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Conservation Genetics
Birds

Samples of genetics and genomics research from the USGS Ecosystems Mission Area about the conservation genetics of birds.

Photo: The Yellow Rail (Coturnicops noveboracencis) is among the most enigmatic and least studied North American birds. Photo credit: © 2010 Susan Haig, USGS. Photo: The Yellow Rail (Coturnicops noveboracencis) is among the most enigmatic and least studied North American birds. Photo credit: © 2010 Susan Haig, USGS. Photo: Micronesian kingfisher. Photo credit: Susan Haig, USGS. Photo: The Least Tern (Sternula antillarum) has undergone large population declines over the last century as a result of direct and indirect anthropogenic factors. Photo credit: © 2010 Susan Haig, USGS.
Variation in Migratory Behavior Influences, American Kestrel Populations (Miller, Haig) Population Bottlenecks and Subtle Genetic Structure in the Yellow Rail (Miller, Haig) Microsatellite recovery using massively parallel sequencing (Haig) Status and Population Genetic Structure of Least Terns (Miller, Haig)
Photo: The Least Tern (Sternula antillarum). Photo credit: Rob Bennetts. American Avocet (Recurvirostra americana) Gunnison sage grouse (Centrocercus minimus). Photo credit: Copyright Robert Bennetts Broad-tailed Hummingbird female (Selasphorus platycerus). Photo credit: San Andres National Wildlife Refuge, USFWS
Decreased Genetic diversity in Least Terns (Haig) Birds and their Prey, Climate Change, and the Great Basin Wetlands (Haig, et al.)

Gunnison Sage-grouse: Population Genetics (Oyler-McCance)

Broad-tailed Hummingbird (Oyler-McCance)
Greater sage grouse. Photo credit: Gary Kramer/USFWS Gunnison sage grouse (Centrocercus minimus). Photo credit: Copyright Dick Williams Mountain plover. Photo credit: Fritz Knopf Kirtland's warbler. Photo credit: D.K. Dawson
Greater Sage-grouse (Oyler-McCance) Gunnison Sage-grouse: Mark-Recapture (Oyler-McCance) Mountain Plover (Oyler-McCance) Kirtland's Warbler (King)
Lesser prairie-chicken (Typmanuchus pallidicinctus). Photo credit: U.S. Fish and Wildlife Service Micronesian kingfisher. Photo credit: Copyright John White Spotted owl Piping Plover. Copyright Paul J. Fusco
Lesser Prairie-chicken (Oyler-McCance) Micronesian Kingfisher (Haig) Spotted Owl (Haig) Piping Plover (Miller)
Endangered Puerto Rican parrot. Photo credit: Tom MacKenzie, USFWS Adult western snowy plover. Photo credit: Courtesy of Morgan Ball Spotted owl Barred owl in a tree along Skyline Drive. Photo credit: Eric Butler, NPS
Puerto Rican Parrot (Haig) Snowy Plover (Haig) Jabiru stork (Jabiru mycteria) (Haig) Spotted/Barred Owl Hybrid (Haig)
Trumpeter swans. Photo credit: NPS photo by Bill Wise White-tailed ptarmigan. Photo credits: Rocky Mountain National Park    
Trumpeter Swan (Oyler-McCance) White-tailed Ptarmigan (Oyler-McCance)    

Variation in Migratory Behavior Influences Regional Genetic Diversity and Structure among American Kestrel Populations (Falco sparverius) in North America
Photo: American kestral (Falco sparverius). Photo credit: Susan Haig, USGS.

Photo: American kestral (Falco sparverius). Photo credit: Susan Haig, USGS.

Birds employ numerous strategies to cope with seasonal fluctuations in high-quality habitat availability. Long distance migration is a common tactic; however, partial migration is especially common among broadly distributed species. Under partial migration systems, a portion of a species migrates, whereas the remainder inhabits breeding grounds year round. Researchers identified effects of migratory behavior variation on genetic structure and diversity of American Kestrels (Falco sparverius), a widespread partial migrant in North America. American Kestrels generally migrate; however, a resident group inhabits the southeastern United States year round. The southeastern group is designated as a separate subspecies (F. s. paulus) from the migratory group (F. s. sparverius). Using mitochondrial DNA and microsatellites from 183 and 211 individuals, respectively, researchers illustrated that genetic structure is stronger among nonmigratory populations, with differentiation measures ranging from 0.060 to 0.189 depending on genetic marker and analysis approach. In contrast, measures from western North American populations ranged from 0 to 0.032. These findings suggest that seasonal migratory behavior is also associated with natal and breeding dispersal tendencies. Researchers also detected significantly lower genetic diversity within nonmigratory populations, reflecting the greater influence of genetic drift in small populations. Differentiation of F. s. paulus and F. s. sparverius reflected subtle differences in allele frequencies. Because migratory behavior can evolve quickly, the analyses suggest recent origins of migratory American Kestrel populations in North America.  Mark P. Miller  (mpmiller@usgs.gov) Sue Haig  susan_haig@usgs.gov  http://jhered.oxfordjournals.org/content/early/2012/05/04/jhered.ess024.full?keytype=ref&ijkey=k8t8xNOfwN7xptd

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Multiplexed microsatellite recovery using massively parallel sequencing
Photo: Micronesian kingfisher. Photo credit: Susan Haig, USGS.

Photo: Micronesian kingfisher. Photo credit: Susan Haig, USGS.

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotypingmethod 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 356 958 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 $0.5 M(USD). Susan M. Haig (susan_haig@usgs.gov)

Title of the related publication: Jennings, T.N., B.J. Knaus, T.D. Mullins, S.M. Haig, and R.C. Cronn. 2011. Multiplexed microsatellite recovery using massively parallel sequencing. Molecular Ecology Resources (online).

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Subspecific Status and Population Genetic Structure of Least Terns (Sternula Antillarum) Inferred by Mitochondrial DNA Control-Region Sequences and Microsatellite DNA
Photo: The Least Tern (Sternula antillarum) has undergone large population declines over the last century as a result of direct and indirect anthropogenic factors. Photo credit: © 2010 Susan Haig, USGS.

Photo: The Least Tern (Sternula antillarum) has undergone large population declines over the last century as a result of direct and indirect anthropogenic factors. Photo credit: © 2010 Susan Haig, USGS.

The taxonomic identity of endangered populations of the Least Tern (Sternula antillarum) has long been debated. Their current conservation status provides even more impetus to examine the taxonomic distinctness of these groups. We used rapidly evolving mitochondrial DNA control-region sequences (840 base pairs; n = 188) and microsatellite DNA data (7 loci; n = 417) to examine genetic structure within and among three subspecies that occur within the United States: California Least Tern (S. a. browni), Interior Least Tern (S. a. athalassos), and Eastern Least Tern (S. a. antillarum). Although significant genetic structure was observed among breeding populations from across the species’ range, the data indicated little evidence of genetic structure within traditional subspecific groups. Isolation-by-distance analyses, however, identified subtle patterns that may reflect sex-specific differences in dispersal behavior. The analyses likewise demonstrated little population subdivision among subspecific groups, which raises questions regarding the taxonomic status of traditionally defined subspecies. Our findings can therefore be used to consider a reevaluation of Least Tern subspecies by the American Ornithologists’ Union’s Committee on Taxonomy and Nomenclature. There remains a need for studies of range-wide breeding-site fidelity and natal philopatry to better understand interpopulation movements of individuals throughout the annual cycle. Mark P. Miller (mpmiller@usgs.gov), Susan M. Haig (susan_haig@usgs.gov) Draheim, H.M., M.P. Miller, P.B. Baird, and S.M. Haig. 2010. Subspecific status and population genetic structure of Least Terns (Sternula antillarum) inferred by mitochondrial DNA control region sequences and microsatellite DNA. Title of the related publication: Auk 127: 807-81

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Temporal analysis of mt DNA variation reveals decreased genetic diversity in Least Terns
Photo: The Least Tern (Sternula antillarum). Photo credit: Rob Bennetts.

Photo: The Least Tern (Sternula antillarum). Photo credit: Rob Bennetts.

The Least Tern (Sternula antillarum) has undergone large population declines over the last century
as a result of direct and indirect anthropogenic factors. The genetic implications of these declines are unknown. Historical museum specimens (pre-1960) and contemporary (2001–2005) samples were used to examine range-wide phylogeographic patterns and investigate potential loss in the species’ genetic variation. We obtained sequences (522 bp) of the mitochondrial gene for NADH dehydrogenase subunit 6 (ND6) from 268 individuals from across the species’ range. Phylogeographic analysis revealed no association with geography or traditional subspecies designations. Potential reductions in genetic diversity were detected in contemporary samples from California and the Atlantic coast Least Tern from that in historical samples, suggesting that current genetic diversity in Least Tern populations is lower than in their pre-1960 counterparts. Results offer unique insights into changes in the Least Tern’s genetic diversity over the past century and highlight the importance and utility of museum specimens in studies of conservation genetics. Susan M. Haig (susan_haig@usgs.gov) Link to related publication http://fresc.usgs.gov/products/papers/1743_Draheim.pdf

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Evidence for Population Bottlenecks and Subtle Genetic Structure in the Yellow Rail
Photo: The Yellow Rail (Coturnicops noveboracencis) is among the most enigmatic and least studied North American birds. Photo credit: © 2010 Susan Haig, USGS.

Photo: The Yellow Rail (Coturnicops noveboracencis) is among the most enigmatic and least studied North American birds. Photo credit: © 2010 Susan Haig, USGS.

The Yellow Rail (Coturnicops noveboracencis) is among the most enigmatic and least studied North American birds. Nesting exclusively in marshes and wetlands, it breeds largely east of the Rocky Mountains in the northern United States and Canada, but there is an isolated population in southern Oregon once believed extirpated. The degree of connectivity of the Oregon population with the main population is unknown. Mitochondrial DNA sequences (mtDNA) and six microsatellite loci were used to characterize the Yellow Rail’s genetic structure and diversity patterns in six areas. The mtDNA-based analyses of genetic structure identified significant population differentiation, but pairwise comparison of regions identified no clear geographic trends. In contrast, microsatellites suggested subtle genetic structure differentiating the Oregon population from those in the five regions sampled in the Yellow Rail’s main breeding range. The genetic diversity of the Oregon population was also the lowest of the six regions sampled, and Oregon was one of three regions that demonstrated evidence of recent
population bottlenecks. Factors that produced population reductions may include loss of wetlands to development and agricultural conversion, drought, and wildfire. It is not yet determined if the high percentage (50%) of populations having experienced bottlenecks is representative of the Yellow Rail’s entire range. Further genetic data from additional breeding populations will be required for this issue to be addressed. Mark P. Miller (mpmiller@usgs.gov), Susan M. Haig (susan_haig@usgs.gov) , Link to related publication http://pubs.er.usgs.gov/publication/70009639.

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Genetic Assessments of Jabiru Storks Important for Conservation
Broad-tailed Hummingbird female (Selasphorus platycerus). Photo credit: San Andres National Wildlife Refuge, USFWS

Photo: Jabiru storks (Jabiru mycteria) in Brazil. Photo credit: © 2010 Susan Haig, USGS.

Jabiru storks are large waterbirds that are found in wetland areas in Central America, northern South America, and southern Brazil. They are considered regionally threatened in Central America due to habitat loss. Little is known about the current and historic population structure of jabirus. USGS scientist Susan Haig and co-authors from Brazil used genetic tools to provide the first species-wide assessment of jabiru storks over their entire range. They also compared historic and contemporary genetic diversity in birds from the same locations. Findings showed lower levels of genetic diversity in Central and northern South American populations when compared to the Brazilian population. If genetic structure is a goal of management agencies, reconnection of populations, particularly in Central America, would be important. The information will be beneficial to the development of conservation strategies to restore genetic diversity in all populations.

Lopes, I.F., Haig, S.M., Del Lama, S.N., 2010, Genetic characterization of neotropical jabiru storks- Insights for conservation: Waterbirds, v. 33, no. 4, p. 425-437. Catalog No: 1740.

For more information view the study description Genetic Characterization of Neotropical Jabiru Storks- Insights for Conservation and contact Susan M. Haig, Forest and Rangeland Ecosystem Science Center.

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Predicting and Managing Climate Change:  Impacts on Semi-Arid Land Wetlands, Migratory Birds, and Their Prey
American Avocet (Recurvirostra americana)

American Avocet (Recurvirostra americana).

Anthropogenic climate change is altering aquatic ecosystems worldwide, particularly small and shallow systems such as wetlands. As a result of these abiotic changes, the terrestrial and aquatic species that depend on such wetlands are also likely to experience significant shifts in range, phenology, and population structure, particularly in arid and semi-arid regions already limited in water quantity and quality. We are developing a framework to determine and manage landscape-level impacts of climate change on wetlands and wetland-dependent species in semi-arid areas of North America’s Great Basin. We begin by determining the scope of abiotic impacts from climate change using remote sensing and ground-level monitoring to create models of the relationships between water volume, water quality, weather, and climate. We will then measure landscape-level population genetic connectivity of the aquatic invertebrates that serve as key prey species to the millions of migratory waterbirds that depend on these wetlands. We can use projections of future climate conditions to model how wetland habitat quality and species connectivity will change in the coming decades by combining estimates of landscape connectivity for these species with a model of the climate drivers of wetland patch quality. This approach will serve as a general model for understanding population- and community-level climate impacts and provide a sound basis for conservation planning and adaptive management by wetland resource managers around the world. The model will be made user-friendly for specific wetland management as well as provide regional perspectives. This novel approach integrates expertise from three USGS divisions and addresses seven of the nine broad goals and 10 more specific goals of the USGS Strategic Science Plan for the U.S. Climate Change Science Program, and will be a contribution to BLM’s Assessment, Inventory, and Monitoring (AIM), USGS Sagebrush Biome coordinated research projects, USGS’s Great Basin Integrated Landscape Monitoring (GBILM) Program, USGS SageMap program, Healthy Lands Initiative, USFWS National Shorebird Plan, North American Waterfowl Management Plan, and Western Hemisphere Shorebird Reserve Network.

Read the project summary Predicting and Managing Climate Change Impacts on Semi-Arid Land Wetlands, Migratory Birds, and Their Prey: An Integration of Remote Sensing, Molecular Genetics, Hydrology, and Environmental Modeling

For more information, contact Susan M. Haig, Forest and Rangeland Ecosystem Science Center; Mark P. Miller, Forest and Rangeland Ecosystem Science Center, Travis Schmidt, Fort Collins Science Center; and John Matthews, World Wildlife Fund (WWF).

See also Conservation Genetics - Landscapes>>

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Assessing Family Relationships in Broad-tailed Hummingbird
Broad-tailed Hummingbird female (Selasphorus platycerus). Photo credit: San Andres National Wildlife Refuge, USFWS

Broad-tailed Hummingbird female (Selasphorus platycerus). Photo credit: San Andres National Wildlife Refuge, USFWS

Based on strong circumstantial evidence on numerous occasions, it is believed that adult female broad-tailed hummingbirds (Selasphorus platycercus) and one or both of her recently-fledged young remain together for two or more weeks after fledging. Due to proximity of banding sites to nesting areas in Rocky Mountain National Park, it cannot be accurately determined how long a family unit could remain together after beginning migration. The literature on broad-tailed hummingbirds reveals that the duration of maternal care beyond the first day is not observed. This study is using DNA analysis to determine whether groups of broad-tailed hummingbirds observed migrating together are family groups. USGS geneticists will isolate a set of polymorphic microsatellite loci directly from the broad-tailed hummingbird. These markers will then be used to determine the relatedness of individuals trapped together in Rocky Mountain National Park. Genotyping is achieved by extracting DNA from a tail feather from each trapped bird. Managers can use this information to monitor levels of genetic variability in populations.

For more information contact Sara J. Oyler-McCance, FORT Molecular Ecology Lab.

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Multilocus Population Genetic Survey of Greater Sage-Grouse Across their Range
Greater sage grouse. Photo credit: Gary Kramer/USFWS

Greater sage grouse. Photo credit: Gary Kramer/USFWS

The Greater Sage-grouse recently was considered for listing under the Endangered Species Act. While it did not warrant the listing based on current science, questions remain about the genetic viability of, and distinctions between, different populations of this bird. Sage-grouse currently inhabit 56% of their historic range, leaving some populations isolated from each other. USGS scientists completed DNA analysis of Greater Sage-grouse sampled across their entire range of 11 states (including Wyoming) and two Canadian provinces. These data evaluate boundaries between Greater and Gunnison Sage-grouse populations as well as the two described subspecies of Greater Sage-grouse. In addition, the data provide information to help understand gene flow, genetic diversity, and evolutionary history between many additional populations. Collecting the same data across the entire species range made it possible to make comparisons between all surveyed populations. This will help managers develop species-wide management strategies that take genetic distinctiveness into account based in part upon the entire "genetic landscape" of the species.

For more information contact Sara J. Oyler-McCance, FORT Molecular Ecology Lab.

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Using DNA as an Individual Marker for Mark-Recapture Analysis of Gunnison Sage-Grouse
Gunnison sage grouse (Centrocercus minimus). Photo credit: Copyright Dick Williams

Gunnison sage grouse (Centrocercus minimus). Photo credit: Copyright Dick Williams

Capture-recapture (CR) is a very important class of methods and models for study of wildlife populations and can be used to obtain movement information and estimate population abundance, survival probabilities, and population trends. Recently, biologists have begun using an individual animal's unique DNA as its mark. This is particularly useful in cases where DNA can be collected non-invasively. In this study USGS investigators are attempting to apply CR methodology to estimate population sizes of Gunnison Sage-grouse, a species of high conservation concern. DNA from Gunnison Sage-grouse is being extracted from fecal pellets collected on leks and used to uniquely identify individuals.

For more information contact Sara J. Oyler-McCance, FORT Molecular Ecology Lab.

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Population Genetics of Gunnison Sage-Grouse

Gunnison sage grouse (Centrocercus minimus). Photo credit: Copyright Robert Bennetts

Gunnison sage grouse (Centrocercus minimus). Photo credit: Copyright Robert Bennetts

The newly described Gunnison Sage-grouse (Centrocercus minimus) is a species of management concern because of marked declines in distribution and abundance, a consequence of the loss and fragmentation of sagebrush habitat. This has caused remaining populations to be unusually small and isolated. USGS scientists used genetic data to assess the extent of population subdivision among Gunnison Sage-grouse populations. They found a high degree of population structure and low amounts of gene flow among all pairs of populations except the geographically adjacent Gunnison and Curecanti populations. Population structure for Gunnison sage-grouse was significantly higher than has been reported for Greater Sage-grouse (C. urophasianus). Further, investigators documented low levels of genetic diversity in some populations, indicating that translocations from larger, more genetically diverse populations may be warranted. This information can be used in conservation plans to guide monitoring and management actions that maintain genetic diversity and help ensure population persistence and species viability.

For more information contact Sara J. Oyler-McCance, FORT Molecular Ecology Lab.

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Delineating Population Structure and Kinship among the Endangered Kirtland’s Warbler

Kirtland's warbler. Photo credit: D.K. Dawson

Kirtland's warbler. Photo credit: D.K. Dawson

Kirtland’s Warbler (Dendroica kirtlandii) is an endangered nearctic/neotropical migratory bird species, utilizing jack pine forests in Michigan, USA as the summer nesting habitat and overwintering in The Bahamas archipelago.  While recent demographic analyses suggest that individual warblers move regularly between geographic colonies no data exist on population structuring or on levels of genetic diversity.  Information on the extent of population structuring, extant levels of genetic diversity, and effective population size is essential to the evaluation of the current recovery program for D. kirtlandii and for any further consideration of the species’ endangered status.  To address these information needs, scientists from the Leetown Science Center, California University of Pennsylvania, and the USDA Forest Service’s International Institute of Tropical Forestry, USDA Forest Service have developed and characterized 23 microsatellite DNA markers for the nearctic/neotropical migrant passerine.  Multilocus genotypes resulting from this suite of markers should reduce the amount of resources required for initiating new genetic studies assessing breeding structure, parentage, demographics, and individual-level ecological interactions for D. kirtlandii

For more information contact Timothy L. King at the Leetown Science Center.

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Metapopulation Dynamics of the Lesser Prairie-Chicken in Southwestern Kansas
Lesser prairie-chicken (Typmanuchus pallidicinctus). Photo credit: U.S. Fish and Wildlife Service

Lesser prairie-chicken (Typmanuchus pallidicinctus). Photo credit: U.S. Fish and Wildlife Service

The Lesser Prairie-Chicken (Tympanuchus pallidicinctus) has one of the most restricted ranges of North American grouse, having sustained marked reductions in suitable habitat over the past 100 years. What remains is a highly fragmented distribution throughout its range. Despite a slowing in the rate of habitat loss, populations have continued to decline range-wide, and the bird is considered a “warranted but precluded” threatened species by the U.S. Fish and Wildlife Service (USFWS). USFWS managers are concerned that genetic diversity within individual populations might not be sufficient to maintain them. Using mitochondrial DNA sequence and nuclear microsatellite analyses on three Kansas populations of Lesser Prairie-Chicken, Fort Collins Science Center scientists and collaborators at Kansas State University are determining if this is the case. The results will help managers determine the best conservation practices for these birds at local and regional levels.

For more information contact Sara J. Oyler-McCance, FORT Molecular Ecology Lab.

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Behavioral Ecology of the Micronesian Kingfisher in Pohnpei: Use of a Surrogate Subspecies in the Recovery of Kingfishers from Guam
Micronesian kingfisher. Photo credit: Copyright John White

Micronesian kingfisher. Photo credit: Copyright John White

The Guam Micronesian kingfisher is extinct in the wild and only occurs in zoos in the United States. In a comprehensive study, molecular markers were used to identify the genetic relatedness among the captive birds so managers could develop a viable breeding strategy and plans for release of the birds back to Guam. Wild Micronesian kingfishers living on Pohnpei also were studied to help develop release plans. Researchers discovered that the Pohnpei birds, hence likely the Guam birds, were cooperative breeders, which means that offspring from previous nests stayed with the parents to help raise the chicks. This was a key clue to improving success in the captive Guam birds because previously older chicks were taken away from parents.  Scientists also learned that kingfishers on Pohnpei were highly territorial, an important fact if their dispersal options are limited by territory vacancies and forest resources as might be the case for the Guam birds. The killing of one sibling by another was also observed which underscores the importance of understanding evolutionary history of the birds.

For more information view the study description Behavioral Ecology of the Micronesian Kingfisher in Pohnpei: Use of a Surrogate Subspecies in the Recovery of Kingfishers from Guam and contact Susan M. Haig, Forest and Rangeland Ecosystem Science Center.

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Population Genetic Analysis of Mountain Plover
Mountain plover. Photo credit: Fritz Knopf

Mountain plover. Photo credit: Fritz Knopf

Mountain Plover (Charadrius montanus) distribution and abundance have drastically declined in the past 30 years, and the conversion of shortgrass prairie to agriculture has caused breeding populations to become geographically isolated. This isolation, coupled with the fact that Mountain Plovers are thought to show fidelity to breeding grounds, leads to the prediction that individual breeding populations would be genetically distinct. If observed, such a pattern would have important management implications for a species of concern. However, when USGS scientists examined genetic variation at two mitochondrial regions for individuals from several breeding sites, they found no evidence of significant population differentiation. Further analysis suggested that the Mountain Plover underwent a population expansion following the Pleistocene glacial period. To explain the lack of detectable genetic differentiation among populations despite their geographic isolation and fidelity to breeding locations, investigators speculate that there is sufficient female-mediated gene flow to homogenize gene pools among populations. Such gene flow might ensue if pair bonds are formed in mixed flocks on wintering grounds rather than on the summer breeding grounds.

For more information contact Sara J. Oyler-McCance, FORT Molecular Ecology Lab.

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Molecular Genetic Analyses of Threatened and Endangered Piping Plovers
Piping Plover. Copyright Paul J. Fusco

Piping Plover. Photo credit: Copyright Paul J. Fusco

The Piping Plover is a small migratory shorebird that is currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. Recent surveys indicate that there are only ~8,000 adult individuals in existence.  The USGS has undertaken an investigation to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species.  The results illustrate strong support for separate Atlantic and Interior Piping Plover subspecies.  Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Genetic analyses also resolved the molecular genetic signal of a population expansion event, which may reflect population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. Overall, differences observed between Interior and Atlantic birds may reflect differences in spatiotemporal stability of Piping Plover nesting habitat between regions.

For more information, view the study description Molecular Population Genetic Structure in the Piping Plover and contact Mark P. Miller, Forest and Rangeland Ecosystem Science Center.

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Individual Identification, Population Structure, and Viability of Puerto Rican Parrots
Endangered Puerto Rican parrot. Photo credit: Tom MacKenzie, USFWS

Endangered Puerto Rican parrot. Photo credit: Tom MacKenzie, USFWS

The Puerto Rican parrot is considered one of the most endangered birds in the world. During Columbus’ time, the parrot population may have exceeded one million but dropped to a low of 13 by 1975. For over 30 years, scientists and managers have studied and nurtured the few remaining wild and captive parrots. USGS scientists at the Forest and Rangeland Ecosystem Science Center and North Carolina Cooperative Research Unit have spent more than a decade working with federal agencies and the Puerto Rican government to establish family trees for the captive and wild populations. Molecular markers have been used to identify individuals and verify their lineage to model potential strategies for moving birds to and from captive and wild populations and to set up pairings for breeding programs to maximize genetic diversity. Recovery of the parrot is far from realized, but some birds are being released into the wild.

For more information view the study description Individual Identification, Population Structure, and Viability of Puerto Rican Parrots and contact Susan M. Haig, Forest and Rangeland Ecosystem Science Center.

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Reconsideration of Definition of Genetic Conservation Units in Western Snowy Plovers
Adult western snowy plover. Photo credit: Courtesy of Morgan Ball

Adult western snowy plover. Photo credit: Courtesy of Morgan Ball

Resting western snowy plovers. Photo credit: Courtesy of Morgan Ball

Resting western snowy plovers. Photo credit: Courtesy of Morgan Ball

Snowy plovers that inhabit the western coast of North America currently are listed under the Endangered Species Act as a distinct population segment (DPS) from other snowy plovers that inhabit the Great Basin and southeastern United States. An analysis of genetic information was conducted to examine whether there were significant genetic divisions, for example subspecies, among snowy plovers in North America and the Caribbean. Using snowy plover data from up to 15 breeding areas and from 155 different snowy plovers, few genetic differences were detected within the continental United States, suggesting there are no separate subspecies within the United States. More specifically, there was no evidence that the western snowy plovers were genetically distinct from those in the Great Basin. Other research has described population characteristics that distinguish the coastal population from inland birds, and this information can be combined with the genetics information in considering taxonomic and management decisions.

For more information view the study description Reconsideration of Definition of Genetic Conservation Units in Western Snowy Plovers and contact Susan M. Haig, Forest and Rangeland Ecosystem Science Center.

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Conservation Genetics of Spotted Owls

Spotted owl

Spotted owl

Spotted owls are mostly non-migratory, long-lived birds whose populations have declined in mature forests of western North America. They are classified as three subspecies: California, northern, and Mexican. Northern and Mexican spotted owls are listed as threatened under the U.S. Endangered Species Act, and California spotted owls are not. In partnership with many others, the USGS has been collecting and analyzing information about spotted owl genetics for over a decade. The distinction of the northern spotted owl as separate subspecies from California and Mexican spotted owls has been reaffirmed. Genetic information also indicates a zone of mixing between northern and California spotted owls in a portion of southern Oregon. This suggests that the range of California spotted owls extends farther north than previously described. Management agencies used these and other genetic information to review the status of the northern spotted owl, and in combination with population estimates and habitat assessments, to consider management options for all three subspecies.

For more information view the study description Conservation Genetics of Spotted Owls and contact Susan M. Haig, Forest and Rangeland Ecosystem Science Center.

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Development of Molecular Markers in Spotted/Barred Owl Hybrids for Use in Forensic Law Enforcement
Barred owl in a tree along Skyline Drive. Photo credit: Eric Butler, NPS

Barred owl in a tree along Skyline Drive. Photo credit: Eric Butler, NPS

Northern spotted owls are hybridizing with barred owls in the Pacific Northwest, and the offspring can be difficult to distinguish from either parent species. From management, law enforcement, and research perspectives, it is important to be able to determine whether a specimen is a northern spotted owl, (a species listed under the Endangered Species Act), a barred owl (protected under the Migratory Bird Treaty Act), or a hybrid (protected under the Migratory Bird Treaty Act). The USGS has worked with the U.S. Forest Service and the U.S. Fish and Wildlife Service to assess maternal and bi-parental gene flow in the process of hybridization between northern spotted owls and barred owls. The results indicate that hybrids have unique genetic combinations, including distinct markers from both parents. The analyses also corroborate the findings of many field studies, which have indicated that most hybrids result from crosses between female barred owls and male spotted owls. These genetic markers allow scientists and managers to clearly identify these species as well as hybrids, and provide solid evidence needed in law enforcement cases.

For more information view the study description Development of Molecular Markers in Spotted/Barred Owl Hybrids for Use in Forensic Law Enforcement and contact Susan M. Haig, Forest and Rangeland Ecosystem Science Center.

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Comparison of Trumpeter Swan Populations Using Nuclear and Mitochondrial Genetic Markers
Trumpeter swans. Photo credit: NPS photo by Bill Wise

Trumpeter swans. Photo credit: NPS photo by Bill Wise

For management purposes, the range of naturally occurring trumpeter swans (Cygnus buccinator) has been divided into two populations, the Pacific Coast Population (PP) and the Rocky Mountain Population (RMP). Little is known about the distribution of genetic variation across the species’ range despite increasing pressure to make difficult management decisions regarding the two populations and flocks within them. To address this issue, USGS scientists used rapidly evolving genetic markers to elucidate the underlying genetic structure of the species. Genetic data revealed a significant difference between the two populations, with the Yukon Territory as a geographic area of mixing and population overlap. Additionally, they found that both populations have somewhat similar levels of genetic diversity (PP is slightly higher), suggesting that the PP underwent a population bottleneck similar to a well-documented one in the RMP. Both genetic structure and diversity results reveal that the Tri-State flock, a suspected unique, non-migratory flock, is not genetically different from the Canadian flock of the RMP and need not be treated as a unique population from a genetic standpoint. Finally, trumpeter swans appear to have much lower mitochondrial DNA variability than other waterfowl studied thus far, which suggests a previous, species-wide bottleneck.

For more information contact Sara J. Oyler-McCance, FORT Molecular Ecology Lab.

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Determining the Effects and Consequences of Climate Change on White-tailed Ptarmigan Using a 41-Year Data Set to Investigate Trends in Demography, Genetic Variability, and Nutritional Ecology
White-tailed ptarmigan. Photo credit: Rocky Mountain National Park

White-tailed ptarmigan. Photo credit: Rocky Mountain National Park

Investigation into the interaction between ecological and evolutionary responses to global change is an important aspect of climate change studies. To address this issue, USGS scientists are documenting changes in genetic diversity and allele frequencies in white-tailed ptarmigan from Mt. Evans, Colo., over a 40-year time span and also are comparing current levels of diversity and patterns of allele frequencies with a northern population on Vancouver Island, British Columbia. Further, they are attempting to identify genetic markers under selection and to determine whether these markers can be correlated with environmental changes associated with climate change, as an understanding of the genetic basis of phenotypes under selection allows for the prediction and mitigation of the effects of climate change on the viability of populations.

For more information contact Sara J. Oyler-McCance, FORT Molecular Ecology Lab.

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Featured Publication

Piping plover. Photo credit: NPSMolecular Genetics at the Fort Collins Science Center
The mission of the U.S. Geological Survey (USGS) at the Fort Collins Science Center Molecular Ecology Laboratory is to use the tools and concepts of molecular genetics to address a variety of complex management questions and conservation issues facing the management of the Nation’s fish and wildlife resources. Together with our partners, we design and implement studies to document genetic diversity and the distribution of genetic variation among individuals, populations, and species. Information from these studies is used to support wildlife-management planning and conservation actions. Current and past studies have provided information to assess taxonomic boundaries, inform listing decisions made under the Endangered Species Act, identify unique or genetically depauperate populations, estimate population size or survival rates, develop management or recovery plans, breed wildlife in captivity, relocate wildlife from one location to another, and assess the effects of environmental change. Read the Fort Collins Molecular Genetics Fact Sheet (pdf) >>

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