This content will become publicly available on September 1, 2024
Several automated molecular methods have emerged for distinguishing eukaryote species based on DNA sequence data. However, there are knowledge gaps around which of these single‐locus methods is more accurate for the identification of microalgal species, such as the highly diverse and ecologically relevant diatoms. We applied genetic divergence, Automatic Barcode Gap Discovery for primary species delimitation (ABGD), Assemble Species by Automatic Partitioning (ASAP), Statistical Parsimony Network Analysis (SPNA), Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) using partial
- Award ID(s):
- 2015674
- NSF-PAR ID:
- 10493908
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Journal of Eukaryotic Microbiology
- Volume:
- 70
- Issue:
- 5
- ISSN:
- 1066-5234
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
Lobophora is a common tropical to temperate genus of brown algae found in a plethora of habitats including shallow and deep‐water coral reefs, rocky shores, mangroves, seagrass beds, and rhodoliths beds. Recent molecular studies have revealed thatLobophora species diversity has been severely underestimated. Current estimates of the species numbers range from 100 to 140 species with a suggested center of diversity in the Central Indo‐Pacific. This study used three molecular markers (cox 3,rbc L,psb A), different single‐marker species delimitation methods (GMYC ,ABGD ,PTP ), and morphological evidence to evaluateLobophora species diversity in the Western Atlantic and the Eastern Pacific oceans.Cox 3 provided the greatest number of primary species hypotheses(PSH), followed byrbc L and thenpsb A.GMYC species delimitation analysis was the most conservative across all three markers, followed byPTP , and thenABGD . The most informative diagnostic morphological characters were thallus thickness and number of cell layers in both the medulla and the dorsal/ventral cortices. Following a consensus approach, 14 distinctLobophora species were identified in the Western Atlantic and five in the Eastern Pacific. Eight new species from these two oceans were herein described:L. adpressa sp. nov.,L. cocoensis sp. nov.,L. colombiana sp. nov.,L. crispata sp. nov.,L. delicata sp. nov.,L. dispersa sp. nov.,L. panamensis sp. nov., andL. tortugensis sp. nov. This study showed that the best approach to confidently identifyLobophora species is to analyzeDNA sequences (preferablycox 3 andrbc L) followed by comparative morphological and geographical assessment. -
Abstract In order to test the congruence of genetic data to the morphologically defined Neotropical catfish genera
Tympanopleura andAgeneiosus and explore species diversity, we generated 17 DNA barcodes from five of six species ofTympanopleura and 12 of 13 species ofAgeneiosus . To discriminate limits between species, an automatic barcode gap discovery (ABGD), a generalised mixed yule‐coalescent model (GYMC) and fixed distance thresholds Kimura two‐parameter (K2P; 3%) were used to discriminate putative species limits from the DNA barcodes. The ABGD, GMYC and K2P methods agreed by each generating 13 clusters: six inTympanopleura (five nominal plus one undescribed species) and seven inAgeneiosus . These clusters corresponded broadly to the described species, except in the case of theAgeneiosus ucayalensis group (A. akamai ,A. dentatus ,A. intrusus ,A. ucayalensis ,A. uranophthalmus andA. vittatus ). Haplotype sharing and low divergences may have prevented molecular methods from distinguishing these species. We hypothesise that this is the result of a recent radiation of a sympatric species group distributed throughout the Amazon Basin. One putative new species ofTympanopleura was also supported by the molecular data. These results taken together highlight the utility of molecular methods such as DNA barcoding in understanding patterns of diversification across large geographic areas and in recognising overlooked diversity. -
Lichens collected worldwide for centuries have resulted in millions of specimens deposited in herbaria that offer the potential to assess species boundaries, phenotypic diversification, ecology, and distribution. The application of molecular approaches to historical collections has been limited due to DNA fragmentation, but high-throughput sequencing offers an opportunity to overcome this barrier. Here, we combined a large dataset of ITS sequences from recently collected material and historical collections, obtained through Sanger, 454, or Illumina Sequencing, to test the performance of ITS barcoding in two genera of lichenized Basidiomycota: Cora and Corella. We attempted to generate new sequence data for 62 fresh specimens (from 2016) and 274 historical collections (collected between 1888 and 1998), for a final dataset of 1325 sequences. We compared various quantitative approaches to delimit species (GMYC, bPTP, ASAP, ABGD) and tested the resolution and accuracy of the ITS fungal barcoding marker by comparison with a six-marker dataset. Finally, we quantitatively compared phylogenetic and phenotypic species delimitation for 87 selected Cora species that have been formally described. Our HTS approach successfully generated ITS sequences for 76% of the historical collections, and our results show that an integrative approach is the gold-standard for understanding diversity in this group.more » « less
-
Abstract Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences (“barcodes”) of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.more » « less
-
In 2016-17, shellfish harvesting closed for the first time in Narragansett Bay, Rhode Island, USA, from domoic acid (DA), a neurotoxin produced by diatoms of the Pseudo-nitzschia genus. Pseudo-nitzschia have occurred frequently for over 60 years in Narragansett Bay’s Long-Term Plankton Time Series (NBPTS), therefore it is surprising that the first closure only recently occurred. Pseudo-nitzschia species are known to vary in their toxin production, thus species identification is critical for understanding the underlying ecological causes of these harmful algal blooms (HABs). DNA in plankton biomass can be preserved for many years, so molecular barcoding of archived samples is useful for delineation of taxa over time. This study used amplification of the Pseudo-nitzschia -specific 18S-5.8S rDNA internal transcribed spacer region 1 (ITS1) in plankton samples and high throughput sequencing to characterize Pseudo-nitzschia species composition over a decade in Narragansett Bay, including eight years before the 2016-17 closures and two years following. This metabarcoding method can discriminate nearly all known Pseudo-nitzschia species. Several species recur as year-round residents in Narragansett Bay ( P. pungens var. pungens, P. americana, P. multiseries , and P. calliantha ). Various other species increased in frequency after 2015, and some appeared for the first time during the closure period. Notably, P. australis , a species prevalent in US West Coast HABs and known for high DA production, was not observed in Narragansett Bay until the 2017 closure but has been present in several years after the closures. Annual differences in Pseudo-nitzschia composition were correlated with physical and chemical conditions, predominantly water temperature. The long-term composition trends of Pseudo-nitzschia in Narragansett Bay serve as a baseline for identifying the introduction of new species, understanding shifting assemblages that contributed to the 2016-17 closures, and monitoring species that may be cause for future concern.more » « less