Taxonomic Overlap Research Articles

Assessing the performance of short 18S rDNA markers for environmental DNA metabarcoding of marine protists

AbstractMarine protists are globally distributed and sensitive to environmental conditions, which makes them a focal group when studying the effects of climate change on biodiversity and ocean health. However, they are a highly diverse group with varying evolutionary histories and morphologies and widely variable preservation potential in the fossil record. Thus, their past diversity and composition are poorly known. Paleogenetics, which relies, among other approaches, on DNA metabarcoding of sedimentary ancient DNA (sedaDNA), provides a promising avenue to explore the past history and responses of marine protists to global change. Choosing the right marker for sedaDNA studies is critical, striking a balance between marker length and taxonomic resolution. While marker guides exist for modern environmental DNA surveys, a thorough assessment of existing short markers for sedaDNA studies targeting protists is lacking. In this study, we report on a comparison of in silico PCR for eight short 18S rDNA markers, including one from the Tara Oceans initiative and a longer marker commonly used in modern marine eDNA studies. We analyze their taxonomic coverage and resolution, taxonomic overlap and uniqueness between markers, co‐amplification of non‐protist taxa, and amplicon size differences across taxonomic groups. Additionally, we provide a detailed analysis of diatoms, dinoflagellates, haptophytes, and chlorophytes. Our study is aimed at supporting project‐specific marker choices for characterizing protist composition and diversity. While we focus on marine protists, our results are applicable to other aquatic and terrestrial environments.

Scratching the surface: The in vitro research that will be critical for conserving exceptional plants to scale

The conservation of threatened exceptional plants, which cannot be conserved by seed banking, requires in vitro technologies for many of the approaches needed for their long-term ex situ conservation. This study evaluated the current in vitro plant literature, as represented in Web of Science, to determine its taxonomic overlap with the families and genera of the 775 species currently listed as exceptional. Web of Science was searched using the terms micropropagation, somatic embryogenesis, zygotic embryo, and cryopreservation, and the target genera and families were identified in the more than 19,000 articles evaluated. There were five families with significant overlap between the in vitro literature and exceptional species: Fabaceae, Asteraceae, Orchidaceae, Arecaceae, and Rutaceae. However, there was less overlap at the level of genus, with Citrus, Coffea, and Quercus having the most articles. Significant gaps were also found, with 14 exceptional families and half of the exceptional genera having no representation in the Web of Science search results. The 20 exceptional species with the most articles were all economically important species, and these had 343 threatened congeners that could be prioritized for research. A highly important group of exceptional plants that was significantly under-represented in the literature was tropical woody species, which form the backbone of the diversity of the world’s threatened rainforests. Overall, there are areas of strength upon which to build future work, but significant gaps where research should be prioritized for effectively conserving exceptional plants.

Optimizing waterborne eDNA capture from waterholes in savanna systems under remote field conditions.

Environmental DNA (eDNA) is used for biodiversity assessments in a variety of ecosystems across the globe, whereby different eDNA concentration, preservation and extraction methods can outperform others depending on the sampling conditions and environment. Tropical and subtropical ecosystems in Africa are among the less studied systems concerning eDNA-based monitoring. Waterholes in arid parts of southern Africa represent important agglomeration points for terrestrial mammals, and the eDNA shed into such waterbodies provides a powerful source of information for monitoring mammalian biodiversity in the surrounding area. However, the applied methods for eDNA sampling, preservation and filtering in different freshwater systems vary greatly, and rigorous protocol testing in African freshwater systems is still lacking. This study represents the first attempt to examine variations in eDNA concentration, preservation and extraction methods under remote field conditions using waterborne eDNA in a savanna system. Collected samples were heavily affected by microalgal and bacterial growth, impeding eDNA capture and PCR success. We demonstrate clear effects of the methodological choices, which also depend on the state of eDNA. A preliminary metabarcoding run showed little taxonomic overlap in mammal species detection between two metabarcoding primers tested. We recommend water filtering (using filters with pore sizes >1 μm) over centrifugation for eDNA concentration, Longmire's solution for ambient temperature sample preservation and Qiagen's DNeasy PowerSoil Pro Kit for DNA extraction of these inhibitor-prone samples. Furthermore, at least two independent metabarcoding markers should be utilized in order to maximize species detections in metabarcoding studies.

RCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R.

The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa then are currently curated by professional staff. Thus there is a growing need for an easy to implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like it's predecessor, relies on sequence homology and PCR primer compatibility instead of keyword-searches to avoid limitations of user-defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user-defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI) formatted nt database using a taxonomic-rank based stratified random sampling approach ( blast_seeds() ). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer-specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.

Polar lake microbiomes have distinct evolutionary histories.

Toward the poles, life on land is increasingly dominated by microorganisms, yet the evolutionary origin of polar microbiomes remains poorly understood. Here, we use metabarcoding of Arctic, sub-Antarctic, and Antarctic lacustrine benthic microbial communities to test the hypothesis that high-latitude microbiomes are recruited from a globally dispersing species pool through environmental selection. We demonstrate that taxonomic overlap between the regions is limited within most phyla, even at higher-order taxonomic levels, with unique deep-branching phylogenetic clades being present in each region. We show that local and regional taxon richness and net diversification rate of regionally restricted taxa differ substantially between polar regions in both microeukaryotic and bacterial biota. This suggests that long-term evolutionary divergence resulting from low interhemispheric dispersal and diversification in isolation has been a prominent process shaping present-day polar lake microbiomes. Our findings illuminate the distinctive biogeography of polar lake ecosystems and underscore that conservation efforts should include their unique microbiota.

Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of seawater in reef environments.

In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (Chaetodon lunulatus) resident to coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater vs gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S and ITS2 sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater based on low levels of taxonomic overlap (3 to 21%) and significant differences between the sampling approaches. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that might include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, epiphytic, symbiotic, or cryptic.

Unravelling bird nest arthropod community structure using metabarcoding

Bird nests are fascinating microcosms harboring a wide range of arthropods parasitizing the nesting birds or feeding on prey remains, feces, and the nest material. Studies of these communities have been entirely based on emergence traps which collect live organisms out of the nests. The analysis of nest contents and environmental DNA (eDNA) via metabarcoding could expand our knowledge and identify prey, exuviae, and other animal remains in bird nests. Here, we investigated the potential of arthropod remains, nest dust, and feathers to better describe arthropod diversity accumulated in 20 bird nests collected in Guelph (Canada). We used subsampling strategies and tested two extraction approaches to investigate the distribution of DNA in nests, account for low-quality DNA, and the presence of inhibitory substances. In total, 103 taxa were detected via metabarcoding. Arthropod remains delivered the highest number of taxa (n = 67), followed by nest dust (n = 29). Extractions with the PowerSoil kit outperformed DNeasy extractions coupled with PowerClean Pro inhibitor removal. Per nest, on average 5.5% taxonomic overlap between arthropod remains of different size classes was detected and subsamples of nest dust extracted with the PowerSoil kit showed 47.3% taxonomic overlap indicating a heterogeneous eDNA distribution in nests. Most detected species were either feeding in the nest, i.e., herbivorous / predatory, or bird food. We also detected molecular traces of 25 bird species, whose feathers were likely used as nest material. Consequently, the metabarcoding of bird nest materials provides a more complete picture of nest communities, which can enable future studies on functional diversity and better comparisons between nesting species.

Mesophotic vs. shallow water reefs: ecosystem connectivity in the Silurian of Gotland

The Lower Silurian Visby Beds (ca. 430 Ma) exposed on the island of Gotland (Sweden) yield the oldest so far described MCE’s (mesophotic coral ecosystems). Several basic questions concerning these ecosystems, including their extent, positioning, and particularly their spatial relation and affinity with the shallow water reefs, remain unanswered. We describe a deeply incised erosional channel infilled by redeposited detrital and biodetrital material including corals and stromatoporoids, which represents a unique example of a fossil depositional structure connecting shallow- and deep-water reef environments of that time. The mesophotic environment is embodied by limestones and marls, in which the channel is incised, while the shallow water habitats are represented by the redeposited material infilling the channel. The erosional channel contains material derived from hypothetical adjacent shallow-water reefal settings, which indicates that it served as an interconnecting zone between shallow- and deep-water benthic communities. The vertical connectivity of the shallow-water reefs and the adjacent mesophotic ecosystems results in a significant taxonomic overlap between these communities. This is especially important when taking into account that the Visby Beds are the oldest example of a fossil mesophotic ecosystem described so far. This indicates that the development of the earliest mesophotic ecosystems should not be attributed solely to gradual expansion of corals and stromatoporoids into greater depths, but probably took place also by means of redistribution of shallow water taxa during high-energy sedimentary events.

Epiphytic and Endophytic Fungi Colonizing Seeds of Two Poaceae Weed Species and Fusarium spp. Seed Degradation Potential In Vitro.

Fungi colonizing the surface and endosphere of two widespread Poaceae weed species, Avena fatua and Echinochloa crus-galli, were isolated to compare the taxonomic composition between the plant species, location, and year of the seed collection. The seed-degrading potential of Fusarium isolated from the seeds was tested by inoculating seeds of E. crus-galli with spore suspension. Molecular identification of epiphytic and endophytic fungal genera was performed by sequencing the ITS region of rDNA. Endophytes comprised of significantly lower fungal richness compared to epiphytes. A significant taxonomic overlap was observed between the endosphere and seed surface. The most abundant genera were Alternaria, Fusarium, Cladosporium, and Sarocladium. Analysis of similarities and hierarchical clustering showed that microbial communities were more dissimilar between the two plant species than between the years. Fusarium isolates with a high potential to infect and degrade E. crus-galli seeds in laboratory conditions belong to F. sporotrichioides and F. culmorum.

Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers.

Molecular gut content analysis is a popular tool to study food web interactions and has recently been suggested as an alternative source for DNA-based biomonitoring. However, the overabundant consumer's DNA often outcompetes that of its diet during PCR. Lineage-specific primers are an efficient means to reduce consumer amplification while retaining broad specificity for dietary taxa. Here, we designed an amplicon sequencing assay to monitor the eukaryotic diet of mussels and other metazoan filter feeders and explore the utility of mussels as natural eDNA samplers to monitor planktonic communities. We designed several lineage-specific rDNA primers with broad taxonomic suitability for eukaryotes. The primers were tested using DNA extracts of different limnic and marine mussel species and the results compared to eDNA water samples collected next to the mussel colonies. In addition, we analysed several 25-year time series samples of mussels from German rivers. Our primer sets efficiently prevent the amplification of mussels and other metazoans. The recovered DNA reflects a broad dietary preference across the eukaryotic tree of life and considerable taxonomic overlap with filtered water samples. We also show the utility of a reversed version of our primers, which prevents amplification of nonmetazoan taxa from complex eukaryote community samples, by enriching fauna associated with the marine brown algae Fucus vesiculosus. Our protocol will enable large-scale dietary analysis in metazoan filter feeders, facilitate aquatic food web analysis and allow surveying of aquacultures for pathogens. Moreover, we show that mussels and other aquatic filter feeders can serve as complementary DNA source for biomonitoring.

Rare biosphere in cultivated Panax rhizosphere shows deterministic assembly and cross-plant similarity

Revealing the ecological patterns of abundant and rare microbial subcommunities in rhizosphere of cultivated plant is critical for understanding plant–microbe interactions and the formation of functionally important rhizosphere microbiome. Based on rhizodeposit support effects and colonization priority effects, the present study outlined two disparate hypotheses predicting the more deterministic assembly of abundant (the “dominance-determinism” hypothesis) and rare subcommunities (the “rare-determinism” hypothesis), respectively. These hypotheses were tested using bacterial and fungal subcommunities in the rhizosphere of three cultivated Panax species (P. ginseng, P. quinquefolium, and P. notoginseng). In each plant species, the abundant and rare taxa exhibited different patterns of distribution and composition, but similar edaphic factors could explain their phylogenetic community variations. Network analysis indicated that the abundant taxa located in more central positions than the rare taxa, and the negative links mainly exhibited between abundant and rare taxa. Null model showed that stochastic and deterministic processes dominated the assembly of abundant (determinism: 11.97–45.30 %) and rare (determinism: 67.24–96.30 %) subcommunities, respectively. In addition, almost all members of the rhizosphere abundant taxa (> 89 %) were also highly abundant in corresponding bulk soil. Among the three Panax species, the rare taxa exhibited stronger taxonomic overlap and phylogenetic similarity compared to the abundant taxa. These results indicate that the assembly of abundant subcommunities in Panax rhizosphere is highly stochastic and may relate to the priority effects, whereas the rare taxa tend to be the results of plant selection and exhibit potentially evolutionary conservatism.

Harnessing aquatic plant growth forms to apply European nutrient-enrichment bioindicators to Canadian waters.

PremiseAquatic macrophyte species abundance and nutrient affinity are used in metrics to assess the trophic condition of lakes and rivers. The development of these indices is often regional, with inter‐regional comparisons being complicated by the lack of taxonomic overlap. Here, we use a traits‐based approach to expand the geographic scope of existing metrics.MethodsWe generalized European trophic affinity values using the response of plant growth form to the light–nutrient gradient, then applied these values to sites in Canada. We evaluated the method's performance against the measured total phosphorus concentration (TP).ResultsFree‐floating and emergent growth forms were associated with enriched waters (>0.2 mg/L TP), whereas rosette forms were associated with oligotrophic conditions (<0.05 mg/L TP). The responses were longitudinally consistent, and the site scores among indices were highly collinear. Growth form–based scores were more strongly correlated with TP than were species‐based scores (0.42–0.56 versus 0.008–0.25).DiscussionWe leveraged the ecological relationship between increased surface water nutrient enrichment and the dominance of particular aquatic plant growth forms to generalize aquatic plant trophic indices. We demonstrated an approach for adapting species‐based indices to plant traits to facilitate a broader geographic application and simpler data collection, which could be used to develop an easily applied trait‐based method of assessing water nutrient status.

Influence of blueback herring, Alosa aestivalis, on zooplankton in a southeastern US reservoir

Grove L, Stell EG, Grove LJW, Wright RA, DeVries DR. 2022. Influence of blueback herring, Alosa aestivalis, on zooplankton in a southeastern US reservoir. Lake Reserv Manage. 38:256–267. Forage fishes like blueback herring (Alosa aestivalis) have been widely introduced, sometimes without careful consideration of potential ecological consequences. We compared biotic and abiotic factors before and after blueback herring introduction into Lewis Smith Lake, Alabama (United States), and tested for diet overlap among planktivorous species to quantify their potential ecological influences. Abiotic and biotic factors varied among regions of the lake, consistent with differences in agricultural practices and nutrient input within each region. Secchi depth increased and zooplankton density decreased, while chlorophyll a remained unchanged relative to before blueback herring introduction. Juvenile and adult blueback herring and threadfin shad (Dorosoma petenense) consumed the same zooplankton taxa; however, blueback herring consumed significantly larger individuals and significantly greater numbers of zooplankton than threadfin shad. Blueback herring also selectively consumed larger zooplankton than the average size in the reservoir population, while threadfin shad did not. Threadfin shad and blueback herring positively selected Bosmina and cyclopoid copepods. The taxonomic overlap and size selectivity in prey choice suggest that if blueback herring reduce larger zooplankton, threadfin shad and blueback herring diets are likely to increasingly overlap. Because of their differences in feeding strategies (i.e., related to zooplankton size differences) and habitat preferences, current evidence for potential competitive interactions between these planktivores appears limited; however, longer term concerns are that blueback herring could eventually reduce larger zooplankton to the extent where they would increasingly compete with threadfin shad as the most abundant forage fish in Lewis Smith Lake.

Functional and Taxonomic Overlap in Shore Fish Assemblages in a Tropical Seascape

The relationships between shore fish assemblages from habitats neighboring coral reefs have received little attention in the Indo-Pacific. The present study is based on the extensive sampling (539,000 fish; 898 taxa) of three fish assemblages: reefs, mangroves, and soft-bottoms in a large bay of New Caledonia. Species area curves indicate that sampling was nearly exhaustive in all three habitats (262 species in mangroves, 342 on soft-bottoms, 594 on reefs). Combinations of life-history traits were used as proxies of ecological functions. The species and functional overlaps were highest between soft-bottoms and mangroves and lowest between mangroves and reefs. These overlaps were lower than most recent studies in the Indo-Pacific, a result probably linked to the extent of the sampling in the present study. The life-history traits of species found exclusively in one habitat as opposed to several habitats were not a random selection within the species pool. Overlapping species were mostly large species that fed on nekton, large invertebrates, or plankton; exclusive species were mostly sedentary, solitary, and of small size, except for plankton-feeding species, which mostly had large home ranges and formed large schools. Herbivores were seldom found in several habitats. Functional redundancy was correlated to species richness, and was highest in reef fish assemblages. Functions common to several habitats had very seldom the same relative redundancy, implying that these functions had not the same importance for each assemblage. Functions exclusive to one habitat generally had low redundancy. These functional attributes and species overlap suggest that these three assemblages have a low level of interaction, despite the fact that they share extensive boundaries. These findings may have important applications in the management of shore fish assemblages.

A fossil assemblage from the mid-late Maastrichtian of Gavdos Island, Greece, provides insights into the pre-extinction pelagic ichthyofaunas of the Tethys.

The global body-fossil record of marine 'fishes' from the time interval immediately preceding the Cretaceous-Paleogene Extinction is markedly poor. This deficiency appears to be further exacerbated with regards to offshore and deep-water taxa, obscuring our understanding of the state and composition of corresponding vertebrate faunas at the onset of this major extinction event. Recent fieldwork in the mid-late Maastrichtian exposures of the Pindos Unit in Gavdos Island, Greece, yielded a small but informative sample of fossil 'fishes', which inhabited the Tethys approximately three to four million years before the extinction. In this work we describe this sample, which comprises between eight and nine discrete morphotypes of various size classes, belonging to †Ichthyodectoidei, Aulopiformes (†Dercetidae, †Enchodontidae, †Ichthyotringidae), cf. †Sardinioididae, as well as the hexanchid shark †Gladioserratus sp. The new material expands the faunal list for the Maastrichtian of Gavdos Island, and the Pindos Unit as a whole, and further allows for the description of a new genus and species of †Enchodontidae and a new species of †Ichthyotringidae. The two new taxa are found to be widespread in the Maastrichtian of the Pindos Unit. The overall character of the assemblage agrees with previous interpretations of an offshore and rather deep depositional environment for the fossiliferous horizons. Furthermore, it exhibits a higher diversity than, and little taxonomic overlap with penecontemporaneous teleost assemblages from the Tethys, and informs on the otherwise poorly known Maastrichtian offshore and deep-water marine ichthyofaunas of the region.

The functional ecology of mangrove fishes across the Isthmus of Panama

AbstractAimBiogeographic history and variation in modern environmental conditions can greatly influence local and regional community structure and, more generally, ecosystem functioning. This is clearly exemplified at the Isthmus of Panama where marine communities and environments from the Caribbean Sea and the Tropical Eastern Pacific Ocean differ despite ancient connections during the Miocene and Pleistocene. Here, we compare the functional (implied from traits) and isotopic structure of mangrove fish communities from those two biogeographic regions, which have been separated by the Isthmus of Panama for ~3 my.LocationCaribbean and Pacific coasts of Panama (Eastern Pacific and Caribbean Sea).MethodsWe gathered data on five functional traits (salinity preference, body mass, diet, position in the water column and lifespan) of mangrove fishes from the sampled regions. We also analysed δ13C and δ15C isotopic values and calculated functional isotopic metrics of the most abundant fish species inhabiting mangroves of these two regions.ResultsThe taxonomic composition and functional and trophic diversity differed between the mangrove fish communities of the Caribbean and the Eastern Pacific. Although the species richness of both assemblages was similar, there was very little taxonomic overlap between them: Snooks (Centropomidae) numerically dominated in the Eastern Pacific, whereas grunts (Haemulidae) and snappers (Lutjanidae) dominated in the Caribbean Sea. Functional divergence (FDiv) and isotopic richness (IRic) were higher in the Caribbean than in the Eastern Pacific, indicating differences in the way fishes use mangroves in these areas.Main conclusionsTaxonomic and functional characteristics of mangrove fish assemblages across biogeographic realms can be strongly influenced by local environmental factors (e.g. tidal regimes, the presence of adjacent coastal ecosystems and productivity), and these can override similarities that recent historical connections of faunas might be expected to produce. All such aspects need to be considered when seeking generalizations about ecosystem functioning.

MARINE FISHES (CHONDRICHTHYES, HOLOCEPHALI, ACTINOPTERYGII) FROM THE UPPER CRETACEOUS (CAMPANIAN) RYBUSHKA FORMATION NEAR BELOE OZERO, SARATOV OBLAST, RUSSIA

A diverse fish paleofauna occurs in the upper Campanian portion of the Rybushka Formation exposed near Saratov city in the Saratov Oblast, Russia. Twenty taxa have been identified, including two holocephalans (Ischyodus bifurcatus and Amylodon karamysh), twelve elasmobranchs (Synechodus sp., Cederstroemia sp., Cretalamna cf. C. borealis, C. cf. C. sarcoportheta, Archaeolamna kopingensis, Eostriatolamia segedini, E. venusta, Pseudocorax laevis, Squalicorax kaupi, Squalicorax morphotype 1, Squalidae indet., and Squatirhina sp.), and six teleosts (Pachyrhizodus sp., Saurocephalus lanciformis, Paralbula casei, Enchodus cf. E. dirus, E. cf. E. gladiolus, and E. petrosus). Many of these taxa are new to the Campanian fish record of Russia, and the assemblage demonstrates that there is significant taxonomic overlap between the Rybushka Formation paleofauna and that of North America.

Testing the agreement of trees with internal labels

BackgroundA semi-labeled tree is a tree where all leaves as well as, possibly, some internal nodes are labeled with taxa. Semi-labeled trees encompass ordinary phylogenetic trees and taxonomies. Suppose we are given a collection {mathcal {P}}= {{mathcal {T}}_1, {mathcal {T}}_2, ldots , {mathcal {T}}_k} of semi-labeled trees, called input trees, over partially overlapping sets of taxa. The agreement problem asks whether there exists a tree {mathcal {T}}, called an agreement tree, whose taxon set is the union of the taxon sets of the input trees such that the restriction of {mathcal {T}} to the taxon set of {mathcal {T}}_i is isomorphic to {mathcal {T}}_i, for each i in {1, 2, ldots , k}. The agreement problems is a special case of the supertree problem, the problem of synthesizing a collection of phylogenetic trees with partially overlapping taxon sets into a single supertree that represents the information in the input trees. An obstacle to building large phylogenetic supertrees is the limited amount of taxonomic overlap among the phylogenetic studies from which the input trees are obtained. Incorporating taxonomies into supertree analyses can alleviate this issue. ResultsWe give a {mathcal {O}}(n k (sum _{i in [k]} d_i + log ^2(nk))) algorithm for the agreement problem, where n is the total number of distinct taxa in {mathcal {P}}, k is the number of trees in {mathcal {P}}, and d_i is the maximum number of children of a node in {mathcal {T}}_i.ConclusionOur algorithm can aid in integrating taxonomies into supertree analyses. Our computational experience with the algorithm suggests that its performance in practice is much better than its worst-case bound indicates.

A synthesis tree of the Copepoda: integrating phylogenetic and taxonomic data reveals multiple origins of parasitism.

The Copepoda is a clade of pancrustaceans containing 14,485 species that are extremely varied in their morphology and lifestyle. Not only do copepods dominate marine plankton and sediment communities and make up a sizeable component of the freshwater plankton, but over 6,000 species are symbiotically associated with every major phylum of marine metazoans, mostly as parasites. Unfortunately, our understanding of copepod evolutionary relationships is relatively limited in part because of their extremely divergent morphology, sparse taxon sampling in molecular phylogenetic analyses, a reliance on only a handful of molecular markers, and little taxonomic overlap between phylogenetic studies. Here, a synthesis tree method is used to integrate published phylogenies into a more comprehensive tree of copepods by leveraging phylogenetic and taxonomic data. A literature review in this study finds fewer than 500 species of copepods have been sampled in molecular phylogenetic studies. Using the Open Tree of Life platform, those taxa that have been sampled in previous phylogenetic studies are grafted together and combined with the underlying copepod taxonomic hierarchy from the Open Tree of Life Taxonomy to make a synthesis phylogeny of all copepod species. Taxon sampling with respect to molecular phylogenetic analyses is reviewed for all orders of copepods and shows only 3% of copepod species have been sampled in phylogenetic studies. The resulting synthesis phylogeny reveals copepods have transitioned to a parasitic lifestyle on at least 14 occasions. We examine the underlying phylogenetic, taxonomic, and natural history data supporting these transitions to parasitism; review the species diversity of each parasitic clade; and identify key areas for further phylogenetic investigation.

Environmental DNA surveys detect distinct metazoan communities across abyssal plains and seamounts in the western Clarion Clipperton Zone.

The deep seafloor serves as a reservoir of biodiversity in the global ocean, with >80% of invertebrates at abyssal depths still undescribed. These diverse and remote deep‐sea communities are critically under‐sampled and increasingly threatened by anthropogenic impacts, including future polymetallic nodule mining. Using a multigene environmental DNA (eDNA) metabarcoding approach, we characterized metazoan communities sampled from sediments, polymetallic nodules and seawater in the western Clarion Clipperton Zone (CCZ) to test the hypotheses that deep seamounts (a) are species richness hotspots in the abyss, (b) have structurally distinct communities in comparison to other deep‐sea habitats, and (c) that seafloor particulate organic carbon (POC) flux and polymetallic nodule density are positively correlated with metazoan diversity. eDNA metabarcoding was effective at characterizing distinct biotas known to occur in association with different abyssal substrate types (e.g., nodule‐ and sediment‐specific fauna), with distinct community composition and few taxa shared across substrates. Seamount faunas had higher overall taxonomic richness, and different community composition and biogeography than adjacent abyssal plains, with seamount communities displaying less connectivity between regions than comparable assemblages on the abyssal plains. Across an estimated gradient of low to moderate POC flux, we find lowest taxon richness at the lowest POC flux, as well as an effect of nodule size on community composition. Our results suggest that while abyssal seamounts are important reservoirs of metazoan diversity in the CCZ, given limited taxonomic overlap between seamount and plains fauna, conservation of seamount assemblages will be insufficient to protect biodiversity and ecosystem function in regions targeted for mining.