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Melanie Culver

Publications and source records attributed to Melanie Culver.

At least 37 records · Page 2Linked to original sources

Genetic variation among island and continental populations of Burrowing Owl (Athene cunicularia) subspecies in North America

Burrowing Owls ( Athene cunicularia ) have a large geographic range spanning both North and South America and resident populations occur on many islands in the eastern Pacific Ocean and the Caribbean Sea. Many owl populations are isolated and disjunct from other populations, but studies on genetic variation within and among populations are limited. We characterized DNA microsatellite variation in populations varying in size and geographic isolation in the Florida ( A. c. floridana ), the Western ( A. c. hypugaea ), and the Clarion ( A. c. rostrata ) subspecies of the Burrowing Owl. We also characterized genetic variation in a geographically isolated population of the western subspecies in central Mexico (near Texcoco Lake). Clarion Burrowing Owls had no intrapopulation variation (i.e., fixation) at 5 out of 11 microsatellite loci, a likely outcome of genetic drift in an isolated and small population. The Florida subspecies had only polymorphic loci but had reduced levels of genetic variation compared with the more-widespread western subspecies that occurs throughout western North America. Despite the extensive geographic distribution of the Western Burrowing Owl, we found genetic differentiation between the panmictic population north of the Trans-Mexican Volcanic Belt and the resident Texcoco Lake population in central Mexico.

Journal of Raptor Research

Genetic assessment of a bighorn sheep population expansion in the Silver Bell Mountains, Arizona

Background: The isolated population of desert bighorn sheep in the Silver Bell Mountains of southern Arizona underwent an unprecedented expansion in merely four years. We hypothesized that immigration from neighboring bighorn sheep populations could have caused the increase in numbers as detected by Arizona Game and Fish Department annual aerial counts. Methods: We applied a multilocus genetic approach using mitochondrial DNA and nuclear microsatellite markers for genetic analyses to find evidence of immigration. We sampled the Silver Bell Mountains bighorn sheep before (2003) and during (2015) the population expansion, and a small number of available samples from the Gila Mountains (southwestern Arizona) and the Morenci Mine (Rocky Mountain bighorn) in an attempt to identify the source of putative immigrants and, more importantly, to serve as comparisons for genetic diversity metrics. Results: We did not find evidence of substantial gene flow into the Silver Bell Mountains population. We did not detect any new mitochondrial haplotypes in the 2015 bighorn sheep samples. The microsatellite analyses detected only one new allele, in one individual from the 2015 population that was not detected in the 2003 samples. Overall, the genetic diversity of the Silver Bell Mountains population was lower than that seen in either the Gila population or the Morenci Mine population. Discussion: Even though the results of this study did not help elucidate the precise reason for the recent population expansion, continued monitoring and genetic sampling could provide more clarity on the genetic demographics of this population. Keywords: Bighorn sheep; Microsatellites; Migration; Mitochondrial DNA; Ovis canadensis; Population growth; Silver Bell Mountains.

Arizona

Genome-wide analysis of SNPs is consistent with no domestic dog ancestry in the endangered Mexican Wolf (Canis lupus baileyi)

The Mexican gray wolf ( Canis lupus baileyi ) was historically distributed throughout the southwestern United States and northern Mexico. Extensive predator removal campaigns during the early 20th century, however, resulted in its eventual extirpation by the mid 1980s. At this time, the Mexican wolf existed only in 3 separate captive lineages (McBride, Ghost Ranch, and Aragón) descended from 3, 2, and 2 founders, respectively. These lineages were merged in 1995 to increase the available genetic variation, and Mexican wolves were reintroduced into Arizona and New Mexico in 1998. Despite the ongoing management of the Mexican wolf population, it has been suggested that a proportion of the Mexican wolf ancestry may be recently derived from hybridization with domestic dogs. In this study, we genotyped 87 Mexican wolves, including individuals from all 3 captive lineages and cross-lineage wolves, for more than 172000 single nucleotide polymorphisms. We identified levels of genetic variation consistent with the pedigree record and effects of genetic rescue. To identify the potential to detect hybridization with domestic dogs, we compared our Mexican wolf genotypes with those from studies of domestic dogs and other gray wolves. The proportion of Mexican wolf ancestry assigned to domestic dogs was only between 0.06% (SD 0.23%) and 7.8% (SD 1.0%) for global and local ancestry estimates, respectively; and was consistent with simulated levels of incomplete lineage sorting. Overall, our results suggested that Mexican wolves lack biologically significant ancestry with dogs and have useful implications for the conservation and management of this endangered wolf subspecies.

Journal of Heredity

Evolutionary and functional mitogenomics associated with the genetic restoration of the Florida panther

Florida panthers are endangered pumas that currently persist in reduced patches of habitat in South Florida, USA. We performed mitogenome reference-based assemblies for most parental lines of the admixed Florida panthers that resulted from the introduction of female Texas pumas into South Florida in 1995. With the addition of 2 puma mitogenomes, we characterized 174 single nucleotide polymorphisms (SNPs) across 12 individuals. We defined 5 haplotypes (Pco1–Pco5), one of which (Pco1) had a geographic origin exclusive to Costa Rica and Panama and was possibly introduced into the Everglades National Park, Florida, prior to 1995. Haplotype Pco2 was native to Florida. Haplotypes Pco3 and Pco4 were exclusive to Texas, whereas haplotype Pco5 had an undetermined geographic origin. Phylogenetic inference suggests that haplotypes Pco1–Pco4 diverged ~202000 (95% HPDI = 83000–345000) years ago and that haplotypes Pco2–Pco4 diverged ~61000 (95% HPDI = 9000–127000) years ago. These results are congruent with a south-to-north continental expansion and with a recent North American colonization by pumas. Furthermore, pumas may have migrated from Texas to Florida no earlier than ~44000 (95% HPDI = 2000–98000) years ago. Synonymous mutations presented a greater mean substitution rate than other mitochondrial functional regions: nonsynonymous mutations, tRNAs, rRNAs, and control region. Similarly, all protein-coding genes were under predominant negative selection constraints. We directly and indirectly assessed the presence of potential deleterious SNPs in the ND2 and ND5 genes in Florida panthers prior to and as a consequence of the introduction of Texas pumas. Screenings for such variants are recommended in extant Florida panthers.

Journal of Heredity

Jaguar taxonomy and genetic diversity for southern Arizona, United States, and Sonora, Mexico

Executive Summary The jaguar is the largest Neotropical felid and the only extant representative of the genus Panthera in the Americas. In recorded history, the jaguars range has extended from the Southern United States, throughout Mexico, to Central and South America, and they occupy a wide variety of habitats. A previous jaguar genetic study found high historical levels of gene flow among jaguar populations over broad areas but did not include any samples of jaguar from the States of Arizona, United States, or Sonora, Mexico. Arizona and Sonora have been part of the historical distribution of jaguars; however, poaching and habitat fragmentation have limited their distribution until they were declared extinct in the United States and endangered in Sonora. Therefore, a need was apparent to have this northernmost (Arizona/Sonora) jaguar population included in an overall jaguar molecular taxonomy and genetic diversity analyses. In this study, we used molecular genetic markers to examine diversity and taxonomy for jaguars in the Northwestern Jaguar Recovery Unit (NJRU; Sonora, Sinaloa, and Jalisco, Mexico; and southern Arizona and New Mexico, United States) relative to jaguars in other parts of the jaguar range (Central and South America). The objectives of this study were to: Collect opportunistic jaguar samples (hide, blood, hair, saliva, and scat), from historical and current individuals, that originated in NJRU areas of Arizona, New Mexico, and Sonora; Use these samples to assess molecular taxonomy of NJRU jaguars compared to data from a previous study of jaguars rangewide; and Develop suggestions for conservation of NJRU jaguars based on the results.

Arizona, Jalisco, New Mexico, Sonora, Sinaloa

Diet of pumas ( Puma concolor ) in Sonora, Mexico, as determined by GPS kill sites and molecular identified scat, with comments on jaguar ( Panthera onca ) diet

We documented puma ( Puma concolor ) and jaguar ( Panthera onca ) prey consumption in northeastern Sonora, Mexico, by investigating global positioning system cluster sites ( n = 220), and conducting molecular analyses of scat ( n = 116) collected between 2011 and 2013. We used camera trap data ( n = 8,976 camera days) to estimate relative abundances of pumas and jaguars. Deer ( Odocoileus virginianus ) was the most frequent prey for puma found at kill sites (67%) and identified from scat (74%), although based on relative numbers of prey consumed, deer represented 45% and lagomorphs 20% of the proportion of all individuals eaten. A variety of small prey (weighing <15 kg) comprised the majority (52%) of the jaguar kill sites. From prey found at kill sites, jaguars killed calves ( Bos taurus ) at a lower frequency than previously reported, whereas pumas preyed on calves at a higher frequency than previously reported in the same area. In our study area, jaguars preyed on calves at approximately the same rate as pumas (jaguars 3.7 calves per year, pumas 4.9 calves per year). Calculated predation rates were limited only to collared animals within our study area and therefore should not be considered applicable to all pumas and jaguars in Sonora.

Sonora

Jaguar surveying and monitoring in the United States

Because of the jaguar&rsquo;s ( Panthera onca ) endangered status under the Endangered Species Act (ESA) of 1973 throughout its range (from Arizona in the north to Argentina in the south), jaguar individuals and populations are monitored to varying degrees throughout their range. Knowledge gained from monitoring jaguars is helpful for wildlife managers who are responsible for conserving this species. The University of Arizona (UA) has conducted a multiyear surveying and monitoring effort for jaguars and ocelots in southern Arizona and New Mexico. The purpose of this work was to establish an effective surveying and monitoring system for jaguars along the United States-Mexico border. Surveying and monitoring in this study focused on the United States side of the border, but the methods could also be used in Mexico. The intent was to develop and implement a surveying and monitoring system that would provide the greatest probability of recording jaguar presence in, and passage through, the border area. This project established and implemented a noninvasive system for detecting and monitoring jaguars. The study area incorporates most of the mountainous areas north of the United States-Mexico international border and south of Interstate 10, from the Baboquivari Mountains in Arizona to the Animas Mountains in New Mexico. We used two primary methods to detect exact jaguar locations: paired motion-sensor trail cameras, and genetic testing of large carnivore scat collected in the field. We emphasize that this project used entirely noninvasive methods and no jaguars were captured, radiocollared, baited, or harassed in any way. Scat sample collection occurred during the entire field part of the study, but was intensified with the use of a trained scat detection dog following the first jaguar photo detection event (photo detection event was October 2012, scat detection dog began working January 2013). We also collected weather, vegetation, and geographic information system (GIS) data to analyze in conjunction with photo and video data. The results of this study are intended to aid and inform future management and conservation practices for jaguars and ocelots in this region.

Arizona, California, New Mexico, Texas

Can captive populations function as sources of genetic variation for reintroductions into the wild? A case study of the Arabian oryx from the Phoenix Zoo and the Shaumari Wildlife Reserve, Jordan

The Arabian oryx ( Oryx leucoryx ) historically ranged across the Arabian Peninsula and neighboring countries until its extirpation in 1972. In 1963&ndash;1964 a captive breeding program for this species was started at the Phoenix Zoo (PHX); it ultimately consisted of 11 animals that became known as the &lsquo;World Herd&rsquo;. In 1978 &ndash; 1979 a wild population was established at the Shaumari Wildlife Reserve (SWR), Jordan, with eight descendants from the World Herd and three individuals from Qatar. We described the mtDNA and nuclear genetic diversity and structure of PHX and SWR. We also determined the long-term demographic and genetic viability of these populations under different reciprocal translocation scenarios. PHX displayed a greater number of mtDNA haplotypes ( n = 4) than SWR ( n = 2). Additionally, PHX and SWR presented nuclear genetic diversities of N &macr; A N&macr;A = 2.88 vs. 2.75, H &macr; O H&macr;O = 0.469 vs. 0.387, and H &macr; E H&macr;E = 0.501 vs. 0.421, respectively. Although these populations showed no signs of inbreeding ( F &macr; IS F&macr;IS &asymp; 0), they were highly differentiated ( G &prime; &prime; ST GST&prime;&prime; = 0.580; P < 0.001). Migration between PHX and SWR ( Nm = 1, 4, and 8 individuals/generation) increased their genetic diversity in the short-term and substantially reduced the probability of extinction in PHX during 25 generations. Under such scenarios, maximum genetic diversities were achieved in the first generations before the effects of genetic drift became predominant. Although captive populations can function as sources of genetic variation for reintroduction programs, we recommend promoting mutual and continuous gene flow with wild populations to ensure the long-term survival of this species.

Conservation Genetics

Assessing models of speciation under different biogeographic scenarios; An empirical study using multi-locus and RNA-seq analyses

Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus . These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNA and four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree. RNA‐seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ∂a∂i serve to test the null hypothesis of no gene flow during divergence. The best‐fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ∂a∂i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).

Ecology and Evolution

Molecular detection of bacteria in the families Rickettsiaceae and Anaplasmataceae in northern crested caracaras ( Caracara cheriway )

Bacterial pathogens of the families Anaplasmataceae and Rickettsiaceae are often spread to humans or other animals from bites from infected arthropod hosts. Recently, an increasing number of studies have implicated migratory birds in the circulation of these pathogens through the spread of arthropod vectors. However, few studies have examined the potential for resident bird populations to serve as reservoirs for these zoonoses. In this study, we used nested PCRs of the GroESL and 17 kDa genes to screen for Anaplasmataceae and Rickettsiaceae , respectively, in a resident population of the northern crested caracara ( Caracara cheriway ) from Florida ( n = 55). Additionally, a small number ( n = 6) of captive individuals from Texas were included. We identified one individual (1.64%) positive for Rickettsia felis and one (1.64%) positive for Ehrlichia chaffeensis; both these individuals were from Florida. Presence of these pathogens demonstrates that these birds are potential hosts; however, the low prevalence of infections suggests that these populations likely do not function as an ecological reservoir.

Ticks and Tick-borne Diseases

Shaping species with ephemeral boundaries: The distribution and genetic structure of desert tortoise ( Gopherus morafkai ) in the Sonoran Desert region

Aim We examine the role biogeographical features played in the evolution of Morafka's desert tortoise ( Gopherus morafkai ) and test the hypothesis that G. morafkai maintains genetically distinct lineages associated with different Sonoran Desert biomes. Increased knowledge of the past and present distribution of the Sonoran Desert region's biota provides insight into the forces that drive and maintain its biodiversity. Location Sonoran Desert biogeographical region; Sonora and Sinaloa, Mexico and Arizona, USA. Methods We examined wild tortoises from Mexico ( n = 155) and Arizona ( n = 78), spanning their known distribution. We used mtDNA sequences to reconstruct matrilineal relationships and 25 microsatellite (STR) loci for Bayesian analyses of gene flow. We performed clinal analyses on both mtDNA and STR loci to determine the position and amount of introgression where lineages co-occur. We used GIS to assess the association of genetic structuring with ecological features. We used these data in a hypothesis-driven approach to assess different models of how genetic diversity is maintained and distributed in G. morafkai . Results Gopherus morafkai was found to comprise genetically and geographically distinct &lsquo;Sonoran&rsquo; and &lsquo;Sinaloan&rsquo; lineages. Both lineages occurred in a relatively narrow zone of overlap in Sinaloan thornscrub, where it transitions into Sonoran desertscrub. Limited introgression occurred at the contact zone. The best-fit model suggests that these lineages diverged in parapatry where the distribution of genotypes is environment-dependent and introgression is inhibited by exogenous selection. Main conclusions The historically shifting ecotone between tropical deciduous forest and Sonoran desertscrub appears to be a boundary that fostered divergence between parapatric lineages of tortoises. The sharp genetic cline between the two lineages suggests that periods of isolation in temporary refugia due to Pleistocene climatic cycling influenced divergence. Despite incomplete reproductive isolation, the Sonoran and Sinaloan lineages of G. morafkai are on separate evolutionary trajectories.

Arizona, Sonora

A new panel of SNP markers for the individual identification of North American pumas

Pumas Puma concolor are one of the most studied terrestrial carnivores because of their widespread distribution, substantial ecological impacts, and conflicts with humans. Over the past decade, managing pumas has involved extensive efforts including the use of genetic methods. Microsatellites have been the most commonly used genetic markers; however, technical artifacts and little overlap of frequently used loci render large-scale comparison of puma genetic data across studies challenging. Therefore, a panel of genetic markers that can produce consistent genotypes across studies without the need for extensive calibrations is essential for range-wide genetic management of puma populations. Here, we describe the development of PumaPlex, a high-throughput assay to genotype 25 single nucleotide polymorphisms in pumas. We validated PumaPlex in 748 North American pumas Puma concolor couguar, and demonstrated its ability to generate reproducible genotypes and accurately identify individuals. Furthermore, in a test using fecal deoxyribonucleic acid (DNA) samples, we found that PumaPlex produced significantly more genotypes with fewer errors than 12 microsatellite loci, 8 of which are commonly used. Our results demonstrate that PumaPlex is a valuable tool for the genetic monitoring and management of North American puma populations. Given the analytical simplicity, reproducibility, and high-throughput capability of single nucleotide polymorphisms, PumaPlex provides a standard panel of markers that promotes the comparison of genotypes across studies and independent of the genotyping technology used.

Journal of Fish and Wildlife Management

Testing taxon tenacity of tortoises: evidence for a geographical selection gradient at a secondary contact zone

We examined a secondary contact zone between two species of desert tortoise, Gopherus agassizii and G. morafkai . The taxa were isolated from a common ancestor during the formation of the Colorado River (4-8 mya) and are a classic example of allopatric speciation. However, an anomalous population of G. agassizii comes into secondary contact with G. morafkai east of the Colorado River in the Black Mountains of Arizona and provides an opportunity to examine reinforcement of species' boundaries under natural conditions. We sampled 234 tortoises representing G. agassizii in California ( n = 103), G. morafkai in Arizona ( n = 78), and 53 individuals of undetermined assignment in the contact zone including and surrounding the Black Mountains. We genotyped individuals for 25 STR loci and determined maternal lineage using mtDNA sequence data. We performed multilocus genetic clustering analyses and used multiple statistical methods to detect levels of hybridization. We tested hypotheses about habitat use between G. agassizii and G. morafkai in the region where they co-occur using habitat suitability models. Gopherus agassizii and G. morafkai maintain independent taxonomic identities likely due to ecological niche partitioning, and the maintenance of the hybrid zone is best described by a geographical selection gradient model.

Ecology and Evolution

Development and characterization of polymorphic microsatellitemarkers for the crested caracara, Caracara cheriway

We isolated novel microsatellites from the crested caracara ( Caracara cheriway ) with a shotgun pyrosequencing approach. We tested 80 loci for polymorphism among 20 individuals from the threatened Florida population. Fourteen loci were polymorphic. The mean number of alleles was 2.21 (range 2–3) and the mean observed heterozygosity was 0.41 (range 0.15–0.65). None of the 14 polymorphic loci exhibited significant linkage disequilibrium nor did they deviate significantly from Hardy–Weinberg expectations. We also report 16 monomorphic loci.

Florida

Characterization of microsatellite loci from two-spotted octopus Octopus bimaculatus Verrill 1883 from pyrosequencing reads

We characterized 22 novel microsatellite loci in the two-spotted octopus Octopus bimaculatus using 454 pyrosequencing reads. All loci were polymorphic and will be used in studies of marine connectivity aimed at increasing sustainability of the resource. The mean number alleles per locus was 13.09 (range 7–19) and observed heterozygosities ranged from 0.50 to 1.00. Four loci pairs were linked and three deviated from Hardy–Weinberg equilibrium. Eighteen and 12 loci were polymorphic in Octopus bimaculoides and Octopus hubbsorum , respectively.

Conservation Genetics Resources

Genetic diversity and demography of two endangered captive pronghorn subspecies from the Sonoran Desert

Species that have experienced population reduction provide valuable case studies for understanding genetic responses to demographic change. Pronghorn (Antilocapra americana) were once widespread across the North American plains but were subject to drastic population reductions due to overexploitation and habitat fragmentation during the late 19th and early 20th centuries. A. a. peninsularis and A. a. sonoriensis, 2 pronghorn subspecies that inhabit the southern edge of the species' distribution, are almost extinct and now breed almost exclusively in captivity. We therefore sequenced the complete mitochondrial control region and genotyped 18 microsatellite loci in 109 individuals to evaluate the impact of population bottlenecks, captive breeding, small population sizes, and isolation on the genetic composition of captive populations of these 2 subspecies. We found extremely low levels of genetic diversity in both subspecies. The 2 subspecies showed high and significant genetic differentiation, indicating the absence of historic and recent gene flow despite their geographic proximity within the Sonoran Desert. Historical effective population size estimates for the 2 subspecies were inferred to be similar, whereas the Sonoran pronghorn has a contemporary effective size (Ne) more than twice as high as the Peninsular subspecies. Our findings suggest the need for careful genetic management of both subspecies in order to minimize the further loss of genetic variability.

Journal of Mammalogy

Severe reduction in genetic variation in a montane isolate: The endangered Mount Graham red squirrel (Tamiasciurus hudsonicus grahamensis)

The Mount Graham red squirrel ( Tamiasciurus hudsonicus grahamensis ; MGRS) is endemic to the Pinaleño Mountains of Arizona at the southernmost extent of the species’ range. The MGRS was listed as federally endangered in 1987, and is currently at high risk of extinction due to declining population size and increasing threats. Here we present a genetic assessment of the MGRS using eight nuclear DNA microsatellite markers and a 472 bp fragment of the mitochondrial cytochrome b gene. We analyzed 34 MGRS individuals and an additional 66 red squirrels from the nearby White Mountains, Arizona ( T. h. mogollonensis ). Both nuclear and mitochondrial DNA analyses revealed an extreme reduction in measures of genetic diversity relative to conspecifics from the White Mountains, suggesting that the MGRS has either experienced multiple bottlenecks, or a single long-term bottleneck. Additionally, we found a high degree of relatedness (mean = 0.75 ± 0.18) between individual MGRS. Our study implies that the MGRS may lack the genetic variation required to respond to a changing environment. This is especially important considering this region of the southwest United States is expected to experience profound effects from global climate change. The reduced genetic variability together with the high relatedness coefficients should be taken into account when constructing a captive population to minimize loss of the remaining genetic variation.

Conservation Genetics

Localized extinction of an arboreal desert lizard caused by habitat fragmentation

We adopted a species’ perspective for predicting extinction risk in a small, endemic, and strictly scansorial lizard ( Urosaurus nigricaudus ), in an old (∼60 year) and highly fragmented (8% habitat remaining) agricultural landscape from the Sonoran Desert, Mexico. We genotyped 10 microsatellite loci in 280 individuals from 11 populations in fragmented and continuous habitat. Individual dispersal was restricted to less than 400 m, according to analyses of spatial autocorrelation and spatially explicit Bayesian assignment methods. Within this scale, continuous areas and narrow washes with native vegetation allowed high levels of gene flow over tens of kilometers. In the absence of the native vegetation, cleared areas and highways were identified as partial barriers. In contrast, outside the scale of dispersal, cleared areas behaved as complete barriers, and surveys corroborated the species went extinct after a few decades in all small (less than 45 ha), isolated habitat fragments. No evidence for significant loss of genetic diversity was found, but results suggested fragmentation increased the spatial scale of movements, relatedness, genetic structure, and potentially affected sex-biased dispersal. A plausible threshold of individual dispersal predicted only 23% of all fragments in the landscape were linked with migration from continuous habitat, while complete barriers isolated the majority of fragments. Our study suggested limited dispersal, coupled with an inability to use a homogeneous and hostile matrix without vegetation and shade, could result in frequent time-delayed extinctions of small ectotherms in highly fragmented desert landscapes, particularly considering an increase in the risk of overheating and a decrease in dispersal potential induced by global warming.

Sonoran Desert