• Application of environmental DNA-based occurrence data in modeling wood frog (Rana sylvatica) distribution in Interior Alaska

      Spangler, Mark A.; López, J. Andrés; Huettmann, Falk (2017)
      Knowledge of wood frog distribution in Alaska is incomplete due to insufficient baseline occurrence data. A short season of activity and difficult access to remote areas restrict implementation of consistent monitoring efforts. Detecting the presence of species in aquatic landscapes using environmental DNA (eDNA) assays is increasingly applied as a monitoring method in wildlife surveys. However, uncertainties regarding the technique’s sensitivity to environmental variables and human error have thus far prevented its widespread adoption in studies of species distribution. Predictive models built on machine learning algorithms can help provide precise descriptions of species distribution using eDNA occurrence data, but they will require ground-truthing efforts to confirm accuracy in under-sampled landscapes. Here we assess the ability of wood frog eDNA occurrence data to inform species distribution models under five criteria for data use. We sampled 60 wetlands for eDNA in the Fairbanks North Star Borough during summer 2015. Samples were processed using a species-specific quantitative PCR assay. Wood frog presence at each site was inferred from the PCR results. This data was used to construct four different wood frog distribution models. From each model we produced a predictive distribution map encompassing the Fairbanks North Star Borough. We assess the performance of each model using available wood frog presence data. Our highest performing model achieves moderate predictive accuracy (Area Under the Curve = 0.74). Weak signals in eDNA occurrence data are important in revealing species presence at low abundance, but strict lab hygiene, quality control practices, and detailed metadata are needed to retain confidence in the results. We show a powerful new way to study wood frog distribution by combining eDNA occurrence data with machine learning techniques. Wider implementation of eDNA surveys and increased availability of high resolution GIS data will help to refine these models.
    • Birding Data for Costa Rica

      Huettmann, Falk (2009)
      These data describe 703 species with geo-referencing information (latitude longitude) for 42 locations in Costa Rica. They are taken from the species lists presented in B. Lawson (2009; A bird-finding guide to Costa Rica. Comstock Publishing Associates and Cornell University Press. ISBN 978-0-8014-7584-9). This database is based on extensive fieldwork by B. Lawson and as described in his book. Here, these extensive species list data got geo-referenced via Google Maps. The resulting database described here consist of 4,829 rows and 8 columns (Page No,Site No,Site Name, latitude, longitude, SpeciesNo,SpeciestoExpect,Source) and is 969KB in size. The following locations were sampled: Arenal Volcano National Park, Bosque de Paz Biological Reserve and Lodge, Bosque del Rio Tigre, Braulio Carrillo National Park, Cabo Blanco Absolute Nature Reserve, Cano Negro National Refuge, Carara National Park, Cerro de la Muerte, Diria National Park, El Copal Biological Reserve, El Rodeo (University for Peace), Esquinas Rainforest Lodge, Irazu Volcano National Park, Kekoldi Hawk Watch, Km 70 (route 2), La Ensenada Wildlife Refuge, La Paz Waterfal Gardens, La Selva Biological Station, Laguna del Lagarto Lodge, Lankester Gardens, Las Alturas, Las Cruces Biological Station, Las Heliconias Lodge, Manuel Antonio National Park, Marenco Beach and Rainforest Lodge, Monteverde Cloud Forest Reserve, Oro Verde Biological Reserve, Palo Verede National Park, Poas Volcano National Park, Rancho Naturalista, Rara Avis Rainforest Lodge, Rincon de la Vieja National Park, Rio Negro, San Gerardo de Dota, Santa Rosa National Park, Selva Bananito Lodge, Talari Mountain Lodge, Tapanti National Park, The Coastline, The University of Costa Rica, Tortuguero National Park, Virgen del Socorro.
    • Compiled occurrence data of migratory Hooded Cranes in Southeast Asia

      Cai, T.; Guo, Y.; Huettmann, F.; Lee, K. (Beijing Forestry University, Beijing China, 2015-01-01)
      This dataset represents the best available science-based ocurrences (presence only) of Hooded Cranes during fall and spring migration along the flyway in Asia. This dataset consists of 115 geo-referenced sightings with the source/observer in a comma delimited file format. The geo-referencing was done in decimal latitude and longitude with six decimals. Each record carries a source information and is derived from 21 sources. The biggest data sections come from field obervations of the local authors as well as GBIF, satellite telemetry, and Higuchi (1994) and Chang (1999). This data set has four columns and 115 rows with a size of 30KB.
    • Compiled Rabies and Trichinosis (presence only) outbreak data for Alaska

      Waltuch, Rebekah (2014-09-01)
      These are two data sets that were compiled during a UAF student research project, Landscape Ecology class 469/669 (eLearning). They represent a value-added data set and can easily be mapped in a Geographic Information System (GIS) etc. For rabies in Alaska, 237 confirmed cases were found of which 158 had complete information (year, coordinates and vector). The rabies cases in this database are from 1914 til 2013; vectors include Dog, Wolf, Red Fox, Coyote, Arctic Fox, Cat, Caribou, Little Brown Bat, Keen's Myotic Bat and Wolverine. The Alaskan trichinosis data cover 1976-2012 and with various details. Species covered are: Walrus Black Bear, Brown Bear, Bear (unspecified) and Polar Bear. These are student project data compiled from various accessible sources (e.g. the State of Alaska Epidiology website <http://www.epi.hss.state.ak.us> and references cited in the Methods), and they are incomplete. However, they can be used for predictive modeling and similar studies and investigations.
    • Development, validation, and evaluation of an assay for the detection of wood frogs (Rana sylvatica) in environmental DNA

      Spangler, Mark A.; Huettmann, Falk; Herriott, Ian C.; López, J. Andrés (Springer, 2017)
      We developed and describe a qPCR assay for the detection of wood frogs (Rana sylvatica) using environmental DNA (eDNA) sampling. A single primer set was designed to amplify a 115-bp region of the wood frog cytochrome B gene and assessed for target specificity. There was no evidence of amplification in eleven non-target species. We evaluated the utility of the primer set in qPCR assay by conducting geo-referenced eDNA field surveys in Interior Alaska. Results indicate that the assay consistently detects wood frog DNA in the environment to 1.83x10-3 pg/μL. The assay provides a complement to traditional survey methods and can be readily applied in a wider conservation and management context.
    • Distribution of White Spruce in Alaska. An Open Access prediction surface from climatic and bioclimatic parameters using ESRI GRID formats.

      Huettmann, Falk (Bettina Ohse, Falk Huettmann, Steffi Ickert-Bond, 2008)
      This open access data set contains a spatially gridded distribution of White Spruce in Alaska (ESRI GRID format), predicted from climatic and bioclimatic parameters (temperature, precipitation, elevation, and aspect). A species distribution model, developed by Bettina Ohse, was used to determine the ecological niche of the species based on the environmental variables. The model was developed within TreeNet, a classification and regression tree software. The ecological niche was then projected into geographical space, resulting in a predictive map of the species distribution in Alaska (4km resolution, tested accuracy of c. 95 %). We used ArcGIS 9.2. Data sources were freely available for the global public, and so were all tools used (prediction algorithms and specific GIS tools). We promote these data and this concept as a role model how to model plant distributions in wilderness areas and for overcoming data gaps in species distributions world-wide. We encourage the use and update of these data for further updating of this concept and its findings.
    • Geo-referenced and documented red squirrel (Tamiasciurus hudsonicus) midden sites from 2016 and 2017 in a highly used forest area behind the University of Alaska, Fairbanks

      Huettmann, Falk; Robold, Richard; Adams, R. (EWHALE Lab, University of Alaska Fairbanks, 2017)
      This dataset consists out of 29 presence points of red squirrel (Tamiasciurus hudsonicus, Taxonomic Serial No.: 180166) midden sites. Data was collected in a highly human-used forest area behind the University of Alaska, Fairbanks for summer 2016 (n= 29) and winter/spring 2017 (n=20).The data set consists of an ESRI shapefile for each year. Data was collected in two consecutive years (2016-2017). The first set of data points (summer 2016) was collected with a land cruising survey design and recorded with a GPS unit, based on an opportunistic course project work by R. Adams. The second data collection campaign took place in spring 2017 to check whether the squirrel midden sites from 2016 are still in use (data collected by R. Robold). The coordinate system is decimal degree (5 decimals) and with a geographic projection NAD_1983_Alaska_Albers. The excel sheet has five columns (site ID, a short description of the vegetation, latitude, longitude, and one if the middens are still used in 2017); the excel document (midden_data_with_control.xlsx) size is 10 KB (2017). The map is a JPEG-file (Midden_sites_2016-27_RR) with a size of 3MB and the shapefiles have an overall size of ca. 50 KB each. This data set is the basis for ongoing study on squirrels in the boreal forest and urban areas.
    • GRID habitat plot survey data for the nesting sea turtles beach La Flor beach, Pacific, southwestern Nicaragua July of 2013

      Huettmann, Falk (Maderas Rainforest Conservancy, 2013-07-29)
      This GRID habitat plot survey was done at a globally relevant sea turtle nesting beach: La Flor (latitude 11.14282, longitude 85.79418, geographic datum WGS84). This sand beach is located at the Pacific Ocean in southwestern Nicaragua, approx. 20 km far from San Juan Del Sur and approx. 30 km far from the Costa Rican border. We did our grid-based habitat survey on the 11th of July in 2013. The GRID points are geo-referenced by latitude and longitude (decimal degrees, WGS84, +- 10 meters acuracy) and were visited only once (no 3 repeats were done because it consists of sand and private/reserve property) and no species information is provided (sand beach). From 25 regular GRID points 13 were inaccessable because of reserve land holdings or dense bush forests. We took three photos (sky, ground vertical view) for every plot, more details can be seen there. This grid can be used for change detection, shoreline location, develeopment questions, and beach erosion questions over time for turtle nest habitat, for instance. Known sea turtles for this region are predominately Olive`s Ridley sea turtle (Lepidochelys olivacea, TSN 173840), but also Hawksbill (Eretmochelys imbricata TSN 208666) and Leatherback sea turtle (Dermochelys coriacea, TSN 173843).
    • GRID survey habitat data for Playa el Coco beach (nesting sea turtles) - Pacific, southwestern Nicaragua July of 2013

      Huettmann, Falk (Maderas Rainforest Conservancy, 2013-07-29)
      This GRID survey was done at the beach of Playa de Coco - near a globally relevant sea turtle nesting beach (La Flor). Playa el Coco (latitude 11.15382, longitude 85.80051, geographic datum WGS84) is situated at the Pacific Ocean in southwestern Nicaragua, approx. 20 km far from San Juan Del Sur and approx. 30 km far from the Costa Rican border, just adjacent to La Flor. We did our grid-based habitat survey on 8th and 9th of July in 2013. The GRID points are geo-referenced by latitude and longitude (decimal degrees, WGS84, +- 10 meters acuracy) and were visited only once (no 3 repeats because it consists of sand and private property) and no species information (mostly empty sand beach). From 25 regular GRID points 9 were inaccessable because of private land holdings or very bushy forests. We took photos for every point (horizontal, vertical, sky), more details can be seen there. This grid can be used for change detection, shoreline location, develeopment, and beach erosion questions over time for turtle nest habitat, for instance. Known sea turtles for this region are predominately Olive`s Ridley turtle (Lepidochelys olivacea, TSN 17384), other species could potentially occur too. On the beach, we also detected Black-throated Magpie-Jay Calocitta colliei 558992, Balck Vulture Coragyps atratus 175272, Groove-billed Ani Crotophaga sulcirostris 177839, Great Kiskadee Pitangus sulphuratus 178301, Magnificent Frigate Bird Fregata magnificens 174763, Black Oystercatcher Haematopus bachman 176475, Sooty Tern Onychoprion fuscatus 824105, Brown Pelican Pelecanus occidentalis 174685, Neotropical Cormorant Phalacrocorax brasilianus 554375 and Banded Wren Thryothorus pleurostictus 563460). This dataset is an MS Excel format and less than 1MB in size.
    • GRID-based habitat plot data for the public nesting sea turtle beach of Pacuare, Caribean Sea, Costa Rica July of 2013

      Huettmann, Falk (Maderas Rainforest Conservancy, 2013-07-29)
      This GRID habitat survey was done at a globally relevant public sea turtle nesting beach: Pacuare (Playa Vigilada). It is situated at the Caribean Sea in Costa Rica ((latitude10.20123 longitude 83.25925; geographic datum WGS84). We did our grid-based habitat survey on 18th of July in 2013. The individual GRID points are geo-referenced by latitude and longitude (decimal degrees, +- 10 meters acuracy) and were visited only once (no 3 repeats because it consists of sand and private property) and no species information was taken (sand beach habitat). From 25 regular GRID points 15 were inaccessable because the nearby jungle and reserve. We took photos for every point (horizontally, ground and sky), more details can be seen there. This grid can for instance be used for change detection, shoreline location, develeopment, and beach erosion questions over time for turtle nest habitat. Known and observed sea turtles to occur for this region are Leatherback sea turtle (Dermochelys coriacea TSN 173843), and presumably Hawksbill sea turtle (Eretmochelys imbricata TSN 208666) and the Green sea turtle (Chelonia mydas TSN 173833). This dataset is in an MS Excel format and is less than 1MB in size.
    • Macro description of public beach attributes that may effect turtle nesting in Playa de Coco, La Flor (Pacific, southwest Nicaragua) and Pacuare and Tortuguero, (Caribbean, Costa Rica), July 2013

      Huettmann, Falk (Maderas Rainforest Conservancy, 2013-07-29)
      We observed several macro beach features of four public sea turtle nesting beaches for Playa Coco (latitude11.15382, longitude 85.80051; geographic datum WGS84) and La Flor (latitude 11.14282, longitude 85.79418) in southwest Nicaragua (Pacific), and Pacuare Reserve (latitude10.20123, longitude, 83.25925) and Tortugero (latitude 10.59583, longitude 83.52520) in Costa Rica (Caribbean). Recorded features included the intensity of tourism, number of different predator species of sea turtle hatchlings, number of tourists, and line transects for density of plastic, wood, metal, and crab burrows. Light and sound disturbances at night were also recorded as well as man-made objects left overnight on the shore of the beaches. This data set is part of a sea turtle class with Maderas Rainforest Conservancy and provides a basic and non-invasive description and a snap shot in time and space for public nesting beaches of relevance for Olive Ridley (Lepidochelys olivacea, TSN 173840), Green (Chelonia mydas TSN 173833), Hawksbill (Eretmochelys imbricata TSN ) and Leatherback (Dermochelys coriacea TSN 173843 ) sea turtles. Some photos were taken for vizualisation purposes.
    • Marine boat surveys for the olive ridley sea turtle (Lepidochelys olivacea) off of the coast of La Flor Playa de Coco, Nicaragua, 9th and 13th July 2013

      Huettmann, Falk (2013-07)
      Two marine monitoring boat surveys were conducted off the coasts of La Flor and Playa de Coco, southwest Nicaragua. Single and mating pairs of Olive Ridley sea turtles (Lepidochelys olivacea, TSN 1738400), were observed and activity and geo-referencing recorded with a GPS (decial latitude and longitude, geographic datum WGS84). Single turtles were seen basking and breathing at the surface of the water and subsequently would dive into the water. Mating pairs were also observed. Males held onto the females via a hook on the front flippers, scars were observed but no tumors were detected. Some photos were taken for visualisation.
    • Marine surveys (at sea and 16 ports) of Atlantic seabirds, passerines and marine mammals during Semester at Sea cruise fall 2014

      Huettmann, Falk (2014-12-08)
      This data set was collected during the Fall 2014 cruise with Semester at Sea (SAS). It covers 2 MS Excel files of marine species surveys (three worksheets: opportunistic 5 minutes, and Distance Sampling 10 minutes, Individual Sightings) as well as harbour species surveys (one file with one worksheet). The SAS cruise of fall 2014 took place in the Atlantic, southern Baltic, the Mediterrean and Caribbean Seas and has the following bounding box coordinates (decimal degrees of latitude and longitude WGS 1984): Highest latitude 59.88929 North, lowest latitude -22.28687 South, most western longitude -81.80984, most eastern longitude -40.91894. The following 16 ports were covered: Southampton (UK), St. Petersburg (Russia), Gdansk (Poland), Rostock (Germany), Antwerp (Belgium), Le Havre (France), Dublin (Ireland), Lisbon (Portugal), Cadiz (Spain), Casablanca (Morocco), Citivecchia (Italy), Barcelona (Spain), Rio De Janeiro (Brazil), Salvador (Brazil), Bridgetown (Barbados), Havanna (Cuba) and Fort Lauderdale (Florida US). The starting date was August 21st and the ending date was Dec 7th 2014. The cruise included app. 632 students and 380 staff and crew (including professors). This dataset includes data from opportunistic 5 minute surveys ('presence only'), as well as 10minute long Distance Sampling surveys (abundances) done 2-3 times per day. All data are geo-referenced. In addition, many additional individual sigthings by the shipboard community and local excursion (terrestrial) data are also included, photos were collected whenever possible. Additional data like state of the ocean, plastic pollution, vessels in view, and weather were also collected. This data set can serve as a basic quantitative large-scale snapshot for the Atlantic region and its ecosystem in fall 2014. The 5 minute-long opportunistic at-sea surveys featured app 102 species; more species were detected in the other surveys. Most of these species are seabirds, with a few mamrine mammals, squid, fish sightings etc. Noteworthy are the high ocurrences of passerines at sea! This dataset has maximum 29 columns, and 314 rows (5 minute Opportunistic Survey), 146 rows (10min abundance surveys) and 271 rows (Individual Opportunistic Sightings); it is <1MB in size. A few photos exist and can be obtained upon request.
    • Marine turtle nesting track survey on Playa de Coco, Nicaragua, and Playa Vigilada (Pacuare) and Tortuguero, Costa Rica, July 2013

      Huettmann, Falk (Maderas Rainforest Conservancy, 2013-07)
      Marine turtle tracks were observed on the beaches of Playa de Coco (Pacific, southwest Nicaragua; latitude 11.15382 , longitude 85.80051; WGS 84 ), Playa Vigilada (Pacuare; latitude 10.20123, longitude 83.25925) and Tortuguero (Caribbean, Costa Rica; latitude 10.59583, longitude 83.52520) during the early morning hours. Number of sea turtle tracks were counted along a transect. This was done by walking along the shore every morning to look for specific tracks that matched the tracks of sea turtle species. Maximum number of tracks observed was 8, while the minimum number obsereved was 0. Tracks had distinct features with flipper tracks visible on the edges of the tracts with a single line down the middle were the tail would drag. Tracks were seen to go straight onto the shore while some came up the shore and curved slightly before going back to the ocean. Tracks were observed near resturants and hotels. We observed Olive Ridely sea turtle (Lepidochelys olivacea, TSN 173840) in Playa de Coco, hatchling Leatherback sea turtles (Dermochelys coriacea, TSN 173843), and Green sea turtles (Chelonya mydas, TSN173833) in Playa Vigilada and Tortuguero,
    • Micro-habitat description of sea turtle nests on three public nesting beaches in LaFlor (Pacific) southeast Nicaragua, and Pacuare Reserve and Tortuguero (Caribbean) Costa Rica during July 2013

      Huettmann, Falk (Maderas Rainforest Conservancy, 2013-07)
      Descriptions of the micro habitat of sea turtle nests were recorded on three public beaches: La Flor (latitude 11.14282, longitude 85.79418, Pacific) in southwest Nicaragua, and Pacuar Reserve (latitude10.20123 longitude 83.25925), and Tourtuguero (latitude 10.59583, longitude 83.52520) at the Caribbean coast of Costa Rica. Species covered are the Olive Ridley sea turtle (Lepidochelys olivacea, TSN 173840), Leatherback sea turtle (Dermochelys coriacea TSN 173843), and presumably Hawksbill sea turtle (Eretmochelys imbricata TSN 208666) and the Green sea turtle (Chelonia mydas TSN 173833). After a nest was identified during night and the turtle left successfully, next day the following micro-habitat attributes were collected with dates: distance from waterline, distance from treeline, slope of beach, nearest known nest, and tree height. The presence of egg shells, tree canopy cover, vegatation type, occurence of plastic and driftwood were also recorded, as well as a description of the sand. Geo-referencing of nests was done with a GPS using decimal latitude and longitude (geographic datum of WGS84). This dataset consists of an MS Excel sheet and is <1MB in size. Some photos are also provided for visual purposes.
    • Minimal covers of the Archimedean tilings, part II Appendices

      Williams, Gordon; Pellicer, Daniel; Mixer, Mark (2013-01-18)
      These files contain a full descriptions of the relations in the presentations of the monodromy groups for the (3.3.4.3.4), (3.3.3.4.4), (4.6.12), and (3.3.3.3.6) tilings. This material was prepared to provide additional material or the possibility of verification of our work for the interested reader of the associated article.
    • Nest and attribute data for 24 Hooded Cranes (Grus monacha) and control plots from field surveys in Northeast China 1993-2010

      Huettmann, Falk (Yu Guo, S. Jiao and colleagues, 2013-05-31)
      This dataset conists of 24 nests and their environmental attributes for the Hooded Crane (Grus monarcha, taxonomic serial number TSN 176186, Avibase ID38F36091DBC85095) in China. It is a legacy dataset, presents the best available information, and covers 9 years of survey work (time window 1993-2010). The Hooded Crane is a vulnerable (VU) species according to the IUCN Red list. The estimated world population of this species is just 10,160 individuals, of which more than 8,000 winter in Izumi, Japan. The Hooded Crane breeds in landscapes of Eastern Russia and Northeastern China. It generally nests in forest swamps, mostly within the permafrost zone. This data set can be used for nest preference studies and is available as an Open Office, ASCII or MS Excel format data sheet. The following environmental attributes have been collected for nests as well as for 81 control plots: elevation (in Meters), aspect (in Degrees), slope position (in degrees), distance to the nearest tree (Meters), distance to the nearest road (meters), distance to the nearest human settlement (Meters), distance to the nearest feeding site (Meters), distance to the nearest skidding road (Meters), water surface area around the nest (Square Meters), average water depth around the nest (Centimeter), canopy coverage (Percent), shrub coverage (Percent), grass coverage (Percent). number of trees (Count).
    • Non-invasive nocturnal surveys of sea turtle nesting beaches at La Flor (Pacific) Nicaragua, and Pacuare Reserve and Tortuguero (Caribbean) Costa Rica, July 2013

      Huettmann, Falk (Maderas Rainforest Conservancy, 2013-07)
      Marine turtles on the nesting beaches of La Flor public beach (latitude11.14282, longitude 11.14282, geographic datum WGS84), Pacific Nicaragua, and Pacuare Reserve public beach (latitude 10.20123, longitude 83.25925) and Tortuguero (latitude 10.59583, longitude 83.52520) , Caribbean, Costa Rica were observed during late hours after sunset. Observations where noninvasive, geo-referenced and observers stayed three meters away from the sea turtles, according to the national requirements (no light, and some limited red light was used for field clarifications). Many surrounding attributes were taken into consideration and measured including date, time, species, location, observed cysts present in the facial region, visually estimated carapace length, other disturbances present on the beach, number of people/tourists and dogs present, plastic encountered, and if applicable, start and end time of specific activities of nesting (such as start of nest time, start of egg laying and start of Ridley dance.) These data are part of a citizen science project and from a sea turtle fieldclass with Maderas Rainforest Conservancy. This dataset consists of an MS Excel sheet and is less than 1MB in size. Some photoes were taken to present the beaches and procedures.