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opencc-zeroNov 2020View details →

DNA sequences for six chloroplast loci concatenated, representing haplotypes found in Colocasia esculenta, and closely related Araceae

As an ancient clonal root and leaf crop, taro (Colocasia esculenta) is highly polymorphic with uncertain genetic and geographic origins. We explored chloroplast DNA variation in wild and cultivated taros and other Colocasia species, and found cultivated taro to be polyphyletic, with tropical and temperate clades originating in Southeast Asia. A third clade was found exclusively in wild populations from Southeast Asia to Australia and Papua New Guinea. Our findings do not support the hypothesis of taro domestication in Papua New Guinea.

opencc-zeroNov 2020View details →

Utilizing next-generation sequencing to identify prey DNA in western North Atlantic grey seal (Halichoerus grypus) diet

Increasing grey seal (Halichoerus grypus) abundance in coastal New England is leading to social, political, economic, and ecological controversies. We studied grey seal feeding habits through next-generation sequencing of prey DNA using 16S amplicons from seal scat (N = 74) collected from a breeding colony on Monomoy Island in Massachusetts, U.S. and report frequency of occurrence and relative read abundance. We also assigned seal sex to scat samples using a revised PCR assay. In contrast to current understanding of grey seal diet from hard parts and fatty acid analysis, we found no significant difference between male and female diet measured by alpha and beta diversity. Overall, we detected 24 prey groups, 18 of which resolved to species. Sand lance (Ammodytes spp.) was the most frequently consumed prey group, with a frequency of occurrence (FO) of 97.3%, consistent with previous studies, but Atlantic menhaden (Brevoortia tyrannus), the second most frequently consumed species (FO = 60.8%), has not been documented in U.S. grey seal diet previously. Our results suggest that a metabarcoding approach to seal food habits can yield important new ecological insights, but that traditional hard parts analysis does not underestimate consumption of Atlantic cod (Gadus morhua; FO = 6.7% Gadidae spp.) and salmon (Salmo salar; FO = 0%), two particularly valuable species of concern.

opencc-by-4.0Jan 2021View details →

Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake's sediment

Supplementary data

opencc-zeroDec 2020View details →

The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species

DNA metabarcoding has become a powerful approach for analyzing complex communities from environmental samples, but there are still methodological challenges limiting its full potential. While conserved DNA markers, like 16S and 18S, often are not able to discriminate among closely related species, other more variable markers – like the fungal ITS region, may include considerable intraspecific variation, which can lead to over-splitting of species during DNA metabarcoding analyses. Here we assess the effects of intraspecific sequence variation in DNA metabarcoding, by analyzing local populations of eleven fungal species. We investigated the allelic diversity of ITS2 haplotypes using both Sanger sequencing and high throughput sequencing (HTS) coupled with error correction with the software dada2. All focal species, except one, included some level of intraspecific variation in the ITS2 region. Overall, we observed a high correspondence between haplotypes generated by Sanger sequencing and HTS, with the exception of a few additional haplotypes detected using either approach. These extra haplotypes, often occurring in low frequencies, were likely due to PCR and sequencing errors or intragenomic variation in the rDNA region. The presence of intraspecific (and possibly intragenomic) variation in ITS2 suggest that haplotypes (or ASVs) should not be used as basic units in ITS-based fungal community analyses, but an extra clustering step is needed to reach species-level resolution.

FIGURE 19 in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)

FIGURE 19. Phylogenetic tree obtained with IQ-TREE. Numbers in nodes, ultrafast bootstrap / SH-like aLRT support.

FIGURES 14–15. 14 in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)

FIGURES 14–15. 14. Geographical distribution of Adelphydraena species. 15. Type locality of Adelphydraena spinosa, in Guyana. Photo. by A. Short.

FIGURES 16–18 in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)

FIGURES 16–18. Habitats of Adelphydraena species. 16–17. Collecting locality of Adelphydraena orchymonti, in Venezuela, Amazonas prov., Cerro Cuau env. 18. Collecting locality of Adelphydraena spangleri, in Venezuela, Bolívar prov., La Gran Sabana, Yaro Parú. Photos. by F. Čiampor.

FIGURES 11–12. 11. Adelphydraena spinosa n in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)

FIGURES 11–12. 11. Adelphydraena spinosa n. sp., spermatheca and terminal abdominal segments. 12. Adelphydraena surinamensis n. sp., spermatheca and terminal abdominal segments.

FIGURES 5–6. 5 in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)

FIGURES 5–6. 5. Adelphydraena spangleri Perkins, non-type aedeagus and last tergites. 6. Adelphydraena surinamensis n. sp., holotype aedeagus and last tergite.

FIGURES 9–10. 9. Adelphydraenaspinosa n in Three new species and DNA sequence data of the rare South American water beetle genus Adelphydraena Perkins, 1989 (Coleoptera: Hydraenidae)

FIGURES 9–10. 9. Adelphydraenaspinosa n. sp., holotypeaedeagus. 10. Adelphydraenaorchymonti Perkins, non-type, aedeagus.

opencc-zeroJan 2021View details →

Mitochondrial DNA sequence phylogeny of Daucus

We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies.

opencc-zeroJan 2021View details →

Data from: Changes in soil microbial communities in post mine ecological restoration: implications for monitoring using high throughput DNA sequencing

The ecological restoration of ecosystem services and biodiversity is a key intervention used to reverse the impacts of anthropogenic activities such as mining. Assessment of the performance of restoration against completion criteria relies on biodiversity monitoring. However, monitoring usually overlooks soil microbial communities (SMC), despite increased awareness of their pivotal role in many ecological functions. Recent advances in cost, scalability and technology has led to DNA sequencing being considered as a cost-effective biological monitoring tool, particularly for otherwise difficult to survey groups such as microbes. However, such approaches for monitoring complex restoration sites such as post-mined landscapes have not yet been tested. Here we examine bacterial and fungal communities across chronosequences of mine site restoration at three locations in Western Australia to determine if there are consistent changes in SMC diversity, community composition and functional capacity. Although we detected directional changes in community composition indicative of microbial recovery, these were inconsistent between locations and microbial taxa (bacteria or fungi). Assessing functional diversity provided greater understanding of changes in site conditions and microbial recovery than could be determined through assessment of community composition alone. These results demonstrate that high-throughput amplicon sequencing of environmental DNA (eDNA) is an effective approach for monitoring the complex changes in SMC following restoration. Future monitoring of mine site restoration using eDNA should consider archiving samples to provide improved understanding of changes in communities over time. Expansion to include other biological groups (e.g. soil fauna) and substrates would also provide a more holistic understanding of biodiversity recovery.

opencc-zeroFeb 2021View details →

Supplementary information for integrating sequence capture and restriction-site associated DNA sequencing to resolve recent radiations of Pelagic seabirds

The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic datasets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds amongst the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq datasets for phylogenetics, divergence time estimation and inference of introgression, and we propose a strategy to optimise RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales.

opencc-zeroDec 2013View details →

Data from: Phylogenetic relationships and timing of diversification in gonorynchiform fishes inferred using nuclear gene DNA sequences (Teleostei: Ostariophysi)

The Gonorynchiformes are the sister lineage of the species-rich Otophysi and provide important insights into the diversification of ostariophysan fishes. Phylogenies of gonorynchiforms inferred using morphological characters and mtDNA gene sequences provide differing resolutions with regard to the sister lineage of all other gonorynchiforms (Chanos vs. Gonorynchus) and support for monophyly of the two miniaturized lineages Cromeria and Grasseichthys. In this study the phylogeny and divergence times of gonorynchiforms are investigated with DNA sequences sampled from nine nuclear genes and a published morphological character matrix. Bayesian phylogenetic analyses reveal substantial congruence among individual gene trees with inferences from eight genes placing Gonorynchus as the sister lineage to all other gonorynchiforms. Seven gene trees resolve Cromeria and Grasseichthys as a clade, supporting previous inferences using morphological characters. Phylogenies resulting from either concatenating the nuclear genes, performing a multispecies coalescent species tree analysis, or combining the morphological and nuclear gene DNA sequences resolve Gonorynchus as the living sister lineage of all other gonorynchiforms, strongly support the monophyly of Cromeria and Grasseichthys, and resolve a clade containing Parakneria, Cromeria, and Grasseichthys. The morphological dataset, which includes 13 gonorynchiform fossil taxa that range in age from Early Cretaceous to Eocene, was analyzed in combination with DNA sequences from the nine nuclear genes and a relaxed molecular clock to estimate times of evolutionary divergence. This "tip dating" strategy accommodates uncertainty in the phylogenetic resolution of fossil taxa that provide calibration information in the relaxed molecular clock analysis. The estimated age of the most recent common ancestor (MRCA) of living gonorynchiforms is slightly older than estimates from previous node dating efforts, but the molecular tip dating estimated ages of Kneriinae (Kneria, Parakneria, Cromeria, and Grasseichthys) and the two paedomorphic lineages, Cromeria and Grasseichthys, are considerably younger.

opencc-zeroDec 2014View details →

Data from: Two new species of Limbodessus diving beetles from New Guinea - short verbal descriptions flanked by online content (digital photography, μCT scans, drawings and DNA sequence data)

Background: To date only one species of Limbodessus diving beetles has been reported from the Island of New Guinea, L. compactus (Clark, 1862), which is widerspread in the Australian region. New information: We describe two new species of microendemic New Guinea Limbodessus and use a compact descriptive format flanked by enriched online content in wiki powered species pages. Limbodessus baliem sp.n. is described from ca. 1,600 m altitude in the Baliem Valley of Papua and Limbodessus alexanderi sp.n. from >3,000 m altitude north of Sugapa, Papua. Based on our analysis, we also transfer three species from other genera to Limbodessus Guignot, 1939, with the following changes: Limbodessus deflectus (Ordish, 1966), new combination; Limbodessus leveri (J. Balfour-Browne, 1944), new combination; and Limbodessus plicatus (Sharp, 1882), new combination.

opencc-zeroDec 2017View details →

Data from: Phylogenetic systematics of subtribe Spiranthinae (Orchidaceae: Orchidoideae: Cranichideae) based on nuclear and plastid DNA sequences of a nearly complete generic sample

Subtribe Spiranthinae is the most species-rich lineage of terrestrial Neotropical orchids, encompassing > 500 species and 40 genera. We conducted maximum parsimony and maximum likelihood phylogenetic analyses of DNA sequence data of plastid matK-trnK and trnL-trnF and nuclear ribosomal ITS sequences for 36 genera and 182 species of Spiranthinae plus appropriate outgroups. The results strongly support monophyly of Spiranthinae (minus Discyphus, Discyphinae and Galeottiella, Galeottiellinae) and five major lineages, namely monospecific Cotylolabium (sister to the remaining Spiranthinae) and the Eurystyles, Pelexia, Spiranthes and Stenorrhynchos clades. Eighteen of the 27 genera of Spiranthinae for which more than one species was included in our analyses are monophyletic. Paraphyly of large genera, such as Cyclopogon and Sarcoglottis, resulted from segregation of particular species or groups of species exhibiting minor modifications of structures directly involved in pollination (e.g. nectary, rostellum and viscidium). Conversely, polyphyly has resulted from convergent evolution of floral attributes in distantly related species (e.g. Mesadenus). Some of the morphological characters used traditionally for generic delimitation and in non-molecular cladistic analyses of Spiranthinae are discussed against the evolutionary framework set by our molecular trees, emphasizing putative synapomorphies and problems derived from inappropriate character coding or incorrect homology assessments. Our ancestral area analysis indicates that Spiranthinae originated in eastern South America, with subsequent migrations and secondary radiations in Mesoamerica and North America, plus a derived migration from the latter region to the Old World (Spiranthes).

opencc-zeroDec 2014View details →

Data from: High-throughput sequencing of nematode communities from total soil DNA extractions

Background: Nematodes are extremely diverse and numbers of species are predicted to be more than a million. Studies on nematode diversity are difficult and laborious using standard methods such as identification based on morphology and therefore high-throughput sequencing is an attractive alternative. Generally, primers that have been used for generating amplicons for sequencing are not nematode specific and also amplify other groups such as fungi and plantae. Thus a nematode enrichment step must be included that may introduce biases. Results: An amplification strategy, including a new primer, which selectively amplifies nematodes and other metazoans was developed. When this strategy was tested on DNA templates from a set of 22 agricultural soils, we obtained 64.4 % sequences of nematode origin in total, whereas the remaining sequences were almost entirely metazoan. The nematode sequences were derived from a broad taxonomic range and most sequences were from nematode taxa that have previously been found to be abundant in soil such as Tylenchida, Rhabditida, Dorylaimida, Triplonchida and Araeolaimida. Conclusions: This amplification and sequencing strategy for assessing nematode diversity was demonstrated to be able to collect a broad taxonomy of nematodes without prior enrichment and thus the method will be highly valuable in ecological studies of nematodes. Keywords: nematode, community, next-generation sequencing, SSU, diversity, 18S, rDNA

opencc-zeroDec 2014View details →

Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure

Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.

opencc-zeroDec 2018View details →

Data from: Pleistocene climate change and phylogeographic structure of the Gymnocarpos przewalskii (Caryophyllaceae) in the northwest China: Evidence from plastid DNA, ITS sequences, and Microsatellite

Northwestern China has a wealth of endemic species, which has been hypothesized to be affected by the complex paleoclimatic and paleogeographic history during Quaternary. In this paper, we used Gymnocarpos przewalskii as a model to address the evolutionary history and current population genetic structure of species in northwestern China. We employed two chloroplast DNA fragments (rps16 and psbB‐psbI), one nuclear DNA fragment (ITS), and simple sequence repeat (SSRs) to investigate the spatial genetic pattern of G. przewalskii. High genetic diversity (cpDNA: hS = 0.330, hT = 0.866; ITS: hS = 0.458, hT = 0.872) was identified in almost all populations, and most of the population have private haplotypes. Moreover, multimodal mismatch distributions were observed and estimates of Tajima's D and Fu's FS tests did not identify significantly departures from neutrality, indicating that recent expansion of G. przewalskii was rejected. Thus, we inferred that G. przewalskii survived generally in northwestern China during the Pleistocene. All data together support the genotypes of G. przewalskii into three groups, consistent with their respective geographical distributions in the western regions—Tarim Basin, the central regions—Hami Basin and Hexi Corridor, and the eastern regions—Alxa Desert and Wulate Prairie. Divergence among most lineages of G. przewalskii occurred in the Pleistocene, and the range of potential distributions is associated with glacial cycles. We concluded that climate oscillation during Pleistocene significantly affected the distribution of the species.