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Species complexes undergoing rapid radiation present a challenge in molecular systematics because of the possibility that ancestral polymorphism is retained in component gene trees. Coalescent theory has demonstrated that gene trees often fail to match lineage trees when taxon divergence times are less than the ancestral effective population sizes. Suggestions to increase the number of loci and the number of individuals per taxon have been proposed; however, phylogenetic methods to adequately analyze these data in a coalescent framework are scarce. We compare two approaches to estimating lineage (species) trees using multiple individuals and multiple loci: the commonly used partitioned Bayesian analysis of concatenated sequences and a modification of a newly developed hierarchical Bayesian method (BEST) that simultaneously estimates gene trees and species trees from multilocus data. We test these approaches on a phylogeny of rapidly radiating species wherein divergence times are likely to be smaller than effective population sizes, and incomplete lineage sorting is known, in the rodent genus, Thomomys. We use seven independent noncoding nuclear sequence loci (total ∼ 4300 bp) and between 1 and 12 individuals per taxon to construct a phylogenetic hypothesis for eight Thomomys species. The majority-rule consensus tree from the partitioned concatenated analysis included 14 strongly supported bipartitions, corroborating monophyletic species status of five of the eight named species. The BEST tree strongly supported only the split between the two subgenera and showed very low support for any other clade. Comparison of both lineage trees to individual gene trees revealed that the concatenation method appears to ignore conflicting signals among gene trees, whereas the BEST tree considers conflicting signals and downweights support for those nodes. Bayes factor analysis of posterior tree distributions from both analyses strongly favor the model underlying the BEST analysis. This comparison underscores the risks of overreliance on results from concatenation, and ignoring the properties of coalescence, especially in cases of recent, rapid radiations.

The underground environment imposes unique demands on life that have led subterranean species to evolve specialized traits, many of which evolved convergently. We studied convergence in evolutionary rate in subterranean mammals in order to associate phenotypic evolution with specific genetic regions. We identified a strong excess of vision- and skin-related genes that changed at accelerated rates in the subterranean environment due to relaxed constraint and adaptive evolution. We also demonstrate that ocular-specific transcriptional enhancers were convergently accelerated, whereas enhancers active outside the eye were not. Furthermore, several uncharacterized genes and regulatory sequences demonstrated convergence and thus constitute novel candidate sequences for congenital ocular disorders. The strong evidence of convergence in these species indicates that evolution in this environment is recurrent and predictable and can be used to gain insights into phenotype–genotype relationships. Over the past 100 million years, many mammals, such as moles or mole rats, for example, have evolved to live almost entirely underground. During their transition to adapt to life underground, many species have reduced or completely lost their sense of sight, and often have only a small remnant of an eye that can sometimes be completely covered by skin and fur. In addition, the sections of the DNA that usually control how the eyes form have changed in these animals. Since there is less need for a working eye in dark environments, DNA related to the eye is no longer protected from damaging mutations in mammals that live underground. So, by comparing the DNA of mammals that live aboveground and underground, scientists can identify the parts of DNA that help form mammals’ eyes. Previous studies have discovered many sections of DNA responsible for producing the proteins that make up the eye. However, scientists know less about which sections of DNA control when and where these proteins are made. To address this, Partha et al. have studied the DNA of four underground mammals: the star-nosed mole, the cape golden mole, the naked mole-rat and the blind mole-rat. By comparing the DNA of these animals with that of mammals that live above ground, Partha et al. identified sections of DNA that contained an abnormally high number of changes in the blind underground mammals. Many of these sections are involved in forming the eye, including controlling when and where proteins are made. Overall, the findings show that comparing rates of evolution in different species can help uncover sections of DNA that guide and influence how organisms develop. Understanding how the eye is formed is not only of interest to scientists studying evolution and biology; it also has wider applications in healthcare. Many people suffer from unexplained eye abnormalities, and insight into the sections of DNA that control the eye’s development could help medical professionals diagnose these cases and design new treatments.

Soil carbon (C) sequestration rates vary widely in abandoned agricultural lands, and factors determining this variation, beyond climate, soil type, and productivity, are poorly understood. One such factor is soil disturbance by burrowing mammals. Despite being ubiquitous in all grasslands, the impact of burrowing mammals on soil C dynamics is not well understood. We quantified the major ecosystem processes that are influenced by one such burrowing mammal, plains pocket gophers (Geomys bursarius), in old field ecosystems located in east-central Minnesota, USA. We found that pocket gopher abundance varied among old fields and that newly formed gopher mounds covered up to 6% of the soil surface annually. We first measured short-term C pool and flux changes induced by gopher activities. Soil N mineralization did not differ between the soil in gopher mounds and undisturbed soil. However, for the soil under gopher mounds, N mineralization was 30% lower compared with the undisturbed soil. We developed a process model to simulate the long-term gopher disturbance impact on old field soil C accumulation. This simulation showed that pocket gophers reduced both the rate of soil C accumulation and the total C pool. This reduction is primarily driven by reduced plant C input due to the time it requires for the vegetation to recolonize gopher mounds. Soil organic matter (SOM) decomposition changes had only a minor impact. The process model showed that the depth from which burrowing mammals redistribute soil to the surface is a key factor in determining the overall impact on SOM. In total, our study indicated that soil disturbance by burrowing animals could significantly reduce C storage in old field ecosystems when the mammals are mostly active at the surface soil and can be a significant factor in decreasing overall C sequestration after land abandonment. However, at our study site, gopher abundance decreased with abandonment age, which was likely to have been cause by successional vegetation changes, therefore the gopher disturbance-induced reduction in soil C is transient and decreases with abandonment age.

Abstract Morphological analyses are critical to quantify phenotypic variation, identify taxa, inform phylogenetic relationships, and shed light on evolutionary patterns. This work is particularly important in groups that display great morphological disparity. Such is the case in geomyoid rodents, a group that includes 2 of the most species-rich families of rodents in North America: the Geomyidae (pocket gophers) and the Heteromyidae (kangaroo rats, pocket mice, and their relatives). We assessed variation in skull morphology (including both shape and size) among geomyoids to test the hypothesis that there are statistically significant differences in skull measurements at the family, genus, and species levels. Our sample includes 886 specimens representing all geomyoid genera and 39 species. We used the geometric mean to compare size across taxa. We used 14 measurements of the cranium and lower jaw normalized for size to compare shape among and within taxa. Our results show that skull measurements enable the distinction of geomyoids at the family, genus, and species levels. There is a larger amount of size variation within Geomyidae than within Heteromyidae. Our phylomorphospace analysis shows that the skull shape of the common ancestor of all geomyoids was more similar to the common ancestor of heteromyids than that of geomyids. Geomyid skulls display negative allometry whereas heteromyid skulls display positive allometry. Within heteromyids, dipodomyines, and non-dipodomyines show significantly different allometric patterns. Future analyses including fossils will be necessary to test our evolutionary hypotheses.

As urbanization continues to increase, it is necessary to understand the ecology of species in both their natural habitat and areas impacted by human activities. Baird's pocket gophers (Geomys breviceps) are often found in suburban habitat such as residential lawns, but little is known about their movements and habitat selection in these areas. The objectives of this study were to examine a population of Baird's pocket gophers in a suburban landscape and determine the size of their home range and which habitat variables best predicted pocket gopher activity. The average home range size for all gophers was 469.44 m2. Average home range was 502.02 m2 for adult females and 371.71 m2 for an adult male. We found that distance to a forest edge and soil sulfur content best predicted pocket gopher activity. As distance to a forest edge decreased, pocket gopher activity increased, and as soil sulfur increased, activity decreased. Plant diversity, especially of forbs, is often higher along a forest edge, providing greater foraging opportunities, and the increased shade from trees decreases soil temperature and increases soil moisture. Soil sulfur content has been shown to decrease with animal burrowing activity because aeration of the soil can alter chemical cycles, creating the significant association between gopher activity and sulfur. Our results provide some evidence that home range size among male and female Baird's pocket gophers in a suburban landscape may differ from populations in a natural habitat. Further, the presence of a forest edge may positively affect gopher activity. A medida que la urbanización continúa en aumento, se vuelve necesario comprender la ecología de las especies tanto en su hábitat natural como en áreas afectadas por actividades humanas. El tuza de Baird (Geomys breviceps) suele encontrarse en entornos suburbanos, como jardines residenciales, pero se sabe poco sobre sus patrones de movimiento y selección de hábitat en estos contextos. Los objetivos de este estudio fueron examinar una población de tuzas de Baird en un paisaje suburbano, determinar el tamaño de su ámbito hogareño y analizar qué variables del hábitat predicen mejor su actividad. El tamaño promedio del área de actividad para todos los individuos fue de 469.44 m2. Para las hembras adultas, el promedio fue de 502.02 m2, y para un macho adulto, de 371.71 m2. Encontramos que la distancia al borde del bosque y el contenido de azufre en el suelo fueron los mejores predictores de la actividad de las tuzas. A medida que disminuía la distancia al borde del bosque, aumentaba la actividad, mientras que un mayor contenido de azufre en el suelo se asoció con una menor actividad. La diversidad vegetal, especialmente de herbáceas de hoja ancha, suele ser mayor cerca del borde del bosque, lo que ofrece mejores oportunidades de alimentación. Además, la sombra de los árboles reduce la temperatura del suelo y aumenta su humedad. Se ha demostrado que el contenido de azufre en el suelo tiende a disminuir con la actividad de excavación de madrigueras por parte de los animales, debido a que la aireación del suelo puede alterar los ciclos químicos, generando la asociación significativa entre la actividad de las tuzas y los niveles de azufre. Nuestros resultados aportan evidencia de que el tamaño del ámbito hogareño de las tuzas de Baird puede diferir entre machos y hembras en hábitats suburbanos, en comparación con poblaciones que habitan en áreas naturales. Además, la presencia del borde de un bosque podría influir positivamente en su actividad.

Abstract Trapping is an important method for controlling pocket gophers. However, the difficulty of setting certain pocket gopher traps presents a barrier to their use. This study evaluates 5 common pocket gopher traps with differing operational mechanisms to determine which design(s) are easiest for applicators to set, using both objective and subjective criteria. The findings aim to assist individuals in selecting traps that match their trap-setting capabilities. Additionally, we describe a tool designed to assist individuals in setting more challenging traps in the field.

Parasitic lice demonstrate an unusual array of mitochondrial genome architectures and gene arrangements. We characterized the mitochondrial genome of Geomydoecus aurei , a chewing louse (Phthiraptera: Trichodectidae) found on pocket gophers (Rodentia: Geomyidae) using reads from both Illumina and Oxford Nanopore sequencing coupled with PCR, cloning, and Sanger sequencing to verify structure and arrangement for each chromosome. The genome consisted of 12 circular mitochondrial chromosomes ranging in size from 1,318 to 2,088 nucleotides (nt). Total genome size was 19,015 nt. All 37 genes typical of metazoans (2 rRNA genes, 22 tRNA genes, and 13 protein-coding genes) were present. An average of 26% of each chromosome was composed of non-gene sequences. Within the non-gene region of each chromosome, there was a 79-nt nucleotide sequence that was identical among chromosomes and a conserved sequence with secondary structure that was always followed by a poly-T region. We hypothesize that these regions may be important in the initiation of transcription and DNA replication, respectively. The G . aurei genome shares 8 derived gene clusters with other chewing lice of mammals, but in G . aurei , genes on several chromosomes are not contiguous.

neighboring countries. Recently, an increase in biological surveys and access to natural preserves has led to a better understanding of species distributions in Nicaragua and across Central America. Here, we provide new departmental records for three species of didelphid, 18 chiropterans (Phyllostomidae, Molossidae, Vespertilionidae), one geomyid, and one mustelid from 21 sites across the country. This work underscores the need for additional sampling across Nicaragua to fill gaps in the known distribution of many species. This information can facilitate or inform conservation actions in established and proposed preserves in Nicaragua.

Abstract Geomyoid rodents provide a great study system for the analysis of sexual dimorphism. They are polygynic and many inhabit harsh arid environments thought to promote sexual dimorphism. In fact, there has been extensive work published on the sexual size dimorphism of individual populations and species within this rodent clade. However, little work has been undertaken to assess the evolutionary patterns and processes associated with this sexual dimorphism. We use multivariate analyses of cranial measurements in a phylogenetic framework to determine the distribution of size and shape dimorphism among geomyoids and test for Rensch’s rule. Our results suggest that sexual dimorphism is more common in geomyids than heteromyids, but it is not in fact universal. There is evidence for variation in sexual dimorphism across populations. Additionally, in many taxa, geographic variation appears to overwhelm existing sexual dimorphism. We find support for the repeated independent evolution of shape and size dimorphism across geomyoid taxa, but we do not find support for an association between size and shape dimorphism. There is no evidence for Rensch’s rule in geomyoids, whether at the superfamily or family level. Together, our findings suggest that there is no single explanation for the evolution of sexual dimorphism in geomyoids and that, instead, it is the product of numerous evolutionary events. Future studies incorporating phylogenetic relationships will be necessary to paint a more complete picture of the evolution of sexual dimorphism in geomyoids.

Because of their cryptic morphology, pocket gophers of the genus Geomys are difficult organisms for examining species boundaries and taxonomic classification. However, this difficulty allows us to examine mechanisms of speciation more thoroughly. The cryptic morphology and complicated taxonomic history of pocket gophers also make identifying species distributions difficult. The use of molecular techniques has allowed for cryptic species to be recognized, including the recently proposed species G. jugossicularis (formally included in G. lutescens and G. bursarius). Previous work identifying the proposed distribution of G. jugossicularis was based on low sample numbers and limited geographical representation, and the data showed evidence of hybridization, further complicating relationships within the Geomys bursarius-lutescens-jugossicularis species complex. Samples suggested to represent G. jugossicularis have been identified in southwestern Nebraska, southeastern Colorado, southwestern Kansas, and, most recently, the Texas panhandle. Its distribution has been proposed to include the Oklahoma panhandle; however, gophers in this region currently are recognized as G. bursarius major. Samples were collected throughout western Oklahoma and the Oklahoma and Texas panhandles to determine identification and evaluate boundaries and distribution of gopher species in this region, as well as to compare our findings with previous work. Using the mitochondrial cytochrome b gene and nuclear microsatellite markers, we showed some support for the recognition of the proposed species G. jugossicularis and determined it occurs in the Oklahoma panhandle. However, our findings indicate the need for additional research to resolve species delimitation within the Geomys bursarius-lutescens-jugossicularis species complex. Debido a su morfología críptica no es fácil examinar los límites de las especies y la clasificación taxonómica de las tuzas del género Geomys. Sin embargo, esta dificultad nos permite examinar más a fondo los mecanismos de especiación. La morfología críptica y su complicada historia taxonómica también hacen difícil la identificación de la distribución de las especies. El uso de técnicas moleculares ha permitido reconocer especies crípticas, incluida la especie G. jugossicularis que se propuso recientemente (formalmente incluida en G. lutescens y G. bursarius). El trabajo previo que identificaba la distribución propuesta de G. jugossicularis contenía un tamaño de muestra reducido, una representación geográfica limitada y mostraba evidencia de hibridación, lo que complica aún más las relaciones dentro del complejo de especies Geomys bursarius-lutescens-jugossicularis. Se han identificado muestras que se cree que representan G. jugossicularis en el suroeste de Nebraska, el sureste de Colorado, el suroeste de Kansas y, más recientemente, en el corredor geográfico (Panhandle en inglés) de Texas. Se ha sugerido que la distribución incluya el área más al norte del corredor geográfico de Oklahoma, no obstante, las tuzas de esta región actualmente se reconocen como G. bursarius major. Se recolectaron muestras en todo el oeste de Oklahoma y en los corredores geográficos de Oklahoma y Texas, para identificar y evaluar los límites de las especies y la distribución de las tuzas en esta región, así como para comparar nuestros hallazgos con trabajos previos. Utilizando el gen del citocromob mitocondrial y los marcadores microsatélites nucleares, mostramos cierto apoyo para el reconocimiento de la especie propuesta G. jugossicularis y determinamos que se encuentra en el corredor geográfico de Oklahoma. Si bien, nuestros hallazgos indican la necesidad de llevar a cabo investigaciones adicionales para resolver la delimitación de especies dentro del complejo de especies Geomys bursarius-lutescens-jugossicularis.