Sustainability management of short-lived freshwater fish in human-altered ecosystems should focus on adult survival.

Fish populations globally are susceptible to endangerment through exploitation and habitat loss. We present theoretical simulations to explore how reduced adult survival (age truncation) might affect short-lived freshwater fish species in human-altered contemporary environments. Our simulations evaluate two hypothetical "average fish" and five example fish species of age 1 or age 2 maturity. From a population equilibrium baseline representing a natural, unaltered environment we impose systematic reductions in adult survival and quantify how age truncation affects the causes of variation in population growth rate. We estimate the relative contributions to population growth rate arising from simulated temporal variation in age-specific vital rates and population structure. At equilibrium and irrespective of example species, population structure (first adult age class) and survival probability of the first two adult age classes are the most important determinants of population growth. As adult survival decreases, the first reproductive age class becomes increasingly important to variation in population growth. All simulated examples show the same general pattern of change with age truncation as known for exploited, longer-lived fish species in marine and freshwater environments. This implies age truncation is a general potential concern for fish biodiversity across life history strategies and ecosystems. Managers of short-lived, freshwater fishes in contemporary environments often focus on supporting reproduction to ensure population persistence. However, a strong focus on water management to support reproduction may reduce adult survival. Sustainability management needs a focus on mitigating adult mortality in human-altered ecosystems. A watershed spatial extent embracing land and water uses may be necessary to identify and mitigate causes of age truncation in freshwater species. Achieving higher adult survival will require paradigm transformations in society and government about water management priorities.

De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis.

Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory-controlled setting and in two different water types, a native and a non-native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.

Self-Fertilization and the Role of Males in Populations of Tadpole Shrimp (Branchiopoda: Notostraca: Triops).

Self-fertilization has both negative and positive fitness effects on species evolution. Selfing can increase inbreeding depression, thereby decreasing genetic diversity. In contrast, self-fertilization can preserve beneficial gene combinations and facilitate colonization success. Within the class of crustaceans Branchiopoda, selfing is a primary reproductive mode. Some species of Triops, in the family Notostraca, are a few of the animal species thought to have a mixed mating system between hermaphrodites and males termed androdioecy. The objective of this study is to validate the reproductive mode utilized by Triops newberryi in southern New Mexico by the use of progeny arrays and population simulations. Individuals were reared in the lab from dried soil collected from temporary ponds inhabited by T. newberryi The adults reared and the encysted embryos contained within their brood pouches were genotyped using 7 T. newberryi specific microsatellite markers to determine the relatedness between parent and offspring. Overall microsatellite diversity was low with few heterozygous individuals and limited polymorphisms. Simulated populations and allele segregation analysis suggest hermaphroditism is the primary reproductive mode for T. newberryi In addition, based on the offspring's alleles, there was no direct evidence that a male (ovisacless) T. newberryi outcrossed with a female. Population simulations further suggest that the rate of successful outcrossing events must be low and could explain why outcrossing was not observed in the laboratory rearing trials.

Discriminating between the effects of founding events and reproductive mode on the genetic structure of Triops populations (Branchiopoda: Notostraca).

Crustaceans that initially colonize a freshwater temporary pond can strongly bias the subsequent genetic composition of the population, causing nearby populations to be genetically distinct. In addition, these crustaceans have various reproductive modes that can influence genetic differentiation and diversity within and between populations. We report on two species of tadpole shrimp, Triops newberryi and Triops longicaudatus "short", with different reproductive modes. Reproduction in the tadpole shrimp can occur clonally (parthenogenesis), with self fertilization (hermaphroditism), or through outcrossing of hermaphrodites with males (androdioecy). For all these reproductive modes, population genetic theory predicts decreased genetic diversity and increased population differentiation. Here we use mitochondrial control region (mtCR) sequences and nuclear microsatellite loci to determine if the difference in reproductive mode affects the high genetic structure typical of persistent founder effects. Previous authors indicated that T. newberryi is androdioecious because populations are composed of hermaphrodites and males, and T. longicaudatus "short" is hermaphroditic or parthenogenetic because males are absent. In our data, T. newberryi and T. longicaudatus "short" populations were highly structured genetically over short geographic distances for mtCR sequences and microsatellite loci (T. newberryi: ΦST = 0.644, FST = 0.252, respectively; T. l. "short": invariant mtCR sequences, FST = 0.600). Differences between the two Triops species in a number of diversity measures were generally consistent with expectations from population genetic theory regarding reproductive mode; however, three of four comparisons were not statistically significant. We conclude the high genetic differentiation between populations is likely due to founder effects and results suggest both species are composed of selfing hermaphrodites with some level of outcrossing; the presence of males in T. newberryi does not appreciably reduce inbreeding. We cannot exclude the possibility that males in T. newberryi are non-reproductive individuals and the two species have the same mating system.

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.

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.

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 progeny's 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.

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.