on population dynamics. However, changes in nestling survival were more consistently correlated with population dynamics as demographic rates were randomly altered. We concluded that conservation practitioners working with endangered Pacific kingfishers should primarily focus efforts on factors affecting nestling and breeder survival, and secondarily address fledgling juveniles and helpers. Further, we described how the generalized base model might be changed to focus on individual populations and discussed the potential application of multi-species models to other conservation situations. ?? 2007 Elsevier Ltd. All rights reserved.

Biological Conservation↗
USGS2007

Territoriality, prospecting, and dispersal in cooperatively breeding Micronesian Kingfishers ( Todiramphus cinnamominus reichenbachii )

We investigated territoriality, prospecting, and dispersal behavior in cooperatively breeding Pohnpei Micronesian Kingfishers ( Todiramphus cinnamominus reichenbachii ) throughout the annual cycle using radiotelemetry and color-band resights. Mean home-range size was 6.3 ha and territories were 8.1 ha. Within territories, Micronesian Kingfishers shared 63% of their home-range space with coterritorial occupants, and 3% was shared with extraterritorial conspecifics. Birds on cooperative territories had larger home ranges that overlapped more with coterritory occupants' home ranges than birds in pair-held territories. Despite evidence suggesting that resources necessary for survival and reproduction occurred on each territory, Micronesian Kingfishers of all age and sex classes made extraterritorial prospecting movements. Prospecting was rare; it comprised only 4.3% of our observations. When birds departed on forays, they were gone for ∼1.9 h and returned to home territories before sunset. Prospecting by dominant birds was temporally correlated with courtship and nest initiation, and birds were observed at neighboring nest sites with opposite-sex conspecifics during the period when females were available for fertilization. Juveniles and helpers prospected throughout the year and made repeated homesteading movements to dispersal destinations before dispersing. Mean dispersal distance for radiomarked individuals was 849 m. Results suggest that prospecting in Micronesian Kingfishers is a complex behavior that provides information for dispersal decisions and familiarity with dispersal destinations. Additionally, extraterritorial movements may provide covert opportunities for reproduction, which have potential to profoundly influence the distribution of fitness among helper and dominant Micronesian Kingfishers.

The Auk↗
USGS2006

Phylogeography and spatial genetic structure of the southern torrent salamander: Implications for conservation and management

The Southern torrent salamander ( Rhyacotriton variegatus ) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.

Oregon, Washington↗
USGS2006

Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act

The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

Conservation Biology↗
USGS2005

Taxonomic relationships among Phenacomys voles as inferred by cytochrome b

Taxonomic relationships among red tree voles (Phenacomys longicaudus longicaudus, P. l. silvicola), the Sonoma tree vole (P. pomo), the white-footed vole (P. albipes), and the heather vole (P. intermedius) were examined using 664 base pairs of the mitochondrial cytochrome b gene. Results indicate specific differences among red tree voles, Sonoma tree voles, white-footed voles, and heather voles, but no clear difference between the 2 Oregon subspecies of red tree voles (P. l. longicaudus and P. l. silvicola). Our data further indicated a close relationship between tree voles and albipes, validating inclusion of albipes in the subgenus Arborimus. These 3 congeners shared a closer relationship to P. intermedius than to other arvicolids. A moderate association between porno and albipes was indicated by maximum parsimony and neighbor-joining phylogenetic analyses. Molecular clock estimates suggest a Pleistocene radiation of the Arborimus clade, which is concordant with pulses of diversification observed in other murid rodents. The generic rank of Arborimus is subject to interpretation of data.

Journal of Mammalogy↗
USGS2004

Seasonal movement and home range of the Mariana Common Moorhen

Adult Mariana Common Moorhens ( Gallinula chloropus guami ) were radio-marked on Guam (n = 25) and Saipan (n = 18) to determine home range, inter- and intraseasonal space use, and movement patterns among the Mariana Islands of Guam, Saipan, Tinian, and Rota. Birds were tracked throughout the dry and wet seasons in 2000 and 2001. During the dry season, no interisland movements were detected and most birds remained at a single wetland. However, some radio-marked adults on Guam (48%) and Saipan (11%) dispersed from their capture site to other wetland sites. Inter-and intraisland movements increased during the wet season. Interisland movement from Saipan to Tinian occurred at the onset of the wet season, although no birds were observed moving off Guam. Radio-marked adults on Guam (71%) and Saipan (70%) dispersed from their capture site to other wetlands. On Guam, moorhens moved farther in the wet season than the dry season. During the wet season frequency of movement among sites was inversely proportional to the average distance between wetlands. Guam moorhens used rivers more often during the wet season. Among nine dispersing adult moorhens captured during the wet season on Fena Reservoir, Guam, 67% returned to Fena Reservoir during the 2001 dry season. Home-range estimates on Guam averaged 3.1 ± 4.8 ha (SD) and did not differ significantly between sexes or seasons. However, during the dry season, females exhibited significantly smaller mean core areas than males.

Mariana Islands↗
USGS2003

Use of radar remote sensing (RADARSAT) to map winter wetland habitat for shorebirds in an agricultural landscape

Many of today's agricultural landscapes once held vast amounts of wetland habitat for waterbirds and other wildlife. Successful restoration of these landscapes relies on access to accurate maps of the wetlands that remain. We used C-band (5.6-cm-wavelength), HH-polarized radar remote sensing (RADARSAT) at a 38?? incidence angle (8-m resolution) to map the distribution of winter shorebird (Charadriiformes) habitat on agricultural lands in the Willamette Valley of western Oregon. We acquired imagery on three dates (10 December 1999, 27 January 2000, and 15 March 2000) and simultaneously collected ground reference data to classify radar signatures and evaluate map accuracy of four habitat classes: (1) wet with ??? 50% vegetation (considered optimal shorebird habitat), (2) wet with > 50% vegetation, (3) dry with ??? 50% vegetation, and (4) dry with > 50% vegetation. Overall accuracy varied from 45 to 60% among the three images, but the accuracy of focal class 1 was greater, ranging from 72 to 80%. Class 4 coverage was stable and dominated maps (40% of mapped study area) for all three dates, while class 3 coverage decreased slightly throughout the study period. Among wet classes, class 1 was most abundant (30% coverage) in December and January, decreasing in March by 15%. Conversely, class 2 increased dramatically from January to March, likely due to transition from class 1 as vegetation grew. This approach was successful in detecting optimal habitat for shorebirds on agricultural lands. For modest classification schemes, radar remote sensing is a valuable option for wetland mapping in areas where cloud cover is persistent. ?? 2003 Springer-Verlag New York Inc.

Environmental Management↗