Effectiveness of DNA barcoding for identifying piscine prey items in stomach contents of piscivorous catfishes

Environmental Biology of Fishes - Introduced predators pose ecological impacts upon prey species and receiving ecosystems. Understanding such ecological interactions creates technical challenges...     

Diets of sympatric native and introduced carnivores in the Barrington Tops,eastern Australia

Invasive predators have severe impacts on global biodiversity, and their effects in Australia have been more extreme than on any other continent. The spotted‐tailed quoll (Dasyurus maculatus), an endangered marsupial carnivore, coexists with three eutherian carnivores, the red fox (Vulpes vulpes), feral cat (Felis catus) and wild dog (Canis lupus ssp.) with which it did not coevolve. No previous study has investigated dietary overlap between quolls and the suite of three eutherian carnivores. By analysing scats, we aimed to quantify dietary overlap within this carnivore assemblage in eastern Australia, and to detect any differences that may facilitate coexistence. We also sought evidence of intraguild predation. Dietary overlap between predators was extensive, with the greatest similarity occurring between foxes and cats. However, some differences were apparent. For example, cats mainly consumed smaller prey, and wild dogs larger prey. Quolls showed greater dietary overlap with foxes and cats than with dogs. Intraguild predation was evident, with fox remains occurring in 3% of wild dog scats. Our results suggest wild dogs competitively dominate invasive foxes, which in turn are likely to compete with the endangered quoll.     

DNA barcoding the native flowering plants and conifers of Wales

We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.     

Molecular identification of prey in the stomach contents of Harp Seals (Pagophilus groenlandicus) using species-specific oligonucleotides

All methods of diet analysis in marine mammals, including hard part analysis (HPA), have biases affecting the accuracy of prey-species identification and frequency in the estimated diet due to differential consumption, digestion and retention. Using PCR amplification of specific prey DNA with species-specific primers, we developed a DNA-based method that complements HPA and provides an alternative means to detect prey from stomach contents of Harp Seals (Pagophilus groenlandicus). The target size that could be reliably amplified was determined using a digestion time-series of Atlantic Cod (Gadus morhua) tissue in simulated seal stomachs. Various target lengths were trialed using general teleost primers; amplicons of approximately 800 bp or less were consistently obtained. Prey species-specific PCR primers for Atlantic Cod, Arctic Cod (Boreogadus saida) and Capelin (Mallotus villosus) were designed and tested with DNA from the stomach contents of 31 Harp Seals. Amplicons were obtained for all three species-specific primer sets. Amplification results compared with HPA revealed: (i) Atlantic Cod hard parts were found in five stomachs where no Atlantic Cod DNA amplified, suggesting that Atlantic Cod may be over-represented in the estimated diet, (ii) amplification of Arctic Cod DNA occurred for 17 stomachs, including all 12 stomachs with, and five stomachs without, Arctic Cod hard parts, and (iii) Capelin DNA amplified for four of five stomachs with Capelin hard parts and for one stomach without Capelin hard parts. We conclude that PCR amplification of specific prey DNA provides a viable means to complement Harp Seal diet analysis by HPA, but suggest that valuable information for quantitative diet analysis rests in a quantitative PCR approach.     

Consumption of introduced prey by native predators: Argentine ants and pit-building ant lions

When populations of native predators are subsidized by numerically dominant introduced species, the structure of food webs can be greatly altered. Surprisingly little is known, however, about the general factors that influence whether or not native predators consume introduced species. To learn more about this issue, we examined how native pit-building ant lions (Myrmeleon) are affected by Argentine ant (Linepithema humile) invasions in coastal southern California. Compared to areas without L. humile, invaded areas contained few native ant species and were deficient in medium-sized and large bodied native ants. Based on these differences, we predicted that Argentine ants would negatively affect ant lion larvae. Contrary to this expectation, observational surveys and laboratory growth rate experiments revealed that Myrmeleon were heavier, had longer mandibles, and grew more quickly when their main ant prey were Argentine ants rather than native ants. Moreover, a field transplant experiment indicated that growth rates and pupal weights were not statistically different for larval ant lions reared in invaded areas compared to those reared in uninvaded areas. Argentine ants were also highly susceptible to capture by larval Myrmeleon. The species-level traits that presumably make Argentine ant workers susceptible to capture by larval ant lions—small size and high activity levels—appear to be the same characteristics that make them unsuitable prey for vertebrate predators, such as horned lizards. These results underscore the difficulties in predicting whether or not numerically dominant introduced species serve as prey for native predators.     

DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads

Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.     

Gape limitation and piscine prey size‐selection by yellow perch in the extreme southern area of Lake Michigan, with emphasis on two exotic prey items

The trophic linkage between yellow perch Perca flavescens and two exotic prey items, alewife Alosa pseudoharengus and round goby Neogobius melanostomus , was investigated in the extreme southern area of Lake Michigan during the summer of 2002. Yellow perch ≥100 mm total length, L _T( n  = 1293) exhibited size selective feeding, with 148 fish containing round gobies and 120 fish containing alewives. The mean round goby L _T, preyed on by yellow perch, was 23% of the predator L _T, with a range of 7 to 47%, and mean alewife L _T was 32% of yellow perch L _T, with a range of 18 to 46%. Although the selection of prey size by yellow perch increased proportionally with yellow perch L _T, prey consumed appeared smaller than theoretically possible based on gape size.     

DNA条形码在入侵植物鉴定中的应用进展

生物入侵对世界经济、环境造成了巨大的影响,已经成为世界关注的焦点。传统的海关检验方法存在鉴定缓慢、准确率低、鉴定专家稀缺等问题,因此急需一种鉴定率高、操作简单和快速的方法对入侵植物的繁殖体进行精确的鉴别。DNA条形码是一种基于DNA序列差异进行物种鉴定的技术,鉴定结果只受样品组织内DNA保存状况影响,不受形态学性状保存状态影响,只需掌握简单分子生物学技术的工作人员即可实现对未知样品的鉴定,在入侵植物检疫鉴定中有很大的应用潜力。根据入侵植物进化快、变异多的特点,可优先考虑种间、种内差异度高的ITS基因作为核心条形码,再以mat K和rbc L基因为辅助条形码。本文分析了植物DNA条形码技术及其衍生出的超级DNA条形码和metabarcoding技术在入侵植物鉴定中的应用潜力,提出构建入侵植物DNA条形码参考数据库与智能植物志(i Flora)相结合,为利用DNA条形码技术对入侵植物进行快速鉴定和相关研究提供参考。     

Performance of distance-based DNA barcoding in the molecular identification of Primates

For comparative primatology proper recognition of basal taxa (i.e. species) is indispensable, and in this the choice of a suitable gene with high phylogenetic resolution is crucial. For the goals of species identification in animals, the cytochrome c oxidase subunit 1 (cox1) has been introduced as standard marker. Making use of the difference in intra- and interspecific genetic variation – the DNA barcoding gap – cox1 can be used as a fast and accurate marker for the identification of animal species. For the Order Primates we compare the performance of cox1 (166 sequences; 50 nominal species) in species-identification with that of two other mitochondrial markers, 16S ribosomal RNA (412 sequences, 92 species) and cytochrome b (cob: 547 sequences, 72 species). A wide gap exist between intra- and interspecific divergences for both cox1 and cob genes whereas this gap is less apparent for 16S, indicating that rRNA genes are less suitable for species delimitation in DNA barcoding. For those species where multiple sequences are available there are significant differences in the intraspecific genetic distances between different mitochondrial markers, without, however, showing a consistent pattern. We conclude that cox1 allows accurate differentiation of species and as such DNA barcoding may have an important role to play in comparative primatology.     

DNA barcoding of Neotropical bats: species identification and discovery within Guyana

Sequence diversity in the cytochrome c oxidase subunit 1 gene has been shown to be an effective tool for species identification and discovery in various groups of animals, but has not been extensively tested in mammals. We address this gap by examining the performance of DNA barcodes in the discrimination of 87 species of bats from Guyana. Eighty‐one of these species showed both low intraspecific variation (mean = 0.60%), and clear sequence divergence from their congeners (mean = 7.80%), while the other six showed deeply divergent intraspecific lineages suggesting that they represent species complexes. Although further work is needed to examine patterns of sequence diversity at a broader geographical scale, the present study validates the effectiveness of barcoding for the identification of regional bat assemblages, even highly diverse tropical faunas.     

Population genetics of Himalayan balsam (Impatiens glandulifera): comparison of native and introduced populations

Background: Invasive species can interfere in the structure and functioning of ecosystems. Better understanding of the evolution of such species will be useful when planning their management and eradication.

Aims: We aimed to compare patterns of genetic variability in Impatiens glandulifera in native and introduced regions.

Methods: We used native samples from India and Pakistan, and non-native samples from Canada, Finland and the UK. Genetic analyses included genotyping using 10 microsatellite markers and sequencing of the nuclear ITS region.

Results: Mean allele numbers from native and introduced samples were even, 8.8 and 8.5, respectively, while expected heterozygosities were higher in native samples (mean 0.738) than in non-native samples (mean 0.477). Hardy–Weinberg equilibrium testing indicated significant heterozygote deficiencies at 70% of the loci. Inbreeding coefficients were high in both native and introduced regions (range 0.201–0.726). STRUCTURE analyses showed that native samples from India and Pakistan possessed similar clustering patterns while non-native samples from the UK and Canada resembled each other. One of the four Finnish populations had a similar pattern with the UK and Canadian populations, while the rest showed similarly unique genetic compositions. ITS sequencing indicated in Pakistani samples two polymorphic sites not found in Indian samples but present in some samples from Canada, Finland and the UK.

Conclusions: Distinct population genetic patterns indicate that human-mediated dispersal is important in I. glandulifera.     

Population genetics of introduced and native populations of the green mussel, Perna viridis: determining patterns of introduction

Genetic variation can be used to determine routes of introduction of non-native species and whether introduced populations lost variation during establishment. The present study sought to determine whether multiple, geographically isolated non-native populations of the green mussel, Perna viridis, were the product of a stepping stone expansion of a single introduction or from multiple independent introductions from the native range. Measurements of genetic variation were compared among five introduced populations and three populations from within the native range. We sequenced 650 bp of the mitochondrial gene cytochrome oxidase I from 280 samples from five introduced populations and another 190 samples from three native populations. Haplotype frequencies of all introduced populations were not significantly different from each other, but virtually all populations differed from samples taken from the native range. Measurements of genetic variation tended to suggest that introduced populations had less variation than most native populations and there was no evidence for admixture in any of the introduced populations. The genetic data and Monte Carlo simulations both provide compelling evidence of a stepping-stone pattern of introduction of P. viridis from the native range to Trinidad, and from Trinidad to other locations in the Caribbean and United States. The lack of genetic variation in introduced populations suggests that the initial introduction was relatively small and the lack of admixture suggests a single original source population.     

DNA barcoding in medicinal plants: Testing the potential of a proposed barcoding marker for identification of Uncaria species from China

DNA barcoding, an increasingly popular mean of species identification, has been widely used for global species identification despite a consensus not being reached regarding which DNA sequences can be used as the best plant barcodes. In this study, we tested the feasibility of five candidate DNA barcodes (nrITS, nrITS2, matk, rbcL and trnH-psbA) for identifying Uncaria species. We collected a total of 54 specimens of 10 Uncaria species across its distributional range. BLAST, barcoding gaps, tree-based methods and TAXONDNA analysis were used to investigate the molecular identification capability of the candidate DNA barcodes. The results showed that the ITS2 is most suitable as a candidate DNA barcode for identification of medicinal plants of the genus Uncaria.     

The population genetics of a biological control introduction: mitochondrial DNA and microsatellie variation in native and introduced populations of Aphidus ervi, a parisitoid wasp

Introductions of biological control agents may cause bottlenecks in population size despite efforts to avoid them. We examined the population genetics of Aphidius ervi (Hymenoptera: Braconidae), a parasitoid that was introduced to North America from Western Europe in 1959 to control pea aphids. To explore the phylogeographical relationships of A. ervi we sequenced 1249 bp of mitochondrial DNA (mtDNA) from 27 individuals from the native range and 51 individuals from the introduced range. Most individuals from Western Europe, the Middle East and North America shared one of two common haplotypes, consistent with the known history of the introduction. However, some A. ervi from the Pacific Northwest have a haplotype that is most similar to haplotypes found in Japan, raising the possibility of a second accidental introduction. To examine population structure and assess whether a bottleneck occurred upon introduction to North America, we assayed variation at 5 microsatellite loci in 62 individuals from 2 native populations and 230 individuals from 6 introduced populations. Introduced samples had fewer rare alleles than native samples (F1,34 = 13.5, P = 0.0008), but heterozygosity did not differ significantly. These results suggest that a mild bottleneck occurred in spite of the introduction of over 1000 individuals. Using a hierarchical Bayesian approach, the founding population size was estimated to be 245 individuals. amova showed significant genetic differentiation between the European and North American samples, and a Bayesian assignment approach clustered individuals into four groups, with most European individuals in one group and most North American individuals in the other three. These results highlight that genetic changes are associated with founder events in rapidly growing natural populations, even when the founding population size is relatively large.     

A comparison of reproductive patterns and adult dispersal in sympatric introduced and native marine crabs: implications for species characteristics of invaders

The introduction and translocation of nonindigenous marine species is widespread and can pose severe threats to biodiversity and ecosystem functioning. Predicting which species are potential invaders is of particular interest to ecologists. One approach is to identify characteristics that predispose a species to becoming a successful invader. Since its introduction in the 1980’s, the invasive Asian shore crab, Hemigrapsus sanguineus, has shown a remarkable ability to colonize rocky intertidal habitats along the east coast of the United States. In Long Island Sound H. sanguineus occurs sympatrically with the functionally equivalent, but non-invasive, native Atlantic mud crab, Panopeus herbstii. The presence of both species at the same site allowed us to make a detailed, simultaneous assessment of life history traits and adult dispersibility of co-occurring invading and native crab species. We investigated fecundity and maturation rates, length of breeding season and brood production for both species, and conducted field experiments using mark–recapture techniques to determine mobility patterns. Our results show that the nonindigenous Asian crab has a greater reproductive potential than the native mud crab as evidenced by a longer breeding season, multiple brood production and higher fecundity rates. Field experiments confirmed previous studies indicating H. sanguineus is a highly mobile crab, and further demonstrated that adult Asian crabs are more likely than mud crabs to disperse from their shelter/refuge sites. Recovery rates for native mud crabs were significantly higher than those for Asian crabs in three experimental trials, across sites and years. This work provides new information about life history characteristics of both species and supports the hypothesis that high reproductive potential combined with high adult dispersal ability may be important factors associated with the invasion/establishment success of the Asian shore crab. More study is needed, however, to determine the applicability of these findings to other highly successful marine invaders.     

Population genetics of the soybean aphid in North America and East Asia: test for introduction between native and introduced populations

Understanding the population genetic diversity and structure of recently introduced pest species is important for determining appropriate strategies for pest control. In recent years, the rate of introduction of new invasive insect pests between continents has continued to increase. About a decade ago, the soybean aphid, Aphis glycines Matsumura, was introduced from East Asia (EA) into North America (NA) and is now widely established in NA. To compare soybean aphid populations between the native and invasive regions, we examined 689 individuals obtained from 28 different collections in NA and EA. A total of 8 microsatellite loci were used for population genetics statistics. Genetic differentiations among NA populations were very low compared to those among EA populations. Gene diversity and mean number of alleles in NA populations averaged 0.40 and 2.70, respectively, whereas in EA they averaged 0.55 and 4.32, respectively. Structure analysis of all populations revealed two distinct structures in the invaded and in the native regions. NA populations were divided into two distinct structures consistent with their geographic distribution. Among EA populations, certain Korean populations were genetically closest to NA populations, especially those from Ohio and Delaware. An approximate Bayesian computation test also supports an introduction into NA from Korea. These suggest that Korea is most likely to be the origin of soybean aphids in North America, rather than China or Japan.     

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 barcoding: a tool for improved taxon identification and detection of species diversity

Recently it was decided that portions of rbcL and matK gene regions are approved and required standard barcode regions for land plants. Ideally, DNA barcoding can provide a fast and reliable way to identify species. Compiling a library of barcodes can be enhanced by the numerous specimens available in botanic gardens, museums and herbaria and in other ex situ conservation collections. Barcoding can strengthen ongoing efforts of botanic gardens and ex situ conservation collections to preserve Earth’s biodiversity. Our study aimed to detect the usability of the universal primers of the standard DNA barcode, to produce standard barcodes for species identification and to detect the discriminatory power of the standard barcode in a set of different groups of plant and fungal taxa. We studied Betula species originating from different parts of the world, and Salix taxa, bryophytes and edible and poisonous fungal species originating from Finland. In Betula and Salix, the standard DNA barcode regions, portions of matK and rbcL, were able to identify species to genus level, but did not show adequate resolution for species discrimination. Thus, supplementary barcode regions are needed for species identification. In Salix, the trnH-psbA spacer was also used, and it proved to have more resolution but, yet, not adequate levels of interspecific divergence for all studied taxa. In a set of bryophyte species, the rbcL gene region was found to possess adequate resolution for species discrimination for most genera studied. In bryophytes, matK failed to amplify properly. In fungi, the combination of ITS1 and ITS2 proved to be effective for species discrimination, although alignment difficulties were encountered. In general, closely related or recently diverged species are the greatest challenge, and the problem is most difficult in plants, both in terms of a suitable combination of barcoding regions and the universality of used primers.