References
Akaike H (1974) A new look at the statistical model identification.IEEE Transactions on Automatic Control 19, 716-723.
Arafat H, Alamaru A, Gissi C, Huchon D (2018) Extensive mitochondrial
gene rearrangements in the Ctenophora: insights from benthic
Playtctenida. BMC Evolutionary Biology 18, 11.
Choy CA, Haddock SHD, Robison BH (2017) Deep pelagic food web structure
as revealed by in situ feeding observations. Proceedings of
the Royal Society B: Biological Sciences 284, 20172116.
Chun C (1880) Die Ctenophoren des Golfes von Neapel und der angrenzenden
Meeres-Abschnitte. Flora und Fauna des Golfes von Neapel,1 Engelmann, Leipzig. 1-311
DeSalle R, Goldstein P (2019) Review and interpretation of trends in DNA
barcoding. Frontiers in Ecology and Evolution 7, 302.
Djurhuus A, Pitz K, Sawaya NA, et al. (2018) Evaluation of marine
zooplankton community structure through environmental DNA metabarcoding.Limnology and Oceanography: Methods 16, 209-221.
Dunn CW, Leys SP, Haddock SHD (2015) The hidden biology of sponges and
ctenophores. Trends in Ecology and Evolution 30,
282-291.
Eble JA, Daly-Engel TS, DiBattista JD, Koziol A, Gaither MR (2020)
Marine Environmental DNA: Approaches, applications, and opportunities.
In: Advances in Marine Biology (ed. Sheppard C), pp. 141-169.
Elsevier Ltd., London, United Kingdom.
Edgar R (2004) MUSCLE: multiple sequence alignment with high accuracy
and high throughput. Nucleic Acids Research 32,
1792-1797.
Folmer O, Black MB, Hoeh WR, Lutz RA, Vrijenhoek RC (1994) DNA primers
for amplification of mitochondrial cytochrome C oxidase subunit I from
metazoan invertebrates. Molecular Marine Biology and
Biotechnology 3, 294-299.
Francis WR, Christianson LC, Kiko R, et al. (2013) A comparison
across non-model animals suggests an optimal sequencing depth forde novo transcriptome assembly. BMC Genomics 14,
167.
Geller J, Meyer C, Parker M, Hawk H (2013) Redesign of PCR primers for
mitochondrial cytochrome c subunit I for marine invertebrates and
application in all-taxa biotic surveys. Molecular Ecology
Resources 13, 851-861.
Günther B, Knebelsberger T, Neumann H, Laakmann S, Arbizu PM (2018)
Metabarcoding of marine environmental DNA based on mitochondrial and
nuclear genes. Scientific Reports 8, 14822.
Haddock SHD (2004) A golden age of gelata: past and future research on
planktonic ctenophores and cnidarians. Hydrobiologica530/531, 549-556.
Haddock SHD, Christianson LM, Francis WR, et al. (2017) Insights
into the biodiversity, behavior, and bioluminescence of deep-sea
organisms using molecular and maritime technology. Oceanography30, 39-47.
Harbison GR, Madin LP, Swanberg NR (1978) On the natural history and
distribution of oceanic ctenophores. Deep-Sea Research25, 233-256.
Hoang D, Chernomor O, von Haeseler A, Minh B, Vinh L (2018) UFBoot2:
Improving the ultrafast bootstrap approximation. Molecular Biology
and Evolution 35, 518-522.
Johnson SB, Winnikoff JR, Schultz DT, et al. (in prep) Speciation
in the midwater; a new lobate ctenophore in the eastern Pacific.
Kohn AB, Citarella MR, Kocot KM, et al. (2012) Rapid evolution of
the compact and unusual mitochondrial genome in the ctenophore,Pleurobrachia bachei. Molecular Phylogenetics and
Evolution 63, 203-207.
Komai T, Tokioka T (1940) Kiyohimea aurita, n. gen., n. sp., type
of a new family of lobate Ctenophora. Annot. Zool. Japan19 , 43-46.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular
Evolutionary Genetics Analysis across computing platforms.Molecular Biology and Evolution 35, 1547-1549.
Lacoursière-Roussel A, Howland K, Normandeau E, et al. (2018)
eDNA metabarcoding as a new surveillance approach for coastal Arctic
biodiversity. Ecology and Evolution 8, 7763-7777.
Lavrov DV, Pett W (2016) Animal mitochondrial DNA as we do not know it:
mt-genome organization and evolution in nonbilaterian lineages.Genome Biology and Evolution 8, 2896-2913.
Leray M, Knowlton N (2015) DNA barcoding and metabarcoding of
standardized samples reveal patterns of marine benthic diversity.Proceedings of the National Academy of Sciences 112,
2076-2081.
Leray M, Yang JY, Meyer CP, et al. (2013) A new versatile primer
set targeting a short fragment of the mitochondrial COI region for
metabarcoding metazoan diversity: application for characterizing coral
reef fish gut contents. Frontiers in Zoology 10, 34.
Lindsay DJ, Miyake H (2007) A novel benthopelagic ctenophore from 7,217
m depth in the Ryukyu Trench, Japan, with notes on the taxonomy of
deep-sea cydippids. Plankton and Benthos Research 2,
98-102.
López-Escardó D, Paps J, C. dV, et al. (2018) Metabarcoding
analysis on European coastal samples reveals new molecular metazoan
diversity. Scientific Reports 8, 9106.
Madin LP, Harbison GR (1978) Bathocyroe fosteri gen.nov.,
sp.nov.: a mesopelagic ctenophore observed and collected from a
submersible. Journal of the Marine Biological Association of the
United Kingdom 58 , 559-564.
Matsumoto GI, Robison BH (1992) Kiyohimea usagi, a new species of
lobate ctenophore from the Monterey submarine canyon. Bulletin of
Marine Science 51, 19-29.
Medlin LK, Elwood HJ, Stickel S, Sogin ML (1988) The characterization of
enzymatically amplified eukaryotic 16S-like rRNA-coding regions.Genetica 71, 491-499.
Mills CE (2017) Phylum ctenophora: list of all valid species
names. https://faculty.washington.edu/cemills/Ctenolist.html
Minh B, Schmidt H, Chernomor O, et al. (2020) IQ-TREE 2: New
models and efficient methods for phylogenetic inference in the genomic
era. Molecular Biology and Evolution 37, 1530-1534.
Nguyen L, Schmidt H, von Haeseler A, Minh B (2015) IQ-TREE: A fast and
effective stochastic algorithm for estimating maximum likelihood
phylogenies. Molecular Biology and Evolution 32,
268-274.
Pett W, Ryan JR, Pang K, et al. (2011) Extreme mitochondrial
evolution in the ctenophore Mnemiopsis leidyi: insights from
mtDNA and the nuclear genome. Mitochondrial DNA 22,
130-142.
Pitz K, Guo J, Johnson SB, et al. (2020) Zooplankton
biogeographic boundaries in the California Current System as determined
from metabarcoding. Plos One 15, e0231519-0231520.
Podar M, Haddock SHD, Sogin ML, Harbison GR (2001) A molecular
phylogenetic framework for the phylum Ctenophora using 18S rRNA genes.Molecular Phylogenetics and Evolution 21, 218-230.
Posada D, Crandall KA (1998) Modeltest: Testing the model of DNA
substitution. Bioinformatics 14, 817-818.
Preston CM, Durkin CA, Yamahara KM (2020) DNA metabarcoding reveals
organisms contributing to particulate matter flux to abyssal depths in
the North East Pacific ocean. Deep-Sea Research Part II173, 104708.
Rambaut A, Drummond A, Xie D, Baele G, Suchard MA (2018) Posterior
summarisation in Bayesian phylogenetics using Tracer 1.7.Systematic Biology syy032.
Ronquist F, Teslenko M, van der Mark P, et al. (2012) MrBayes
3.2: Efficient Bayesian phylogenetic inference and model choice across a
large model space. Systematic Biology 61, 539-542.
Rozas J, Ferrer-Mata A, Sánchez D, JC, et al. (2017) DnaSP 6: DNA
sequence polymorphism analysis of large datasets. Molecular
Biology and Evolution 34, 3299-3302.
Schroeder A, Stanković D, Pallavicini A, et al. (2020) DNA
metabarcoding and morphological analysis - Assessment of zooplankton
biodiversity in transitional waters. Marine Environmental
Research 160, 104946.
Schultz DT, Eizenga JM, Corbett-Detig RB, et al. (2020) Conserved
novel ORFs in the mitochondrial genome of the ctenophore Beroe
forskalii. PeerJ 8.
Siddall ME, Fontanella FM, Watson SC, Kvist S, Erséus C (2009) Barcoding
bamboozled by bacteria: convergence to metazoan mitochondrial primer
targets by marine microbes. Systematic Biology 4,
445-451.
Simion P, Bekkouche N, Jager M, Quéinnec E, Manuel M (2015) Exploring
the potential of small RNA subunit and ITS sequences for resolving
phylogenetic relationships within phylum Ctenophora. Zoology118, 102-114.
Ralph PM, Kaberry C (1950) New Zealand Coelenterates. Ctenophores from
Cook Straight. Zoology Publications from Victoria University
College 3 , 1-11.
R Team (2015) RStudio: Integrated Development for R. RStudio Inc,
Boston, MA.
Thiebot J-B, McInnes JC (2020) Why do marine endotherms eat gelatinous
prey? ICES Journal of Marine Science 77, 58-71.
Trifinopoulos J, Nguyen L, von Haeseler A, Minh B (2016) W-IQ-TREE: a
fast online phylogenetic tool for maximum likelihood analyses.Nucleic Acids Research 44, W232-W235.
Untergasser A, Cutcutache I, Koressaar T, et al. (2012)
Primer3—new capabilities and interfaces. Nucleic Acids Research40, e115.
Vrijenhoek RC, Waples RS (2012) Popular misconceptions. Molecular
Ecology 21, 4155-4156.
Wickham H (2016) ggplot2: Elegant graphics for data analysisSpringer-Verlag, New York.
Xia X (2018) DAMBE7: New and improved tools for data analysis in
molecular biology and evolution. Molecular Biology and Evolution35, 1550-1552.
Xia X, Hafner MS, Sudman PD (1996) On transition bias in mitochondrial
genes of pocket gophers. Journal of Molecular Evolution43 , 32-40.
Yeh HD, Questel JM, Maas KR, Bucklin A (2020) Metabarcoding analysis of
regional variation in gut contents of the copepod Calanus
finmarchicus in the North Atlantic Ocean. Deep-Sea Research Part
II.