Detection of invasive freshwater fish species using environmental DNA survey

Invasive species are one of the most significant problem in freshwater ecosystems. Most common non-native freshwater species in Turkish freshwater fish fauna are Prussian Carp (Carassius gibelio), North African Catfish (Clarias gariepinus), Nile Tilapia (Oreochromis niloticus) and Topmouth Gudgeon (Pseudorasbora parva).Recent studies showed that environmental DNA could be used to detect target species inhabiting the ecosystem with higher precision and less effort compared to traditional field surveys. In this study, eDNA approach was used to investigate non-native freshwater fish species from fifteen different locations of Upper Sakarya Basin. eDNA was successfully extracted from the water samples of locations where the species were visually observed. Mean amplification rate of eDNA was calculated as 77.03%.This study is the first environmental DNA study used in detection of four of the most common invasive freshwater fish species. Results clearly indicating that eDNA surveys could be used as an important molecular tool to monitor invasive fish species in freshwater ecosystems.     

Temporal variation in dwarf sperm whale (Kogia sima) habitat use and group size off Great Abaco Island, Bahamas

Dwarf sperm whales (Kogia sima) are among the most commonly stranded yet least known pelagic cetaceans. Few studies have occurred at sea, and none have quantified temporal and spatial variation in dwarf sperm whale abundance and group size. We assessed seasonal and spatial variation in dwarf sperm whale group size and abundance off Great Abaco Island, Bahamas using surveys within a 126 km² study area with depths between 2 and 1,600 m. After correcting for survey effort and variation in sighting efficiency among sea states, we found that dwarf sperm whale group size and habitat use varied seasonally. In summer, dwarf sperm whale groups were small (median = 2.5, range = 1–8) and were found only in the two deep habitats within the study area (slope 400–900 m, deep 900–1,600 m). In winter, group sizes increased (median = 4, range = 1–12) and sightings were almost six times higher in the slope habitat, where vertical relief is highest, than other habitats. Our results suggest that studies of pelagic cetaceans and conservation plans must explicitly account for seasonal variation in group size and habitat use.     

Riverine distribution of mussel environmental DNA reflects a balance among density,transport, and removal processes

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Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA‐based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water‐limited ecosystem where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for noninvasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment and water filtered through glass fibre filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus‐specific PCRs were tested on environmental samples for two genera producing fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non‐African mammals showed that baits covering 30% of nontarget mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over‐representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100‐fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.     

Foraging ecology and niche overlap in pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales from waters of the U.S. mid‐Atlantic coast

A complementary approach of stomach content and stable isotope analyses was used to characterize the foraging ecology and evaluate niche overlap between pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales stranded on the U.S. mid‐Atlantic coast between 1998 and 2011. Food habits analysis demonstrated both species were primarily teuthophagous, with 35 species of cephalopods, and 2 species of mesopelagic fishes represented in their overall diets. Pianka's Index of niche overlap suggested high overlap between whale diets (O_n = 0.92), with squids from the families Histioteuthidae, Cranchidae, and Ommastrephidae serving as primary prey. Pygmy sperm whales consumed slightly larger prey sizes (mean mantle length [ML] = 10.8 cm) than dwarf sperm whales (mean ML = 7.8 cm). Mean prey sizes consumed by pygmy sperm whales increased with growth, but showed no trend in dwarf sperm whales. Significant differences were not detected in δ¹⁵N and δ¹³C values of muscle tissues from pygmy (10.8‰ ± 0.5‰, ?17.1‰ ± 0.6‰), and dwarf sperm whales (10.7‰ ± 0.5‰, ?17.0‰ ± 0.4‰), respectively. Isotopic niche widths also did not differ significantly and dietary overlap was high between the two species. Results suggest the feeding ecologies of the pygmy and dwarf sperm whales are similar and both species occupy equivalent trophic niches in the region.     

Assessment of littoral algal diversity from the northern Gulf of Mexico using environmental DNA metabarcoding

Traditional methods for algal biodiversity monitoring are costly and time inefficient because they rely on high‐level taxonomic expertise to address species identity problems involving phenotypic plasticity and morphological convergence. These problems are exacerbated in regions such as the Gulf of Mexico, that has a limited history of phycological exploration, but that are economically important or threatened by numerous anthropogenic stressors. Given the high pace of disturbance to natural systems, there is a critical need for expedient and cost‐effective tools for the study of benthic algal communities. Here we document the use of environmental DNA metabarcoding, using the partial LSU rDNA and 23S rDNA plastid molecular markers, to elucidate littoral algal diversity in the Northern Gulf of Mexico. We assigned 73.7% of algal OTUs to genus and 59.6% to species ranks. Our current study detected molecular signals for 35 algal/protist species with no previous reports in the Gulf of Mexico, thus providing an important, molecular‐validated, baseline of species richness for this region. We also make several bioinformatic recommendations for the efficient use of high‐throughput sequence data to assess biological communities.     

Use of environmental DNA to detect Eastern Sand Darter (Ammocrypta pellucida Putnam, 1863) in large Laurentian Great Lakes embayments

A single-species environmental DNA (eDNA) method was developed to sample for a small, benthic rare species, Eastern Sand Darter (Ammocrypta pellucida Putnam, 1863) in two large Lake Ontario embayments. Summer water sampling allowed for: (a) surveys of habitats (Wellers Bay) where traditional fish sampling gear could not be used; and, (b) a comparison between eDNA and seining-based detection probabilities at known occupied habitats (West Lake). In 2018, replicate (n = 3) 1 L water samples were collected from 90 Wellers Bay sites and 71 West Lake sites. A site-occupancy model, a hierarchical logistic regression model, was fitted to determine site occupancy, sample occupancy (presence of Eastern Sand Darter DNA in a water sample) and probability of detection (p) based on replicate quantitative polymerase chain reaction (qPCR) results for each water sample. Eastern Sand Darter was detected at 10 West Lake sites, but not from Wellers Bay. Mean site occupancy was 0.31 (0.12–0.70; 95% CLs), mean sample occupancy was 0.28 (0.09–0.58; 95% CLs), and mean detection probability in a subsample (i.e., successful qPCR amplification) given it was present was 0.40 (0.25–0.55; 95% CLs). While the eDNA method successfully detected Eastern Sand Darter from known occupied areas in West Lake, it was not more effective for assessing local site occupancy than traditional sampling methods, such as the seine.     

Effects of Sika Deer (Cervus nippon) and Dwarf Bamboo (Sasa senanensis) on Trillium Populations in Akan National Park,Eastern Hokkaido,Japan

The competition between Trillium spp. and other species could modify the utility of Trillium spp. as indicators of the impact of deer on forest vegetation. To evaluate whether Trillium spp. (T. camschatcense and T. tschonoskii) are appropriate indicators of the impact of sika deer (Cervus nippon) in the presence of dwarf bamboo (Sasa senanensis), which competes with Trillium populations, we examined the size class of large‐growth‐stage Trillium plants, the frequency of the presence of deer pellets and the coverage of S. senanensis in deer‐excluded sites (where deer have been eliminated since 1995) and unfenced control sites in Akan National Park, eastern Hokkaido, Japan. The result of a cumulative link mixed model (CLMM) suggests that size class at deer‐excluded sites is influenced by competitive understory species, even without deer grazing. The CLMM result for unfenced control sites suggests that C. nippon negatively influences the size class of Trillium populations; however, the negative effect weakened with increasing S. senanensis coverage. Thus, S. senanensis can function as an unpalatable neighbor that makes it difficult for C. nippon to detect Trillium plants. We conclude that the size class structure of Trillium spp. can be a useful index of C. nippon usage under sparse or medium S. senanensis understories; however, it is difficult to use these indices under dense S. senanensis understories because of the weakened negative effect of C. nippon grazing.     

Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Aquatic environmental DNA (eDNA) surveys are transforming how marine ecosystems are monitored. The time-consuming preprocessing step of active filtration, however, remains a bottleneck. Hence, new approaches that eliminate the need for active filtration are required. Filter-feeding invertebrates have been proven to collect eDNA, but side-by-side comparative studies to investigate the similarity between aquatic and filter-feeder eDNA signals are essential. Here, we investigated the differences among four eDNA sources (water; bivalve gill-tissue; sponges; and ethanol in which filter-feeding organisms were stored) along a vertically stratified transect in Doubtful Sound, New Zealand using three metabarcoding primer sets targeting fish and vertebrates. Combined, eDNA sources detected 59 vertebrates, while concurrent diver surveys observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was successfully extracted from the ethanol in which sponges were stored, although a reduced number of species were detected. Bivalve gill-tissue dissections, on the other hand, failed to reliably detect eDNA. Overall, our results show that vertebrate eDNA signals obtained from water samples and marine sponges are highly concordant. The strong similarity in eDNA signals demonstrates the potential of marine sponges as an additional tool for eDNA-based marine biodiversity surveys, by enabling the incorporation of larger sample numbers in eDNA surveys, reducing plastic waste, simplifying sample collection, and as a cost-efficient alternative. However, we note the importance to not detrimentally impact marine communities by, for example, nonlethal subsampling, specimen cloning, or using bycatch specimens.     

First record of a potential neonate tiger shark (Galeocerdo cuvier) at a remote oceanic island in the Eastern Tropical Pacific

Tiger sharks (Galeocerdo cuvier) play an important ecological role as top predators, yet knowledge of their reproductive ecology is scarce. Here, the authors report the first observation of a potential neonate G. cuvier at Cocos Island, a predator-dominated oceanic island in the Eastern Tropical Pacific (ETP). The individual was detected using baited remote underwater video stations (BRUVS). The cameras also detected female individuals potentially pregnant, suggesting that parturition may take place at or near the island. Nonetheless, it is still unclear if the presence of a single neonate is an isolated event or evidence that the species is using the island for reproduction.     

In vitro sperm characterization and development of a sperm cryopreservation method using directional solidification in the killer whale (Orcinus orca)

Research was conducted to characterize seminal traits and to develop a sperm cryopreservation method using directional freezing (DF) for the killer whale (Orcinus orca). Experiments evaluated effects of: (i) freezing rate (SLOW, MED, FAST) by diluent (BF5F, Biladyl®, EYC) in 0.5 mL straws; and (ii) freezing method (straw or DF) by glycerol (3, 6, or 9% final concentration, v:v) on in vitro sperm quality. Fresh ejaculates (n = 161) were (mean ± SD) 7.8 ± 7.4 mL at 740 × 10⁶ sperm/mL with 92.2 ± 6.3% total motility (TM), 85.4 ± 6.9% progressive motility (PM), 89.6 ± 9.0% viability and 89.8 ± 9.2% acrosome integrity. Samples frozen using straws by the MED or SLOW method were improved (P < 0.05) over FAST across all diluents. At 3 h post thaw (PT), TM, PM, Rapid motility (RM), VAP, VCL, ALH and viability for 3% and 6% glycerol were improved (P < 0.05) over 9% glycerol. Directional freezing samples at 0 h and 3 h PT, at all glycerol concentrations, displayed higher (P < 0.001) TM, PM, RM, VAP, VSL, VCL and viability /intact acrosomes (PI/FITC-PNA) than straw. These data provided the first information on ejaculate characteristics and the development of a semen cryopreservation method using DF in the killer whale.     

Two new species of gorgonian octocorals from the Tropical Eastern Pacific Biogeographic Region (Cnidaria,Anthozoa, Gorgoniidae)

The gorgoniid Eugorgia is exclusively an eastern Pacific genus. It has a wide geographic and bathymetric range of distribution, found from California to Perú and extends down to 65 m deep. Two new species are herein described. The morphological characters were analyzed and illustrated by light and scanning electron microscopy. Eugorgia beebeisp. n. can be distinguished by its white, ascending, sparse colony growth. Eugorgia mutabilissp. n. can be distinguished by its white colony that changes color after collection, and the conspicuous sharp-crested disc sclerites. From a morphological point of view the new species are related to the daniana-group, the rubens-group and the siedenburgae-group of Eugorgia; their affiliations, and the proposal of a new group are discussed. These new species increases the number of species in the genus to 15, and contribute to the knowledge of the eastern Pacific octocoral biodiversity.     

Rapid degradation of longer DNA fragments enables the improved estimation of distribution and biomass using environmental DNA

The advent of environmental DNA (eDNA) analysis methods has enabled rapid and wide‐range ecological monitoring in aquatic ecosystems, but there is a dearth of information on eDNA degradation. The results of previous studies suggest that the decay rate of eDNA varies depending on the length of DNA fragments. To examine this hypothesis, we compared temporal change in copy number of long eDNA fragments (719 bp) with that of short eDNA fragments (127 bp). First, we isolated rearing water from a target fish species, Japanese Jack Mackerel (Trachurus japonicus), and then quantified the copy number of the long and short eDNA fragments in 1 L water samples after isolating the water from the fish. Long DNA fragments showed a higher decay rate than short fragments. Next, we measured the eDNA copy numbers of long and short DNA fragments using field samples, and compared them with fish biomass as measured by echo intensity. Although a previous study suggested that short eDNA fragments could be overestimated because of nontarget eDNA from a nearby fish market and carcasses, the eDNA concentrations of long fragments were correlated with echo intensity. This suggests that the concentration of longer eDNA fragments reflects fish biomass more accurately than the previous study by removing the effects of the fish market and carcasses. The length‐related differences in eDNA have a substantial potential to improve estimation of species biomass.     

Molecular studies on two variant repeat types of the common cetacean DNA satellite of the sperm whale, and the relationship between Physeteridae (sperm whales) and Ziphiidae (beaked whales)

In the sperm whale (Physeter macrocephalus) two different repeat types (A and B) of the common cetacean DNA satellite were identified. The evolution of each group of repeats appears to be independent from that of the other. The sequence similarity between the two groups is less than the similarity between group A and repeats of the satellite in related whale species. The systematic relationship within and between the families Physeteridae (sperm whales) and Ziphiidae (beaked whales) was addressed by both sequence analysis of the satellite and comparisons with the families Delphinidae and Phocoenidae. The mysticete blue whale (Balaenoptera musculus) was used as an outgroup in the comparisons. The molecular phylogeny, when maximum-parsimony analysis and the neighbor-joining method were used, grouped together species of each family. At the family level the ziphiids grouped closet to the families Phocoenidae and Delphinidae. The similarities between the common cetacean satellite of the blue whale and the sperm whale were greater than those between the blue whale and the other odontocetes included, suggesting that the evolution of the satellite is slower in the sperm whale than in the other odontocetes.      

Cetopsis varii,a new species of whale catfish (Siluriformes: Cetopsidae) from the Meta Basin,Colombia

Cetopsis varii sp. nov. Cetopsidae (Cetopsinae) is described from the Río Meta basin in eastern Colombia, at middle portions of the Río Orinoco basin. The new species differs from congeners by a combination of features: the absence of a humeral spot, presence of eye, conical teeth on vomer and dentary and rounded posterior nares, along with details of body, dorsal and caudal‐fin pigmentation. The osteology of the new species is investigated through high‐resolution X‐ray computed tomography and cleared and stained specimens. Data thus obtained are used to code the new species for character states utilized in a previous phylogenetic analysis of Cetopsidae. Analysis of the expanded matrix shows that C. varii is the sister group to C. orinoco.     

Upper quaternary vegetational and climatic sequence of the fuquene area (Eastern Cordillera,Colombia)

In this paper the results of a pollen-analytical study of three bore holes of lake deposits in the Fuquene-Valle de Ubaté area, Colombian Cordillera Oriental (5° N; elev. 2,580 m) are given. By means of ¹⁴C dates and comparison with other pollen diagrams and dates from the Eastern Cordillera, it was possible to correlate the local pollen zones and chronostratigraphical units with the European chronostratigraphical sequence. The longest diagram (Fuquene II) represents some 30, 000 years, including part of the Middle Pleniglacial, the Upper Pleniglacial, the Late Glacial and the Holocene.During the Middle Pleniglacial, Polylepis wood was an important constituent of the vegetation. During climatic extremes of the Upper Pleniglacial an open páramo vegetation existed.During the main part of the Upper Pleniglacial (from ca. 21,000 to ca. 13,000 B.P.) the lake level was low and the climate dry. The lake level rose again in the beginning of the Late Glacial, and the area around the lake became forested. At the beginning of the El Abra Stadial (Late Dryas Stadial) there was a marked cooling and the lake became lower once more; this had a great impact on the vegetation which became partly open again. The beginning of the Holocene is marked by a gradual increase of forest elements, especially of Quercus (oak.) Oak forests dominated the area during the greater part of the Holocene. During the “hypithermal”, elements growing today at a lower level, such as Cecropia, Acalypha (and possibly Alchornea), must have been growing in the area, intermixed with the oak forest. At the same time there was a considerable increase of Urticaceae in the undergrowth of these forests. The vegetation zones were probably situated several hundreds of metres higher than they are at the present time.The influence of man on vegetation had started already before the beginning of our era, but there is a sudden increase of this influence (e.g., increase of Dodonaea, decrease of Quercus and Urticaceae) somewhere around 2,000 B.P. Later on, the diagram shows the rapid ultimate decline of the forest elements and an increase of Gramineae. Today nothing is left of the original oak forests and their place is taken by arable land or by secondary plant communities with low brushwood.In the lake sediments, thin layers of volcanic ash were found dated approximately 9,000 B.P., 11,000 B.P., and 21,000 B.P., respectively; a series of three ash-layers was deposited between approximately 22,000 B.P. and 26,000 B.P. and one possibly at approximately 30,000 B.P. These layers have been found in several other sections in the Eastern Cordillera and are the basis for a tephrochronology.     

Effect of exogenous DNA on bovine sperm functionality using the sperm mediated gene transfer (SMGT) technique

Sperm mediated gene transfer (SMGT) could provide the opportunity to carry out transgenesis on a mass scale using spermatozoa as vectors for exogenous DNA. However, the efficiency of sperm‐mediated DNA transfer is still questionable, and the mode of transmission to the egg has not yet been well understood. Our aim was to investigate the capacity of bovine spermatozoa to carry exogenous DNA and its relationship to sperm functionality. We studied these parameters using flow cytometry to measure viability (necrosis and apoptosis) and capacitation status, computer‐assisted semen analysis (CASA) to measure motility parameters and in vitro fertilization (IVF) to assess fertilizing capacity. Furthermore, we studied the effect of capacitation status on interaction with exogenous DNA, and the role of heparin supplementation in this process. Bull spermatozoa showed a high capacity to bind DNA quickly and reached a maximum after 30 min, with approximately half of the DNA‐bound spermatozoa being viable. Incubation with exogenous DNA induced a decrease in sperm viability and motility and increased the proportion of apoptotic cells, but did not affect the cleavage rate in IVF assay. Heparin increased high‐lipid disorder and the number of sperm with DNA bound (viable and dead). In conclusion, this study shows that live spermatozoa can bind exogenous DNA with a slight negative effect in some parameters of sperm function that in our opinion, would not drastically compromise fertility. Mol. Reprod. Dev. 77: 687–698, 2010. © 2010 Wiley‐Liss, Inc.     

Assessing habitat suitability for the translocation of Ochrosia tahitensis (Apocynaceae), a critically endangered endemic plant from the island of Tahiti (South Pacific)

Reintroduction or translocation of threatened plant species, as part of in situ conservation efforts, often failed because of the lack or the poor quality of remaining natural habitats due to human disturbances and invasion by alien species, especially in island ecosystems. We conducted a study on Ochrosia tahitensis (Apocynaceae), a critically endangered endemic small tree in the tropical high volcanic island of Tahiti (French Polynesia, South Pacific) to find the most suitable sites for future translocation. Distribution models were produced based on climate, topography, and plant community inventories (i.e. species composition and abundance, canopy height and openness, basal area of woody species) of the few remnant populations. Results show that this species, comprising 32 reproductive trees within 16 populations known in the wild, remains restricted to a few ecological refuges representing a very small part of its potential ecological range located on the northwest side of the island, and shares its current habitats with a set of more common native woody species found in mesic-wet forests. The use of native plant communities as a proxy for habitat suitability along with species distribution modelling can enhance translocation success in island ecosystems, but only if the major threats causing population decrease, mainly forest destruction and fragmentation and invasive alien species, are effectively managed.