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At least 685 records · Page 38Linked to original sources

USGS1991

Mitochondrial DNA in wildlife forensic science: Species identification of tissues

A common problem in wildlife law enforcement is identifying the species of origin of carcasses, meat, or blood when morphological characters such as hair or bones are not available. Immunological and protein electrophoretic (allozyme or general protein) procedures have been used in species identification with considerable success (Bunch et al. 1976, McClymont et al. 1982, Wolfe 1983, Mardini 1984, Pex and Wolfe 1985, Dratch 1986), However, immunological tests often are not sensitive enough to distinguish closely related species. Furthermore, electrophoretically detectable protein polymorphisms may be lacking in certain populations or species and may not be species-specific. Analysis of DNA in human and wildlife forensics has been shown to be a potentially powerful tool for identification of individuals (Jeffreys et al. 1985, Vassartet al. 1987, Thommasen et al. 1989). Differences in copy number and nucleotide sequence of repetitive sequences in the nuclear (chromosomal) DNA result in hypervariability and individual-specific patterns which have been termed DNA "fingerprints." However, these patterns may be too variable for species identification necessitating analyses of more conservative parts of the genome. Mitochondrial DNA (mtDNA) is haploid, maternally inherited, similar in nucleotide sequence among conspecifics from the same geographic region, and more suitable for species identification, in contrast to hypervariable DNA fingerprints. MtDNA has several characteristics which make it useful as a species-specific marker. In mammals, individuals have a single mtDNA genotype shared by all tissues. Because mtDNA is haploid and reflects only maternal ancestry, the mtDNA gene number in a population is 4 times less than the nuclear gene number (Birky et al. 1983). This can result in relatively rapid loss or fixation of mtDNA genotypes so that all individuals in a population may be descended from a single ancestral female in as few as 4N ( N = population size) generations (Avise et al., 1984). This suggests there is great potential for identification of species-specific or population-specific mtDNA genotypes, Within species, mtDNA genotypes are thought to be selectively neutral, i.e., there is little evidence that genotypes differ in fitness (Nigro and Prout 1990).

Wildlife Society Bulletin↗

USGS1998

Impact of alternative regeneration methods on genetic diversity in coastal Douglas-fir

Genetic implications of natural and artificial regeneration following three regeneration methods (group selection, shelterwood, and clearcut) were investigated in coastal Douglas-fir ( Pseudotsuga menziesii var. menziesii [Mirb.] Franco) using genetic markers (17 allozyme loci). In general, harvesting followed by either natural or artificial regeneration resulted in offspring populations little altered from those in the previous generation. Cutting the smallest trees to form shelterwoods, however, resulted in the removal of rare, presumably deleterious, alleles, such that slightly fewer alleles per locus were observed among residual trees (2.76) and natural regeneration (2.75) than found in uncut (control) stands (2.86). Thus, although the shelterwood regime appears quite compatible with gene conservation, it would be best to leave parent trees of a range of sizes in shelterwoods designated as gene conservation reserves, in order to maximize the number of alleles (regardless of current adaptive value) in naturally regenerated offspring. Seedling stocks used for artificial regeneration in clearcut, shelterwood, and group selection stands (7 total) had significantly greater levels of genetic diversity, on average, than found in natural regeneration. This is probably because the seeds used in artificial seedling stocks came from many wild stands and thus, sampled more diversity than found in single populations. For. Sci. 44(3): 390-396.

Forest Science↗

USGS1999

Intraspecific phylogeography of Lasmigona subviridis (Bivalvia: Unionidae): Conservation implications of range discontinuity

A nucleotide sequence analysis of the first internal transcribed spacer region (ITS-1) between the 5.8S and 18S ribosomal DNA genes (640 bp) and cytochrome c oxidase subunit I (COI) of mitochondrial DNA (mtDNA) (576 bp) was conducted for the freshwater bivalve Lasmigona subviridis and three congeners to determine the utility of these regions in identifying phylogeographic and phylogenetic structure. Sequence analysis of the ITS-1 region indicated a zone of discontinuity in the genetic population structure between a group of L. subviridis populations inhabiting the Susquehanna and Potomac Rivers and more southern populations. Moreover, haplotype patterns resulting from variation in the COI region suggested an absence of gene exchange between tributaries within two different river drainages, as well as between adjacent rivers systems. The authors recommend that the northern and southern populations, which are reproductively isolated and constitute evolutionarily significant lineages, be managed as separate conservation units. Results from the COI region suggest that, in some cases, unionid relocations should be avoided between tributaries of the same drainage because these populations may have been reproductively isolated for thousands of generations. Therefore, unionid bivalves distributed among discontinuous habitats (e.g. Atlantic slope drainages) potentially should be considered evolutionarily distinct. The DNA sequence divergences observed in the nuclear and mtDNA regions among the Lasmigona species were congruent, although the level of divergence in the COI region was up to three times greater. The genus Lasmigona, as represented by the four species surveyed in this study, may not be monophyletic.

Conference Paper↗

USGS2009

Diffusion-equation representations of landform evolution in the simplest circumstances: Appendix C

The diffusion equation is one of the three great partial differential equations of classical physics. It describes the flow or diffusion of heat in the presence of temperature gradients, fluid flow in porous media in the presence of pressure gradients, and the diffusion of molecules in the presence of chemical gradients. [The other two equations are the wave equation, which describes the propagation of electromagnetic waves (including light), acoustic (sound) waves, and elastic (seismic) waves radiated from earthquakes; and LaPlace’s equation, which describes the behavior of electric, gravitational, and fluid potentials, all part of potential field theory. The diffusion equation reduces to LaPlace’s equation at steady state, when the field of interest does not depend on t. Poisson’s equation is LaPlace’s equation with a source term.] Joseph Fourier developed the diffusion equation for heat conduction in 1807, and it has significant associations with probability theory (Narasimhan, 2009), as we will see shortly. In a novel and fascinating application, Gene Humphreys has employed solutions of the diffusion equation to describe the density of desert tortoises in the presence of population gradients caused by new dirt roads cut in the Mojave Desert. These new dirt roads induce an immediate line sink for unsuspecting tortoises. As of this writing in early September, I am not sure whether Gene has published this work. Most of us here know that the diffusion equation has also been used to describe the evolution through time of scarp-like landforms, including fault scarps, shoreline scarps, or a set of marine terraces. The methods, models, and data employed in such studies have been described in the literature many times over the past 25 years. For most situations, everything you will ever need (or want) to know can be found in Hanks et al. (1984) and Hanks (2000), the latter being a review of numerous studies of the 1980s and 1990s and a summary of available estimates of the mass diffusivity κ. The geometric parameterization of scarp-like landforms is shown in Figure 1.

Book↗

USGS2013

Population genetic structure of rare and endangered plants using molecular markers

This study was initiated to assess the levels of genetic diversity and differentiation in the remaining populations of Phyllostegia stachyoides and Melicope zahlbruckneri in Hawai`i Volcanoes National Park and determine the extent of gene flow to identify genetically distinct individuals or groups for conservation purposes. Thirty-six Amplified Fragment Length Polymorphic (AFLP) primer combinations generated a total of 3,242 polymorphic deoxyribonucleic acid (DNA) fragments in the P. stachyoides population with a percentage of polymorphic bands (PPB) ranging from 39.3 to 65.7% and 2,780 for the M. zahlbruckneri population with a PPB of 18.8 to 64.6%. Population differentiation (Fst) of AFLP loci between subpopulations of P. stachyoides was low (0.043) across populations. Analysis of molecular variance of P. stachyoides showed that 4% of the observed genetic differentiation occurred between populations in different k ī puka and 96% when individuals were pooled from all k ī puka. Moderate genetic diversity was detected within the M. zahlbruckneri population. Bayesian and multivariate analyses both classified the P. stachyoides and M. zahlbruckneri populations into genetic groups with considerable sub-structuring detected in the P. stachyoides population. The proportion of genetic differentiation among populations explained by geographical distance was estimated by Mantel tests. No spatial correlation was found between genetic and geographic distances in both populations. Finally, a moderate but significant gene flow that could be attributed to insect or bird-mediated dispersal of pollen across the different k ī puka was observed. The results of this study highlight the utility of a multi-allelic DNA-based marker in screening a large number of polymorphic loci in small and closely related endangered populations and revealed the presence of genetically unique groups of individuals in both M. zahlbruckneri and P. stachyoides populations. Based on these findings, approaches that can assist conservation efforts of these species are proposed.

Hawai`i↗

USGS2001

Immunogenetics and resistance to avian malaria in Hawaiian honeycreepers (Drepanidinae)

Although a number of factors have contributed to the decline and extinction of Hawai‘i’s endemic terrestrial avifauna, introduced avian malaria ( Plasmodium relicturn ) is probably the single most important factor preventing recovery of these birds in low-elevation habitats. Continued decline in numbers, fragmentation of populations, and extinction of species that are still relatively common will likely continue without new, aggressive approaches to managing avian disease. Methods of intervention in the disease cycle such as chemotherapy and vaccine development are not feasible because of efficient immune-evasion strategies evolved by the parasite, technical difficulties associated with treating wild avian populations, and increased risk of selection for more virulent strains of the parasite. We are investigating the natural evolution of disease resistance in some low-elevation native bird populations, particularly Hawai‘i ‘Amakihi ( Hemignathus virens ), to perfect genetic methods for identifying individuals with a greater immunological capacity to survive malarial infection. We are focusing on genetic analyses of the major histocompatibility complex, due to its critical role in both humoral and cell-mediated immune responses. In the parasite, we are evaluating conserved ribosomal genes as well as variable genes encoding cell-surface molecules as a first step in developing a better understanding of the complex interactions between malarial parasites and the avian immune system. A goal is to provide population managers with new criteria for maintaining long-term population stability for threatened species through the development of methods for evaluating and maintaining genetic diversity in small populations at loci important in immunological responsiveness to pathogens.

Hawai'i↗

USGS2006

Genetic characterization of brown bears of the Kodiak Archipelago

Here we examine genetic characteristics of brown bears of Kodiak and Afognak islands, using 14 variable nuclear microsatellite loci and nucleotide sequence information including the hypervariable domain I of the mtDNA control region (Wakely 1993). Because these markers, or a subset of them, have been used to characterize brown bears of the Kenai Peninsula (Jackson et al. 2005), Katmai National Park, Seward Peninsula, and nine other populations in Alaska (Talbot, unpublished data), we compared levels of genetic diversity and relationships among populations when possible. In addition, we obtained preliminary comparative information from class II DQA and DQB genes of the brown bear MHC, to examine levels of variation at this important immunology-mediating supergene. These data were used to answer the following questions: 1) are earlier findings of extremely low levels of variability at nuclear (biparentallyinherited) microsatellite loci from a small geographic area (Paetkau et al. 1998b) representative of Kodiak Archipelago populations as a whole? 2) Is the level and type of variation at the maternally-inherited mtDNA lower, or similar to, levels found in other populations in Alaska? 3) Is there concordance between low levels of genetic variation observed at neutral markers with levels of variation observed at functional genes? 4) Is there population substructuring within Kodiak and Afognak islands? 5) What is the connectivity between populations on Afognak Island and Kodiak Island? 6) What are the phylogeographic relationships between bears of the Kodiak Archipelago with brown bears on mainland Alaskan and other western Beringian populations? We also test whether these markers will provide an appropriate baseline for designing genetic tagging studies for use in future research and management activities, such as mark-recapture efforts, on the Refuge.

Alaska↗

USGS2018

A test of sex specific genetic markers in the Hawaiian hoary bat and relevance to population studies

We tested the utility of a protocol using genetic markers that previously proved successful to identify the sex of Vespertilionid bats on tissues collected from live bats and carcasses of varying age from the Hawaiian hoary bat (Lasiurus cinereus semotus). This molecular method is based on genes unique to X and Y chromosomes in mammals and previously was used successfully on North American hoary bats (L. c. cinereus). We amplified two markers within intron regions of the zinc-finger-X (Zfx) and zinc-finger-Y (Zfy) genes using a multiplexed polymerase chain reaction technique and obtained product bands that were easily visualized using gel electrophoresis. Genotyping determined the sex of 36 individual Hawaiian hoary bat carcasses previously assigned sex only by external genitalia and identified sex for 29 “unknown” bat carcasses that could not be classified by external genitalia. Employing this method for sexing Hawaiian hoary bats will permit more reliable evaluation of the ratio of males to females in subpopulations affected by fatalities from emerging threats. This is critical to the conservation and management of this endangered bat.

Technical Report↗

USGS2019

Using environmental DNA (eDNA) to assess the presence of cavefish and cave crayfish populations in caves of the Ozark Highlands

Many cavefishes and cave crayfishes are considered of conservation concern; however, sampling these species is inherently difficult given their occupied environments. The goal of our project was to verify the presence of select karst organisms while developing the foundation for sampling approaches that might be useful to conservation and management agencies. Our project objectives were to develop assays to amplify deoxyribonucleic acid (DNA) from several species of Ozark cavefishes and cave crayfishes and complete an initial surveillance of locations across the Ozark Highlands using environmental DNA (eDNA). Using DNA either provided by agency cooperators or that we extracted from tissue samples, we PCR amplified and then sequenced the Cytochrome Oxidase 1 (CO1) gene for cave crayfishes and the NADH Dehydrogenase Subunit 2 (ND2) gene for cavefishes. We developed species-specific primers and probes for five cave crayfishes and two cavefishes. From February 2017 to May 2017, we sampled 1–5 sampling units from 42 caves, wells, and springs (i.e., sites) using eDNA and traditional visual surveys. We measured physicochemical parameters at each sampling unit to estimate detection probability associated with both techniques. We also calculated two occupancy covariates for each site using geospatial data. We successfully amplified Troglichthys rosae DNA from the environment and detected DNA representing this species at 24 of 40 sites. At 16 of the sites where we detected T. rosae DNA, we did not visually observe the species. Although our assay for Typlichthys eigenmanni successfully amplified the target DNA from the environment, it also resulted in false absences where the species was visually confirmed. Using eDNA to detect cave crayfishes was much more difficult. The assay for Cambarus subterraneus did not work for eDNA samples and we were unable to pick up DNA from the environment, even at locations where it was visually confirmed. Alternatively, the eDNA surveys worked well for C. tartarus and we were able to amplify DNA at every site where it was visually observed. Our assay for C. aculabrum was based on a single sample obtained from GenBank, and did not amplify eDNA from field samples. Lastly, our eDNA results from samples in the known range of Orconectes stygocaneyi suggested the species may be found at an additional cave. Detection using eDNA based on our O. stygocaneyi assay was likely low because it was designed from a pseudogene; however, positive eDNA samples were sequenced to confirm species-specific DNA. Detection probability of both cavefishes and cave crayfishes varied by survey technique and was influenced by water volume, water clarity, water velocity, and substrate. Detection of cavefishes and cave crayfishes via visual surveys decreased when water volume increased, whereas detection using eDNA increased with greater water volume. Detection between taxa using either sample method was highest in habitats classified by fine substrates, except for eDNA detection of crayfishes which was greatest in coarse substrates. Detection of cavefishes increased with water clarity, but detection of cave crayfishes increased with turbidity. Detection probability of both cavefishes and crayfishes using eDNA increased slightly with water velocity, but decreased with visual surveys as water velocity increased. Occupancy by both taxa was positively related to particular geologic series. Crayfish occupancy was negatively related to fine-scale anthropogenic disturbance (i.e., 500-m buffer around the site), whereas crayfish showed no relationship with disturbance. Our results suggest possible range extensions, provide insights to factors driving detection using both sample techniques, and suggest areas where recharge zones may be shared among caves. Future efforts focused on a comprehensive evaluation of genetic diversity among cave crayfishes to improve assay design could improve detection and the applicability of eDNA as a supplemental and non-invasive sampling approach.

Cooperator Science Series↗

USGS2000

Description and identification of American Black Duck, Mallard, and hybrid wing plumage

We developed a key to identify wings of hybrids between American Black Ducks (Anas rubripes) and Mallards (A. platyrhynchos). Material for analysis included review of historical descriptions dating from the late 1700's, older museum collections in Europe and North America, wings collected from hunters in North America and Great Britain, birds banded in Canada and the United States, and a flock of propagated hybrids. All first filial generation (F1) American Black Duck - Mallard hybrids were identified correctly with the key. A lower proportion of other hybrid cohorts (i.e., backcrosses of F1 to parental forms (P1), and second and third filial generations (F2, F3, etc.) were identified. We successfully identified a larger portion of male than female hybrids for all hybrid progeny cohorts examined except F1. The new key identified 2.37 times more hybrids in the 1977 U.S. Fish and Wildlife Service Parts Collection Survey (annual determination of the species, age, and sex composition of the waterfowl harvest using detached wings contributed by hunters) than were identified by standard techniques. The proportion of American Black Duck - Mallard hybrids to the American Black Duck parental population (the ratio: hybrids/[hybrids + American Black Ducks]) may therefore be closer to 0.132 than 0.056, the historically reported value. The hybrid key is suggested for use from North Carolina north in the Atlantic Flyway and Arkansas and Tennessee north in the Mississippi Flyway (areas where other members of the Mallard group will not confound assessment). We provide suggestions for further research that would assist identification of wings in parts collection surveys and permit estimation of the proportional representation of Mallard genes in the American Black Duck gene pool.

Report↗

USGS2016

A network model framework for prioritizing wetland conservation in the Great Plains

Context Playa wetlands are the primary habitat for numerous wetland-dependent species in the Southern Great Plains of North America. Plant and wildlife populations that inhabit these wetlands are reciprocally linked through the dispersal of individuals, propagules and ultimately genes among local populations. Objective To develop and implement a framework using network models for conceptualizing, representing and analyzing potential biological flows among 48,981 spatially discrete playa wetlands in the Southern Great Plains. Methods We examined changes in connectivity patterns and assessed the relative importance of wetlands to maintaining these patterns by targeting wetlands for removal based on network centrality metrics weighted by estimates of habitat quality and probability of inundation. Results We identified several distinct, broad-scale sub networks and phase transitions among playa wetlands in the Southern Plains. In particular, for organisms that can disperse > 2 km a dense and expansive wetland sub network emerges in the Southern High Plains. This network was characterized by localized, densely connected wetland clusters at link distances ( h ) >2 km but <5 km and was most sensitive to changes in wetland availability ( p ) and configuration when h = 4 km, and p = 0.2–0.4. It transitioned to a single, large connected wetland system at broader spatial scales even when the proportion of inundated wetland was relatively low ( p = 0.2). Conclusions Our findings suggest that redundancy in the potential for broad and fine-scale movements insulates this system from damage and facilitates system-wide connectivity among populations with different dispersal capacities.

New Mexico, Texas↗

USGS2022

Exploring genetic variation and population structure in a threatened species, Noturus placidus, with whole-genome sequence data

The Neosho madtom ( Noturus placidus ) is a small catfish, generally less than 3 inches in length, unique to the Neosho-Spring River system within the Arkansas River Basin. It was federally listed as threatened in 1990, largely due to habitat loss. For conservation efforts, we generated whole-genome sequence data from 10 Neosho madtom individuals originating from 3 geographically separated populations to evaluate genetic diversity and population structure. A Neosho madtom genome was de novo assembled, and genome size and content were assessed. Single nucleotide polymorphisms were assessed from de Bruijn graphs, and via reference alignment with both the channel catfish ( Ictalurus punctatus) reference genome and Neosho madtom reference genome. Principal component analysis and structure analysis indicated weak population structure, suggesting fish from the 3 locations represent a single population. Using a novel method, genome-wide conservation and divergence between the Neosho madtom, channel catfish, and zebrafish ( Danio rerio ) was assessed by pairwise contig alignment, which demonstrated that genes important to embryonic development frequently had conserved sequences. This research in a threatened species with no previously published genomic resources provides novel genetic information to guide current and future conservation efforts and demonstrates that using whole-genome sequencing provides detailed information of population structure and demography using only a limited number of rare and valuable samples.

Arkansas, Kansas, Missouri, Oklahoma↗

USGS2022

Avian-associated Aspergillus fumigatus displays broad phylogenetic distribution, no evidence for host specificity, and multiple genotypes within epizootic events

Birds are highly susceptible to aspergillosis, which can manifest as a primary infection in both domestic and wild birds. Aspergillosis in wild birds causes mortalities ranging in scale from single animals to large-scale epizootic events. However, pathogenicity factors associated with aspergillosis in wild birds have not been examined. Specifically, it is unknown whether wild bird-infecting strains are host-adapted (i.e. phylogenetically related). Similarly, it is unknown whether epizootics are driven by contact with clonal strains that possess unique pathogenic or virulence properties, or by distinct and equally pathogenic strains. Here, we use a diverse collection of Aspergillus fumigatus isolates taken from aspergillosis-associated avian carcasses, representing 24 bird species from a wide geographic range, and representing individual bird mortalities as well as epizootic events. These isolates were sequenced and analyzed along with 130 phylogenetically diverse human clinical isolates to investigate the genetic diversity and phylogenetic placement of avian-associated A. fumigatus , the geographic and host distribution of avian isolates, evidence for clonal outbreaks among wild birds, and the frequency of azole resistance in avian isolates. We found that avian isolates were phylogenetically diverse, with no clear distinction from human clinical isolates, and no sign of host or geographic specificity. Avian isolates from the same epizootic events were diverse and phylogenetically distant, suggesting that avian aspergillosis is not contagious among wild birds and that outbreaks are likely driven by environmental spore loads or host comorbidities. Finally, all avian isolates were susceptible to Voriconazole and none contained the canonical azole resistance gene variants.

G3 Genes|Genomes|Genetics↗

USGS1999

Molecular and immunogenetic analysis of major histocompatibility haplotypes in northern bobwhite enable direct identification of corresponding haplotypes in an endangered subspecies, the masked bobwhite

The major histocompatibility complex (MHC) is a group of genetic loci coding for haplotypes that have been associated with fitness traits in mammals and birds. Such associations suggest that MHC diversity may be an indicator of overall genetic fitness of endangered or threatened species. The MHC haplotypes of a captive population of 12 families of northern bobwhites ( Colinus virginianus ) were identified using a combination of immunogenetic and molecular techniques. Alloantisera were produced within families of northern bobwhites and were then tested for differential agglutination of erythrocytes of all members of each family. The pattern of reactions determined from testing these alloantisera identified a single genetic system of alloantigens in the northern bobwhites, resulting in the assignment of a tentative genotype to each individual within the quail families. Restriction fragment patterns of the DNA of each bird were determined using the chicken MHC B-G cDNA probe bg11 . The concordance between the restriction fragment patterns and the alloantisera reactions showed that the alloantisera had identified the MHC of the northern bobwhite and supported the tentative genotype assignments, identifying at least 12 northern bobwhite MHC haplotypes. Eighteen northern bobwhite alloantisera were then used to detect a minimum of 17 masked bobwhite MHC haplotypes. Subsequent restriction fragment pattern analyses using cDNA probes for chicken MHC genes were in agreement with agglutination patterns displayed by the antisera, showing that the immunogenetically identified alloantigen system constituted the MHC of the masked bobwhite. These data demonstrate that a non-endangered species may be used to provide antisera for differentiating MHC haplotypes in a closely related endangered species, thus providing a practical basis for long-range monitoring of MHC haplotypes of birds surviving in their native habitats.

Zoo Biology↗

USGS2017

Spatial heterogeneity of within-stream methane concentrations

Streams, rivers, and other freshwater features may be significant sources of CH 4 to the atmosphere. However, high spatial and temporal variabilities hinder our ability to understand the underlying processes of CH 4 production and delivery to streams and also challenge the use of scaling approaches across large areas. We studied a stream having high geomorphic variability to assess the underlying scale of CH 4 spatial variability and to examine whether the physical structure of a stream can explain the variation in surface CH 4 . A combination of high-resolution CH 4 mapping, a survey of groundwater CH 4 concentrations, quantitative analysis of methanogen DNA, and sediment CH 4 production potentials illustrates the spatial and geomorphic controls on CH 4 emissions to the atmosphere. We observed significant spatial clustering with high CH 4 concentrations in organic-rich stream reaches and lake transitions. These sites were also enriched in the methane-producing mcrA gene and had highest CH 4 production rates in the laboratory. In contrast, mineral-rich reaches had significantly lower concentrations and had lesser abundances of mcrA . Strong relationships between CH 4 and the physical structure of this aquatic system, along with high spatial variability, suggest that future investigations will benefit from viewing streams as landscapes, as opposed to ecosystems simply embedded in larger terrestrial mosaics. In light of such high spatial variability, we recommend that future workers evaluate stream networks first by using similar spatial tools in order to build effective sampling programs.

Journal of Geophysical Research G: Biogeosciences↗

USGS2021

The role of genome duplication in big sagebrush growth and fecundity

Premise Adaptive traits can be dramatically altered by genome duplication. The study of interactions among traits, ploidy, and the environment are necessary to develop an understanding of how polyploidy affects niche differentiation and to develop restoration strategies for resilient native ecosystems. Methods Growth and fecundity were measured in common gardens for 39 populations of big sagebrush ( Artemisia tridentata ) containing two subspecies and two ploidy levels. General linear mixed-effect models assessed how much of the trait variation could be attributed to genetics (i.e., ploidy and climatic adaptation), environment, and gene–environment interactions. Results Growth and fecundity variation were explained well by the mixed models (80% and 91%, respectively). Much of the trait variation was attributed to environment, and 15% of variation in growth and 34% of variation in seed yield were attributed to genetics. Genetic trait variation was mostly attributable to ploidy, with much higher growth and seed production in diploids, even in a warm-dry environment typically dominated by tetraploids. Population-level genetic variation was also evident and was related to the climate of each population's origin. Conclusions Ploidy is a strong predictor growth and seed yield, regardless of common-garden environment. The superior growth and fecundity of diploids across environments raises the question as to how tetraploids can be more prevalent than diploids, especially in warm-dry environments. Two hypotheses that may explain the abundance of tetraploids on the landscape include selection for drought resistance at the seedling stage, and greater competitive ability in water uptake in the upper soil horizon.

American Journal of Botany↗

USGS2019

Detecting the undetectable: Characterization, optimization, and validation of an eDNA detection assay for the federally endangered dwarf wedgemussel, Alasmidonta heterodon (Bivalvia: Unionoida)

Environmental (e)DNA assays are valuable tools for monitoring presence and distribution of cryptic species. Like many freshwater mussels, the dwarf wedgemussel, Alasmidonta heterodon numbers have dwindled and its range has diminished. As of its listing in 1993, only 10 to 20 locations were known to persist of the 70 Atlantic slope locations known historically. A qPCR assay to detect the presence of A. heterodon was developed that uses two probes to accommodate a single nucleotide polymorphism (SNP) in the probe binding site within the cytochrome oxidase I (COI) gene. This SNP defines northern and southern major phylogenetic lineages. The primers match exactly the previously determined cytochrome oxidase I sequences of twenty dwarf wedgemussel individuals representing Atlantic slope populations from North Carolina, Virginia, Maryland, New York, and New Hampshire. Other than for the qPCR assay described here these primers can be used for sequencing and/or metabarcoding to further delineate dwarf wedgemussel populations phylogenetically. A simple eDNA preparation method is introduced using flocculation to concentrate free DNA in solution as well as cellular material (including shed animal cells, bacteria, virus, and dissolved DNA). In addition to the specific application described here, the methodological approaches used in this study are widely applicable to the study of conservation issues including, but not limited to general aquatic biodiversity, phylogenetic studies, and detection of pathogenic microbes.

North Carolina, Virginia, Maryland, New York, New ↗

USGS2003

Left-Right Asymmetric Morphogenesis in the Xenopus Digestive System

The morphogenetic mechanisms by which developing organs become left-right asymmetric entities are unknown. To investigate this issue, we compared the roles of the left and right sides of the Xenopus embryo during the development of anatomic asymmetries in the digestive system. Although both sides contribute equivalently to each of the individual digestive organs, during the initial looping of the primitive gut tube, the left side assumes concave topologies where the right side becomes convex. Of interest, the concave surfaces of the gut tube correlate with expression of the LR gene, Pitx2, and ectopic Pitx2 mRNA induces ectopic concavities in a localized manner. A morphometric comparison of the prospective concave and convex surfaces of the gut tube reveals striking disparities in their rate of elongation but no significant differences in cell proliferation. These results provide insight into the nature of symmetry-breaking morphogenetic events during left-right asymmetric organ development. ?? 2003 Wiley-Liss, Inc.

Developmental Dynamics↗