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opencc-zeroJan 2021View details →

Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics

Amplicon metabarcoding is an established technique to analyse the taxonomic composition of communities of organisms using high-throughput DNA sequencing, but there are doubts about its ability to quantify the relative proportions of the species, as opposed to the species list. Here, we bypass the enrichment step and avoid the PCR-bias, by directly sequencing the extracted DNA using shotgun metagenomics. This approach is common practice in prokaryotes, but not in eukaryotes, because of the low number of sequenced genomes of eukaryotic species. We tested the metagenomics approach using insect species whose genome is already sequenced and assembled to an advanced degree. We shotgun-sequenced, at low-coverage DNA, 18 species of insects in 22 single-species and 6 mixed-species libraries and mapped the reads against 110 reference genomes of insects. We used the single-species libraries to calibrate the process of assignation of reads to species and the libraries created from species mixtures to evaluate the ability of the method to quantify the relative species abundance. Our results showed that the shotgun metagenomic method is easily able to set apart closely-related insect species, like four species of Drosophila included in the artificial libraries. However, to avoid the counting of rare misclassified reads in samples, it was necessary to use a rather stringent detection limit of 0.001, so species with a lower relative abundance are ignored. We also identified that approximately half the raw reads were informative for taxonomic purposes. Finally, using the mixed-species libraries, we showed that it was feasible to quantify with confidence the relative abundance of individual species in the mixtures.

opencc-zeroDec 2010View details →

Data from: An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

BACKGROUND: Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea. RESULTS: Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea. CONCLUSION: An updated phylogenetic framework for tunicates is provided based on phylogenetic analyses using the most realistic evolutionary models currently available for ribosomal molecules and an unprecedented taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear definition of the major tunicate groups and revealed contrasting evolutionary dynamics among major lineages. The resolving power of this gene nevertheless appears limited within the clades composed of Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae, which were delineated as spots of low resolution. These limitations underline the need to develop new nuclear markers in order to further resolve the phylogeny of this keystone group in chordate evolution.

opencc-zeroDec 2018View details →

Data from: Differential resource consumption in leaf litter mixtures by native and non-native amphipods

Leaf litter processing is an essential ecosystem function in freshwater systems, since much of the carbon and nutrients moving through freshwater food webs come from the surrounding terrestrial ecosystems. Thus, it is important to understand how the species performing this function differ, especially because many native species are being replaced by non-native species in aquatic ecosystems. We used a field experiment to examine leaf consumption rates of two common shredding macroinvertebrates (the native Gammarus fossarum and the non-native Gammarus roeselii). Leaves from three species, varying in resource quality, were added both in leaf monocultures and as a three-species mixture. Biomass-adjusted daily consumption rates were similar between the two amphipod species, and each consumed nitrogen-rich alder leaves faster than oak or beech leaves. However, because adult G. roeselii are approximately twice the size of G. fossarum, this led to systematic, though nonsignificant, differences in consumption rates at the per-capita or population level. Furthermore, we found nuanced effects of decomposer identity on leaf decomposition in mixtures. Only G. roeselii showeding increased consumption of the preferred resource (alder) in the mixture, while G. fossarum consumed all leaves at the same proportional rates as in monocultures. This is an important distinction, as most measures of macroinvertebrate leaf shredding are made in the laboratory with only a single leaf resource available. Our results, based on a field experiment which could control the presence of dominant macroinvertebrates while still providing natural, biologically realistic context, suggests that even functionally-similar species may subtly shift ecosystem processes.

opencc-zeroDec 2013View details →

Data from: A comparative study of egg recognition signature mixtures in Formica ants

Processing of information from the environment, such as assessing group membership in social contexts, is a major determinant of inclusive fitness. For social insects, recognizing brood origin is crucial for inclusive fitness in many contexts, such as social parasitism and kin conflicts within colonies. Whether or not a recognition signature is informative in kin conflicts, depends on the extent of a genetic contribution into the cues. We investigated colony and matriline specific variation in egg surface hydrocarbons in seven species of Formica ants. We show that chemical variance is distributed similarly to genetic variation, suggesting a significant genetic contribution to eggs odors in the genus. Significant among matriline components, and significant correlations between chemical and genetic similarity among individuals also indicate kin informative egg odors in several species. We suggest that egg odor surface variation could play a large role in within colony conflicts, and that a comparative method can reveal novel insight into communication of identity.

opencc-zeroDec 2019View details →

Field evaluation of abundance estimates under binomial and multinomial N‐mixture models

Assessing and modelling abundance from animal count data is a very common task in ecology and management. Detection is arguably never perfect, but modern hierarchical models can incorporate detection probability and yield abundance estimates that are corrected for imperfect detection. Two variants of these models rely on counts of unmarked individuals, or territories, (binomial N‐mixture models, or binmix) and on detection histories based on territory mapping data (multinomial N‐mixture models or multimix). However, calibration studies which evaluate these two N‐mixture model approaches are needed. We analysed conventional territory mapping data (three surveys in 2014 and four in 2015) using both binmix and multimix models to estimate abundance for two common avian cavity‐nesting forest species (Great Tit Parus major and Eurasian Blue Tit Cyanistes caeruleus). In the same study area, we used two benchmarks: (i) occupancy data from a dense nest box scheme; (ii) total number of detected territories. To investigate variance in estimates due to the territory assignment, three independent ornithologists conducted territory assignments. Nest box occupancy yields a minimum number of territories, since some natural cavities may have been used, and binmix model estimates were generally higher than this benchmark. Estimates under the multimix model were slightly more precise than binmix model estimates. Depending on the person assigning the territories, the multimix model estimates became quite different, either overestimating or underestimating the "truth". We conclude that N‐mixture‐models estimated abundance reliably, even for our very small sample sizes. Territory‐mapping counts depended on territory assignment and this carried over to estimates under the multimix model. This limitation has to be taken into account when abundance estimates are compared between sites or years. Whenever possible, accounting for such hidden heterogeneity in the raw data of bird surveys, via including a "territory editor" factor, is recommended. Distributing the surveys randomly (in time and space) to editors may also alleviate this problem.

opencc-zeroDec 2017View details →

Data from: Estimating transient populations of unmarked individuals at a migratory stopover site using generalized N-mixture models

1. Migration counts are popular indices used to monitor population trends over time. Advanced analytical methods for estimating abundance of unmarked, open populations now incorporate population growth models and simultaneously test for covariate effects on abundance and detection probability. However, estimating population abundance at a staging site is complicated by daily immigration and emigration of unmarked individuals. 2. We applied a set of generalized N-mixture models to simulated count data to test their applicability for transient populations. Using simulated datasets, parameters were unbiased when the apparent survival rate varied within a season or was mis-specified in a model, but not when the immigration or detection probability was mis-specified. 3. With knowledge from the simulated data, we applied these models to daily counts of staging migratory shorebirds and estimated daily abundances accounting for variation in the detection and immigration rates. Daily counts of ruddy turnstones (Arenaria interpres) staging at Westhampton Island, New York, were collected during northward migration (1997–1999). We tested the effects of weather and tides on detection probability, and we modeled within-season variation in immigration rates as a function of time. 4. Covariates affecting the detection probability differed among years, but tide height consistently was correlated with detection probability. Accounting for detection and immigration rates, the predicted maximum single-day populations of ruddy turnstones were 172%, 165%, and 129% of the observed counts for each year. 5. Synthesis and applications. Management and conservation plans for migratory species require abundance estimates that are near the true population size though they are difficult to obtain. Our study is the first empirical application of the generalized N-mixture model that incorporates temporal trends in immigration and estimates daily abundance of a staging unmarked migratory population. Correct estimation of population sizes and the environmental factors affecting them can aid the conservation prioritization of species and staging sites. Moreover, the use of generalized N-mixture models can improve our understanding of the environmental factors that shape migratory movements.

opencc-zeroDec 2013View details →

Data from: Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages

Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modelled accurately using the Γ distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or under-parameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10,000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42,337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these 3 sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modelled by a combination of 8 edge-specific rate matrices (4 for V1 and 4 for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the 7 species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.

opencc-zeroDec 2016View details →

Data from: Mapping tropical dry forest succession using multiple criteria spectral mixture analysis

Tropical dry forests (TDFs) in the Americas are considered the first frontier of economic development with less than 1% of their total original coverage under protection. Accordingly, accurate estimates of their spatial extent, fragmentation, and degree of regeneration are critical in evaluating the success of current conservation policies. This study focused on a well-protected secondary TDF in Santa Rosa National Park (SRNP) Environmental Monitoring Super Site, Guanacaste, Costa Rica. We used spectral signature analysis of TDF ecosystem succession (early, intermediate, and late successional stages), and its intrinsic variability, to propose a new multiple criteria spectral mixture analysis (MCSMA) method on the shortwave infrared (SWIR) of HyMap image. Unlike most existing iterative mixture analysis (IMA) techniques, MCSMA tries to extract and make use of representative endmembers with spectral and spatial information. MCSMA then considers three criteria that influence the comparative importance of different endmember combinations (endmember models): root mean square error (RMSE); spatial distance (SD); and fraction consistency (FC), to create an evaluation framework to select a best-fit model. The spectral analysis demonstrated that TDFs have a high spectral variability as a result of biomass variability. By adopting two search strategies, the unmixing results showed that our new MCSMA approach had a better performance in root mean square error (early: 0.160/0.159; intermediate: 0.322/0.321; and late: 0.239/0.235); mean absolute error (early: 0.132/0.128; intermediate: 0.254/0.251; and late: 0.191/0.188); and systematic error (early: 0.045/0.055; intermediate: −0.211/−0.214; and late: 0.161/0.160), compared to the multiple endmember spectral mixture analysis (MESMA). This study highlights the importance of SWIR in differentiating successional stages in TDFs. The proposed MCSMA provides a more flexible and generalized means for the best-fit model determination than common IMA methods.

FIGURE 41 in Is Montandoniola moraguesi (Puton, 1896) a mixture of different species? (Hemiptera: Heteroptera: Anthocoridae)

FIGURE 41. Distribution of the four Montandoniola species studied in the present paper, as is revealed through the examined material.

FIGURES 27–28 in Is Montandoniola moraguesi (Puton, 1896) a mixture of different species? (Hemiptera: Heteroptera: Anthocoridae)

FIGURES 27–28. Metapleural evaporative area and ostiolar peritreme (left metapleura). 27, M. moraguesi; 28, M. confusa sp. nov.; scale bar: 0.1 mm.

FIGURES 6–13. Montandoniola thripodes, male holotype. 6 in Is Montandoniola moraguesi (Puton, 1896) a mixture of different species? (Hemiptera: Heteroptera: Anthocoridae)

FIGURES 6–13. Montandoniola thripodes, male holotype. 6, type specimen with its labels; 7, 8, habitus, dorsal view; scale bar: 0.5 mm; 9, head and pronotum (part), lateral view; scale bar: 0.5 mm; 10, evaporative area and ostiolar peritreme of the metathoracic glands (left metapleura), lateral view; scale bar: 0.1 mm; 11, pygophore dorsal view; scale bar: 0.1 mm; 12, paramere, dorsal view; 13, idem, lateral view; scale bars: 0.1 mm.

FIGURES 1–5. Montandoniola moraguesi, female holotype. 1 in Is Montandoniola moraguesi (Puton, 1896) a mixture of different species? (Hemiptera: Heteroptera: Anthocoridae)

FIGURES 1–5. Montandoniola moraguesi, female holotype. 1, type specimen with its labels; 2, habitus, dorsal view; scale bar: 1 mm; 3, head and pronotum, lateral view; scale bar: 1 mm; 4, evaporative area and ostiolar peritreme of the metathoracic glands (left metapleura), lateral view; scale bar: 0.1 mm. 5, base of ovipositor and copulatory tube, internal ventral view; scale bar: 0.2 mm.

FIGURES 38–40. Female copulatory tube, internal ventral view. 38, M in Is Montandoniola moraguesi (Puton, 1896) a mixture of different species? (Hemiptera: Heteroptera: Anthocoridae)

FIGURES 38–40. Female copulatory tube, internal ventral view. 38, M. moraguesi; 39, M. pictipennis; 40, M. confusa sp. nov.; scale bar: 0.1 mm. ct = copulatory tube; StVII = sternite VII.

FIGURES 20–26 in Is Montandoniola moraguesi (Puton, 1896) a mixture of different species? (Hemiptera: Heteroptera: Anthocoridae)

FIGURES 20–26. Montandoniola confusa sp. nov., male holotype (except Figs. 22, 23: paratype). 20, type specimen and its labels; 21, habitus, dorsal view; scale bar: 1 mm; 22, head and thorax, lateral view; scale bar: 1 mm; 23, evaporative area and ostiolar peritreme of the metathoracic glands (left metapleura), lateral view; scale bar: 0.1 mm; 24, pygophore with paramere, dorsal view; scale bar: 0.1 mm; 25, paramere, dorsal view; 26, idem, lateral view; scale bars: 0.1 mm.

FIGURES 29–37 in Is Montandoniola moraguesi (Puton, 1896) a mixture of different species? (Hemiptera: Heteroptera: Anthocoridae)

FIGURES 29–37. Comparison of the male genitalia between M. moraguesi, M. thripodes, and M. confusa sp. nov. 29– 31, pygophore, dorsal view; 32–34, paramere, dorsal view; 35–37, paramere, lateral view; scale bars: 0.1 mm. d = denticule; f = flagelle; l = lame.

FIGURES 14–19. Montandoniola pictipennis, female holotype. 14 in Is Montandoniola moraguesi (Puton, 1896) a mixture of different species? (Hemiptera: Heteroptera: Anthocoridae)

FIGURES 14–19. Montandoniola pictipennis, female holotype. 14, type specimen with its labels; 15, habitus, dorsal view; scale bar: 1 mm; 16, habitus, lateral view; scale bar: 1 mm; 17, habitus, ventral view; scale bar: 1 mm;18, evaporative area and ostiolar peritreme (somewhat damaged) of the metathoracic glands (left metapleura), lateral view; scale bar: 0.1 mm; 19, base of ovipositor and copulatory tube, internal ventral view; scale bar: 0.2 mm.

FIGURES 5A–5B. Cochylis notulana Zeller, 1847 lectotype male genitalia. Fig. 5A in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species

FIGURES 5A–5B. Cochylis notulana Zeller, 1847 lectotype male genitalia. Fig. 5A: male genitalia (phallus removed). Fig. 5B: Phallus.

FIGURE 9 in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species

FIGURE 9. Neighbor-Joining tree (Kimura 2 Parameter model) of Phalonidia and Gynnidomorpha COI (DNA barcode) sequences. The scale bar indicates 1% sequence difference.

FIGURES 6A–6B in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species

FIGURES 6A–6B. Cochylis udana Guenée, 1845 lectotype male genitalia. Fig. 6A: male genitalia (phallus removed). Fig. 6B: Phallus.

FIGURES 1A–1F. Adult specimens. Fig. 1A in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species

FIGURES 1A–1F. Adult specimens. Fig. 1A: Phalonidia udana male (Finland). Fig. 1B: Phalonidia udana male (Finland), Fig. 1C: P. m a n n i a n a male (Finland), Fig. 1D: P. m a n n i a n a male (Austria), Fig. 1E: P. m a n n i a n a male (Germany), Fig. 1F: P. manniana male (Germany).