Meta-Fish-Lib: A generalised,dynamic DNA reference library pipeline for metabarcoding of fishes

The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish-12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta-Fish-Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib .     

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.

     

Isotopic change throughout the life history of a Lake Malawi cichlid fish

Clear changes in body size-isotope (carbon and nitrogen) trajectories of Pseudotropheus callainos , a cichlid belonging to the endemic haplochromine species radiation in Lake Malawi, were found that corresponded with an ontogenetic dietary shift from predominantly planktonic to benthic food sources. The results indicated that dietary switching was a proximate cause of isotopic change over the life history of this species and confirmed the value of stable isotope signatures for inferring diet. The data also illustrated that possible variability of signatures over the life history of a species should be considered when using stable isotope ratios to investigate fine-scale ecological differentiation among taxa.     

Continental shelf-wide response of a fish assemblage to rapid warming of the sea

Climate change affects marine biological processes from genetic to ecosystem levels [1-3]. Recent warming in the northeast Atlantic [4, 5] has caused distributional shifts in some fish species along latitudinal and depth gradients [6,?7], but such changes, as predicted by climate envelope models [8], may often be prevented because population movement requires availability of suitable habitat. We assessed the full impacts of warming on the commercially important European continental shelf fish assemblage using a data-driven Eulerian (grid-based) approach that accommodates spatial heterogeneity in ecological and environmental conditions. We analyzed local associations of species abundance and community diversity with climatic variables, assessing trends in 172 cells from records of >100 million individuals sampled over 1.2 million km(2) from 1980-2008. We demonstrate responses to warming in 72% of common species, with three times more species increasing in abundance than declining, and find these trends reflected in international commercial landings. Profound reorganization of the relative abundance of species in local communities occurred despite decadal stability in the presence-absence of species. Our analysis highlights the importance of focusing on changes in species abundance in established local communities to assess the full consequences of climate change for commercial fisheries and food security.     

Levels of connectivity between longnose skate (Dipturus oxyrinchus) in the Mediterranean Sea and the north-eastern Atlantic Ocean

Sequencing of a partial region of the mitochondrial control region has revealed no shared haplotypes between longnose skate (Dipturus oxyrinchus L.) sampled in the north-eastern Atlantic (Norway and Rockall) and those sampled in the Mediterranean (Mallorca). Bayesian estimation of the migration rate suggests little, if any, gene flow occurs between the regions and that the populations separated 20,000?years ago. These conclusions provide a genetic basis for long-standing observations, based on egg capsule and adult size, that longnose skate in the Mediterranean may be genetically isolated from other stocks. This result has important conservation implications for the threatened longnose skate.     

SEQUENTIAL FEMALE ASSESSMENT DRIVES COMPLEX SEXUAL SELECTION ON BOWER SHAPE IN A CICHLID FISH

In many animals, sexual selection on male traits results from female mate choice decisions made during a sequence of courtship behaviors. We use a bower‐building cichlid fish, Nyassachromis cf. microcephalus, to show how applying standard selection analysis to data on sequential female assessment provides new insights into sexual selection by mate choice. We first show that the cumulative selection differentials confirm previous results suggesting female choice favors males holding large volcano‐shaped sand bowers. The sequential assessment analysis reveals these cumulative differentials are the result of selection acting on different bower dimensions during the courtship sequence; females choose to follow males courting from tall bowers, but choose to engage in premating circling with males holding bowers with large diameter platforms. The approach we present extends standard selection analysis by partitioning the variances of increasingly accurate estimates of male reproductive fitness and is applicable to systems in which sequential female assessment drives sexual selection on male traits.     

Foraging of rocky habitat cichlid fishes in Lake Malawi: coexistence through niche partitioning?

The haplochromine cichlid fish communities of the rocky habitats of Lake Malawi are highly diverse; however, many species live side by side with apparently very similar resource requirements. There is a long-standing debate concerning whether these species partition their resources on a finer scale than has been previously reported or if species that are truly ecologically indistinguishable can coexist. A field study of food resource use was conducted to determine whether coexisting species segregate their diet and foraging sites. Significant differences between species were found, yet considerable inter-specific resource use overlap was commonplace. The data indicate that these cichlid species coexist both with and without niche differentiation. We propose that alternatives to niche differentiation should be considered to explain how many species coexist in Lake Malawi cichlid communities. Received: 5 October 1998 / Accepted: 30 June 1999     

Niche segregation among Lake Malawi cichlid fishes? Evidence from stable isotope signatures

The fish communities of the rocky littoral zone of Lake Malawi contain a large number of ecologically similar cichlid species. It has been suggested that dietary niche segregation may play a role in the coexistence of these species, but previous studies have yielded ambiguous results. Stable isotope analysis was used to determine whether five sympatric species are segregated by diet. Significant differences were found between the mean isotopic signatures of the study species, but there was considerable interspecific overlap between three species from the same subgenus that were anatomically almost indistinguishable. The implication that this was due to substantial dietary similarity was supported by stomach content analysis. We propose that ecological segregation may not always be necessary to allow coexistence of Lake Malawi cichlids.     

Losing cichlid fish biodiversity: genetic and morphological homogenization of tilapia following colonization by introduced species

Among the many negative impacts of invasive species, hybridization with indigenous species has increasingly become recognized as a major issue. However, relatively few studies have characterized the phenotypic outcomes of hybridization following biological invasions. Here we investigate the genetic and morphological consequences of stocking invasive tilapia species in two water bodies in central Tanzania. We sampled individuals from the Mindu Reservoir on the Ruvu river system, and at Kidatu on the Great Ruaha–Rufiji river system. We screened individuals at 16 microsatellite loci, and quantified morphology using geometric morphometrics and linear measurements. In both the Mindu and Kidatu systems, we identified evidence of hybridization between indigenous Wami tilapia (Oreochromis urolepis) and the introduced Nile tilapia (Oreochromis niloticus) or blue-spotted tilapia (Oreochromis leucostictus). At both sites, purebred individuals could largely be separated using geometric morphometric variables, with hybrids occupying a broad morphospace among the parental species. Our data demonstrate that the gene pools and phenotypic identity of the indigenous O. urolepis have been severely impacted by the stocking of the invasive species. Given the lack of evidence for clear commercial benefits from stocking invasive tilapia species in waters already populated by indigenous congenerics, we suggest further spread of introduced species should be undertaken with considerable caution.