Research Interests: Evolutionary Biology, Genetics, Mate Choice, Population Genetics, Biology, and 15 moreArgentina, Medicine, Heredity, Genetic Diversity, Software, Phylogeny, Female, Animals, Male, Regression Analysis, Major histocompatibility complex, Genetic Polymorphism, Genetic variation, Spheniscidae, and Molecular Sequence Data
Research Interests: Genetics, Conservation, Conservation Genetics, Biology, Biodiversity, and 12 moreEndangered Species, Genetic Diversity, Biological Sciences, Population viability analysis, Environmental Sciences, Habitat loss, Local adaptation, Inbreeding Depression, Genetic variation, Management Strategy, Initial Condition, and Management Tool
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Research Interests: Genetics, Geography, Demography, Gene Flow, Biology, and 15 moreMedicine, Molecular Ecology, Biological Sciences, Mitochondrial DNA, Population, Haplotypes, Ecology and Evolutionary Biology, Animals, Effective Population Size, Galliformes, Genetic variation, Demographic History, Indexation, Bottleneck, and Mutation Rate
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Research Interests: Evolutionary Biology, Genetics, Biology, Medicine, Natural Selection, and 15 moreHeredity, Genetic Diversity, Animals, Goats, Balancing selection, Local adaptation, Major histocompatibility complex, Genetic variation, Demographic History, Amino Acid Sequence, Base Sequence, Allele, Molecular Sequence Data, microsatellite loci, and Gene frequency
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Although population genetic structure and geographic differentiation have been reported for many bird species with insular distributions, high vagility typically results in high levels of gene flow and thus little local differentiation... more
Although population genetic structure and geographic differentiation have been reported for many bird species with insular distributions, high vagility typically results in high levels of gene flow and thus little local differentiation among continental populations. This study provides the first survey of population genetic variation in a South American ratite, suggesting that, in an agricultural landscape, recent fragmentation and isolation
Research Interests: Geography, Genetic Drift, Gene Flow, Population Genetics, Biology, and 15 moreAgriculture, Landscape, Genetic Diversity, Biological Sciences, Environmental Sciences, Population, Biological Conservation, Genetic Structure, Fragmentation, Analysis of Molecular Variance, Genetic Differentiation, Population Genetic Structure, Genetic variation, Agricultural landscape, and Genetic Variability
Conservation genetics studies of populations bottlenecks are commonly framed under the detrimental paradigm of inbreeding depression. This conceptual paradigm presupposes a direct and unambiguous relationship between population size,... more
Conservation genetics studies of populations bottlenecks are commonly framed under the detrimental paradigm of inbreeding depression. This conceptual paradigm presupposes a direct and unambiguous relationship between population size, genetic diversity, fitness, and extinction. Here, I review a series of studies that emphasize the role of chance, selection, and history in determining the genetic consequences of population bottlenecks. The variable responses
Research Interests: Evolutionary Biology, Genetics, Conservation Genetics, Biology, Biodiversity, and 12 moreMolecular Genetics, Fitness, Genetic Diversity, Biological Sciences, Population viability analysis, Environmental Sciences, Population, Population Size, Extinction, Inbreeding, Inbreeding Depression, and Phenotypic variation
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111 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 1998.In addition, genetic analysis of four extant populations of the greater prairie chicken and museum specimens from a prebottlenecked population along with ecological... more
111 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 1998.In addition, genetic analysis of four extant populations of the greater prairie chicken and museum specimens from a prebottlenecked population along with ecological data on population fitness allowed me to directly assess the effects of a demographic bottleneck on the genetic diversity and fitness of a natural population. Microsatellite analysis of current populations showed that Illinois prairie chickens, which have undergone an extreme demographic contraction and an associated decline in population fitness, had the lowest estimate of mean heterozygosity per locus and approximately 2/3 the allelic diversity, sharing 95-100% of all their alleles with each of 3 other populations that have no known bottleneck history or associated declines in fitness. This finding suggests that the Illinois prairie chickens originally had higher levels of genetic diversity that were consequently lost through an extreme demographic contraction. These results were further supported by the DNA analysis of museum specimens of Illinois prairie chickens collected in the 1930s and 1960s, which revealed the loss of specific alleles (known to have been present earlier in this century) following the demographic contraction. In addition to most of the currently extant alleles, I identified in museum specimens 9 alleles not present in the current Illinois population. These "lost" alleles included both common alleles present in all other populations and others unique to the Illinois population.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD
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Research Interests: Genetics, Health Sciences, Conservation, Conservation Genetics, Science, and 15 moreBiology, Ecology, Provenance, Biodiversity, Biological Chemistry, Biological Sciences, Conservation Status, Environmental Sciences, Mitochondrial DNA, Range Expansion, DNA analysis, Museum Collection, Genetic Differentiation, Growth rate, and Mortality rate
Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped... more
Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, diving, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth.
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In many animals a small number of primordial germ cells (PGCs) are set aside early in development, mitosis and mitochondrial DNA syntheses are arrested, transcription is stopped or reduced, and the PGCs migrate later to the emerging... more
In many animals a small number of primordial germ cells (PGCs) are set aside early in development, mitosis and mitochondrial DNA syntheses are arrested, transcription is stopped or reduced, and the PGCs migrate later to the emerging gonads and become germ cells. What could be the evolutionary advantage of sequestering non-dividing PGCs early in development? A commonly cited advantage is a reduction in the number of new deleterious mutations that would occur if there were additional divisions in PGCs early in development. We would like to add to this advantage the fact that these additional mutations in PGCs give rise to germinal mosaics (i.e., premeiotic clusters of mutation) in multiple progeny of the same individual, thus having a larger detrimental effect on the evolutionary fitness of their carriers. Here, we reviewed published studies providing evidence that germinal mosaics of deleterious mutant alleles are not rare, occur for all types of genetic damage, and have been observed in all tested organisms and in nature. We propose the hypothesis that PGC sequestration during early animal development may have evolved in part in response to selection for preventing the occurrence of premeiotic clusters of deleterious mutant alleles, and describe a series of predictions that would allow the assessment of the potential role of germinal mosaics on the evolution of PGC sequestration.
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Research Interests: Arsenic, Biology, Environmental Chemistry, Medicine, Microbial Population Biology, and 15 moreGreat Lakes Region, Biological Sciences, Heavy metals, Environmental Sciences, Heavy Metal, Bacteria, Pollution, Cadmium, Lake Erie, Local adaptation, Ecosystem, Fresh water, Geologic Sediments, Microbial community, and Medical and Health Sciences
Research Interests: Adaptation, Biology, Ecology, Comparative Study, Medicine, and 15 moreGreat Lakes Region, Enzymes, Bacteria, Functional diversity, Dissolved organic matter, Lake Erie, Local adaptation, Carbohydrate metabolism, Fresh water, Dissolved Organic Carbon, Availability, Enzyme activity, Large Scale, Geologic Sediments, and Extracellular
ABSTRACT Lake Erie is a large freshwater ecosystem with three distinct basins that exhibit an east-to-west gradient of increasing productivity, as well as allochthonous inputs of nutrients and xenobiotics. To evaluate microbial community... more
ABSTRACT Lake Erie is a large freshwater ecosystem with three distinct basins that exhibit an east-to-west gradient of increasing productivity, as well as allochthonous inputs of nutrients and xenobiotics. To evaluate microbial community composition throughout this ecosystem, 435 16S rDNA environmental clones were sequenced from 11 sediment samples throughout the Western, Central, and Eastern basins, as well as the hypoxic “dead zone” of Lake Erie in the hypolimnetic region of the Central basin. Rank abundance distributions of bacterial taxa within each location revealed that Gamma- and Betaproteobacteria, microbes capable of metabolizing a wide range of organic matter pools, comprised a greater fraction of the microbial community within inshore sites of the Central and Western basins compared to the Eastern basin. While geophysical characteristics of the three major basins and the dead zone did not drive significant differences in species diversity, Fast UniFrac analyses revealed microbial community spatial structuring, with the Central basin showing higher phylogenetic uniqueness of bacterial lineages. Principal component analyses based on phylogenetic distances consistently grouped the dead zone with the Central basin and highlighted the distinctiveness of microbial communities from the Eastern basin. Results from this study provide evidence for the local adaptation of microbial communities and the potential role of riverine inputs in modulating taxonomic composition of lacustrine bacterial communities. These results are consistent with previous functional studies on microbial metabolism, which showed that differences in geochemistry across the three basins of Lake Erie play an important role in the local adaptation of microbial communities.
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Microorganisms have adapted intricate signal transduction mechanisms to coordinate tolerance to toxic levels of metals, including two-component regulatory systems (TCRS). In particular, both cop and czc operons are regulated by TCRS; the... more
Microorganisms have adapted intricate signal transduction mechanisms to coordinate tolerance to toxic levels of metals, including two-component regulatory systems (TCRS). In particular, both cop and czc operons are regulated by TCRS; the cop operon plays a key role in bacterial tolerance to copper, whereas the czc operon is involved in the efflux of cadmium, zinc, and cobalt from the cell. Although the molecular physiology of heavy metal tolerance genes has been extensively studied, their evolutionary relationships are not well-understood. Phylogenetic relationships among heavy-metal efflux proteins and their corresponding two-component regulatory proteins revealed orthologous and paralogous relationships from species divergences and ancient gene duplications. The presence of heavy metal tolerance genes on bacterial plasmids suggests these genes may be prone to spread through horizontal gene transfer. Phylogenetic inferences revealed nine potential examples of lateral gene transfer associated with metal efflux proteins and two examples for regulatory proteins. Notably, four of the examples suggest lateral transfer across major evolutionary domains. In most cases, differences in GC content in metal tolerance genes and their corresponding host genomes confirmed lateral gene transfer events. Three-dimensional protein structures predicted for the response regulators encoded by cop and czc operons showed a high degree of structural similarity with other known proteins involved in TCRS signal transduction, which suggests common evolutionary origins of functional phenotypes and similar mechanisms of action for these response regulators.
Research Interests: Evolutionary Biology, Genetics, Molecular Evolution, Biology, Horizontal Gene Transfer, and 15 moreMedicine, Phylogeny, Copper, Escherichia coli, Salmonella Typhimurium, Zinc, Genome, Gene, Gene Duplication, Plasmids, Biological evolution, Cadmium, Pseudomonas Syringae, Phylogenetic Tree, and Biochemistry and cell biology
A variety of conservation management strategies have been developed to address rapid, anthropogenically-driven biodiversity loss. The translocation of individuals from viable populations to those experiencing significant decline is one... more
A variety of conservation management strategies have been developed to address rapid, anthropogenically-driven biodiversity loss. The translocation of individuals from viable populations to those experiencing significant decline is one such strategy to increase genetic diversity and avoid extirpation, yet efficacy of this strategy has rarely been examined in detail utilizing genomic data. Here, we employ a conservation icon, the greater prairie-chicken ( Tympanuchus cupido pinnatus ), as a case study to demonstrate how genome-wide SNPs derived from RADseq offer the ability to assess translocation success with respect to the genomic aspects of genetic restoration, encompassing (1) the alleviation of inbreeding (2) the restoration of evolutionary potential, and (3) the maintenance of local variation. Genome-wide diversity estimates calculated from 356,778 SNPs demonstrate that translocations rescued the Illinois population from severe inbreeding and lack of genetic diversity, restoring variation to levels comparable to the three non-bottlenecked source populations. Delineation of genetic structure using non-linked and ubiquitously genotyped SNPs reveal distinct genetic variation among the source and recipient populations as well as high levels of admixture in the post-translocation population resulting from translocations. Estimated ancestry derived from private alleles uncover introgression of unique variation from each source population as well as the maintenance of substantial levels of variation unique to Illinois. Our findings demonstrate that genome-wide analysis of variation is a valuable management tool for measuring the genomic effects of translocations and, subsequently, gauging genetic restoration success.
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The Kelp Gull (Larus dominicanus), a common seabird in coastal Patagonia, has recently increased in overall abundance and distribution, creating some concerns for the protection and conservation of other native, threatened species. We... more
The Kelp Gull (Larus dominicanus), a common seabird in coastal Patagonia, has recently increased in overall abundance and distribution, creating some concerns for the protection and conservation of other native, threatened species. We combined genetic and demographic data of four large Kelp Gull colonies distributed along 1800 km of the northern Patagonian coast of Argentina to further understand patterns of population growth and migration of the species. DNA analysis of variable intron sequences of two separate genes (myelin proteolipid protein, β-fibrinogen) revealed similar intra-colony levels of DNA sequence diversity. Pairwise FST comparisons revealed significant differentiation of the northernmost colony, Islote La Pastosa, from the two southern colonies, Punta Tombo and Isla Vernaci Sudoeste (p 6). Demographic estimates revealed that Islote La Pastosa showed an increase in the number of breeding individuals over time (λ = 1.075), representing an area of potential population e...
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Research Interests: Metabolism, Adaptation, Microbial Ecology, Ecology, Comparative Study, and 15 moreGreat Lakes Region, Enzymes, Bacteria, Functional diversity, Dissolved organic matter, Lake Erie, Local adaptation, Carbohydrate metabolism, Fresh water, Availability, Enzyme activity, Large Scale, Geologic Sediments, Extracellular, and Microbial community
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ABSTRACT Lake Erie is a large freshwater ecosystem with three distinct basins that exhibit an east-to-west gradient of increasing productivity, as well as allochthonous inputs of nutrients and xenobiotics. To evaluate microbial community... more
ABSTRACT Lake Erie is a large freshwater ecosystem with three distinct basins that exhibit an east-to-west gradient of increasing productivity, as well as allochthonous inputs of nutrients and xenobiotics. To evaluate microbial community composition throughout this ecosystem, 435 16S rDNA environmental clones were sequenced from 11 sediment samples throughout the Western, Central, and Eastern basins, as well as the hypoxic “dead zone” of Lake Erie in the hypolimnetic region of the Central basin. Rank abundance distributions of bacterial taxa within each location revealed that Gamma- and Betaproteobacteria, microbes capable of metabolizing a wide range of organic matter pools, comprised a greater fraction of the microbial community within inshore sites of the Central and Western basins compared to the Eastern basin. While geophysical characteristics of the three major basins and the dead zone did not drive significant differences in species diversity, Fast UniFrac analyses revealed microbial community spatial structuring, with the Central basin showing higher phylogenetic uniqueness of bacterial lineages. Principal component analyses based on phylogenetic distances consistently grouped the dead zone with the Central basin and highlighted the distinctiveness of microbial communities from the Eastern basin. Results from this study provide evidence for the local adaptation of microbial communities and the potential role of riverine inputs in modulating taxonomic composition of lacustrine bacterial communities. These results are consistent with previous functional studies on microbial metabolism, which showed that differences in geochemistry across the three basins of Lake Erie play an important role in the local adaptation of microbial communities.
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Research Interests: Evolutionary Biology, Genetics, Natural Selection, Heredity, Genetic Diversity, and 14 morePhylogeny, Animals, Phylogenetic analysis, Goats, Positive Selection, Local adaptation, Major histocompatibility complex, Genetic variation, Demographic History, Amino Acid Sequence, Base Sequence, Molecular Sequence Data, microsatellite loci, and Gene frequency
The extent to which inbreeding depression affects longevity and patterns of survivorship is an important issue from several research perspectives, including evolutionary biology, conservation biology, and the genetic analysis of... more
The extent to which inbreeding depression affects longevity and patterns of survivorship is an important issue from several research perspectives, including evolutionary biology, conservation biology, and the genetic analysis of quantitative traits. However, few previous inbreeding depression studies have considered longevity as a focal life-history trait. We maintained laboratory populations of Drosophila melanogaster at census population sizes of 2 and 10 male-female pairs for up to 66 generations and performed repeated assays of male survivorship throughout this time period. On average, significant levels of inbreeding depression were observed for median life span and age-specific mortality. For age-specific mortality, the severity of inbreeding depression increased over the life span. We found that a baseline inbreeding load of 0.307 lethal equivalents per gamete affected age-specific mortality, and that this value increased at a rate of 0.046 per day of the life span. With resp...
Research Interests: Evolutionary Biology, Genetics, Conservation Biology, Evolutionary genetics, Drosophila melanogaster, and 15 moreLongevity, Mutation, Survivors, Female, Animals, Male, Population Size, Aging and Longevity, Biological evolution, Inbreeding, Inbreeding Depression, Genetic variation, Mutation Accumulation, Life Span, and Haploidy
Research Interests: Genetics, Evolutionary genetics, Stress, Environmental Stresses, Drosophila melanogaster, and 15 moreQuantitative Genetics, Natural Selection, Genetica, Female, Animals, Male, Temperature, Heritability, Selection, High Temperature, Analysis of Variance, Model System, Environmental Stress, Genetic variation, and Environment
The magnitude of inbreeding depression in small populations may depend on the effectiveness with which natural selection purges deleterious recessive alleles from populations during inbreeding. The effectiveness of this purging process,... more
The magnitude of inbreeding depression in small populations may depend on the effectiveness with which natural selection purges deleterious recessive alleles from populations during inbreeding. The effectiveness of this purging process, however, may be influenced by the rate of inbreeding and the environment in which inbreeding occurs. Although some experimental studies have examined these factors individually, no study has examined their joint effect or potential interaction. In the present study, therefore, we performed an experiment in which 180 lineages of Drosophila melanogaster were inbred at slow and fast inbreeding rates within each of three inbreeding environments (benign, high temperature, and competitive). The fitness of all lineages was then measured in a common benign environment. Although slow inbreeding reduced inbreeding depression in lineages inbred under high temperature stress, a similar reduction was not observed with respect to the benign or competitive treatments. Overall, therefore, the effect of inbreeding rate was nonsignificant. The inbreeding environment, in contrast, had a larger and more consistent effect on inbreeding depression. Under both slow and fast rates of inbreeding, inbreeding depression was significantly reduced in lineages inbred in the presence of a competitor D. melanogaster strain. A similar reduction of inbreeding depression occurred in lineages inbred under high temperature stress at a slow inbreeding rate. Overall, our findings show that inbreeding depression is reduced when inbreeding takes place in a stressful environment, possibly due to more effective purging under such conditions.
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The influence of natural selection on the magnitude of inbreeding depression is an important issue in conservation biology and the study of evolution. It is generally expected that the magnitude of inbreeding depression in small... more
The influence of natural selection on the magnitude of inbreeding depression is an important issue in conservation biology and the study of evolution. It is generally expected that the magnitude of inbreeding depression in small populations will depend upon the average homozygosity of individuals, as measured by the coefficient of inbreeding (F). However, if deleterious recessive alleles are selectively purged from populations during inbreeding, then inbreeding depression may differ among populations in which individuals have the same inbreeding coefficient. In such cases, the magnitude of inbreeding depression will partly depend on the ancestral inbreeding coefficient (fa), which measures the cumulative proportion of loci that have historically been homozygous and therefore exposed to natural selection. We examined the inbreeding depression that occurred in lineages of Drosophila melanogaster maintained under pedigrees that led to the same inbreeding coefficient (F = 0.375) but different levels of ancestral inbreeding (fa = 0.250 or 0.531). Although inbreeding depression varied substantially among individual lineages, we observed a significant 40% decrease in the median level of inbreeding depression in the treatment with higher ancestral inbreeding. Our results demonstrate that high levels of ancestral inbreeding are associated with greater purging effects, which reduces the inbreeding depression that occurs in isolated populations of small size.
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Although population genetic structure and geographic differentiation have been reported for many bird species with insular distributions, high vagility typically results in high levels of gene flow and thus little local differentiation... more
Although population genetic structure and geographic differentiation have been reported for many bird species with insular distributions, high vagility typically results in high levels of gene flow and thus little local differentiation among continental populations. This study provides the first survey of population genetic variation in a South American ratite, suggesting that, in an agricultural landscape, recent fragmentation and isolation
Research Interests: Genetic Drift, Gene Flow, Population Genetics, Agriculture, Landscape, and 14 moreGenetic Diversity, Biological Sciences, Environmental Sciences, Biological Conservation, Genetic Structure, Fragmentation, Reproductive Success, RAPD, Genetic Differentiation, Reproductive Isolation, Population Genetic Structure, Genetic variation, Agricultural landscape, and Genetic Variability
Research Interests: Evolutionary Biology, Genetics, Natural Selection, Heredity, Genetic Diversity, and 14 morePhylogeny, Animals, Phylogenetic analysis, Goats, Positive Selection, Local adaptation, Major histocompatibility complex, Genetic variation, Demographic History, Amino Acid Sequence, Base Sequence, Molecular Sequence Data, microsatellite loci, and Gene frequency
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Although population genetic structure and geographic differentiation have been reported for many bird species with insular distributions, high vagility typically results in high levels of gene flow and thus little local differentiation... more
Although population genetic structure and geographic differentiation have been reported for many bird species with insular distributions, high vagility typically results in high levels of gene flow and thus little local differentiation among continental populations. This study provides the first survey of population genetic variation in a South American ratite, suggesting that, in an agricultural landscape, recent fragmentation and isolation
Research Interests: Genetic Drift, Gene Flow, Population Genetics, Agriculture, Landscape, and 14 moreGenetic Diversity, Biological Sciences, Environmental Sciences, Biological Conservation, Genetic Structure, Fragmentation, Reproductive Success, RAPD, Genetic Differentiation, Reproductive Isolation, Population Genetic Structure, Genetic variation, Agricultural landscape, and Genetic Variability
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Research Interests: Genetics, Conservation, Conservation Genetics, Endangered Species, Genetic Diversity, and 10 moreBiological Sciences, Population viability analysis, Environmental Sciences, Habitat loss, Local adaptation, Inbreeding Depression, Genetic variation, Management Strategy, Initial Condition, and Management Tool
Quantifiable geographic variation in DNA or morphology is often used to gauge past and present levels of population interchange and has thus helped define taxonomic boundaries, resolve evolutionary histories, and develop effective... more
Quantifiable geographic variation in DNA or morphology is often used to gauge past and present levels of population interchange and has thus helped define taxonomic boundaries, resolve evolutionary histories, and develop effective conservation strategies to preserve evolutionary diversity. We examined rangewide patterns of genetic (mtDNA and microsatellites) and morphological diversity within the Lark Sparrow (Chondestes grammacus), focusing on diversity patterns across potentially independent Western, Central, and Eastern USA regional breeding zones. Phylogenetic analysis of mtDNA sequences did not support phylogeographic patterns associated with previously characterized subspecies, though the presence of regionally specific clades suggests incipient evolutionary diversification. Regional differentiation was evidenced by significant differences in morphological traits, significant levels of genetic differentiation, reduced estimates of migration among regions, and the characterizat...
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The Kelp Gull ( Larus dominicanus ), a common seabird in coastal Patagonia, has recently increased in overall abundance and distribution, creating some concerns for the protection and conservation of other native, threatened species. We... more
The Kelp Gull ( Larus dominicanus ), a common seabird in coastal Patagonia, has recently increased in overall abundance and distribution, creating some concerns for the protection and conservation of other native, threatened species. We combined genetic and demographic data of four large Kelp Gull colonies distributed along 1800 km of the northern Patagonian coast of Argentina to further understand patterns of population growth and migration of the species. DNA analysis of variable intron sequences of two separate genes (myelin proteolipid protein, β-fibrinogen) revealed similar intra-colony levels of DNA sequence diversity. Pairwise F ST comparisons revealed significant differentiation of the northernmost colony, Islote La Pastosa, from the two southern colonies, Punta Tombo and Isla Vernaci Sudoeste (p 6). Demographic estimates revealed that Islote La Pastosa showed an increase in the number of breeding individuals over time (λ = 1.075), representing an area of potential populatio...