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At least 91 records · Page 5Linked to original sources
USGS2015

Nest predation research: Recent findings and future perspectives

Nest predation is a key source of selection for birds that has attracted increasing attention from ornithologists. The inclusion of new concepts applicable to nest predation that stem from social information, eavesdropping or physiology has expanded our knowledge considerably. Recent methodological advancements now allow focus on all three players within nest predation interactions: adults, offspring and predators. Indeed, the study of nest predation now forms a vital part of avian research in several fields, including animal behaviour, population ecology, evolution and conservation biology. However, within nest predation research there are important aspects that require further development, such as the comparison between ecological and evolutionary antipredator responses, and the role of anthropogenic change. We hope this review of recent findings and the presentation of new research avenues will encourage researchers to study this important and interesting selective pressure, and ultimately will help us to better understand the biology of birds.

Journal of Ornithology↗
USGS1993

Natural range expansion and local extirpation of an exotic psittacine--an unsuccessful colonization attempt

The Brown-throated Parakeet Aratinga pertinax is native to Panama, northern South America, and the islands off the northern coast of Venezuela. It is widely believed that the parakeet was introduced to St. Thomas, Virgin Islands, from Curacao before the mid-19th century, although no records exist as to when and how this may have occurred. The parakeet was not recorded from Vieques or Culebra islands or mainland Puerto Rico before 1975. However, in that year A. pertinax underwent an apparent natural range expansion from St. Thomas into each of these sites. The 5 birds in the eastern Puerto Rico population made 5 breeding attempts and fledged 11 young since their discovery in April1975. That population grew to a maximum size of 10 birds in June 1979. However there was only 1 bird left by July 1980, and the population no longer existed at the beginning of what would have been the 1982 breeding season. The populations on Culebra and Vieques islands were apparently extirpated by 1976. Losses in the eastern Puerto Rico population were low during the first four years of colonization, when reproduction was adequate and the mortality was low. However, between 1978 and the time of population disappearance in 1982, the expected extirpation was 0.999. Habitat use, general behavior, breeding biology, competitors and predators of the colonizing population in eastern Puerto Rico are described. Biogeographic, evolutionary, and conservation implications of these observations are discussed.

Ornitologia Neotropical↗
USGS2001

Microsatellite DNA variation Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) and cross-species amplification the Acipenseridae

O verharvest and habitat alteration have led to a collapse of most commercial Atlantic sturgeon( Acipenser oxyrinchus oxyrinchus )fisheries while pushing the species to rarity or extirpation in most of its historical range. A biologically sound conservation program for this species requires knowledge of its genetic diversity and of the evolutionary relationships among geographic populations. To address these research needs, six microsatellite loci were isolated from A. o. oxyrinchus . Pedigree analysis suggested that all are inherited in a codominant Mendelian pattern. The six loci were tested in ten additional sturgeon species from three genera and three apparent ploidy levels (4n, 8n, 16n). Approximately 70% of successful locus-species amplifications were polymorphic. Polysomy was observed most often in 8n and 16n species. Genetic diversity and population structure of A. o. oxyrinchus were assayed using three polymorphic Aox markers and four markers developed from lake sturgeon ( A. fulvescens ). A. o. oxyrinchus were sampled from the Altamaha River, Georgia, USA north to the St. Lawrence River, Quebec, Canada. Gulf sturgeon, A. o. desotoi , were sampled from the Suwannee River, Florida, USA, to assess differentiation between the subspecies. Seventy-seven alleles were observed to segregate into unique multilocus genotypes for each of the 392 individuals assayed. Mean diversity was greatest in the Chesapeake Bay (9.7 alleles per locus) and Delaware River (7.4 alleles per locus) collections, and lowest in the St. Lawrence River (4.6 alleles per locus). Mean heterozygosity across seven loci ranged from 44.3% (St. Lawrence River) to 62.6% (Altamaha River). Significant allelic heterogeneity was observed in 82% of pairwise comparisons as well as a global test (p < 0.0001) for A. o. oxyrinchus collections. Genetic distance suggests the presence of at least six subpopulations in A. o. oxyrinchus : St. Lawrence River, St. John River, Hudson River, Delaware River, Albemarle Sound, and Altamaha River. Genetic and geographic distances were positively correlated (r = 0.57, p < 0.03) among A. o. oxyrinchus , suggesting isolation by distance and philopatry. Hierarchical gene diversity analysis indicated significant genetic population structure at every level. Maximum likelihood assignment tests correctly assigned individual fish to collection with a high rate of success (mean = 87.5%); this and other lines of evidence indicated that the Chesapeake Bay collection represents a mixed population of sub-adult sturgeon from northern and southern Atlantic coast populations. Population structure was correlated with that suggested by earlier mitochondrial (mt) DNA analyses. Significant diversity was observed between two Canadian populations from which only a single mt DNA haplotype has been reported.

Conservation Genetics↗
USGS2024

Molecular sexing of birds using quantitative PCR (qPCR) of sex-linked genes and logistic regression models

The ability to sex individuals is an important component of many behavioural and ecological investigations and provides information for demographic models used in conservation and species management. However, many birds are difficult to sex using morphological characters or traditional molecular sexing methods. In this study, we developed probabilistic models for sexing birds using quantitative PCR (qPCR) data. First, we quantified distributions of gene copy numbers at a set of six sex-linked genes, including the sex-determining gene DMRT1 , for individuals across 17 species and seven orders of birds ( n = 150). Using these data, we built predictive logistic models for sex identification and tested their performance with independent samples from 51 species and 13 orders ( n = 209). Models using the two loci most highly correlated with sex had greater accuracy than models using the full set of sex-linked loci, across all taxonomic levels of analysis. Sex identification was highly accurate when individuals to be assigned were of species used in model building. Our analytical approach was widely applicable across diverse neognath bird lineages spanning millions of years of evolutionary divergence. Unlike previous methods, our probabilistic framework incorporates uncertainty around qPCR measurements as well as biological variation within species into decision-making rules. We anticipate that this method will be useful for sexing birds, including those of high conservation concern and/or subsistence value, that have proven difficult to sex using traditional approaches. Additionally, the general analytical framework presented in this paper may also be applicable to other organisms with sex chromosomes.

Molecular Ecology Resources↗
USGS2015

Arctic biodiversity: Increasing richness accompanies shrinking refugia for a cold-associated tundra fauna

As ancestral biodiversity responded dynamically to late-Quaternary climate changes, so are extant organisms responding to the warming trajectory of the Anthropocene. Ecological predictive modeling, statistical hypothesis tests, and genetic signatures of demographic change can provide a powerful integrated toolset for investigating these biodiversity responses to climate change, and relative resiliency across different communities. Within the biotic province of Beringia, we analyzed specimen localities and DNA sequences from 28 mammal species associated with boreal forest and Arctic tundra biomes to assess both historical distributional and evolutionary responses and then forecasted future changes based on statistical assessments of past and present trajectories, and quantified distributional and demographic changes in relation to major management regions within the study area. We addressed three sets of hypotheses associated with aspects of methodological, biological, and socio-political importance by asking (1) what is the consistency among implications of predicted changes based on the results of both ecological and evolutionary analyses; (2) what are the ecological and evolutionary implications of climate change considering either total regional diversity or distinct communities associated with major biomes; and (3) are there differences in management implications across regions? Our results indicate increasing Arctic richness through time that highlights a potential state shift across the Arctic landscape. However, within distinct ecological communities, we found a predicted decline in the range and effective population size of tundra species into several discrete refugial areas. Consistency in results based on a combination of both ecological and evolutionary approaches demonstrates increased statistical confidence by applying cross-discipline comparative analyses to conservation of biodiversity, particularly considering variable management regimes that seek to balance sustainable ecosystems with other anthropogenic values. Refugial areas for cold-adapted taxa appear to be persistent across both warm and cold climate phases and although fragmented, constitute vital regions for persistence of Arctic mammals.

Ecosphere↗
USGS2021

Exploiting the physiology of lampreys to refine methods of control and conservation

Lampreys (order: Petromyzontiformes) represent one of two extant groups of jawless fishes, also called cyclostomes. Lampreys have a variety of unique features that distinguish them from other fishes. Here we review the physiological features of lampreys that have contributed to their evolutionary and ecological success. The term physiology is used broadly to also include traits involving multiple levels of biological organization, like swimming performance, that have a strong but not exclusively physiological basis. We also provide examples of how sea lamprey traits are currently being used or investigated to control invasive populations in the Great Lakes, such as reduced capacity to detoxify lampricides, inability to surmount low barriers or dams, and sensitivity to several lamprey-specific chemosensory pheromones and alarm cues. Specific suggestions are also provided for how an improved knowledge of lamprey physiological traits could be exploited for more effective conservation of native lampreys and lead to the development of next generation sea lamprey control and conservation tools.

Journal of Great Lakes Research↗
USGS2012

Discordant introgression in a rapidly expanding hybrid swarm

The erosion of species boundaries can involve rapid evolutionary change. Consequently, many aspects of the process remain poorly understood, including the formation, expansion, and evolution of hybrid swarms. Biological invasions involving hybridization present exceptional opportunities to study the erosion of species boundaries because timelines of interactions and outcomes are frequently well known. Here, we examined clinal variation across codominant and maternally inherited genetic markers as well as phenotypic traits to characterize the expansion and evolution of a hybrid swarm between native Cyprinella venusta and invasive Cyprinella lutrensis minnows. Discordant introgression of phenotype, microsatellite multilocus genotype, and mtDNA haplotype indicates that the observable expansion of the C. venusta x C. lutrensis hybrid swarm is a false invasion front. Both parental and hybrid individuals closely resembling C. lutrensis are numerically dominant in the expansion wake, indicating that the non-native parental phenotype may be selectively favored. These findings show that cryptic introgression can extend beyond the phenotypic boundaries of hybrid swarms and that hybrid swarms likely expand more rapidly than can be documented from phenotypic variation alone. Similarly, dominance of a single parental phenotype following an introduction event may lead to instances of species erosion being mistaken for species displacement without hybridization.

Evolutionary Applications↗
USGS2025

The future of biocontrol in the Anthropocene: A review of climate change impacts on biocontrol agents and their hosts

Biological control, the practice of using one species (biocontrol agent) to control the population of another (a host or prey species, hereafter target), can be a successful method to reduce pest species in agricultural and natural systems worldwide. Successful biocontrol agents often share a deep evolutionary history with their targets that results in high target specificity and synchronized phenology. However, with rapidly changing climatic conditions, users of biocontrol agents have questioned how climate change will affect both well-established and more recent biological control relationships. Using a meta-analysis of data collected from a systematic literature review, we evaluated the evidence for the impact of changing temperatures on the efficacy of biocontrol agents and corresponding responses in their targets. Overall, most studies of climate change impacts on biocontrol agents take place in the laboratory and focus on arthropod agents that are parasitoids. Results from our meta-analysis reveal that changes in temperature are projected to impact biocontrol agents and their targets similarly, with no overall significant changes to biocontrol agent or target performance. However, our results also show that temperature responses vary widely across study systems, as illustrated by case studies showing both positive, neutral, and negative effects of temperature on biocontrol agent efficacy, as well as variation in responses across the three core biological control measures of success: survival, reproduction, and efficacy. Our work highlights important knowledge gaps including how climate change will affect both biocontrol agents and their targets simultaneously. Additionally, we find that most current studies of climate impacts examined temperature relationships, predominantly of agricultural biocontrol agents. Increasing the breadth of studies is crucial for understanding the potential for climate change to affect the success of current and future biological control programs.

Ecological Applications↗
USGS2026

Diverging mineral chemistry of iron and nickel throughout Earth’s changing redox conditions reveals foundation for their evolution as protein cofactors

Iron (Fe) and nickel (Ni) were both foundational to early metabolism, yet their biological trajectories diverged as Earth’s surface redox state changed. Here, we integrate mineral chemistry network analysis, protein metal-site coordination-sphere analysis, and curated redox comparisons to test how geochemistry and metalloprotein architecture co-evolved. Mineral network analyses show broader electronegativity variation and network diversity for Fe-bearing minerals through time relative to Ni-bearing minerals. In structural analyses of protein metal centers in a combined Fe/Ni protein structure set, it is shown that Fe- and Ni-associated environments differ in amino-acid composition, hydropathy structure, and cysteine representation. The greater chemical diversity and electronegativity variation in Fe minerals mirror the higher redox and structural versatility of Fe-binding proteins. The presence of Fe in a broader range of mineral and protein environments demonstrates the chemical adaptability of the metal, from the anoxic Archean to oxidative Earth surface conditions following the Great Oxidation Event. Iron, with its broad redox potential range in Fe-oxidoreductases, has a central role in both anaerobic and aerobic metabolisms. Nickel, by contrast, is less widespread in biology. Today, Ni is predominantly employed in deeply branching anaerobic pathways and by proteins with narrower redox potential ranges. Our results show that evolutionary processes, constrained by metal chemistry, habitually utilize Fe as a redox generalist while retaining Ni in specialized roles. The divergent paths of Ni and Fe, from rocks to proteins, demonstrate the intimate relationship between planetary geochemistry and metabolic origins on Earth and suggest that Fe/Ni geochemistry may inform habitability assessments in extraterrestrial environments when interpreted within specific planetary environmental contexts.

Life↗
USGS2000

Environmental quality and preservation; bedrock beneath reefs; the importance of geology in understanding biological decline in a modern reef ecosystem

Environmental Quality and Preservation-Bedrock Beneath Reefs: the Importance of Geology in Understanding Biological Decline in a Modern Ecosystem' is a four-page and one-plate full-color discussion of the geologic framework and evolutionary history of the coral reef ecosystem that lines the outer shelf off the Florida Keys.

Open-File Report↗
USGS2020

Nanopore amplicon sequencing reveals molecular convergence and local adaptation of rhodopsin in Great Lakes salmonids

Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus ) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle and MinION. We sequenced five visual opsin genes for individuals of C. artedi , C. hoyi , C. kiyi , and C. zenithicus. Comparisons revealed species-specific differences in a key spectral tuning amino acid in rhodopsin (Tyr261Phe substitution), suggesting local adaptation of C. kiyi to the blue-shifted depths of Lake Superior. Ancestral state reconstruction demonstrates that parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

Lake Superior↗
USGS2011

Individual condition and stream temperature influence early maturation of rainbow and steelhead trout, ncorhynchus mykiss

Alternative male phenotypes in salmonine fishes arise from individuals that mature as larger and older anadromous marine-migrants or as smaller and younger freshwater residents. To better understand the processes influencing the expression of these phenotypes we examined the influences of growth in length (fork length) and whole body lipid content in rainbow trout ( Oncorhynchus mykiss ). Fish were sampled from the John Day River basin in northeast Oregon where both anadromous ("steelhead") and freshwater resident rainbow trout coexist. Larger males with higher lipid levels had a greater probability of maturing as a resident at age-1+. Among males, 38% were maturing overall, and the odds ratios of the logistic model indicated that the probability of a male maturing early as a resident at age-1+ increased 49% (95% confidence interval (CI) = 23-81%) for every 5 mm increase in length and 33% (95% CI = 10-61%) for every 0.5% increase in whole body lipid content. There was an inverse association between individual condition and water temperature as growth was greater in warmer streams while whole body lipid content was higher in cooler streams. Our results support predictions from life history theory and further suggest that relationships between individual condition, maturation, and environmental variables (e.g., water temperature) are shaped by complex developmental and evolutionary influences.

Oregon↗
USGS1999

Habitat invasibility and dominance by alien annual plants in the western Mojave Desert

Patterns of habitat invasibility and alien dominance, respectively measured as species richness and biomass of alien annual plants, were evaluated in association with four habitat factors at the Desert Tortoise Research Natural Area (DTNA) in the western Mojave Desert, USA. Habitat factors varied in levels of disturbance outside (high) and inside (low) the DTNA, and in levels of soil nutrients in washlet (high) and hummock (low) topographic positions, in Larrea -north (high), Larrea -south (medium), and interspace (low) microhabitats near creosote bushes ( Larrea tridentata ), and during 1995 when rainfall was 207% (high) and 1994 when rainfall was 52% (low) of the long-term average. Dominant alien plants included the annual grasses Bromus rubens , Bromus trinii , and Schismus spp., and the forb Erodium cicutarium . Species richness and dominance of alien annual plants were slightly higher where disturbance was high, and much higher where soil nutrients were high. B. rubens and B. trinii were most dominant in washlets and in the Larrea -north microhabitats during both years. These two species evolved in mesic ecosystems, and appeared to be particularly limited by soil nutrients at this site. Schismus spp. and E. cicutarium were also most dominant in washlets, but their dominance varied between interspaces in 1994 and the Larrea -south microhabitat in 1995. Monitoring to detect the invasion of new annual plants should focus on regions of high rainfall and nitrogen deposition and on washes and beneath-canopy microhabitats. The ecological range of each alien species should be evaluated separately, because their evolutionary origins may greatly affect their patterns of invasion and dominance in the Mojave Desert.

California↗
USGS2022

Spatially explicit management of genetic diversity using ancestry probability surfaces

1. Ecological restoration and conservation efforts are increasing worldwide and the management of intraspecific genetic variation in plants and animals, an important component of biodiversity, is increasingly valued. As a result, tailorable, spatially explicit approaches to map genetic variation are needed to support decision-making and management frameworks related to the recovery of threatened and endangered species and the maintenance of genetic resources in species utilized by humans, such as for restoration or agricultural purposes. 2. Here, we describe and demonstrate a workflow to spatially interpolate patterns of genetic differentiation using novel functions in the R package POPMAPS ( Pop ulation M anagement using A ncestry P robability S urfaces). Our approach uses empirical genetic data to estimate ancestry coefficients across a user-defined landscape correlated with patterns of differentiation in the focal species. The resulting surface, which we term the ancestry probability surface, includes two components: hard population boundaries and estimations of uncertainty that represent confidence in population assignments (i.e., ancestry probabilities). 3. An ancestry probability surface developed for Hilaria jamesii , an important graminoid utilized in restoration across the western United States, demonstrates the functionality of POPMAPS . Genetic distances among empirical sites correlated better with least-cost distances across suitable habitat than with geographic distances, informing the surface over which the interpolation was conducted (i.e., a model indicating habitat suitability). A jackknifing procedure identified parameter values resulting in robust population assignments across the species’ range, which were utilized in downstream analyses to estimate ancestry coefficients from empirical data. Ancestry coefficients were translated into ancestry probabilities, which tended to be low for cells that were intermediate in distance between empirical sampling locations representing different populations or when influenced by empirical sampling locations with mixed genetic ancestry. 4. POPMAPS allows users to tailor parameter values and analytical approaches and thereby incorporate species-specific biological characteristics and desired levels of uncertainty into maps illustrating patterns of genetic differentiation. Ancestry probability surfaces may be used to guide management or investigate further ecological or evolutionary hypotheses. We discuss how maps produced by POPMAPS can inform multiple management challenges including species recovery planning and the utilization of commonly used species in restoration.

Methods in Ecology and Evolution↗
USGS2020

Climate dipoles as continental drivers of plant and animal populations

Ecological processes, such as migration and phenology, are strongly influenced by climate variability. Studying these processes often relies on associating observations of animals and plants with climate variability indices, such as the El Niño–Southern Oscillation. A characteristic of climate indices is the simultaneous emergence of opposite extremes of temperature and precipitation across continental scales, known as climate dipoles. The role of climate dipoles in shaping ecological and evolutionary processes has been largely overlooked. We review emerging evidence that climate dipoles can entrain species dynamics, and offer a framework for identifying ecological dipoles using broad-scale biological data. Given future changes in climatic and atmospheric processes, climate and ecological dipoles will likely shift in their intensity, distribution, and timing.

Trends in Ecology and Evolution↗
USGS2002

Intercontinental convergence of stream fish community traits along geomorphic and hydraulic gradients

Community convergence across biogeographically distinct regions suggests the existence of key, repeated, evolutionary mechanisms relating community characteristics to the environment. However, convergence studies at the community level often involve only qualitative comparisons of the environment and may fail to identify which environmental variables drive community structure. We tested the hypothesis that the biological traits of fish communities on two continents (Europe and North America) are similarly related to environmental conditions. Specifically, from observations of individual fish made at the microhabitat scale (a few square meters) within French streams, we generated habitat preference models linking traits of fish species to local scale hydraulic conditions (Froude number), Using this information, we then predicted how hydraulics and geomorphology at the larger scale of stream reaches (several pool-riffle sequences) should quantitatively influence the trait composition of fish communities. Trait composition for fishes in stream reaches with low Froude number at low flow or high proportion of pools was predicted as nonbenthic, large, fecund, long-lived, nonstreamlined, and weak swimmers. We tested our predictions in contrasting stream reaches in France (n = 11) and Virginia, USA (n = 76), using analyses of covariance to quantify the relative influence of continent vs. physical habitat variables on fish traits. The reach-scale convergence analysis indicated that trait proportions in the communities differed between continents (up to 55% of the variance in each trait was explained by "continent"), partly due to distinct evolutionary histories. However, within continents, trait proportions were comparably related to the hydraulic and geomorphic variables (up to 54% of the variance within continents explained). In particular, a synthetic measure of fish traits in reaches was well explained (50% of its variance) by the Froude number independently of the continent. The effect of physical variables did not differ across continents for most traits, confirming our predictions qualitatively and quantitatively. Therefore, despite phylogenetic and historical differences between continents, fish communities of France and Virginia exhibit convergence in biological traits related to hydraulics and geomorphology. This convergence reflects morphological and behavioral adaptations to physical stress in streams. This study supports the existence of a habitat template for ecological strategies. Some key quantitative variables that define this habitat template can be identified by characterizing how individual organisms use their physical environment, and by using dimensionless physical variables that reveal common energetic properties in different systems. Overall, quantitative tests of community convergence are efficient tools to demonstrate that some community traits are predictable from environmental features.

Virginia↗
USGS2014

Hybridization of an invasive shrub affects tolerance and resistance to defoliation by a biological control agent

Evolution has contributed to the successful invasion of exotic plant species in their introduced ranges, but how evolution affects particular control strategies is still under evaluation. For instance, classical biological control, a common strategy involving the utilization of highly specific natural enemies to control exotic pests, may be negatively affected by host hybridization because of shifts in plant traits, such as root allocation or chemical constituents. We investigated introgression between two parent species of the invasive shrub tamarisk ( Tamarix spp.) in the western United States, and how differences in plant traits affect interactions with a biological control agent. Introgression varied strongly with latitude of origin and was highly correlated with plant performance. Increased levels of T. ramosissima introgression resulted in both higher investment in roots and tolerance to defoliation and less resistance to insect attack. Because tamarisk hybridization occurs predictably on the western U.S. landscape, managers may be able to exploit this information to maximize control efforts. Genetic differentiation in plant traits in this system underpins the importance of plant hybridization and may explain why some biological control releases are more successful than others.

Colorado↗