Archaeological Evidence of Validity of Fish Populations on Unexploited Reefs as Proxy Targets for Modern Populations

Reef‐fish management and conservation is hindered by a lack of information on fish populations prior to large‐scale contemporary human impacts. As a result, relatively pristine sites are often used as conservation baselines for populations near sites affected by humans. This space‐for‐time approach can only be validated by sampling assemblages through time. We used archaeological remains to evaluate whether the remote, uninhabited Northwestern Hawaiian Islands (NWHI) might provide a reasonable proxy for a lightly exploited baseline in the Main Hawaiian Islands (MHI). We used molecular and morphological techniques to describe the taxonomic and size composition of the scarine parrotfish catches present in 2 archaeological assemblages from the MHI, compared metrics of these catches with modern estimates of reproductive parameters to evaluate whether catches represented by the archaeological material were consistent with sustainable fishing, and evaluated overlap between size structures represented by the archaeological material and modern survey data from the MHI and the NWHI to assess whether a space‐for‐time substitution is reasonable. The parrotfish catches represented by archaeological remains were consistent with sustainable fishing because they were dominated by large, mature individuals whose average size remained stable from prehistoric (AD approximately 1400–1700) through historic (AD 1700–1960) periods. The ancient catches were unlike populations in the MHI today. Overlap between the size structure of ancient MHI catches and modern survey data from the NWHI or the MHI was an order of magnitude greater for the NWHI comparison, a result that supports the validity of using the NWHI parrotfish data as a proxy for the MHI before accelerated, heavy human impacts in modern times. Evidencia Arqueológica de la Validez de Poblaciones de Peces en Arrecifes Sin Explotar como Objetivos de Apoderamiento para Poblaciones Actuales     

Level of environmental threat posed by horticultural trade in Cactaceae

Ornamental horticulture has been identified as an important threat to plant biodiversity and is a major pathway for plant invasions worldwide. In this context, the family Cactaceae is particularly challenging because it is considered the fifth most threatened large taxonomic group in the world; several species are among the most widespread and damaging invasive species; and Cactaceae is one of the most popular horticultural plant groups. Based on the Convention on International Trade in Endangered Species of Wild Flora and Fauna and the 11 largest online auction sites selling cacti, we documented the international cactus trade. To provide an in‐depth look at the dynamics of the industry, we surveyed the businesses involved in the cactus trade in South Africa (a hotspot of cactus trade and invasions). We purchased seeds of every available species and used DNA barcoding to identify species to the genus level. Although <20% of this trade involved threatened species and <3% involved known invasive species, many species were identified by a common name. However, only 0.02% of the globally traded cacti were collected from wild populations. Despite a large commercial network, all South African imports (of which 15% and 1.5% were of species listed as threatened and invasive, respectively) came from the same source. With DNA barcoding, we identified 24% of the species to genus level. Based on our results, we believe that if trade restrictions are placed on the small proportion of cacti that are invasive and there is no major increase in harvesting of native populations, then the commercial trade in cactus poses a negligible environmental threat. However, there are currently no effective methods for easily identifying which cacti are traded, and both the illicit harvesting of cacti from the wild and the informal trade in invasive taxa pose on‐going conservation challenges.     

Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity

Monitoring communities of fish is important for the management and sustainability of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are among the most effective nondestructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, BRUVs sample visually conspicuous biota; hence, some taxa are undersampled or not recorded at all. We compared the diversity of fishes characterized using BRUVs with diversity detected via environmental DNA (eDNA) metabarcoding. We sampled seawater and captured BRUVs imagery at 48 locales that included reef and seagrass beds inside and outside a marine reserve (Jurien Bay in Western Australia). Eighty-two fish genera from 13 orders were detected, and the community of fishes described using eDNA and BRUVs combined yielded >30% more generic richness than when either method was used alone. Rather than detecting a homogenous genetic signature, the eDNA assemblages mirrored the BRUVs’ spatial explicitness; differentiation of taxa between seagrass and reef was clear despite the relatively small geographical scale of the study site (∼35 km²). Taxa that were not sampled by one approach, due to limitations and biases intrinsic to the method, were often detected with the other. Therefore, using BRUVs and eDNA in concert provides a more holistic view of vertebrate marine communities across habitats. Both methods are noninvasive, which enhances their potential for widespread implementation in the surveillance of marine ecosystems.     

Use of genetic,climatic, and microbiological data to inform reintroduction of a regionally extinct butterfly

Species reintroductions are increasingly used as means of mitigating biodiversity loss. Besides habitat quality at the site targeted for reintroduction, the choice of source population can be critical for success. The butterfly Melanargia russiae (Esper´s marbled white) was extirpated from Hungary over 100 years ago, and a reintroduction program has recently been approved. We used museum specimens of this butterfly, mitochondrial DNA data (mtDNA), endosymbiont screening, and climatic‐similarity analyses to determine which extant populations should be used for its reintroduction. The species displayed 2 main mtDNA lineages across its range: 1 restricted to Iberia and southern France (Iberian lineage) and another found throughout the rest of its range (Eurasian lineage). These 2 lineages possessed highly divergent wsp alleles of the bacterial endosymbiont Wolbachia. The century‐old Hungarian specimens represented an endemic haplotype belonging to the Eurasian lineage, differing by one mutation from the Balkan and eastern European populations. The Hungarian populations of M. russiae occurred in areas with a colder and drier climate relative to most sites with extant known populations. Our results suggest the populations used for reintroduction to Hungary should belong to the Eurasian lineage, preferably from eastern Ukraine (genetically close and living in areas with the highest climatic similarity). Materials stored in museum collections can provide unique opportunities to document historical genetic diversity and help direct conservation.     

Transforming ecology and conservation biology through genome editing

As the conservation challenges increase, new approaches are needed to help combat losses in biodiversity and slow or reverse the decline of threatened species. Genome-editing technology is changing the face of modern biology, facilitating applications that were unimaginable only a decade ago. The technology has the potential to make significant contributions to the fields of evolutionary biology, ecology, and conservation, yet the fear of unintended consequences from designer ecosystems containing engineered organisms has stifled innovation. To overcome this gap in the understanding of what genome editing is and what its capabilities are, more research is needed to translate genome-editing discoveries into tools for ecological research. Emerging and future genome-editing technologies include new clustered regularly interspaced short palindromic repeats (CRISPR) targeted sequencing and nucleic acid detection approaches as well as species genetic barcoding and somatic genome-editing technologies. These genome-editing tools have the potential to transform the environmental sciences by providing new noninvasive methods for monitoring threatened species or for enhancing critical adaptive traits. A pioneering effort by the conservation community is required to apply these technologies to real-world conservation problems.     

A spatially explicit empirical model of structural development processes in natural forests based on climate and topography

Stand structure develops with stand age. Old-growth forests with well-developed stand structure support many species. However, development rates of stand structure likely vary with climate and topography. We modeled structural development of 4 key stand variables and a composite old-growth index as functions of climatic and topographic covariates. We used a hierarchical Bayesian method for analysis of extensive snap-shot National Forest Inventory (NFI) data in Japan (n = 9244) to account for differences in stand age. Development rates of structural variables and the old-growth index exhibited curvilinear responses to environmental covariates. Flat sites were characterized by high rates of structural development. Approximately 150 years were generally required to attain high values (approximately 0.8) of the old-growth index. However, the predicted age to achieve specific values varied depending on environmental conditions. Spatial predictions highlighted regional variation in potential structural development rates. For example, sometimes there were differences of >100 years among sites, even in the same catchment, in attainment of a medium index value (0.5) after timber harvesting. The NFI data suggested that natural forests, especially old natural forests (>150 years), remain generally on unproductive ridges, steep slopes, or areas with low temperature and deep snow, where many structural variables show slow development rates. We suggest that maintenance and restoration of old natural forests on flat sites should be prioritized for conservation due to the likely rapid development of stand structure, although remaining natural forests on low-productivity sites are still important and should be protected.     

Use of Ancient Sedimentary DNA as a Novel Conservation Tool for High‐Altitude Tropical Biodiversity

Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment‐based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro‐alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high‐quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro‐alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human‐induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited. Uso de ADN Sedimentario Antiguo como una Herramienta Novedosa de Conservación para la Biodiversidad Tropical de Grandes Altitudes     

Degradation of ammonium dinitramide (ADN) in digested sewage sludge under strict anaerobic conditions

The biodegradation of one popular nitramine energetics, ammonium dinitramide (ADN) by mixture of denitrifying bacterial species was investigated. ADN was observed to be effectively mineralized in the anaerobic mixed culture. The initial ADN concentration of 250 mg/L was reduced to non‐detectable levels (> 99% removal efficiency) in 5 days of incubation under anaerobic conditions. Final products generated from anaerobic degradation of nitramine energetics by anaerobic metabolism were NH₄ ⁺, CH₄, and CO₂ that were released to the environment with the denitrifiers’ growth. In addition, it was found that the activity of denitrifiers was inhibited by high concentration of ammonia generated through the degradation reactions of energetic nitrites.     

New Genetic Approach to Detecting Individuals of Rare and Endangered Species

Abstract: Many rare and endangered species are difficult to locate, observe, and study. Consequently, many individuals, breeding pairs, and even populations of such species could remain undetected. Genetic markers can potentially be used to detect the existence of undiscovered individuals and populations, and we propose a method to do so that requires 3 conditions. First, sampling of the known population(s) of the target species must be comprehensive. Second, the species must display a reasonable level of philopatry and genetic structuring. Third, individuals must be able to be caught outside of breeding locations (e.g., at courtship or feeding areas, in flight), and the level of recapture must be reasonably high. We applied our method to the Chatham Island Taiko (Pterodroma magentae), one of the world's most endangered seabirds. We sequenced the Taiko mitochondrial cytochrome b gene and both copies of a fragment of the duplicated domain I of the control region. Twenty‐one haplotypes were revealed, including 4 (19%) not found in birds at known burrows. These results suggest there are more burrow groups yet to be located. The species is a pelagic gadfly petrel that inhabits land only in the breeding season during which it is nocturnal and nests in burrows. Taiko burrows are situated in dense forest in a remote area of Chatham Island, and are consequently difficult to locate and study. It is important that all Taiko burrows be discovered to enable monitoring and protection of the birds from exotic predators.     

Comparison of metabolic nitramine degradation by denitrifying species

The biodegradation of two popular nitramine energetics were investigated. The HMX (octa‐hydro‐1,3,5,7‐tetranitro‐1,3,5,7‐tetrazocine) was mineralized by anaerobic mixed denitrifiers in digested sewage sludge culture. An initial HMX concentration of 120 mg/L decreased to a non‐detectable level (> 99% removal efficiency) in 8 days of incubation under strict anaerobic conditions. It was, however, not effectively metabolized by single denitrifying species, P. aeruginosa, B. subtilis in a nitrogen limiting condition under their optimum growth conditions. The other nitramine energetic, ADN (ammonium dinitramide), was mineralized well in the anaerobic mixed culture. The initial ADN concentration of 250 mg/L was reduced to non‐detectable levels (> 99% removal efficiency) in 5 days of incubation under anaerobic conditions. These results show that the anaerobic mixed culture, compared to the pure monoculture, is superior in the degradation of nitramine energetics.