Genetic Identification of Spotted Owls, Barred Owls, and Their Hybrids: Legal Implications of Hybrid Identity

Abstract:  Recent population expansion of Barred Owls (  Strix varia ) into western North America has led to concern that they may compete with and further harm the Northern Spotted Owl (  S. occidentalis caurina ), which is already listed as threatened under the U.S. Endangered Species Act (ESA). Because they hybridize, there is a legal need under the ESA for forensic identification of both species and their hybrids. We used mitochondrial control-region DNA and amplified fragment-length polymorphism (AFLP) analyses to assess maternal and biparental gene flow in this hybridization process. Mitochondrial DNA sequences (524 base pairs) indicated large divergence between Barred and Spotted Owls (13.9%). Further, the species formed two distinct clades with no signs of previous introgression. Fourteen diagnostic AFLP bands also indicated extensive divergence between the species, including markers differentiating them. Principal coordinate analyses and assignment tests clearly supported this differentiation. We found that hybrids had unique genetic combinations, including AFLP markers from both parental species, and identified known hybrids as well as potential hybrids with unclear taxonomic status. Our analyses corroborated the findings of extensive field studies that most hybrids genetically sampled resulted from crosses between female Barred Owls and male Spotted Owls. These genetic markers make it possible to clearly identify these species as well as hybrids and can now be used for research, conservation, and law enforcement. Several legal avenues may facilitate future conservation of Spotted Owls and other ESA-listed species that hybridize, including the ESA similarity-of-appearance clause (section 4[e]) and the Migratory Bird Treaty Act. The Migratory Bird Treaty Act appears to be the most useful route at this time.     

芳香族化合物生物降解代谢及其分子遗传研究

芳香族碳水化合物（烃）是自然环境中普遍存在的。由于这些芳香烃在环境中的化学稳定性高、水溶性低且许多可能是致癌因子，由此引起的环境问题是一个世界性的难题。利用生物工程技术阵解芳香烃是一条较为有效和快速分解的新途径。为此，本文综述了几种芳香烃生物降解途径的多样性、引发生物降解的生化和分子遗传机制及其所涉基因的克隆分析和应用研究进展。     

Climate change and population genetic structure of marine species

Climate change influences populations by reducing or extirpating local populations, by disrupting patterns of migration and by shifting geographical distributions. These events can affect genetic population structure in several ways. Molecular markers have been used in numerous population genetic and phylogeographical studies of marine species and have detected population responses to climate change in the last few decades, such as range expansions, adaptative shifts and declines or increases in abundance. Little is known, however, about the molecular and physiological basis of adaptive responses to climate change in marine Mediterranean species. The Mediterranean Sea ecosystem is a ‘living laboratory’ with native species that are challenged by environmental change and by invasive species and a ‘gene-climate’ approach should be adopted as a way of focusing on the relationship between climate warming and genetic diversity.     

微生物降解多环芳烃有机污染物分子遗传学研究进展

多环芳烃是环境中广泛存在的一类难降解危险性致癌污染物 ,微生物酶在降解转化多环芳烃的过程及其归趋中起着重要作用。本文就微生物降解多环芳烃代谢途径的多样性和分子遗传学机制的研究进展进行了综述     

Survival Under Conditions of Environmental Stress: Variability of Brain Morphology and Behavior in the House Mouse

Two populations of laboratory mice lived outdoors in open pens for two years. Thereafter, some of them were bred in the laboratory. Morphometric analysis showed that the size of the synaptic projection area of mossy fibers (in the CA3 region of the hippocampus), which has an important functional role, and some behavioral traits of the open-pen mouse progeny had significant genetically determined differences from those in the initial population. This was attributed to differential breeding accounted for by the influence of severe environmental factors. Under environmental stress, selection occurred in the population and the mice with behavioral and neuromorphological characteristics differing from those of the control group proved to be better adapted to such conditions.     

Phylogeography and Limited Genetic Connectivity in the Endangered Boring Giant Clam across the Coral Triangle

Abstract: The Coral Triangle is the global center of marine biodiversity; however, its coral reefs are critically threatened. Because of the bipartite life history of many marine species with sedentary adults and dispersive pelagic larvae, designing effective marine protected areas requires an understanding of patterns of larval dispersal and connectivity among geographically discrete populations. We used mtDNA sequence data to examine patterns of genetic connectivity in the boring giant clam (Tridacna crocea) in an effort to guide conservation efforts within the Coral Triangle. We collected an approximately 485 base pair fragment of mtDNA cytochrome c oxidase 1 (CO1) from 414 individuals at 26 sites across Indonesia. Genetic structure was strong between regions (φ_ST=0.549, p < 0.00001) with 3 strongly supported clades: one restricted to western Sumatra, another distributed across central Indonesia, and a third limited to eastern Indonesia and Papua. Even within the single largest clade, small but significant genetic structure was documented (φ_ST=0.069, p < 0.00001), which indicates limited gene flow within and among phylogeographic regions. Significant patterns of isolation by distance indicated an average dispersal distance of only 25–50 km, which is far below dispersal predictions of 406–708 km derived from estimates of passive dispersal over 10 days via surface currents. The strong regional genetic structure we found indicates potent limits to genetic and demographic connectivity for this species throughout the Coral Triangle and provides a regional context for conservation planning. The recovery of 3 distinct evolutionarily significant units within a well‐studied taxonomic group suggests that biodiversity in this region may be significantly underestimated and that Tridacna taxa may be more endangered than currently recognized.     

Nonparametric spatial covariance functions: Estimation and testing

Spatial autocorrelation techniques are commonly used to describe genetic and ecological patterns. To improve statistical inference about spatial covariance, we propose a continuous nonparametric estimator of the covariance function in place of the spatial correlogram. The spline correlogram is an adaptation of a recent development in spatial statistics and is a generalization of the commonly used correlogram. We propose a bootstrap algorithm to erect a confidence envelope around the entire covariance function. The meaning of this envelope is discussed. Not all functions that can be drawn inside the envelope are candidate covariance functions, as they may not be positive semidefinite. However, covariance functions that do not fit, are not supported by the data. A direct estimate of the L₀ spatial correlation length with associated confidence interval is offered and its interpretation is discussed. The spline correlogram is found to have high precision when applied to synthetic data. For illustration, the method is applied to electrophoretic data of an alpine grass (Poa alpina).     

Toward an integrative molecular approach to wildlife disease

Pathogens pose serious threats to human health, agricultural investment, and biodiversity conservation through the emergence of zoonoses, spillover to domestic livestock, and epizootic outbreaks. As such, wildlife managers are often tasked with mitigating the negative effects of disease. Yet, parasites form a major component of biodiversity that often persist. This is due to logistical challenges of implementing management strategies and to insufficient understanding of host–parasite dynamics. We advocate for an inclusive understanding of molecular diversity in driving parasite infection and variable host disease states in wildlife systems. More specifically, we examine the roles of genetic, epigenetic, and commensal microbial variation in disease pathogenesis. These include mechanisms underlying parasite virulence and host resistance and tolerance, and the development, regulation, and parasite subversion of immune pathways, among other processes. Case studies of devil facial tumor disease in Tasmanian devils (Sarcophilus harrisii) and chytridiomycosis in globally distributed amphibians exemplify the broad range of questions that can be addressed by examining different facets of molecular diversity. For particularly complex systems, integrative molecular analyses present a promising frontier that can provide critical insights necessary to elucidate disease dynamics operating across scales. These insights enable more accurate risk assessment, reconstruction of transmission pathways, discernment of optimal intervention strategies, and development of more effective and ecologically sound treatments that minimize damage to the host population and environment. Such measures are crucial when mitigating threats posed by wildlife disease to humans, domestic animals, and species of conservation concern.     

The effect of metal pollution on the population genetic structure of brown trout (Salmo trutta L.) residing in the River Hayle, Cornwall, UK

The River Hayle in south-west England is impacted with metals and can be divided into three regions depending on the copper and zinc concentrations: a low-metal upper section; a highly-contaminated middle section and a moderately contaminated lower section. Hayle river water is toxic to metal-naive brown trout, but brown trout are found in the upper and lower regions. The study aimed to evaluate the population genetic structure of River Hayle brown trout and to determine if the highly-contaminated section acts as a chemical barrier to migration. Population genetic analysis indicated that metals were not a barrier to gene flow within the river, but there was a high level of differentiation observed between fish sampled at two sites in the upper region, despite being separated by only 1 km. The metal tolerance trait exhibited by this brown trout population may represent an important component of the species genetic diversity in this region.     

Linking life history to landscape for threatened species conservation in a multiuse region

Landscape-scale conservation that considers metapopulation dynamics will be essential for preventing declines of species facing multiple threats to their survival. Toward this end, we developed a novel approach that combines occurrence records, spatial–environmental data, and genetic information to model habitat, connectivity, and patterns of genetic structure and link spatial attributes to underlying ecological mechanisms. Using the threatened northern quoll (Dasyurus hallucatus) as a case study, we applied this approach to address the need for conservation decision-making tools that promote resilient metapopulations of this threatened species in the Pilbara, Western Australia, a multiuse landscape that is a hotspot for biodiversity and mining. Habitat and connectivity were predicted by different landscape characteristics. Whereas habitat suitability was overwhelmingly driven by terrain ruggedness, dispersal was facilitated by proximity to watercourses. Although there is limited evidence for major physical barriers in the Pilbara, areas with high silt and clay content (i.e., alluvial and hardpan plains) showed high resistance to dispersal. Climate subtlety shaped distributions and patterns of genetic turnover, suggesting the potential for local adaptation. By understanding these spatial–environmental associations and linking them to life-history and metapopulation dynamics, we highlight opportunities to provide targeted species management. To support this, we have created habitat, connectivity, and genetic uniqueness maps for conservation decision-making in the region. These tools have the potential to provide a more holistic approach to conservation in multiuse landscapes globally.