Ecology and Evolution (2018)
Curry CM, Ross JD, Contina AJ, Bridge ES. (2018) Varying dataset resolution alters predictive accuracy of spatially explicit ensemble models for avian species distribution. Ecol Evol. 2018;00:1–12. https://doi.org/10.1002/ece3.4725
Abstract
Species distribution models can be made more accurate by use of new “Spatiotemporal Exploratory Models” (STEMs), a type of spatially explicit ensemble model (SEEM) developed at the continental scale that averages regional models pixel by pixel. Although SEEMs can generate more accurate predictions of species distributions, they are computationally expensive. We compared the accuracies of each model for 11 grassland bird species and examined whether they improve accuracy at a statewide scale for fine and coarse predictor resolutions. We used a combination of survey data and citizen science data for 11 grassland bird species in Oklahoma to test a spatially explicit ensemble model at a smaller scale for its effects on accuracy of current models. We found that only four species performed best with either a statewide model or SEEM; the most accurate model for the remaining seven species varied with data resolution and performance measure. Policy implications: Determination of nonheterogeneity may depend on the spatial resolution of the examined dataset. Managers should be cautious if any regional differences are expected when developing policy from range‐wide results that show a single model or timeframe. We recommend use of standard species distribution models or other types of nonspatially explicit ensemble models for local species prediction models. Further study is necessary to understand at what point SEEMs become necessary with varying dataset resolutions.
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IBIS (2018)
Contina A, Alcantara JL, Bridge ES, Ross JD, Oakley WF, Kelly JF, Ruegg KC (2018) Genetic structure of the Painted Bunting and its implications for conservation of migratory populations. https://doi.org/10.1111/ibi.12641
Abstract
The Painted Bunting Passerina ciris is a Neotropical songbird which breeds primarily in the United States during the summer and migrates to Mexico, Central America, southern Florida, and the Caribbean over the winter. Male Painted Buntings are brightly coloured, which makes them highly sought after as pets, particularly in Mexico, Central America and Europe. We used short sequence repeats (microsatellite DNA) to investigate the population genetic structure of the Painted Bunting and its implications in conservation management of migratory populations. We found a detectable level of population differentiation as revealed by pairwise FST and RST comparisons and Bayesian clustering analyses, with strong support for differentiation between eastern and western Painted Buntings (e.g. Oklahoma and Georgia FST = 0.1; P = 0.005; RST = 0.18; P = 0.04) in accordance with previous mitochondrial DNA analysis. We recovered additional support for two sub‐groups within the western clade. While linking migrant songbirds captured outside of the United States to their breeding populations remains a challenge, we show that natural levels of population genetic differentiation can be detected via microsatellite DNA markers and exploited in migratory connectivity studies. We also demonstrate the potential utility of our low‐cost markers for population identification of birds recovered from the pet trade by screening a small subset of samples (n = 5) collected as part of wildlife tracking. We discuss the implications of our results for future efforts to understand patterns of population decline in Painted Buntings more generally, as well as how we might expand this methodology to combat illegal pet‐trade activity in this and other songbird species.
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PLOS ONE (2018)
Contina A, Bridge ES, Ross JD, Shipley JR, Kelly JF (2018) Examination of Clock and Adcyap1 gene variation in a neotropical migratory passerine. PLoS ONE 13(1): e0190859. https://doi.org/10.1371/journal.pone.0190859
Abstract
Complex behavioral traits, such as those making up a migratory phenotype, are regulated by multiple environmental factors and multiple genes. We investigated possible relationships between microsatellite variation at two candidate genes implicated in the control of migratory behavior, Clock and Adcyap1, and several aspects of migratory life-history and evolutionary divergence in the Painted Bunting (Passerina ciris), a species that shows wide variation in migratory and molting strategies across a disjunct distribution. We focused on Clock and Adcyap1 microsatellite variation across three Painted Bunting populations in Oklahoma, Louisiana, and North Carolina, and for the Oklahoma breeding population we used published migration tracking data on adult males to explore phenotypic variation in individual migratory behavior. We found no correlation between microsatellite allele size within either Clock and Adcyap1 relative to the initiation or duration of fall migration in adult males breeding in Oklahoma. We also show the lack of significant correlations with aspects of the migratory phenotype for the Louisiana population. Our research highlights the limitations of studying microsatellite allelic mutations that are of undetermined functional influence relative to complex behavioral phenotypes.
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Movement Ecology (2018)
Zenzal TJ, Contina AJ, Kelly, JF, Moore FR. 2018. Temporal migration patterns between a Gulf Coast stopover site and natal locations of Ruby-throated Hummingbirds (Archilochus colubris). Movement Ecology 6:2DOI 10.1186/s40462-017-0120-2
Abstract
Autumn latitudinal migrations generally exhibit one of two different temporal migration patterns: type 1 where southern populations migrate south before northern populations, or type 2 where northern populations overtake southern populations en route. The ruby-throated hummingbird (Archilochus colubris) is a species with an expansive breeding range, which allows opportunities to examine variation in the timing of migration. Our objective was to determine a relationship between natal origin of ruby-throated hummingbirds and arrival at a Gulf coast stopover site; and if so, what factors, such as differences in body size across the range as well as the cost of migration, might drive such a pattern. To carry out our objectives, we captured hummingbirds at a coastal stopover site during autumn migration, at which time we collected feathers from juveniles for analysis of hydrogen stable isotopes. Using the hydrogen stable isotope gradient of precipitation across North America and published hydrogen isotope values of feathers from populations of breeding ruby-throated hummingbirds, we assigned migrants to probable natal latitudes. Our results confirm that individuals from across the range (30–50° N) stopover along the Gulf of Mexico and there is a positive relationship between arrival day and latitude, suggesting a type 1 migration pattern. We also found no relationship between fuel load (proxy for migration cost) or fat-free body mass (proxy for body size) and natal latitude. Our results, coupled with previous work on the spatial migration patterns of hummingbirds, show a type 1 chain migration pattern. While the mechanisms we tested do not seem to influence the evolution of migratory patterns, other factors such as resource availability may play a prominent role in the evolution of this migration system.
Keywords: Migration – Stable-hydrogen isotope ratio – Spatial patterns – Temporal patterns – Evolution – Deuterium – Gulf of Mexico – Stopover – Ruby-throated hummingbirds – Alabama
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Conservation Genetics Resources (2017)
Contina A, Bay R, Underwood VL, Smith TB, Bridge ES, Kelly JF, Ruegg KC. 2017. Characterization of SNPs markers for the Painted Bunting (Passerina ciris) and their relevance in population differentiation and genome evolution studies. Conservation Genetics Resources. doi: 10.1007/s12686-017-0950-7
Abstract
We developed nuclear single nucleotide polymorphism (SNP) markers for the Painted Bunting (Passerina ciris) using next-generation sequencing genotyping on the Illumina HiSeq4000 platform. Following the best-RAD approach, we sequenced 96 individuals from five breeding populations occurring in the United States. We assessed the discerning power of 105,000 SNPs and confirmed the quality of these markers in population differentiation studies. We detected outlier SNPs within or near protein coding genes, including sequences coding for olfactory receptors which may relate to migratory navigation. Finally, we provide a novel list of 33 primer pairs flanking SNPs to link individuals to regional populations and improve our understanding of the evolution of this migratory songbird.
Keywords: SNPs development – Painted Bunting – Illumina HiSeq4000 – Protein coding regions – Olfactory receptors – Songbird migration
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Integrative Zoology (2016)
Contina A, Bridge ES, Kelly JF. 2016. Exploring novel candidate genes from the Mouse Genome Informatics Database: potential implications for avian migration research. Integrative Zoology DOI: 10.1111/1749-4877.12199
Abstract
To search for genes associated with migratory phenotypes in songbirds, we selected candidate genes through annotations from the Mouse Genome Informatics database and assembled an extensive candidate-gene library. Then, we implemented a next-generation sequencing approach to obtain DNA sequences from the Painted Bunting genome. We focused on those sequences that were conserved across avian species and that aligned with candidate genes in our mouse library. We genotyped short sequence repeats from the following candidate genes: ADRA1d, ANKRD17, CISH and MYH7. We studied the possible correlations between allelic variations occurring in these novel candidate migration genes and avian migratory phenotypes available from the published literature. We found that allele variation at MYH7 correlated with a calculated index of speed of migration (km/day) across 11 species of songbirds. We highlight the potential of the Mouse Genome Informatics database in providing new candidate genes that might play a crucial role in regulating migration in birds and possibly in other taxa. Our research effort shows the benefits and limitations of working with extensive genomic datasets and offers a snapshot of the challenges related to cross-species validation in behavioral and molecular ecology studies.
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Conservation Genetics Resources (2016)
Contina A, Harrigan RJ, Pollinger JP, Bridge ES, Kelly JF, Smith TB. 2016. Genome-wide identification and characterization of simple sequence repeats in the Painted Bunting (Passerina ciris) for population and forensic analyses. Conservation Genetics ResourcesDOI 10.1007/s12686-016-0522-2
Suppl. material 12686_2016_522_MOESM13_ESM.zip (27 kb)
Abstract
The Painted Bunting, Passerina ciris, is a migratory songbird distributed in the United States and Central America and is suffering from habitat loss, habitat fragmentation, and illegal pet-trade. We describe twenty microsatellite loci isolated from Passerina ciris for population genetic analyses and forensic pet-trade investigations. We tested these markers on two distinct breeding populations in Oklahoma, United States. The mean number of alleles of the first population screened for tetra-nucleotides was 13.235 ± 1.922, and the mean of the observed and expected heterozygosities was 0.753 ± 0.045 and 0.761 ± 0.038, respectively. The mean number of alleles of the second population screened for di-nucleotides was 15.333 ± 2.186, and the mean of the observed and expected heterozygosities was 0.916 ± 0.044 and 0.879 ± 0.024, respectively. We provide a new tool for the conservation management of the Painted Bunting and closely related species of the genus Passerina.
Keywords: illegal pet-trade, polymorphic DNA, Painted Bunting, Passerina ciris.
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Behavioral Ecology (2015)
Bridge ES, Ross JD, Contina AJ, Kelly JF. 2015. Do molt-migrant songbirds optimize migration routes based on primary productivity? Behavioral Ecology, Volume 27, Issue 3, 1 January 2016, Pages 784–792. https://doi.org/10.1093/beheco/arv199
Abstract
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Journal of Field Ornithology (2013)
Bridge ES, Kelly JF, Contina A, Gabrielson RM, MacCurdy RB, and Winkler DW. 2013. Advances in tracking small migratory birds: a technical review of light-level geolocation. Journal of Field Ornithology 84(2):121-137.DOI.10.1111/jofo.12011
Abstract
Light-level geolocation data loggers, or geologgers, have recently been miniaturized to the extent that they can be deployed on small songbirds, allowing us to determine many previously unknown migration routes, breeding locations, and wintering sites. Use of geologgers on small birds has great potential to help address major research and conservation questions, but the method is not without its shortcomings. Among these shortcomings are the need to recapture birds after they have carried a device throughout a migration cycle and the potential for the devices to affect survival and behavior. We examined return rates of birds with geologgers in published and unpublished studies and found no evidence of a general negative effect of geologgers on survival, although there were a few individual studies where such an effect was evident. From these same studies, we found that most currently used harness materials are equivalent in terms of failure rates, and the most reliable geologgers are those made by the British Antarctic Survey (although these were also the largest geologgers used in the studies we examined). With regard to analysis methods, we believe there is much room for improvement. Use of online archiving of both data and analysis parameters would greatly improve the repeatability and transparency of geologger research.
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The Auk: Ornithological Advances (2013)
Contina A, Bridge ES, Seavy NE, Duckles JM, and Kelly JF. 2013. Using geologgers to investigate bimodal isotope patterns in Painted Buntings (Passerina ciris). The Auk: Ornithological Advances 130(2): 265-272.DOI: 10.1525/auk.2013.13003
Abstract
Painted Buntings (Passerina ciris) that breed in Oklahoma and molt in Sinaloa, Mexico, demonstrate a clear bimodal pattern of stable isotope ratios in their flight feathers. Some birds had a C3 carbon signature in primary 1 (P1, the first feather replaced during wing molt) and a C4 carbon signature in primary 9 (P9, the last primary to molt), whereas other sympatric birds evinced a C4-based diet throughout feather molt. The bimodal pattern of stable isotope ratios in flight feathers suggests that some birds may initiate molt immediately upon arrival in northwestern Mexico (and carry a C3 signature with them from the breeding grounds) whereas others may delay molt (and grow feathers solely from C4 plants of Sinaloa). From 2010 to 2012, we used geologger tags to test whether differences in the timing and route of fall migration movements were related to stable isotope signatures in primary feathers. We analyzed stable isotopes of hydrogen and carbon in P1 and P9 from 25 individuals fitted with geologger tags in two consecutive years. Of these, 60% changed the diet (C3 vs. C4) that was used to grow P1 between years. We also observed variation among individuals in migration routes, wherein birds from the same breeding population differed greatly in their use of molting and wintering locations. However, we did not find a relationship between isotope signatures and the timing or route of fall migration. We speculate that the bimodal isotope signature we observed represents a carryover effect related to local landscapes (grassland or agriculture vs. shrubland) used during the late breeding season and early molting period, and that these effects diminish as molt progresses. If this is the case, there is the potential for breeding-season diet to directly affect plumage quality in this molt migrant.
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The Auk: Ornithological Advances (2013)
Shipley JR, Contina A, Batbayar N, Bridge ES, Peterson AT, and Kelly JF. 2013. Niche conservatism and disjunct populations: a case study with Painted Buntings (Passerina ciris). The Auk: Ornithological Advances 130:476-486. Featured on the journal cover.doi.org/10.1525/auk.2013.12151
Abstract
Painted Buntings (Passerina ciris) breed in a variety of habitat s across the southern United States; however, a 500-km gap divides the species into eastern and western populations with dramatically different molting schedules. By contrast, the closely related Indigo Bunting (P. cyanea) is syntopic with Painted Buntings, but its range includes the 500-km gap. To date, no well-supported hypothesis explains the gap in the range of Painted Buntings. We used MaxEnt to describe ecological niches of both species and performed comparative analyses of model results to evaluate niche similarity between the two Painted Bunting breeding populations and the range gap. All present-day niche models for both species predicted a single contiguous breeding range, which suggests that the gap in the Painted Bunting range is not bioclimatic in origin. Comparative analyses of the three different environments suggest little bioclimatic divergence. Distribution models during the Last Glacial Maximum suggest that Painted Buntings likely bred as far north as ∼28°N latitude, with two disjunct populations in what are now Florida and northern Mexico. Although alternatives exist, the most parsimonious explanation is that the Gulf of Mexico serves as a migratory divide and there are fitness costs to birds attempting to fly around or over the Gulf to reach their molting or wintering grounds. This was a primary factor contributing to the origin of the current allopatric breeding distribution. Historical distribution models imply that the species may not have filled the 500-km gap as their breeding range expanded northward; divergent molting schedules may reinforce the existing range disjunction.
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Canadian Journal of Zoology (2011)
Bridge ES, Fudickar A, Kelly JF, Contina A, and Rohwer S. 2011. Divergent stable isotope signatures in the feathers of a population molt-migrant songbirds. Canadian Journal of Zoology 89:951-959. https://doi.org/10.1139/z11-064
Abstract
Stable isotope ratios of hydrogen (δD) and carbon (δ13C) in feathers collected from Painted Buntings (Passerina ciris (L., 1758)) breeding in the midwestern United States revealed a surprising degree of variation in δD, as well as a clear bimodal signal in δ13C in the innermost primary feather. Because this population does not molt on the breeding grounds, we reasoned that these observations could be due (i) to birds migrating to two (or possibly more) distinct molting areas or (ii) to differences in the timing of molt (as opposed to molt location) relative to arrival at the stopover site. To evaluate these hypotheses, we collected feathers at a molting location in northwestern Mexico, which revealed patterns similar to those from the birds in the US (favoring the second hypothesis above). We suspect that some birds arrive at stopover sites and begin molting before their body tissues equilibrate to the new isoscape so that the first feathers grown represent a blend of materials from the breeding and stopover locations. Other birds may delay molt after arriving at the molting site, allowing them to equilibrate with the local isoscape and produce feathers with isotope signatures of the molting location.
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BOOK REVIEWS & BOOK CHAPTERS
The Condor: Ornithological Applications (2012)
Contina A. 2012. The Stokes Field Guide to the Birds of North America. The Condor: Ornithological Applications Vol.114, 4-874-875. doi/full/10.1525/cond.2012.114.4.874
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Springer (2018)
Aeroecology. 2018. Editors: Phillip B. Chilson, Winifred F. Frick, Jeffrey F. Kelly, Felix Liechti. Chapter 11: Bridge ES, Ross JD, Contina AJ, Kelly JF: Using Agent Based Models to Scale from Individuals to Populations. http://www.springer.com/us/book/9783319685748
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BROAD AUDIENCE SCIENCE MAGAZINES
BirdWatching (2013)
BirdWatching. Dec. 2013 “Why the Painted Bunting has two separate breeding populations”. Article featuring the paper “Niche conservatism and disjunct populations: a case study with Painted Buntings (Passerina ciris) published a few months earlier in the Auk: Ornithological Advances.
EurekAlert! AAAS (2018)
“A University of Oklahoma researcher, Andrea Contina, and his team have identified the genetic structure of the Painted Bunting, a neotropical migratory songbird, using microsatellite DNA and single nucleotide polymorphisms to develop high-resolution markers to differentiate between individual birds breeding in different Oklahoma populations and across the United States.” Read full article here
