Geology topics

Adrian Munguia-Vega

Publications and source records attributed to Adrian Munguia-Vega.

10 recordsLinked to original sources

USGS2023

Chromosome-level genome assembly of the blacktail brush lizard, Urosaurus nigricaudus, reveals dosage compensation in an endemic lizard

Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87 Gb distributed in 327 scaffolds, with an N50 of 279 Mb and an L50 of 3. Approximately 98.4% of the genome is contained in 14 scaffolds, with 6 large scaffolds (334–127 Mb) representing macrochromosomes and 8 small scaffolds (63–22 Mb) representing microchromosomes. Using standard gene modeling and transcriptomic data, we predicted 17,902 protein-coding genes on the genome. The repeat content is characterized by a large proportion of long interspersed nuclear elements that are relatively old. Synteny analysis revealed some microchromosomes with high repeat content are more prone to rearrangements but that both macro- and microchromosomes are well conserved across reptiles. We identified scaffold 14 as the X chromosome. This microchromosome presents perfect dosage compensation where the single X of males has the same expression levels as two X chromosomes in females. Finally, we estimated the effective population size for U. nigricaudus was extremely low, which may reflect a reduction in polymorphism related to it becoming a peninsular endemic.

Genome Biology and Evolution↗

USGS2022

Tracking the desert's edge with a Pleistocene relict

In addition to the Sky Islands of the southwestern U.S. and northwestern Mexico, a series of 900–1200 m desert peaks surrounded by arid lowlands support temperate affiliated species at their summits. The presence of disjunct long-lived plant taxa on under-explored desert mountains, especially Isla Tiburón at 29° latitude in the Gulf of California, suggests a more southerly extent of Ice Age woodlands than previously understood. The phylogeography of the desert edge species Canotia holacantha (Celastraceae) was investigated to test the hypothesis that insular desert peak populations represent remnants of Pleistocene woodlands rather than recent dispersal events. Sequences of four chloroplast DNA regions totaling 2032 bp were amplified from 74 individuals of 14 populations across the entire range of C. holacantha as well as nine individuals that represented the other two species in its clade ( C. wendtii and Acanthothamnus aphyllus ) and two outgroups. Results suggest that a Canotia common ancestor occurred on the landscape, which underwent a population contraction ca. 15 kya. The Isla Tiburón C. holacantha population and the Chihuahuan Desert microendemic C. wendtii have the greatest genetic differentiation, are sister to one another, and basal to all other Canotia populations. Three haplotypes within C. holacantha were recovered, which correspond to regional geography and thus identified as the Arizona, Sonora, and Tiburón haplotypes, within which Acanthothamnus aphyllus is nested rather than as a sister genus. These results indicate a once broad distribution of Canotia / Acanthothamnus when the current peripheral desert ecotone habitat was more widespread during the Pleistocene, now present in relict populations on the fringes of the southern desert, in the Chihuahuan Desert, with scattered populations on desert peaks, and a common or abundant distribution at the northern boundary of the Sonoran Desert. These results suggest Canotia has tracked the shift of the desert's edge both in latitude and elevation since the end of the last Ice Age.

Journal of Arid Environments↗

USGS2022

Integrating Earth–life systems: A geogenomic approach

For centuries, scientists have recognized and worked to understand how Earth’s mutable landscape and climate shape the distribution and evolution of species. Here, we describe the emerging field of geogenomics, which uses the reciprocal and deep integration of geologic, climatic, and population genomic data to define and test cause–effect relationships between Earth and life at intermediate spatial and temporal scales (i.e., the mesoscale). Technological advances now power the detailed reconstruction of landscape and evolutionary histories, but transdisciplinary collaborations and new quantitative tools are needed to better integrate Earth–life data. Geogenomics can help build a more unified theory and characterize the boundary conditions under which geologic and climatic processes generate new biodiversity, how species’ responses differ, and why.

Trends in Ecology & Evolution↗

USGS2020

Use of museum specimens to refine historical pronghorn subspecies boundaries

Endangered Sonoran ( Antilocapra americana sonoriensis ) and Peninsular ( A. a. peninsularis ) pronghorn persist largely because of captive breeding and reintroduction efforts. Recovery team managers want to re-establish pronghorn in their native range, but there is currently uncertainty regarding the subspecies status of extinct pronghorn populations that historically inhabited southern California, USA, and northern Baja California, Mexico. To address this uncertainty, we genotyped museum specimens and conducted phylogenetic and population genetic analyses of historical data in the context of 3 contemporary pronghorn populations. The historical northern Baja California pronghorn share the most ancestry with contemporary Peninsular pronghorn, whereas pronghorn in southern California share more ancestry with contemporary American ( A. a. americana ) pronghorn. For reintroductions into northern Baja California, the Peninsular subspecies is more appropriate based on museum genetic data. For reintroductions into Southern California, ecological and genetic factors are both important, as the subspecies most genetically related to historical populations (American) may not be well-adapted to the hot, low-elevation deserts of the reintroduction area. © 2019 The Wildlife Society.

California↗

USGS2015

Assessing the geologic and climatic forcing of biodiversity and evolution surrounding the Gulf of California

For almost a century the Baja California peninsula (Peninsula), Gulf of California (Gulf), and broader Sonoran Desert region (figure 1) have drawn geologists and biologists alike to study its unique physical and evolutionary processes (e.g., Wittich 1920; Darton 1921; Nelson 1921; Johnston 1924; Beal 1948; Durham and Allison 1960). The challenge remains to untangle the long, intricate, and at times enigmatic geological and climatological histories that have shaped the high levels of endemism and biodiversity observed in the region today (Van Devender 1990; Grismer 2000; Riddle et al. 2000).

Gulf of California↗

USGS2014

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↗

USGS2013

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↗

USGS2012

New microsatellite loci isolated via next-generation sequencing for two endangered pronghorn from the Sonoran Desert

We isolated 16 novel microsatellite loci in two subspecies of endangered desert pronghorns (Antilocapra americana sonoriensis and Antilocapra americana peninsularis) using a shotgun pyrosequencing approach. All and 87.5 % of the loci were polymorphic within each subspecies, respectively. The mean number of alleles per locus was 4.86 (range 2–8) and 2.5 alleles per locus (range 1–4 alleles), and observed heterozygosity ranged from 0.13 to 0.78 (mean 0.48) and 0.00 to 0.61 (mean 0.31), respectively. We did not find significant linkage disequilibrium among loci pairs and only one locus deviated significantly from Hardy–Weinberg equilibrium in peninsularis.

Conservation Genetics Resources↗

USGS2011

Novel primers for complete mitochondrial cytochrome b genesequencing in mammals

Sequence-based species identification relies on the extent and integrity of sequence data available in online databases such as GenBank. When identifying species from a sample of unknown origin, partial DNA sequences obtained from the sample are aligned against existing sequences in databases. When the sequence from the matching species is not present in the database, high-scoring alignments with closely related sequences might produce unreliable results on species identity. For species identification in mammals, the cytochrome b (cyt b ) gene has been identified to be highly informative; thus, large amounts of reference sequence data from the cyt b gene are much needed. To enhance availability of cyt b gene sequence data on a large number of mammalian species in GenBank and other such publicly accessible online databases, we identified a primer pair for complete cyt b gene sequencing in mammals. Using this primer pair, we successfully PCR amplified and sequenced the complete cyt b gene from 40 of 44 mammalian species representing 10 orders of mammals. We submitted 40 complete, correctly annotated, cyt b protein coding sequences to GenBank. To our knowledge, this is the first single primer pair to amplify the complete cyt b gene in a broad range of mammalian species. This primer pair can be used for the addition of new cyt b gene sequences and to enhance data available on species represented in GenBank. The availability of novel and complete gene sequences as high-quality reference data can improve the reliability of sequence-based species identification.

Molecular Ecology Resources↗

USGS2011

Spatial and temporal interactions of sympatric mountain lions in Arizona

Spatial and temporal interactions among individual members of populations can have direct applications to habitat management of mountain lions ( Puma concolor ). Our objectives were to evaluate home range overlap and spatial/temporal use of overlap zones (OZ) of mountain lions in Arizona. We incorporated spatial data with genetic analyses to assess relatedness between mountain lions with overlapping home ranges. We recorded the space use patterns of 29 radio-collared mountain lions in Arizona from August 2005 to August 2008. We genotyped 28 mountain lions and estimated the degree of relatedness among individuals. For 26 pairs of temporally overlapping mountain lions, 18 overlapped spatially and temporally and eight had corresponding genetic information. Home range overlap ranged from 1.18% to 46.38% (x̄=2443, SE = 2.96). Male–male pairs were located within 1 km of each other on average, 0.04% of the time, whereas male–female pairs on average were 3.0%. Two male–male pairs exhibited symmetrical spatial avoidance and two symmetrical spatial attractions to the OZ. We observed simultaneous temporal attraction in three male–male pairs and four male–female pairs. Individuals from Tucson were slightly related to one another within the population ( n = 13, mean R = 0.0373 ± 0.0151) whereas lions from Payson ( n = 6, mean R = -0.0079 ± 0.0356) and Prescott ( n = 9, mean R = -0.0242 ± 0.0452) were not as related. Overall, males were less related to other males ( n = 20, mean R = -0.0495 ± 0.0161) than females were related to other females ( n = 8, mean R = 0.0015 ± 0.0839). Genetic distance was positively correlated with geographic distance ( r 2 = 0.22, P = 0.001). Spatial requirements and interactions influence social behavior and can play a role in determining population density.

Arizona↗