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"John W Fitzpatrick"
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Climate change causes upslope shifts and mountaintop extirpations in a tropical bird community
Montane species worldwide are shifting upslope in response to recent temperature increases. These upslope shifts are predicted to lead to mountaintop extinctions of species that live only near mountain summits, but empirical examples of populations that have disappeared are sparse. We show that recent warming constitutes an “escalator to extinction” for birds on a remote Peruvian mountain—high-elevation species have declined in both range size and abundance, and several previously common mountaintop residents have disappeared from the local community. Our findings support projections that warming will likely drive wide-spread extirpations and extinctions of high-elevation taxa in the tropical Andes. Such climate change-driven mountaintop extirpations may be more likely in the tropics, where temperature seems to exert a stronger control on species’ range limits than in the temperate zone. In contrast, we show that lowland bird species at our study site are expanding in range size as they shift their upper limits upslope and may thus benefit from climate change.
Journal Article
Deconstructing isolation-by-distance: The genomic consequences of limited dispersal
Geographically limited dispersal can shape genetic population structure and result in a correlation between genetic and geographic distance, commonly called isolation-by-distance. Despite the prevalence of isolation-by-distance in nature, to date few studies have empirically demonstrated the processes that generate this pattern, largely because few populations have direct measures of individual dispersal and pedigree information. Intensive, long-term demographic studies and exhaustive genomic surveys in the Florida Scrub-Jay (Aphelocoma coerulescens) provide an excellent opportunity to investigate the influence of dispersal on genetic structure. Here, we used a panel of genome-wide SNPs and extensive pedigree information to explore the role of limited dispersal in shaping patterns of isolation-by-distance in both sexes, and at an exceedingly fine spatial scale (within ~10 km). Isolation-by-distance patterns were stronger in male-male and male-female comparisons than in female-female comparisons, consistent with observed differences in dispersal propensity between the sexes. Using the pedigree, we demonstrated how various genealogical relationships contribute to fine-scale isolation-by-distance. Simulations using field-observed distributions of male and female natal dispersal distances showed good agreement with the distribution of geographic distances between breeding individuals of different pedigree relationship classes. Furthermore, we built coalescent simulations parameterized by the observed dispersal curve, population density, and immigration rate, and showed how incorporating these extensions to Malécot's theory of isolation-by-distance allows us to accurately reconstruct observed sex-specific isolation-by-distance patterns in autosomal and Z-linked SNPs. Therefore, patterns of fine-scale isolation-by-distance in the Florida Scrub-Jay can be well understood as a result of limited dispersal over contemporary timescales.
Journal Article
Allele frequency dynamics in a pedigreed natural population
A central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes—variation in individual survival, reproductive success, and movement—are often difficult to quantify. Fully understanding these processes requires the population pedigree, the set of relationships among all individuals in the population through time. Here, we use extensive pedigree and genomic information from a long-studied natural population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of different evolutionary processes in shaping patterns of genetic variation through time. We performed gene dropping simulations to estimate individual genetic contributions to the population and model drift on the known pedigree. We found that observed allele frequency changes are generally well predicted by accounting for the different genetic contributions of founders. Our results show that the genetic contribution of recent immigrants is substantial, with some large allele frequency shifts that otherwise may have been attributed to selection actually due to gene flow. We identified a few SNPs under directional short-term selection after appropriately accounting for gene flow. Using models that account for changes in population size, we partitioned the proportion of variance in allele frequency change through time. Observed allele frequency changes are primarily due to variation in survival and reproductive success, with gene flow making a smaller contribution. This study provides one of the most complete descriptions of short-term evolutionary change in allele frequencies in a natural population to date.
Journal Article
Batch-produced, GIS-informed range maps for birds based on provenanced, crowd-sourced data inform conservation assessments
Accurate maps of species ranges are essential to inform conservation, but time-consuming to produce and update. Given the pace of change of knowledge about species distributions and shifts in ranges under climate change and land use, a need exists for timely mapping approaches that enable batch processing employing widely available data. We develop a systematic approach of batch-processing range maps and derived Area of Habitat maps for terrestrial bird species with published ranges below 125,000 km 2 in Central and South America. (Area of Habitat is the habitat available to a species within its range.) We combine existing range maps with the rapidly expanding crowd-sourced eBird data of presences and absences from frequently surveyed locations, plus readily accessible, high resolution satellite data on forest cover and elevation to map the Area of Habitat available to each species. Users can interrogate the maps produced to see details of the observations that contributed to the ranges. Previous estimates of Areas of Habitat were constrained within the published ranges and thus were, by definition, smaller—typically about 30%. This reflects how little habitat within suitable elevation ranges exists within the published ranges. Our results show that on average, Areas of Habitat are 12% larger than published ranges, reflecting the often-considerable extent that eBird records expand the known distributions of species. Interestingly, there are substantial differences between threatened and non-threatened species. Some 40% of Critically Endangered, 43% of Endangered, and 55% of Vulnerable species have Areas of Habitat larger than their published ranges, compared with 31% for Near Threatened and Least Concern species. The important finding for conservation is that threatened species are generally more widespread than previously estimated.
Journal Article
Dynamics of reduced genetic diversity in increasingly fragmented populations of Florida scrub jays,Aphelocoma coerulescens
Understanding the genomic consequences of population decline is important for predicting species' vulnerability to intensifying global change. Empirical information about genomic changes in populations in the early stages of decline, especially for those still experiencing immigration, remains scarce. We used 7834 autosomal SNPs and demographic data for 288 Florida scrub jays (Aphelocoma coerulescens; FSJ) sampled in 2000 and 2008 to compare levels of genetic diversity, inbreeding, relatedness, and lengths of runs of homozygosity (ROH) between two subpopulations within dispersal distance of one another but have experienced contrasting demographic trajectories. At Archbold Biological Station (ABS), the FSJ population has been stable because of consistent habitat protection and management, while at nearby Placid Lakes Estates (PLE), the population declined precipitously due to suburban development. By the onset of our sampling in 2000, birds in PLE were already less heterozygous, more inbred, and on average more related than birds in ABS. No significant changes occurred in heterozygosity or inbreeding across the 8‐year sampling interval, but average relatedness among individuals decreased in PLE, thus by 2008 average relatedness did not differ between sites. PLE harbored a similar proportion of short ROH but a greater proportion of long ROH than ABS, suggesting one continuous population of shared demographic history in the past, which is now experiencing more recent inbreeding. These results broadly uphold the predictions of simple population genetic models based on inferred effective population sizes and rates of immigration. Our study highlights how, in just a few generations, formerly continuous populations can diverge in heterozygosity and levels of inbreeding with severe local population decline despite ongoing gene flow.
Journal Article
Effects of Habitat Fragmentation on Effective Dispersal of Florida Scrub-Jays
Studies comparing dispersal in fragmented versus unfragmented landscapes show that habitat fragmentation alters the dispersal behavior of many species. We used two complementary approaches to explore Florida Scrub-Jay ( Aphelocoma cœrulescens) dispersal in relation to landscape fragmentation. First, we compared dispersal distances of color-marked individuals in intensively monitored continuous and fragmented landscapes. Second, we estimated effective dispersal relative to the degree of fragmentation (as inferred from two landscape indexes: proportion of study site covered with Florida Scrub-Jay habitat and mean distance to nearest habitat patch within each study site) by comparing genetic isolation-by-distance regressions among 13 study sites having a range of landscape structures. Among color-banded individuals, dispersal distances were greater in fragmented versus continuous landscapes, a result consistent with other studies. Nevertheless, genetic analyses revealed that effective dispersal decreases as the proportion of habitat in the landscape decreases. These results suggest that although individual Florida Scrub-Jays may disperse farther as fragmentation increases, those that do so are less successful as breeders than those that disperse short distances. Our study highlights the importance of combining observational data with genetic inferences when evaluating the complex biological and life-history implications of dispersal.
Journal Article
Food, weather, and population density, not number of helpers, drive overwinter survival in Florida Scrub-Jays
Survival is affected by many ecological factors including food, weather, population density, and predation pressure, but documenting survival rates together with all these associated variables requires long-term observational and ecological data from a large, marked population. We used 33 years of data on Florida Scrub-Jay (
Aphelocoma coerulescens)
demography
,
local weather, and food availability to assess determinants of jay survival during the non-breeding season (September to February). We used the known-fate model from program MARK to analyze the probability of survival for breeders and juveniles while independently testing multiple covariates. Breeder survival increased when territory size was larger, decreased when local population density was higher, and did not vary with mean daily minimum temperature in the winter. Juvenile survival slightly increased with mean daily minimum temperature in the winter but showed no association with territory size or local population density. For both breeders and juveniles, odds of survival increased with presence of both breeders in the territory and higher acorn availability, and decreased with higher total winter rainfall. Neither breeder nor juvenile survival was correlated with number of helpers or juveniles in the group. Our results emphasize the importance of environmental variables in driving adult and juvenile survival in this declining endangered bird.
Journal Article
Fire history and weather interact to determine extent and synchrony of mast-seeding in rhizomatous scrub oaks of Florida
In disturbance-prone ecosystems, fitness consequences of plant reproductive strategies are often determined by the relative timing of seed production and disturbance events, but the role of disturbances as proximate drivers of seed production has been overlooked. We use long-term data on seed production in Quercus chapmanii, Q. geminata and Q. inopina, rhizomatous oaks found in south central Florida's oak scrub, to investigate the role of fire history and its interaction with weather in shaping acorn production and its synchrony. Acorn production increased with the time since last fire, combined with additive or interactive effects of spring precipitation (+) or drought (–). Furthermore, multiple matrix regression models revealed that ramet pairs with shared fire history were more synchronous in seed production than ones that burned in different years. Long-term trends suggest that increasingly drier spring weather, in interaction with fire frequency, may drive a decline of seed production. Such declines could affect the community of acorn-reliant vertebrates in the Florida scrub, including endangered Florida scrub-jays (Aphelocoma coerulescens). These results illustrate that fire can function as a proximate driver of seed production in mast-seeding species, highlighting the increasingly recognized importance of interactions among reproductive strategies and disturbance regimes in structuring plant populations and communities.
This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.
Journal Article
Marion A. Jenkinson AOU Service Award, 2011
Generous partnerships with the AOU have accompanied his leadership roles at the Field Museum of Natural History, as executive director of the Archibold Research Station (1988-1995), and as director of the Cornell Lab of Ornithology (1995-present).
Journal Article