David E. Cowley

DEVELOPMENT AND QUANTITATIVE GENETICS OF CORRELATION STRUCTURE AMONG BODY PARTS OF DROSOPHILA MELANOGASTER

The relationships between developmental components and correlation structure are explored for 17 head and thorax traits of Drosophila melanogaster. A developmental basis for the patterns of genetic and phenotypic correlation is described and related to information on the growth of various imaginal discs. In general, correlations between traits are positive, reflecting the similarity of cell doubling times of the various imaginal discs and the overlapping times of their growth during the larval instars. Positive correlations between traits provide a mechanism that can constrain radical evolutionary divergence from the fundamental body plan recognized as a fly. Phenotypic and genetic correlation structures are generally consistent with a hypothesis that traits derived from the same imaginal disc are more highly correlated than those derived from different discs. This structure is consistent with observed patterns of morphological divergence within the order Diptera. Furthermore, higher within-disc correlations provide a mechanism for evolutionary fine-tuning of the phenotype of a population of organisms to variable environmental conditions.

Quantitative genetic models for development, epigenetic selection, and phenotypic evolution

Herein we describe a general multivariate quantitative genetic model that incorporates two potentially important developmental phenomena, maternal effects and epigenetic effects. Maternal and epigenetic effects are defined as partial regression coefficients and phenotypic variances are derived in terms of age‐specific genetic and environmental variances. As a starting point, the traditional quantitative genetic model of additive gene effects and random environmental effects is cast in a developmental time framework. From this framework, we first extend a maternal effects model to include multiple developmental ages for the occurrence of maternal effects. An example of maternal effects occurring at multiple developmental ages is prenatal and postnatal maternal effects in mammals. Subsequently, a model of intrinsic and epigenetic effects in the absence of maternal effects is described. It is shown that genetic correlations can arise through epigenetic effects, and in the absence of other developmental effects, epigenetic effects are in general confounded with age‐specific intrinsic genetic effects. Finally, the two effects are incorporated into the basic quantitative genetic model. For this more biologically realistic model combining maternal and epigenetic effects, it is shown that the phenotypic regressions of offspring on mother and offspring on father can be used in some cases to estimate simultaneously maternal effects and epigenetic effects.

Across the great divide: genetic forensics reveals misidentification of endangered cutthroat trout populations

Accurate assessment of species identity is fundamental for conservation biology. Using molecular markers from the mitochondrial and nuclear genomes, we discovered that many putatively native populations of greenback cutthroat trout (Oncorhynchus clarkii stomias) comprised another subspecies of cutthroat trout, Colorado River cutthroat trout (Oncorhynchus clarkii pleuriticus). The error can be explained by the introduction of Colorado River cutthroat trout throughout the native range of greenback cutthroat trout in the late 19th and early 20th centuries by fish stocking activities. Our results suggest greenback cutthroat trout within its native range is at a higher risk of extinction than ever before despite conservation activities spanning more than two decades.

Estimation of introgression in cutthroat trout populations using microsatellites

Introgressive hybridization, mediated by anthropogenic activity, poses a threat to numerous and diverse taxa. The management of introgressed individuals or populations within species of conservation concern is currently the subject of scientific and political debate. We investigate the utility of 10 non-diagnostic microsatellite loci for investigating admixture from introduced Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (O. mykiss) within 25 putative Rio Grande cutthroat trout (O. c. virginalis) populations. We apply five different approaches (correspondence analysis, maximum-likelihood assignment tests, an admixture estimator based on allele frequencies, an admixture estimator based on coalescent theory and an admixture estimator implementing a Bayesian method) and use two alternative O. c. virginalis reference samples. All approaches were capable of identifying one population that consisted entirely of introduced O. c. bouvieri, and three out of five approaches enabled us to discriminate those populations with relatively high levels of non-native introgression from those populations with little or none. Actual estimates of admixture coefficients within a test population, varied, however, with the approach and reference sample used. These results have important implications for policies dividing populations into different management categories according to the estimated proportion of non-native genetic material that they contain.

UTERINE EFFECTS, EPIGENETICS, AND POSTNATAL SKELETAL DEVELOPMENT IN THE MOUSE

Reciprocal embryo transfer experiments show that skeletal dimensions in adult mice are significantly influenced by the genotype of the female providing the uterine environment in which they were raised. Embryo transfers among C3HeB/FeJ, SWR/J, and the C3SWF, hybrid strain (C3H females x SWR males) permit separation of uterine maternal genotype effects from effects arising from the progenys own genotype. Many different aspects of adult skeletal form are significantly influenced by uterine genotype and, in some instances, the pattern of these effects correlates with events during skeletal embryology. Analyses involving the highly heterozygous C3SWF1 strain demonstrate the existence of significant dominance in maternal genes affecting skeletal development in the progeny. Further, there is a large skeletal effect due to progeny heterosis. Uterine Utter size can be manipulated as a nonheritable component of variability in embryo transfer experiments, and it has a large and systemic effect on skeletal growth and morphogenesis that persists in adult mice. Heritable uterine maternal effects are epigenetic interactions during development that can be incorporated into models of evolutionary change to provide a more complete picture of the causal agents producing morphological change.

Strategies for Ecological Restoration of the Middle Rio Grande in New Mexico and Recovery of the Endangered Rio Grande Silvery Minnow

Issues relevant to management of arid land aquatic ecosystems include: (1) a poor understanding of the extent and linkages of an aquatic ecosystem, (2) human population growth coupled with a highly variable water supply, (3) hydrologic modifications of rivers associated with dams, levees, canalizations, and diversions, (4) impairment of water quality, (5) alteration of vegetative communities of catchments and riparian zones, (6) introduction of invasive non-native species, and (7) imperiled native species. All of these issues occur in the Middle Rio Grande of New Mexico and the first six in combination have been responsible for the imperilment of its native aquatic biota. The extinction of two fish species, extirpation of 13 others, and endangerment of the Rio Grande silvery minnow, a pelagic-spawning species with an enormous potential for recolonization of habitats, has been caused by a century of river and landscape modifications. Erosion from heavily grazed grasslands coupled with appropriation of surface flows for irrigation, both associated with human population expansion in New Mexico, led to increased sediment deposition in the Middle Rio Grande. Sediment deposition exacerbated problems due to flooding and droughts, which led to a series of political and technological actions that progressively extirpated most of the large-bodied native fishes and all but one of the pelagic-spawning minnows. Restoration of the Middle Rio Grande and recovery of the endangered silvery minnow will require many changes in the way humans use the river and its floodplain. If those changes occur, they should consider the Rio Grande within a landscape context that includes strategies for humans to live in arid regions without damaging fragile arid lands and their aquatic ecosystems.

CORRELATED RESPONSE IN THE DEVELOPMENTAL CHOREOGRAPHIES OF THE MOUSE MANDIBLE TO SELECTION FOR BODY COMPOSITION

The correlated response to 13 generations of selection for percent fatness and leanness is investigated in 11 mandible traits in mice. Five selection lines are examined including high fat (HF), low fat (LF), high lean (HL), low lean (LL) and a randomly selected control strain (RC. The ontogenetic patterns of growth in the RC strain serve as a model to evaluate the developmental consequences of directional selection. Selection has systematically altered the patterns of mandible growth in selection lines relative to the control strain. Further, selection has significantly altered the age‐specific phenotypic covariance among these traits. In the HF strain, growth in the mandible is completed by 12 weeks of age for most traits. In other selected strains, notably LF and LL, there is a significant growth spurt that occurs between 12 and 15 weeks of age. Changes in the patterns of mandibular growth produce significant differences among strains in the final form of the mandible. Because of the changes in the patterns of growth, the differences among strains are themselves shown to vary at different postnatal ages. The phenotypically similar strains, i.e., HF and LL or LF and HL, show different but correlated patterns of divergence. Multivariate statistical analyses suggest that the temporal strain differences in these traits are multidimensional.

Ecology of the Rio Grande Silvery Minnow (Cyprinidae: Hybognathus amarus) Inferred from Specimens Collected in 1874

The Rio Grande silvery minnow (Hybognathus amarus) was historically an abundant and widespread species in the Rio Grande Basin. Its decline to endangered status had many probable causes and has spanned more than a century. Specimens of H. amarus collected in July 1874 at San Ildefonso, near Santa Fe, New Mexico, allowed a retrospective assessment of the ecology and morphology of the species and the environmental conditions of the Rio Grande in areas foraged by these minnows. Analysis of diatoms from the gut showed that H. amarus foraged mainly in nutrient-enriched areas on mud substrates in 1874 and to lesser extents on periphyton associated with plant, sand, and rock substrates. Gut contents included a considerable amount of fine-grained sediment and a wide variety of organic materials including detritus, pine pollen, cyanobacteria, algae, and diatoms. Scale annuli showed that H. amarus was once a relatively long-lived minnow; all age classes from 1 to 5 were present in 1874. The presence of multiple individuals of several ages suggested that annual survival rates were high historically and that the species may be iteroparous, rather than short-lived and semelparous as widely held. The morphology of H. amarus from a captive stock in 2003 was consistent with the morphology of the 1874 specimens.

Morphologic and Genetic Variation in Triops (Branchiopoda: Notostraca) from Ephemeral Waters of the Northern Chihuahuan Desert of North America

Abstract Tadpole shrimp are known to be important animals in the ecology of ephemeral wetlands. In the northern Chihuahuan Desert of North America, the tadpole shrimp fauna is composed of possibly three species in the genus Triops, which have variously been referred to as species, subspecies, and intraspecific variation. Our results support the presence of three morphologically distinct forms, which will be referred to herein as T. newberryi, T. longicaudatus “short,” and T. longicaudatus “long.” We report analyses of Triops spp. sampled in summer 2008 from 14 natural playas and man-made flood retention ponds. Data were recorded on meristic counts and quantitative measurements of morphological features. We also sequenced portions of the mitochondrial COI and ND1 genes for 72 shrimp, including individuals from all three morphological forms and for multiple ponds for each form where possible. The three forms were morphologically distinct for multiple characters and molecular analyses showed large differences in DNA nucleotide sequence and the presence of multiple unique amino acid substitutions in each form. Finally, prior literature suggests the three forms exhibit different reproductive systems, with populations of T. longicaudatus “long” thought to be gonochoric (equal sex ratios and obligate outcrossing), T. longicaudatus “short” having only self-fertilizing hermaphrodites, and T. newberryi being androdioecious, having both self-fertilizing hermaphrodites and males. While these three forms may be sufficiently distinct in morphology, mitochondrial DNA, and reproductive life history to warrant elevation to species level, additional geographical sampling and an examination of the various type specimens are necessary for a formal taxonomic revision.

Genetic Diversity within Fragmented Cutthroat Trout Populations

Abstract Interior cutthroat trout Oncorhynchus clarkii have undergone severe declines over the past 150 years. Many subspecies now persist in a highly fragmented state, primarily within headwater streams. We used 12 microsatellites to investigate the population genetic characteristics of 22 remnant populations of Rio Grande cutthroat trout O. c. virginalis isolated in montane streams in New Mexico. Populations varied markedly in the amount of genetic diversity they contained. There was no significant relationship between estimated adult population size or habitat size and heterozygosity; however, populations occurring above natural barriers were significantly less diverse. Seven population samples exhibited significant deviations from Hardy-Weinberg equilibrium. Interlocus variance in the population inbreeding coefficient F IS was correlated with habitat size, and several population samples exhibited a significantly higher variance in interindividual relatedness, or a significantly higher median individua...