Diet overlap of non‐native common carp and native Nile tilapia: A potential cause for population reduction of Nile tilapia stock in Lake Ziway,Ethiopia

Lake Ziway harbours indigenous and exotic fish species including Nile tilapia (Oreochromis niloticus) and common carp (Cyprinus carpio). Nile tilapia was the dominant and preferred fish. However, its contribution to total catch has dramatically declined from 89.3% in 1994 to 27% in 2014 while the introduced common carp has increased from 0% before 2012 to 25% in 2014. Common carp potentially compete with Nile tilapia for available resources and could be a cause for the decline. Thus, the study explored the dietary overlap of the two species from April to August 2017. Schoener's overlap index (α) revealed significant dietary overlap between the two species (α = 0.84, between juveniles and α = 0.63, between adults). Juveniles fed mainly on animal origin (zooplankton and insects), while adult Nile tilapia have consumed plant origin (macrophyte and phytoplankton), and adult common carp fed on macrophytes and detritus. The presence of significant dietary overlap between the two species, particularly due to intense competition among juveniles, might cause the reduction of Nile tilapia stock because the native species has shown a competitive disadvantage for food in the presence of common carp. This study provides baseline information to researchers and decision makers working towards the sustainable resource utilisation of the system.     

Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics

This study assessed the major histocompatibility complex (MHC) and neutral genetic variation and structure in two percid species, perch Perca fluviatilis and zander Sander lucioperca, in a unique brackish ecosystem, the Baltic Sea. In addition, to assess the importance of MHC diversity to disease susceptibility in these populations, comparisons were made to an introduced, disease susceptible, P. fluviatilis population in Australia. Eighty‐three MHC class II B exon 2 variants were amplified: 71 variants from 92 P. fluviatilis samples, and 12 variants from 82 S. lucioperca samples. Microsatellite and MHC data revealed strong spatial genetic structure in S. lucioperca, but not P. fluviatilis, across the Baltic Sea. Both microsatellite and MHC data showed higher levels of genetic diversity in P. fluviatilis from the Baltic Sea compared to Australia, which may have facilitated the spread of an endemic virus, EHNV in the Australian population. The relatively high levels of genetic variation in the Baltic Sea populations, together with spatial genetic structure, however, suggest that there currently seems to be little risk of disease epidemics in this system. To ensure this remains the case in the face of ongoing environmental changes, fisheries and habitat disturbance, the conservation of local‐scale genetic variation is recommended.     

Diet of the critically endangered blackchin guitarfish Glaucostegus cemiculus revealed using DNA metabarcoding

We present the first assessment of the diet of the blackchin guitarfish Glaucostegus cemiculus (Geoffroy Saint-Hilaire, 1817) for West Africa using DNA metabarcoding on stomach contents of individuals captured in the Bijagós Archipelago, Guinea-Bissau. The diet was dominated by crustaceans, particularly caramote prawn Penaeus kerathurus (frequency of occurrence [FO] = 74%, numerical frequency [NF] = 54%) and fiddler crab Afruca tangeri (FO = 74%, NF = 12%). Bony fishes were present in 30% of the stomachs. We highlight the importance of conservation action for intertidal habitats and their associated benthic invertebrates for the survival of the critically endangered blackchin guitarfish.     

Making a master filterer: Ontogeny of specialized filtering plates in silver carp (Hypophthalmichthys molitrix)

Filter feeding fishes possess several morphological adaptations necessary to capture and concentrate small particulate matter from the water column. Filter feeding teleosts typically employ elongated and tightly packed gill rakers with secondary bony or epithelial modifications that increase filtering efficiency. The gill rakers of Hypophthalmichthys molitrix, silver carp, are anatomically distinct from and more complex than the filtering apparatus of other teleostean fishes. The silver carp filtering apparatus is composed of biserial, fused filtering plates used to capture particles ranging in size from 4 to 80 μm. Early in ontogeny, at 15–25 mm standard length (SL), silver carp gill rakers are reminiscent of other more stereotypical teleostean rakers, characterized by individual lanceolate rakers that are tightly packed along the entirety of the branchial arches. At 30 mm SL, secondary epithelial projections and concomitant dermal ossification begin to stitch together individual gill rakers. During later juvenile stages, dermal bone further modifies the individual gill rakers and creates a bony scaffold that supports the now fully fused and porous epithelium. By adulthood, the stitching of bone and complete fusion of the overlying epithelium creates rigid filtering plates with morphologically distinct faces. The inner face of the plates is organized into a net‐like matrix while the outer face has a sponge‐like appearance comprised of differently sized pores. Here, we present morphological data from an ontogenetic series of the filtering apparatus within silver carp. These data inform hypotheses regarding both how these gill raker plates may have evolved from a more basal condition, as well as how this novel architecture allows this species to feed on exceedingly small phytoplankton, particles that represent a greater filtering challenge to the typical anatomy of the gill rakers of fishes.     

动物食性分析在生态学中的应用研究进展——基于DNA宏条形码技术

动物食性分析是动物营养生态学的重要研究手段,可用于解析动物与环境因素的关联性、捕食者与猎物之间的关系,以及动物物种多样性等科学问题。近年来,基于新一代测序技术的DNA宏条形码技术被广泛应用到生态学多个研究领域,极大地促进了生命科学交叉学科的发展。其中,DNA宏条形码技术在动物食性分析中具有高分辨、高效率、低样本量等优势,具有重要的应用前景。综述了基于DNA宏条形码技术的动物食性分析在生态学中的应用研究进展,并进一步总结了DNA宏条形码技术原理和食性分析方法,着重探讨了基于DNA宏条形码技术的动物食性分析在珍稀濒危动物保护、生物多样性监测、农业害虫防治等生态学研究领域中的应用,并对DNA宏条形码技术在动物食性分析中存在的问题及应用前景进行小结与展望。     

DNA barcoding reveals novel insights into pterygophagy and prey selection in distichodontid fishes (Characiformes: Distichodontidae)

DNA barcoding was used to investigate dietary habits and prey selection in members of the African‐endemic family Distichodontidae noteworthy for displaying highly specialized ectoparasitic fin‐eating behaviors (pterygophagy). Fin fragments recovered from the stomachs of representatives of three putatively pterygophagous distichodontid genera (Phago, Eugnathichthys, and Ichthyborus) were sequenced for the mitochondrial gene co1. DNA barcodes (co1 sequences) were then used to identify prey items in order to determine whether pterygophagous distichodontids are opportunistic generalists or strict specialists with regard to prey selection and, whether as previously proposed, aggressive mimicry is used as a strategy for successful pterygophagy. Our findings do not support the hypothesis of aggressive mimicry suggesting instead that, despite the possession of highly specialized trophic anatomies, fin‐eating distichodontids are opportunistic generalists, preying on fishes from a wide phylogenetic spectrum and to the extent of engaging in cannibalism. This study demonstrates how DNA barcoding can be used to shed light on evolutionary and ecological aspects of highly specialized ectoparasitic fin‐eating behaviors by enabling the identification of prey species from small pieces of fins found in fish stomachs.     

DNA barcodes of the native ray‐finned fishes in Taiwan

Species identification based on the DNA sequence of a fragment of the cytochrome c oxidase subunit I gene in the mitochondrial genome, DNA barcoding, is widely applied to assist in sustainable exploitation of fish resources and the protection of fish biodiversity. The aim of this study was to establish a reliable barcoding reference database of the native ray‐finned fishes in Taiwan. A total of 2993 individuals, belonging to 1245 species within 637 genera, 184 families and 29 orders of ray‐finned fishes and representing approximately 40% of the recorded ray‐finned fishes in Taiwan, were PCR amplified at the barcode region and bidirectionally sequenced. The mean length of the 2993 barcodes is 549 bp. Mean congeneric K2P distance (15.24%) is approximately 10‐fold higher than the mean conspecific one (1.51%), but approximately 1.4‐fold less than the mean genetic distance between families (20.80%). The Barcode Index Number (BIN) discordance report shows that 2993 specimens represent 1275 BINs and, among them, 86 BINs are singletons, 570 BINs are taxonomically concordant, and the other 619 BINs are taxonomically discordant. Barcode gap analysis also revealed that more than 90% of the collected fishes in this study can be discriminated by DNA barcoding. Overall, the barcoding reference database established by this study reveals the need for taxonomic revisions and voucher specimen rechecks, in addition to assisting in the management of Taiwan's fish resources and diversity.     

Spatial patterns of flower colour variation in native and introduced ranges of Convolvulus arvensis (Convolvulaceae) revealed by citizen-science data and machine learning

• Flower colour polymorphism refers to the presence of multiple colour variants in plant populations. Investigation of this phenomenon led to multiple discoveries, including the principles of heredity and the foundations of population genetics. I examined flower colour variation across native and introduced ranges of Convolvulus arvensis, which exhibits flower colour polymorphism (individuals have white or pink petals).
• To study flower colour variation of this species throughout large geographic scale, I used observations gathered from the iNaturalist platform. To handle a large amount of data, I trained a neural network to classify the plants' morphs based on photographs. After which I performed spatial analyses to examine the patterns of the colour frequency, also in relation to environmental factors.
• The results show that flower colours are polymorphic across the whole species range, but the frequency of pink versus white flowers varies. In the Palearctic, I observed geographic clines of colour morph frequencies: a higher frequency of the pink morph in populations from Northwest Europe, whereas in South and East Europe, towards the eastern edge of the range, the white morph was dominant. In contrast, pattern of colour distribution in North America (where the species is invasive) seems random, but the model indicates a link between higher proportions of pink morphs in mild and humid climates.
• The mechanisms behind the observed patterns remain largely unknown, as changes in a morphs' frequency are not strongly linked to abiotic factors. To understand the spatial pattern, a detailed investigation, accounting for the species' phylogeography is needed. This study provides another example of how the general public may collect data relevant to ecological studies, even when the data are not collected for a specific project.

     

16S rRNAgene-based metagenomic analysis of the gut microbial community associated with the DUI species Unio crassus (Bivalvia: Unionidae)

What factors determine biome richness: genetic or environmental? Sex, phylogeny, and tolerance indicated by other symbionts (e.g., endosymbionts) or simply is it related to local habitat, especially if the gut biome is considered? To answer these questions, we investigated the gut microbial profile of both sexes of three Unio crassus populations, species with unique system of mitochondrial DNA inheritance called doubly uniparental inheritance (DUI), living in different ecological conditions. High-throughput sequencing of the V3–V4 hypervariable regions in the bacterial 16S rRNA gene fragment was performed, which resulted in a total of 1,051,647 reads, with 58,424 reads/65 OTUs (operational taxonomic units) per sample on average. We identified a core microbiome, with all individual mussels sharing 69 OTUs (representing 23% of the total number of OTUs). Proteobacteria was the dominant phylum in all samples, followed by Firmicutes, Actinobacteria, and Bacteroidetes. There were no significant differences in gut microbiome compositions between the two sexes of this species; however, we observed different phyla in geographically isolated populations. A non-metric multidimensional scaling plot and dendrogram showed that the bacterial profile complies with the genetic structure of populations. Although we found differences in microbiomes between populations, their genetic structure suggests that the microbiome is weakly related to habitat, and more strongly to phylogeography (on both F and M mitotypes). We found no significant differences in beta diversity between the individuals of the bacterial communities measured using the Bray–Curtis index. Finally, we also examined whether OTUs were represented by symbiotic bacteria that enable cellulose digestion and by endosymbiotic bacteria that play important functions in the biology of their hosts and also affect microevolutionary processes and population phenomena. With regard to the endosymbionts, however, there was no relation to sex of the studied individuals, which suggests that there are no straightforward relations between DUI and microbiome.     

Checklist of parasites for Ponto-Caspian gobies (Actinopterygii: Gobiidae) in their native and non-native ranges

This study provides a comprehensive checklist of parasites reported for native and non-native populations of seven Ponto-Caspian goby species, i.e. Babka gymnotrachelus, Neogobius fluviatilis, N. melanostomus, Ponticola gorlap, P. kessleri, Proterorhinus semilunaris and P. semipellucidus, all of which have recently expanded their natural range, either by transoceanic translocation or along the three main European intracontinental invasion corridors. In some cases, invasion success is facilitated by loss of natural enemies, such as predators and parasites; thus, knowledge of a species natural parasite fauna is essential for assessments of enemy release in the host's non-native range. The study is based on published literature and personal unpublished data related to parasites of Ponto-Caspian gobiids. A total of 249 parasite taxa have been reported during 1931—2019, with higher numbers reported from native (214) than non-native (151) ranges. This checklist indicates apparent reduction in native parasites in non-native ranges in all goby species, although parasite colonisation in non-native ranges differs between fish species and invasion corridors. Interestingly, the cumulative number of species reported is still gradually increasing in both ranges. Acquisition of high number of local parasite species also indicates competence of Ponto-Caspian gobies to a wide range of generalist parasites.     

Trophic ecology of three stingrays (Myliobatoidei: Dasyatidae) off the Brazilian north-eastern coast: Habitat use and resource partitioning

Understanding the ecological role of species with overlapping distributions is central to inform ecosystem management. Here we describe the diet, trophic level and habitat use of three sympatric stingrays, Hypanus guttatus, H. marianae and H. berthalutzae, through combined stomach content and stable isotope (δ¹³C and δ¹⁵N) analyses. Our integrated approach revealed that H. guttatus is a mesopredator that feeds on a diverse diet of benthic and epibenthic marine and estuarine organisms, principally bivalve molluscs, Alpheus shrimp and teleost fishes. Isotopic data supported movement of this species between marine and estuarine environments. H. berthalutzae is also a marine generalist feeder, but feeds primarily on teleost fishes and cephalopods, and consequently occupies a higher trophic level. In contrast, H. marianae is a mesopredator specialized on shrimps and polychaetas occurring only in the marine environment and occupying a low niche breadth. While niche overlap occurred, the three stingrays utilized the same prey resources at different rates and occupied distinct trophic niches, potentially limiting competition for resources and promoting coexistence. These combined data demonstrate that these three mesopredators perform different ecological roles in the ecosystems they occupy, limiting functional redundancy.     

Assessment of loci for DNA barcoding in the genus Thrips (Thysanoptera:Thripidae)

Identification of the juveniles of economically important thrips species on imports by morphology alone can be challenging and culturing is usually required. In the case of EU quarantine species such as Thrips palmi, rapid and accurate identification is essential. DNA barcoding using the Cytochrome oxidase I (COI) gene has become a popular technique for species identification; however, in some invertebrate genera COI has been shown to provide insufficient variability for species discrimination. This study presents a comparison of five different loci to investigate their ability to discriminate a small number of Thrips species. All five loci discriminated the species by neighbour-joining tree and varying degrees of discrimination were determined upon further investigation of the intraspecific and interspecific distances. Two distinct COI clades were observed for T. Palmi and judged to be COI haplotypes when data from the other four additional loci and geographical collection data were taken into consideration. COI was shown to provide sufficient variation to be used in future DNA barcoding efforts within the genus Thrips.     

Detection of feeding behaviour in common carp Cyprinus carpio by using an acceleration data logger to identify mandibular movement

Miniaturized acceleration data loggers were attached to the lower mandible of common carp Cyprinus carpio to remotely identify feeding behaviour. Whether the acceleration signal could distinguish the quantity and quality of food was also investigated. The frequency and amplitude of the lower mandible stroke, calculated from surging acceleration determined by continuous wavelet transformation, significantly increased during the feeding period compared to that during the non-feeding period. These characteristic movement patterns were maintained for mean ±s.e. 187·3 ± 38·2 s when the fish were fed a single item of food and for mean ±s.e. 419·3 ± 28·6 s when they consumed multiple items. The dominant cycle and amplitude calculated according to feeding event duration, however, did not differ significantly between the two types of diets the fish consumed. Surging acceleration could detect mean ±s.e. 89·8 ± 13·5% of feeding events, although the false detection rate was mean ±s.e. 25·9 ± 10·9%. The results indicate that the mandible acceleration measurement method could be utilized to detect and record the feeding events in fishes that use a suction feeding mode similar to C. carpio.     

DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea)

The analysis of apex predator diet has the ability to deliver valuable insights into ecosystem health, and the potential impacts a predator might have on commercially relevant species. The Australian sea lion (Neophoca cinerea) is an endemic apex predator and one of the world's most endangered pinnipeds. Given that prey availability is vital to the survival of top predators, this study set out to understand what dietary information DNA metabarcoding could yield from 36 sea lion scats collected across 1,500 km of its distribution in southwest Western Australia. A combination of PCR assays were designed to target a variety of potential sea lion prey, including mammals, fish, crustaceans, cephalopods, and birds. Over 1.2 million metabarcodes identified six classes from three phyla, together representing over 80 taxa. The results confirm that the Australian sea lion is a wide‐ranging opportunistic predator that consumes an array of mainly demersal fauna. Further, the important commercial species Sepioteuthis australis (southern calamari squid) and Panulirus cygnus (western rock lobster) were detected, but were present in <25% of samples. Some of the taxa identified, such as fish, sharks and rays, clarify previous knowledge of sea lion prey, and some, such as eel taxa and two gastropod species, represent new dietary insights. Even with modest sample sizes, a spatial analysis of taxa and operational taxonomic units found within the scat shows significant differences in diet between many of the sample locations and identifies the primary taxa that are driving this variance. This study provides new insights into the diet of this endangered predator and confirms the efficacy of DNA metabarcoding of scat as a noninvasive tool to more broadly define regional biodiversity.     

Anatomical features and histology of the digestive tract of two related neotropical omnivorous fishes (Characiformes; Anostomidae)

The estimated mean intestinal coefficients of Leporinus friderici Bloch, 1794 and L. taeniofasciatus Britski, 1997, from the Upper Tocantins River, central-western Brazil, were 1·25±0·15 and 1·14±0·07, respectively. The external surfaces of the lips have taste buds. The histological structure is composed of four layers: mucosa, submucosa, muscular, and serosa. No muscularis mucosa is detected. The oesophageal epithelium is stratified in L. friderici and pseudostratified in L. taeniofasciatus , the latter with PAS+ basal cells and eosinophilic apical cells. A thick layer of adipose tissue was found within the submucosa. Leporinus taeniofasciatus has a sphincter separating the cardiac and fundic portions of the stomach. In both species, gastric glands are present in the stomach, except in its pyloric portion. The pyloric caeca possess a simple columnar epithelium with brush border and three types of goblet cells. Rodlet cells were found in L. friderici . The three portions of the intestine showed no histological differences. Anatomical and histological features of the digestive tract are consistent with the omnivorous habit of both these species.     

LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome

Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR’s divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms.     

Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf‐feeding monkey (Pygathrix nemaeus)

Faecal samples are of great value as a non‐invasive means to gather information on the genetics, distribution, demography, diet and parasite infestation of endangered species. Direct shotgun sequencing of faecal DNA could give information on these simultaneously, but this approach is largely untested. Here, we used two faecal samples to characterize the diet of two red‐shanked doucs langurs (Pygathrix nemaeus) that were fed known foliage, fruits, vegetables and cereals. Illumina HiSeq produced ~74 and 67 million paired reads for these samples, of which ~10 000 (0.014%) and ~44 000 (0.066%), respectively, were of chloroplast origin. Sequences were matched against a database of available chloroplast ‘barcodes’ for angiosperms. The results were compared with ‘metabarcoding’ using PCR amplification of the P6 loop of trnL. Metagenomics identified seven and nine of the likely 16 diet plants while six and five were identified by metabarcoding. Metabarcoding produced thousands of reads consistent with the known diet, but the barcodes were too short to identify several plant species to genus. Metagenomics utilized multiple, longer barcodes that combined had greater power of identification. However, rare diet items were not recovered. Read numbers for diet species in metagenomic and metabarcoding data were correlated, indicating that both are useful for determining relative sequence abundance. Metagenomic reads were uniformly distributed across the chloroplast genomes; thus, if chloroplast genomes were used as reference, the precision of identifications and species recovery would improve further. Metagenomics also recovered the host mitochondrial genome and numerous intestinal parasite sequences in addition to generating data useful for characterizing the microbiome.     

Four cleaved amplified polymorphic sequence (CAPS) markers for the detection of the Juglans ailantifolia chloroplast in putatively native J. cinerea populations

Hybridization between butternut (Juglans cinerea), a forest tree native to eastern North America, and Japanese walnut (J. ailantifolia), a tree tolerant to the lethal fungal disease butternut canker, casts doubt on the genetic identity of the remaining butternuts. We report a diagnostic test to distinguish the J. cinerea chloroplast from the J. ailantifolia chloroplast using cleaved amplified polymorphic sequences resolvable in 1.5% agarose gels. J. ailantifolia maternal ancestry in naturally regenerated stands provides a site selection criterion for studies of introgression dynamics when the non-native parent and the hybrids tolerate a disease to which the native species is susceptible.