Persistence of environmental DNA in marine systems

As environmental DNA (eDNA) becomes an increasingly valuable resource for marine ecosystem monitoring, understanding variation in its persistence across contrasting environments is critical. Here, we quantify the breakdown of macrobial eDNA over a spatio-temporal axis of locally extreme conditions, varying from ocean-influenced offshore to urban-inshore, and between winter and summer. We report that eDNA degrades 1.6 times faster in the inshore environment than the offshore environment, but contrary to expectation we find no difference over season. Analysis of environmental covariables show a spatial gradient of salinity and a temporal gradient of pH, with salinity—or the biotic correlates thereof—most important. Based on our estimated inshore eDNA half-life and naturally occurring eDNA concentrations, we estimate that eDNA may be detected for around 48 h, offering potential to collect ecological community data of high local fidelity. We conclude by placing these results in the context of previously published eDNA decay rates

Limited hybridization between introduced and Critically Endangered indigenous tilapia fishes in northern Tanzania

Hybridization between introduced and indigenous species can lead to loss of unique genetic resources and precipitate extinction. In Tanzania, the Nile tilapia (Oreochromis niloticus) and blue-spotted tilapia (Oreochromis leucostictus) have been widely introduced to non-native habitats for aquaculture and development of capture fisheries. Here, we aimed to quantify interspecific hybridization between these introduced species and the indigenous species Oreochromis esculentus, Oreochromis jipe and Oreochromis korogwe. In the Pangani basin, several hybrids were observed (O. niloticus × O. jipe, O. leucostictus × O. jipe, O. niloticus × O. korogwe), although hybrids were relatively uncommon within samples relative to purebreds. Hybrids between the native O. jipe × O. korogwe were also observed. In the Lake Victoria basin, no evidence of hybrids was found. Analysis of body shape using geometric morphometrics suggested that although purebreds could be discriminated from one another, hybrids could not be readily identified on body and head shape alone. These results provide the first evidence of hybridization between the introduced species and the Critically Endangered O. jipe in Tanzania. Given uncertainty regarding benefits of introduced species over large-bodied indigenous species in aquaculture and capture fisheries, we suggest that future introductions of hybridization-prone species should be carefully evaluated

Reproduction influences seasonal eDNA variation in a temperate marine fish community

Many factors influence how environmental DNA (eDNA) abundance varies in natural environments. One of the least studied contributors to eDNA variation is that of reproduction. Marine organisms that broadcast spawn are expected to shed increased quantities of DNA in association with the release of gametes and the elevated levels of activity associated with reproduction. To test this hypothesis at the community level, we present a year-long eDNA time-series of a temperate sea-shelf fish assemblage combined with adult fish and ichthyoplankton abundance data. Our results show that eDNA is associated with species abundance estimated by conventional fish surveys at all life stages (adult, larval, and egg), and was on average 2.3-fold more abundant during predicted fish reproductive periods

Molecular phylogeny of Oreochromis (Cichlidae: Oreochromini) reveals mito-nuclear discordance and multiple colonisation of adverse aquatic environments

Although the majority of cichlid diversity occurs in the African Great Lakes, these fish have also diversified across the African continent. Such continental radiations, occurring in both rivers and lakes have received far less attention than lacustrine radiations despite some members, such as the oreochromine cichlids (commonly referred to as ‘tilapia’), having significant scientific and socioeconomic importance both within and beyond their native range. Unique among cichlids, several species of the genus Oreochromis exhibit adaptation to soda conditions (including tolerance of elevated temperatures and salinity), which are of interest from evolutionary biology research and aquaculture perspectives. Questions remain regarding the factors facilitating the diversification of this group, which to date have not been addressed within a phylogenetic framework. Here we present the first comprehensive (32/37 described species) multi-marker molecular phylogeny of Oreochromis and closely related Alcolapia, based on mitochondrial (1583 bp) and nuclear (3092 bp) sequence data. We show widespread discordance between nuclear DNA and mitochondrial DNA trees. This could be the result of incomplete lineage sorting and/or introgression in mitochondrial loci, although we didn’t find a strong signal for the latter. Based on our nuclear phylogeny we demonstrate that adaptation to adverse conditions (elevated salinity, temperature, or alkalinity) has occurred multiple times within Oreochromis, but that adaptation to extreme (soda) conditions (high salinity, temperature, and alkalinity) has likely arisen once in the lineage leading to O. amphimelas and Alcolapia. We also show Alcolapia is nested within Oreochromis, which is in agreement with previous studies, and here revise the taxonomy to synonymise the genus in Oreochromis, retaining the designation as subgenus Oreochromis (Alcolapia)

Environmental DNA captures elasmobranch diversity in a temperate marine ecosystem

Many sharks, skates, and rays (elasmobranchs) are highly threatened by the activities of commercial fisheries, and a clear understanding of their distributions, diversity, and abundance can guide protective measures. However, surveying and monitoring elasmobranch species can be highly invasive or resource-intensive, and utilization of non-invasive environmental DNA-based methods may overcome these problems. Here, we studied spatial and seasonal variation in the elasmobranch community of the Western English Channel using environmental DNA (eDNA) collected from surface and bottom waters periodically over an annual cycle (2017–2018). In total we recovered 13 elasmobranch species within eDNA samples, and the number of transformed eDNA reads was positively associated with species (hourly) catch data resolved from 105-year time series trawl data (1914–2018). These results demonstrate the ability of eDNA to detect and semi-quantitatively reflect the prevalence of historically dominant and rare elasmobranch species in this region. Notably, eDNA recorded a greater number of species per sampling event than a conventional trawl survey in the same area over the same sampling years (2017–2018). Several threatened species were recovered within the eDNA, including undulate ray, porbeagle shark, and thresher shark. Using eDNA, we found differences in elasmobranch communities among sampling stations and between seasons, but not between sampling depths. Collectively, our results suggest that non-invasive eDNA-based methods can be used to study the spatial and seasonal changes in the diversity and abundance of whole elasmobranch communities within temperate shelf habitats. Given the threatened status of many elasmobranchs in human-impacted marine environments, eDNA analysis is poised to provide key information on their diversity and distributions to inform conservation-focused monitoring and management

Stable Isotope Evidence for Dietary Overlap between Alien and Native Gastropods in Coastal Lakes of Northern KwaZulu-Natal, South Africa

Tarebia granifera (Lamarck, 1822) is originally from South-East Asia, but has been introduced and become invasive in many tropical and subtropical parts of the world. In South Africa, T. granifera is rapidly invading an increasing number of coastal lakes and estuaries, often reaching very high population densities and dominating shallow water benthic invertebrate assemblages. An assessment of the feeding dynamics of T. granifera has raised questions about potential ecological impacts, specifically in terms of its dietary overlap with native gastropods.A stable isotope mixing model was used together with gut content analysis to estimate the diet of T. granifera and native gastropod populations in three different coastal lakes. Population density, available biomass of food and salinity were measured along transects placed over T. granifera patches. An index of isotopic (stable isotopes) dietary overlap (IDO, %) aided in interpreting interactions between gastropods. The diet of T. granifera was variable, including contributions from microphytobenthos, filamentous algae (Cladophora sp.), detritus and sedimentary organic matter. IDO was significant (>60%) between T. granifera and each of the following gastropods: Haminoea natalensis (Krauss, 1848), Bulinus natalensis (Küster, 1841) and Melanoides tuberculata (Müller, 1774). However, food did not appear to be limiting. Salinity influenced gastropod spatial overlap. Tarebia granifera may only displace native gastropods, such as Assiminea cf. ovata (Krauss, 1848), under salinity conditions below 20. Ecosystem-level impacts are also discussed.The generalist diet of T. granifera may certainly contribute to its successful establishment. However, although competition for resources may take place under certain salinity conditions and if food is limiting, there appear to be other mechanisms at work, through which T. granifera displaces native gastropods. Complementary stable isotope and gut content analysis can provide helpful ecological insights, contributing to monitoring efforts and guiding further invasive species research

Environmental DNA reveals ecologically relevant spatial and temporal variation in fish assemblages between estuaries and seasons

Estuarine ecosystems are threatened by numerous anthropogenic pressures. Fish assemblages are a dominant component of estuarine macrofauna and serve as indicators for the health of these transitional water ecosystems. Environmental DNA (eDNA) metabarcoding is increasingly used to assess the biodiversity of fishes in estuaries. However, there is a need to further establish how effective eDNA metabarcoding can be relative to conventional fish sampling methods across multiple estuaries and seasons. This study compared fish assemblages detected via eDNA metabarcoding of surface water samples to contemporary sampling with conventional fishing gears in three temperate estuaries (UK), during early summer and autumn. Most species caught by fishing were detected by eDNA. Species richness estimates from eDNA were two to ten times higher than estimates based on fishing, and included taxa of conservation importance and a non-native species. The eDNA assemblage composition was significantly different to the assemblage detected by seine nets. Importantly, eDNA methods could effectively discriminate between fish assemblages of different estuaries and seasons. Fish assemblages in estuaries are often not monitored due to resource constraints. The dynamic nature of estuaries may make fishing gear deployment difficult and inconsistent. The findings indicate that eDNA metabarcoding is suited to gathering large amounts of information on fish biodiversity, at a relatively low sampling effort, compared to established fishing methods. Therefore, eDNA shows promise as an assessment tool for fish assemblage structure and ecosystem health in estuarine environments, with application to statutory monitoring

Widespread colonisation of Tanzanian catchments by introduced Oreochromis tilapia fishes: the legacy from decades of deliberate introduction

From the 1950s onwards, programmes to promote aquaculture and improve capture fisheries in East Africa have relied heavily on the promise held by introduced species. In Tanzania these introductions have been poorly documented. Here we report the findings of surveys of inland water bodies across Tanzania between 2011 and 2017 that clarify distributions of tilapiine cichlids of the genus Oreochromis. We identified Oreochromis from 123 sampling locations, including 14 taxa restricted to their native range and three species that have established populations beyond their native range. Of these three species, the only exotic species found was blue-spotted tilapia (Oreochromis leucostictus), while Nile tilapia (Oreochromis niloticus) and Singida tilapia (Oreochromis esculentus), which are both naturally found within the country of Tanzania, have been translocated beyond their native range. Using our records, we developed models of suitable habitat for the introduced species based on recent (1960–1990) and projected (2050, 2070) East African climate. These models indicated that presence of suitable habitat for these introduced species will persist and potentially expand across the region. The clarification of distributions provided here can help inform the monitoring and management of biodiversity, and inform policy related to the future role of introduced species in fisheries and aquaculture

Asymmetric Reproductive Isolation between Two Sympatric Annual Killifish with Extremely Short Lifespans

BACKGROUND: Interspecific reproductive isolation is typically achieved by a combination of intrinsic and extrinsic barriers. Behavioural isolating barriers between sympatric, closely related species are often of primary importance and frequently aided by extrinsic factors causing spatial and temporal interspecific separation. Study systems with a severely limited role of extrinsic factors on reproductive isolation may provide valuable insights into how reproductive isolation between sympatric species is maintained. We used no-choice experimental set-up to study reproductive barriers between two closely related sympatric African killifish species, Nothobranchius furzeri and Nothobranchius orthonotus. These fish live in small temporary savannah pools and have complete spatial and temporal overlap in reproductive activities and share a similar ecology. PRINCIPAL FINDINGS: We found that the two species display largely incomplete and asymmetric reproductive isolation. Mating between N. furzeri males and N. orthonotus females was absent under standard experimental conditions and eggs were not viable when fish were forced to mate in a modified experimental setup. In contrast, male N. orthonotus indiscriminately mated with N. furzeri females, the eggs were viable, and offspring successfully hatched. Most spawnings, however, were achieved by male coercion and egg production and embryo survival were low. Behavioural asymmetry was likely facilitated by mating coercion from larger males of N. orthonotus and at relatively low cost to females. Interestingly, the direction of asymmetry was positively associated with asymmetry in post-mating reproductive barriers. SIGNIFICANCE: We showed that, in fish species with a promiscuous mating system and multiple matings each day, selection for strong mate preferences was relaxed. This effect was likely due to the small proportion of resources allocated to each single mating and the high potential cost to females from mating refusal. We highlight and discuss the fact that males of rarer species may often coercively mate with females of a related, more abundant species