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USGS2019

Puerto Rico Sicydium goby diversity: Species-specific insights on population structures and distributions

Sicydiine gobies are major contributors to Caribbean stream fish biodiversity, and ecosystem functions and services. In the Caribbean, Sicydiine gobies are represented by a single genus, Sicydium, but species-level Sicydium taxonomy and distributions remain unresolved in this region. A previous study posited that four species of Sicydium are present in Puerto Rico, including the recently described Sicydium gilberti; however, that study relied solely on morphological characters, and samples from a limited number of locations. Identification of Sicydium to species in studies with more comprehensive sampling has not occurred due to the impracticality of field identification. In our study, we employed morphological data and Mitochondrial Cytochrome C Oxidase I (mtCOI) genetic sequence data, collected from over 500 Sicydium spp. individuals at 16 broadly distributed sites, to provide an inventory of the species of Sicydium that occur in Puerto Rico. Additionally, we reveal new information on the spatial patterns of distribution, relative abundance, population structure, and observed molecular diversity among Sicydium taxa in Puerto Rico’s river systems. This information is essential to advance ecological and evolutionary knowledge of Caribbean fish assemblages, guide stream fish conservation, and for effective management of fisheries.

Neotropical Biodiversity↗

USGS2023

Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis

Spiny lizards (genus Sceloporus ) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis , is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis , as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis , the species status of the California endemic island fence lizard ( S. becki ), and the spectacular radiation of Sceloporus lizards.

California↗

USGS2006

Global phylogeographic limits of Hawaii's avian malaria

The introduction of avian malaria (Plasmodium relictum) to Hawaii has provided a model system for studying the influence of exotic disease on naive host populations. Little is known, however, about the origin or the genetic variation of Hawaii's malaria and traditional classification methods have confounded attempts to place the parasite within a global ecological and evolutionary context. Using fragments of the parasite mitochondrial gene cytochrome b and the nuclear gene dihydrofolate reductase-thymidylate synthase obtained from a global survey of greater than 13 000 avian samples, we show that Hawaii's avian malaria, which can cause high mortality and is a major limiting factor for many species of native passerines, represents just one of the numerous lineages composing the morphological parasite species. The single parasite lineage detected in Hawaii exhibits a broad host distribution worldwide and is dominant on several other remote oceanic islands, including Bermuda and Moorea, French Polynesia. The rarity of this lineage in the continental New World and the restriction of closely related lineages to the Old World suggest limitations to the transmission of reproductively isolated parasite groups within the morphological species. ?? 2006 The Royal Society.

Proceedings of the Royal Society B: Biological Sci↗

USGS2016

Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones

Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural selection acting on invasive introgression within and among natural populations occupying diverse environments. We quantified genome-wide patterns of admixture across multiple independent hybrid zones of native westslope cutthroat trout and invasive rainbow trout, the world's most widely introduced fish, by genotyping 339 individuals from 21 populations using 9380 species-diagnostic loci. A significantly greater proportion of the genome appeared to be under selection favouring native cutthroat trout (rather than rainbow trout), and this pattern was pervasive across the genome (detected on most chromosomes). Furthermore, selection against invasive alleles was consistent across populations and environments, even in those where rainbow trout were predicted to have a selective advantage (warm environments). These data corroborate field studies showing that hybrids between these species have lower fitness than the native taxa, and show that these fitness differences are due to selection favouring many native genes distributed widely throughout the genome.

Proceedings of the Royal Society B: Biological Sci↗

USGS2016

Demographic mechanisms underpinning genetic assimilation of remnant groups of a large carnivore

Current range expansions of large terrestrial carnivores are occurring following human-induced range contraction. Contractions are often incomplete, leaving small remnant groups in refugia throughout the former range. Little is known about the underlying ecological and evolutionary processes that influence how remnant groups are affected during range expansion. We used data from a spatially explicit, long-term genetic sampling effort of grizzly bears ( Ursus arctos ) in the Northern Continental Divide Ecosystem (NCDE), USA, to identify the demographic processes underlying spatial and temporal patterns of genetic diversity. We conducted parentage analysis to evaluate how reproductive success and dispersal contribute to spatio-temporal patterns of genetic diversity in remnant groups of grizzly bears existing in the southwestern (SW), southeastern (SE) and east-central (EC) regions of the NCDE. A few reproductively dominant individuals and local inbreeding caused low genetic diversity in peripheral regions that may have persisted for multiple generations before eroding rapidly (approx. one generation) during population expansion. Our results highlight that individual-level genetic and reproductive dynamics play critical roles during genetic assimilation, and show that spatial patterns of genetic diversity on the leading edge of an expansion may result from historical demographic patterns that are highly ephemeral.

Northern Continental Divide Ecosystem↗

USGS2017

Effects of host species and environment on the skin microbiome of Plethodontid salamanders

The amphibian skin microbiome is recognized for its role in defence against pathogens, including the deadly fungal pathogen Batrachochytrium dendrobatidis (Bd). Yet, we have little understanding of evolutionary and ecological processes that structure these communities, especially for salamanders and closely related species. We investigated patterns in the distribution of bacterial communities on Plethodon salamander skin across host species and environments. Quantifying salamander skin microbiome structure contributes to our understanding of how host-associated bacteria are distributed across the landscape, among host species, and their putative relationship with disease. We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring Plethodon salamander species (35 Plethodon cinereus , 17 Plethodon glutinosus , 10 Plethodon cylindraceus ) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of P. cinereus along an elevational gradient ( n = 50, 700–1,000 m a.s.l.) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members. Co-occurring salamanders had similar microbiome structure, but among sites salamanders had dissimilar microbiome structure for beta-diversity and abundance of 28 bacterial OTUs. We found that alpha-diversity increased with elevation, beta-diversity and the abundance of 17 bacterial OTUs changed with elevation (16 OTUs decreasing, 1 OTU increasing). We detected 11 putatively anti-Bd bacterial OTUs that were present on 90% of salamanders and made up an average relative abundance of 83% ( SD ± 8.5) per salamander. All salamanders tested negative for Bd. We conclude that environment is more influential in shaping skin microbiome structure than host differences in these congeneric species, and suggest that environmental characteristics that covary with elevation influence microbiome structure. High prevalence and abundance of anti-Bd bacteria may contribute to low Bd levels in these populations of Plethodon salamanders.

Journal of Animal Ecology↗

USGS2015

Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout ( Salvelinus confluentus ) populations from 24 watersheds (i.e., ~4–7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity ( r = −0.77; P < 0.001); watersheds containing populations with lower average genetic diversity generally had the lowest habitat complexity, warmest stream temperatures, and greatest frequency of winter flooding. Together, these findings have important conservation implications for bull trout and other imperiled species. Genetic diversity is already depressed where climatic vulnerability is highest; it will likely erode further in the very places where diversity may be most needed for future persistence.

Global Change Biology↗

USGS2014

Nutritional stress affects corticosterone deposition in feathers of Caspian tern chicks

Stressful environmental conditions affect the adrenocortical function of developing animals, which can have consequences for their fitness. Discovery of the avian stress hormone corticosterone (CORT) in feathers has the potential to broaden the application of endocrine research in ecological and evolutionary studies of wild birds by providing a long-term measure of CORT secretion. Mechanisms of CORT deposition in feathers are not well known and few studies have related feather CORT to circulating plasma CORT during feather growth. Our objective was to experimentally test the validity of using feather CORT as a measure of CORT secretion in developing birds experiencing nutritional stress. Caspian tern Hydroprogne caspia chicks were fed ad libitum or restricted (35% less than ad libitum) diets for four weeks. We measured CORT in feathers from these chicks to examine the relationship between feather CORT concentrations and nutritional limitation, circulating plasma CORT, and feather development. We found that feather CORT was higher in controls fed ad libitum than in restricted individuals, despite higher levels of plasma CORT in restricted chicks compared to controls. Feather mass and growth rates were strongly and positively related to feather CORT concentrations in both treatments. This is the first experimental study to show that feather CORT concentrations can be lower in response to nutritional stress, even when plasma CORT concentrations are elevated. Our results indicate that CORT deposition in feathers may be confounded when feather mass and growth rates are compromised by nutritional stress. We conclude that feather CORT can be used for assessing nutritional stress in growing birds, but the direction of response depends on how strongly stress affects feather development.

Journal of Avian Biology↗

USGS2020

Latitudinal patterns of alien plant invasions

Latitudinal patterns of biodiversity have long been a central topic in ecology and evolutionary biology. However, while most previous studies have focused on native species, little effort has been devoted to latitudinal patterns of plant invasions (with a few exceptions based on data from sparse locations). Using the most up‐to‐date worldwide native and alien plant distribution data from 801 regions (including islands), we compared invasion levels (i.e. alien richness/total richness) in the Northern and Southern Hemispheres and across continental regions and islands around the globe. Results from quantile regressions using B‐splines to model nonlinearity showed (1) declining richness with increasing latitude, although the highest alien richness occurs at around 40 degrees in both hemispheres, (2) decreasing invasion levels towards higher latitudes on islands but a unimodal pattern in invasion level in continental regions in each hemisphere, (3) significantly higher invasion levels on islands than in continental regions and (4) a greater variability in invasion levels on islands at low latitudes than on high‐latitude islands. In continental regions, only the mid‐latitudes had high variability with both low and high invasion levels. Our findings identified latitudes with invasion hotspots where management is urgently needed, and latitudes with many areas of low invasions but high conservation potential where prevention of future invasions should be the priority.

Journal of Biogeography↗

USGS2021

Sarcoptic mange: An emerging panzootic in wildlife

Sarcoptic mange, a skin infestation caused by the mite Sarcoptes scabiei , is an emerging disease for some species of wildlife, potentially jeopardizing their welfare and conservation. Sarcoptes scabiei has a near-global distribution facilitated by its forms of transmission and use of a large diversity of host species (many of those with broad geographic distribution). In this review, we synthesize the current knowledge concerning the geographic and host taxonomic distribution of mange in wildlife, the epidemiological connections between species, and the potential threat of sarcoptic mange for wildlife conservation. Recent sarcoptic mange outbreaks in wildlife appear to demonstrate ongoing geographic spread, increase in the number of hosts and increased virulence. Sarcoptic mange has been reported in at least 12 orders, 39 families and 148 species of domestic and wild mammals, making it one of the most generalist ectoparasites of mammals. Taxonomically, the orders with most species found infested so far include Perissodactyla (67% species from the entire order), Artiodactyla (47%), and Diprotodontia (67% from this order). This suggests that new species from these mammal orders are likely to suffer cross-species transmission and be reported positive to sarcoptic mange as surveillance improves. We propose a new agenda for the study of sarcoptic mange in wildlife, including the study of the global phylogeography of S. scabiei , linkages between ecological host traits and sarcoptic mange susceptibility, immunology of individuals and species, development of control strategies in wildlife outbreaks and the effects of global environmental change in the sarcoptic mange system. The ongoing transmission globally and sustained spread among areas and wildlife species make sarcoptic mange an emerging panzootic in wildlife. A better understanding of sarcoptic mange could illuminate the aspects of ecological and evolutionary drivers in cross-species transmission for many emerging diseases.

Transboundary and Emerging Diseases↗

USGS2016

Formation of the Isthmus of Panama

The formation of the Isthmus of Panama stands as one of the greatest natural events of the Cenozoic, driving profound biotic transformations on land and in the oceans. Some recent studies suggest that the Isthmus formed many millions of years earlier than the widely recognized age of approximately 3 million years ago (Ma), a result that if true would revolutionize our understanding of environmental, ecological, and evolutionary change across the Americas. To bring clarity to the question of when the Isthmus of Panama formed, we provide an exhaustive review and reanalysis of geological, paleontological, and molecular records. These independent lines of evidence converge upon a cohesive narrative of gradually emerging land and constricting seaways, with formation of the Isthmus of Panama sensu stricto around 2.8 Ma. The evidence used to support an older isthmus is inconclusive, and we caution against the uncritical acceptance of an isthmus before the Pliocene.

Science Advances↗

USGS2024

Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology

The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind. To that end, EEB is developing new tools to analyze the massive, complex, transdisciplinary datasets that result from such studies. The American Society for Microbiology’s Council on Microbial Sciences hosted a virtual retreat in 2023 to identify the trajectory of EEB both within the Society and microbiology at large. Retreat presentations and discussions collectively emphasized the interconnectedness of microbes and their outsized global influence on environmental and host health. The retreat repeatedly emphasized that the future of science is through transdisciplinary collaborations that promote integration of diverse datasets and advanced technologies, while also genuinely fostering inclusivity, global collaborations, and public engagement. The American Society for Microbiology and EEB stand poised to lead a paradigm shift that will result in a new era of collaboration, innovation, and societal relevance for microbiology.

mSphere↗

USGS1979

Exploitation of marine mammals: r-selection of K-strategists?

The importance of marine mammals as predators to the organization of marine communities is poorly known, although in several structurally analogous systems the ecological and evolutionary roles of predators are known to be of considerable importance. Occupation of the marine environment by mammals probably carried physiological constraints for single-young pregnancies thereby limiting all species to low intrinsic rates of population increase. As such, species subjected to high mortality rates from predation or other natural disturbances became extinct; those that survived probably were largely resource limited. In view of this scenario it is suggested that stable populations of marine mammals can be maintained at high levels without being manipulated in most communities. Exploitation probably constitutes a rather dramatic environmental change to marine mammals consequently subjecting them to selective forces fundamentally different from many of those under the influence of which they evolved.

Journal of the Fisheries Research Board of Canada↗

USGS2021

Age-structured Jolly-Seber model expands inference and improves parameter estimation from capture-recapture data

Understanding the influence of individual attributes on demographic processes is a key objective of wildlife population studies. Capture-recapture and age data are commonly collected to investigate hypotheses about survival, reproduction, and viability. We present a novel age-structured Jolly-Seber model that incorporates age and capture-recapture data to provide comprehensive information on population dynamics, including abundance, age-dependent survival, recruitment, age structure, and population growth rates. We applied our model to a multi-year capture-recapture study of polar bears (Ursus maritimus) in western Hudson Bay, Canada (20122018), where management and conservation require a detailed understanding of how polar bears respond to climate change and other factors. In simulation studies, the age-structured Jolly-Seber model improved precision of survival, recruitment, and annual abundance estimates relative to standard Jolly-Seber models that omit age information. Furthermore, incorporating age information improved precision of population growth rates, increased power to detect trends in abundance, and allowed direct estimation of age-dependent survival and changes in annual age structure. Our case study provided detailed evidence for senescence in polar bear survival. Median survival estimates were lower (<0.95) for individuals aged <5 years, remained high (>0.95) for individuals aged 722 years, and subsequently declined to near zero for individuals >30 years. We also detected cascading effects of large recruitment classes on population age structure, which created major shifts in age structure when these classes entered the population and then again when they reached prime breeding ages (1015 years old). Overall, age-structured Jolly-Seber models provide a flexible means to investigate ecological and evolutionary processes that shape populations (e.g., via senescence, life expectancy, and lifetime reproductive success) while improving our ability to investigate population dynamics and forecast population changes from capture-recapture data.

PLoS ONE↗

USGS2008

Length variation in age-0 westslope cutthroat trout at multiple spatial scales

Phenotypic diversity provides ecological and evolutionary functions, stabilizing populations in variable environments. Although benefits of larger body size in juvenile fishes are well documented, size variation may have value as well. We explored the distribution of length and length variation in age-0 westslope cutthroat trout Oncorhynchus clarkii lewisi at three spatial scales: area (102 km2), stream (101 km2), and site (100 km2). In addition, we examined relationships between length variables (mean length and interquartile range of length) and instream (temperature and conductivity) and landscape (aspect, elevation, headwater distance, and valley width) variables that were expected to be associated with fish size. Conductivity was included as a surrogate for productivity. Most variation in mean length and interquartile range of fish length was found among areas (62.2% and 62.6%, respectively). Mean length also varied among streams and sites (21.9% and 15.8%, respectively). Similarly, interquartile range of fish length varied among streams and sites (19.1% and 18.3%, respectively). Both length variables were associated with temperature and elevation. Mean fish length was also associated with conductivity, but the association between interquartile length range and conductivity was weak. We conclude that the conservation of variation in phenotypic attributes, such as length, in westslope cutthroat trout may require conservation of viable populations across broad areas and across environmental gradients that are associated with growth. ?? Copyright by the American Fisheries Society 2008.

North American Journal of Fisheries Management↗

USGS2011

Hybridization and cytonuclear associations among native westslope cutthroat trout, introduced rainbow trout, and their hybrids within the Stehekin River drainage, North Cascades National Park

Historic introductions of nonnative rainbow trout Oncorhynchus mykiss into the native habitats of cutthroat trout O. clarkii have impacted cutthroat trout populations through introgressive hybridization, creating challenges and concerns for cutthroat trout conservation. We examined the effects of rainbow trout introductions on the native westslope cutthroat trout O. c. lewisii within the Stehekin River drainage, North Cascades National Park, Washington, by analyzing 1,763 salmonid DNA samples from 18 locations with nine diagnostic nuclear DNA markers and one diagnostic mitochondrial DNA (mtDNA) marker. Pure westslope cutthroat trout populations only occurred above upstream migration barriers in the Stehekin River and Park Creek. Two categories of rainbow trout admixture were observed: (1) less than 10% within the Stehekin River drainage above the Bridge Creek confluence and the middle and upper Bridge Creek drainage and (2) greater than 30% within the Stehekin River below the Bridge Creek confluence and in lower Bridge Creek. Hybrid indices and multilocus genotypes revealed an absence of rainbow trout and reduced hybrid diversity within the Stehekin River above the Bridge Creek confluence relative to hybrid diversity in the Stehekin River below the confluence and within lower Bridge Creek. Cytonuclear disequilibrium statistics revealed assortative mating between westslope cutthroat and rainbow trout but not among hybrids within the same locations. This suggests that a randomly mating hybrid swarm does not currently exist. However, continual migration of parental genotypes into the study location could also create significant cytonuclear disequilibria. The Stehekin River represents a novel and unique example of a dynamic hybridization zone where the invasion of rainbow trout alleles into the Stehekin River westslope cutthroat trout population above the Bridge Creek confluence appears to be impeded, suggesting that divergent ecological or evolutionary mechanisms promote the population structure within the Stehekin River drainage, depending upon location.

Washington↗

USGS2024

Thermal traits of anurans database for the southeastern United States (TRAD): A database of thermal trait values for 40 anuran species

Thermal traits, or how an animal responds to changing temperatures, impacts species persistence and thus biodiversity. Trait databases, as repositories of consolidated, measured organismal attributes, allow researchers to link study species with specific trait values, enabling comparisons within and among species. Trait databases also help lay the groundwork to build mechanistic linkages between organisms and the environment. However, missing or hidden physiological trait data preclude building mechanistic estimates of climate change vulnerability for many species. Thus, physiologically focused trait databases present an opportunity to consolidate data and enable species-specific or multispecies, mechanistic evaluations of climate change vulnerability. Here, we present TRAD: thermal traits of anurans database for the southeastern United States, a database of thermal trait values related to physiological thermoregulation (critical thermal minima and maxima, preferred temperature), behavioral thermoregulation (activity period, retreat emergence temperature, basking temperature, minimum and maximum foraging temperatures), and body mass for 37 anuran species found within the southeastern United States. In total, TRAD contains 858 reported trait values for 37 of 40 species found in the region from 267 peer-reviewed papers, dissertations, or theses and is easily linked with trait data available in ATraiU, an ecological trait database for anurans in the United States. TRAD contains trait values for multiple life stages and a summarization of interspecific adult trait values. Availability of trait data varied widely among traits and species. Estimates of mass were the most common trait values reported, with values available for 32 species. Behavioral trait values comprised 23% of our database, with activity period available for 34 species. We found the most trait values for Cope's Gray Treefrog ( Dryophytes chrysoscelis ), with at least one trait value for eight traits in the database. Conversely, species in the genus Pseudacris generally had the fewest trait values available. Species with the largest geographic range sizes also had the greatest coverage of data across traits (rho 5 0.75, P , 0.001). TRAD can aid studies of anuran response to changing temperatures, physiological niche space and limitations, and potential drivers of anuran geographic range limits, influencing our understanding of other ecological and evolutionary patterns and processes and enabling multispecies comparisons of potential risk and resilience in the face of climate change.

southeastern United States↗

USGS2023

Condition and coloration of lingual lures of Alligator Snapping Turtles

The lingual lures of Macrochelys (alligator snapping turtles) are believed to be the only prey-capturing lures within the mouths of modern reptiles. To date, no formal assessment of lure condition in Macrochelys has been published, and few researchers record lure data. Herein, we report damaged or missing lures from 25 Macrochelys temminckii (Alligator Snapping Turtle; 7 adults, 18 juveniles) from a sample of more than 2000 lure assessments in 4 states, indicating this is a rare occurrence. We also describe lingual lure color observed in these assessments and introduce standardized terminology and color categories. We suggest researchers record data on the condition and coloration of the lingual lure to further our understanding of this ecological and evolutionary adaptation.

Southeastern Naturalist↗