Bibliography
Abdelkrim, J., Fedosov, A., Kantor, Y., Lozouet, P., Phuong, M.,
Zaharias, P., & Puillandre, N. (2018). Exon-capture based phylogeny and
diversification of the venomous gastropods (Neogastropoda, Conoidea).Molecular Biology and Evolution , 35 (10), 2355–2374. doi:
10.1093/molbev/msy144/5056056
Aberer, A. J., Kobert, K., & Stamatakis, A. (2014). ExaBayes: Massively
parallel Bayesian tree inference for the whole-genome era.Molecular Biology and Evolution , 31 (10), 2553–2556. doi:
10.1093/molbev/msu236
Avila, C., Núñez-Pons, L., & Moles, J. (2018). From the tropics to the
poles: chemical defensive strategies in sea slugs (Mollusca:
Heterobranchia). In M. P. Puglisi & M. A. Becerro (Eds.),Chemical Ecology: The Ecological Impacts of Marine Natural
Products (pp. 71–163). Boca Raton: CRC Press.
Barker, G. M. (2001). Gastropods on land: phylogeny, diversity, and
adaptive morphology. In G. M. Barker (Ed.), The Biology of
Terrestrial Molluscs (pp. 1–146). doi: 10.1079/9780851993188.0001
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible
trimmer for Illumina sequence data. Bioinformatics ,30 (15), 2114–2120. doi: 10.1093/bioinformatics/btu170
Brenzinger, B., Haszprunar, G., & Schrödl, M. (2013). At the limits of
a successful body plan - 3D microanatomy, histology and evolution ofHelminthope (Mollusca: Heterobranchia: Rhodopemorpha), the most
worm-like gastropod. Frontiers in Zoology , 10 (1), 1–26.
doi: 10.1186/1742-9994-10-37
Carmona, L., Pola, M., Gosliner, T. M., & Cervera, J. L. (2013). A tale
that morphology fails to tell: A molecular phylogeny of Aeolidiidae
(Aeolidida, Nudibranchia, Gastropoda). PLoS ONE , 8 (5).
doi: 10.1371/journal.pone.0063000
Castresana, J. (2000). Selection of conserved blocks from multiple
alignments for their use in phylogenetic analysis. Molecular
Biology and Evolution , 17 (4), 540–552. doi:
10.1093/oxfordjournals.molbev.a026334
Chaban, E. M., Ekimova, I. A., Schepetov, D. M., Kohnert, P. C.,
Schrödl, M., & Chernyshev, A. V. (2019). Euopisthobranch mollusks of
the order Cephalaspidea (Gastropoda: Heterobranchia) of the
Kuril-Kamchatka Trench and the adjacent Pacific abyssal plain with
descriptions of three new species of the genus Spiraphiline(Philinidae). Progress in Oceanography , 178 , 102185. doi:
10.1016/j.pocean.2019.102185
Choo, L. Q., Bal, T. M. P., Choquet, M., Smolina, I., Ramos-Silva, P.,
Marlétaz, F., … Peijnenburg, K. T. C. A. (2020). Novel genomic
resources for shelled pteropods: a draft genome and target capture
probes for Limacina bulimoides , tested for cross-species
relevance. BMC Genomics , 21 (1), 11. doi:
10.1186/s12864-019-6372-z
Colgan, D. J., Ponder, W. F., Beacham, E., & Macaranas, J. (2007).
Molecular phylogenetics of Caenogastropoda (Gastropoda: Mollusca).Molecular Phylogenetics and Evolution , 42 (3), 717–737.
doi: 10.1016/j.ympev.2006.10.009
Colgan, D. J., Ponder, W. F., Beacham, E., & Macaranas, J. M. (2003).
Gastropod phylogeny based on six segments from four genes representing
coding or non-coding and mitochondrial or nuclear DNA. Molluscan
Research , 23 (2), 123–148. doi: 10.1071/MR03002
Colgan, D. J., Ponder, W. F., & Eggler, P. E. (2000). Gastropod
evolutionary rates and phylogenetic relationships assessed using partial
28s rDNA and histone H3 sequences. Zoologica Scripta ,29 (1), 29–63. doi: 10.1046/j.1463-6409.2000.00021.x
Crawford, N. G., Faircloth, B. C., McCormack, J. E., Brumfield, R. T.,
Winker, K., & Glenn, T. C. (2012). More than 1000 ultraconserved
elements provide evidence that turtles are the sister group of
archosaurs. Biology Letters , 8 (5), 783–786. doi:
10.1098/rsbl.2012.0331
Crotty, S. M., Minh, B. Q., Bean, N. G., Holland, B. R., Tuke, J.,
Jermiin, L. S., & Haeseler, A. Von. (2020). GHOST: Recovering
Historical Signal from Heterotachously Evolved Sequence Alignments.Systematic Biology , 69 (2), 249–264. doi:
10.1093/sysbio/syz051
Cunha, T. J., & Giribet, G. (2019). Deep gastropod relationships
resolved. Proceedings of the Royal Society B: Biological
Sciences , 286 , 20182776.
Derkarabetian, S., Benavides, L. R., & Giribet, G. (2019). Sequence
capture phylogenomics of historical ethanol‐preserved museum specimens:
unlocking the rest of the vault. Molecular Ecology Resources ,
1755-0998.13072. doi: 10.1111/1755-0998.13072
Derkarabetian, S., Starrett, J., Tsurusaki, N., Ubick, D., Castillo, S.,
& Hedin, M. (2018). A stable phylogenomic classification of
Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence
capture of ultraconserved elements. ZooKeys , 2018 (760),
1–36. doi: 10.3897/zookeys.760.24937
Dimitrov, D., Benavides, L. R., Arnedo, M. A., Giribet, G., Griswold, C.
E., Scharff, N., & Hormiga, G. (2017). Rounding up the usual suspects:
a standard target-gene approach for resolving the interfamilial
phylogenetic relationships of ecribellate orb-weaving spiders with a new
family-rank classification (Araneae, Araneoidea). Cladistics ,33 (3), 221–250. doi: 10.1111/cla.12165
Dinapoli, A., Zinssmeister, C., & Klussmann-Kolb, A. (2011). New
insights into the phylogeny of the Pyramidellidae (Gastropoda).Journal of Molluscan Studies , 77 (1), 1–7. doi:
10.1093/mollus/eyq027
Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith,
S. A., … Giribet, G. (2008). Broad phylogenomic sampling improves
resolution of the animal tree of life. Nature , 452 (7188),
745–749. doi: 10.1038/nature06614
Epstein, H. E., Hallas, J. M., Johnson, R. F., Lopez, A., & Gosliner,
T. M. (2018). Reading between the lines: revealing cryptic species
diversity and colour patterns in Hypselodoris nudibranchs
(Mollusca: Heterobranchia: Chromodorididae). Zoological Journal of
the Linnean Society , 186 (1), 116–189.
Faircloth, B. C. (2013). Illumiprocessor: a trimmomatic wrapper for
parallel adapter and quality trimming. Retrieved from
http://dx.doi.org/10.6079/J9ILL
Faircloth, B. C. (2016). PHYLUCE is a software package for the analysis
of conserved genomic loci. Bioinformatics , 32 (5),
786–788. doi: 10.1093/bioinformatics/btv646
Faircloth, B. C., McCormack, J. E., Crawford, N. G., Harvey, M. G.,
Brumfield, R. T., & Glenn, T. C. (2012). Ultraconserved elements anchor
thousands of genetic markers spanning multiple evolutionary timescales.Systematic Biology , 61 (5), 717–726. doi:
10.1093/sysbio/sys004
Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012). CD-HIT: Accelerated
for clustering the next-generation sequencing data.Bioinformatics , 28 (23), 3150–3152. doi:
10.1093/bioinformatics/bts565
Giribet, G., Okusu, A., Lindgren, A. R., Huff, S. W., Schrödl, M., &
Nishiguchi, M. K. (2006). Evidence for a clade composed of molluscs with
serially repeated structures: Monoplacophorans are related to chitons.Proceedings of the National Academy of Sciences of the United
States of America , 103 (20), 7723–7728. doi:
10.1073/pnas.0602578103
Glenn, T., Nilsen, R., Kieran, T., Finger, J., Pierson, T., Bentley, K.,
… Faircloth, B. (2016). Adapterama I: universal stubs and primers
for thousands of dual-indexed Illumina libraries (iTru & iNext).BioRxiv , 049114 . doi: https://doi.org/10.1101/049114
González, V. L., Andrade, S. C. S., Bieler, R., Collins, T. M., Dunn, C.
W., Mikkelsen, P. M., … Giribet, G. (2015). A phylogenetic
backbone for Bivalvia: an RNA-seq approach. Proceedings of the
Royal Society B: Biological Sciences , 282 (1801),
20142332–20142332. doi: 10.1098/rspb.2014.2332
Goodheart, J. A. (2017). Insights into the systematics, phylogeny, and
evolution of Cladobranchia (Gastropoda: Heterobranchia). American
Malacological Bulletin , 35 (1), 73–81.
Goodheart, J. A., Bazinet, A. L., Collins, A. G., & Cummings, M. P.
(2015). Relationships within Cladobranchia (Gastropoda: Nudibranchia)
based on RNA-Seq data: an initial investigation. Royal Society
Open Science , 2 (9), 150196. doi: 10.1098/rsos.150196
Goodheart, J. A., Bazinet, A. L., Valdés, Á., Collins, A. G., &
Cummings, M. P. (2017). Prey preference follows phylogeny: Evolutionary
dietary patterns within the marine gastropod group Cladobranchia
(Gastropoda: Heterobranchia: Nudibranchia). BMC Evolutionary
Biology , 17 , 221. doi: 10.1186/s12862-017-1066-0
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D.
A., Amit, I., … Regev, A. (2010). Full-length transcriptome
assembly from RNA-Seq data without a reference genome. Nature
Biotechnology , 29 , 644–652. doi: 10.1038/nbt.1883
Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J.,
Tomkins-Tinch, C. H., … Team, T. B. (2018). Bioconda: Sustainable
and comprehensive software distribution for the life sciences.Nature Methods , 15 (7), 475–476. doi:
10.1038/s41592-018-0046-7
Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D.,
Bowden, J., … Regev, A. (2013). De novo transcript
sequence reconstruction from RNA-seq using the Trinity platform for
reference generation and analysis. Nature Protocols , 8 (8),
1494–1512. doi: 10.1038/nprot.2013.084
Harasewych, M. G., Adamkewicz, S. L., Blake, J. A., Saudek, D., Spriggs,
T., & Bult, C. J. (1997). Neogastropod phylogeny: A molecular
perspective. Journal of Molluscan Studies , 63 (3),
327–351. doi: 10.1093/mollus/63.3.327
Harasewych, M. G., Adamkewicz, S. L., Plassmeyer, M., & Gillevet, P. M.
(1998). Phylogenetic relationships of the lower Caenogastropoda
(Mollusca, Gastropoda, Architaenioglossa, Campaniloidea, Cerithioidea)
as determined by partial 18S rDNA sequences. Zoologica Scripta ,27 (4), 361–372. doi: 10.1111/j.1463-6409.1998.tb00467.x
Harasewych, M. G., & McArthur, A. G. (2000). A molecular phylogeny of
the Patellogastropoda (Mollusca: Gastropoda). Marine Biology ,137 (2), 183–194. doi: 10.1007/s002270000332
Haszprunar, G. (1985). The Heterobranchia: a new concept of the
phylogeny and evolution of the higher Gastropoda. Journal of
Zoological Systematics and Evolutionary Research , 23 , 15–37.
doi: 10.1111/j.1439-0469.1985.tb00567.x
Huang, W., Li, L., Myers, J. R., & Marth, G. T. (2012). ART: A
next-generation sequencing read simulator. Bioinformatics ,28 (4), 593–594. doi: 10.1093/bioinformatics/btr708
Jackman, S., Vandervalk, B., Mohamadi, H., Chu, J., Yeo, S., Hammond,
S., … Birol, I. (2017). ABySS 2.0: resource-efficient assembly of
large genomes using a Bloom filter. Genome Research , 27 ,
768–777.
Jörger, K. M., Stöger, I., Kano, Y., Fukuda, H., Knebelsberger, T., &
Schrödl, M. (2010). On the origin of Acochlidia and other enigmatic
euthyneuran gastropods, with implications for the systematics of
Heterobranchia. BMC Evolutionary Biology , 10 (1), 323. doi:
10.1186/1471-2148-10-323
Kandel, E. R. (1979). Behavioral biology of Aplysia. A
contribution to the comparative study of opisthobranch molluscs (WH
Freeman). San Francisco: WH Freeman.
Kano, Y., Brenzinger, B., Nützel, A., Wilson, N. G., & Schrödl, M.
(2016). Ringiculid bubble snails recovered as the sister group to sea
slugs (Nudipleura). Scientific Reports , 6 , 30908. doi:
10.1038/srep30908
Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment
software version 7: Improvements in performance and usability.Molecular Biology and Evolution , 30 (4), 772–780. doi:
10.1093/molbev/mst010
Keul, N., Peijnenburg, K. T. C. A., Andersen, N., Kitidis, V., Goetze,
E., & Schneider, R. R. (2017). Pteropods are excellent recorders of
surface temperature and carbonate ion concentration. Scientific
Reports , 7 , 12645. doi: 10.1038/s41598-017-11708-w
Klussmann-Kolb, A., & Dinapoli, A. (2006). Systematic position of the
pelagic Thecosomata and Gymnosomata within Opisthobranchia (Mollusca,
Gastropoda) - Revival of the Pteropoda. Journal of Zoological
Systematics and Evolutionary Research , 44 (2), 118–129. doi:
10.1111/j.1439-0469.2006.00351.x
Klussmann-Kolb, A., Dinapoli, A., Kuhn, K., Streit, B., & Albrecht, C.
(2008). From sea to land and beyond–new insights into the evolution
of euthyneuran Gastropoda (Mollusca). BMC Evolutionary Biology ,8 , 57. doi: 10.1186/1471-2148-8-57
Kocot, K. M., Cannon, J. T., Todt, C., Citarella, M. R., Kohn, A. B.,
Meyer, A., … Halanych, K. M. (2011). Phylogenomics reveals deep
molluscan relationships. Nature , 477 (7365), 452–456. doi:
10.1038/nature10382
Kocot, K. M., Halanych, K. M., & Krug, P. J. (2013). Phylogenomics
supports Panpulmonata: opisthobranch paraphyly and key evolutionary
steps in a major radiation of gastropod molluscs. Molecular
Phylogenetics and Evolution , 69 (3), 764–771. doi:
10.1016/j.ympev.2013.07.001
Kocot, K. M., Poustka, A. J., Stöger, I., Halanych, K. M., & Schrödl,
M. (2020). New data from Monoplacophora and a carefully-curated dataset
resolve molluscan relationships. Scientific Reports ,10 (1), 1–8. doi: 10.1038/s41598-019-56728-w
Kocot, K. M., Todt, C., Mikkelsen, N. T., & Halanych, K. M. (2019).
Phylogenomics of Aplacophora (Mollusca, Aculifera) and a solenogaster
without a foot. Proceedings of the Royal Society B: Biological
Sciences , 286 (1902), 20190115. doi: 10.1098/rspb.2019.0115
Korshunova, T., Fletcher, K., Picton, B., Lundin, K., Kashio, S. H. O.,
Sanamyan, N., … Martynov, A. (2020). The Emperor ’sCadlina , hidden diversity and gill cavity evolution new insights
for the taxonomy and phylogeny of dorid nudibranchs (Mollusca:
Gastropoda). Zoological Journal of the Linnean Society , 1–66.
Krug, P. J., Vendetti, J. E., & Valdés, Á. (2016). Molecular and
morphological systematics of Elysia Risso, 1818 (Heterobranchia:
Sacoglossa) from the Caribbean region. Zootaxa , 4148 (1),
1–137.
Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with
Bowtie 2. Nature Methods , 9 (4), 357–359. doi:
10.1038/nmeth.1923
Lemer, S., Bieler, R., & Giribet, G. (2019). Resolving the
relationships of clams and cockles: Dense transcriptome sampling
drastically improves the bivalve tree of life. Proceedings of the
Royal Society B: Biological Sciences , 286 (1896), 20182684. doi:
10.1098/rspb.2018.2684
Lemer, S., González, V. L., Bieler, R., & Giribet, G. (2016). Cementing
mussels to oysters in the pteriomorphian tree: A phylogenomic approach.Proceedings of the Royal Society B: Biological Sciences ,283 (1833), 20160857. doi: 10.1098/rspb.2016.0857
Lemmon, A. R., Emme, S. A., & Lemmon, E. M. (2012). Anchored hybrid
enrichment for massively high-throughput phylogenomics. Systematic
Biology , 61 (5), 727–744. doi: 10.1093/sysbio/sys049
Lemmon, A. R., & Lemmon, E. M. (2012). High-throughput identification
of informative nuclear loci for shallow-scale phylogenetics and
phylogeography. Systematic Biology , 61 (5), 745–761. doi:
10.1093/sysbio/sys051
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N.,
… 1000 Genome Project Data Processing Subgroup. (2009). The
Sequence alignment/map (SAM) format and SAMtools. Bioinformatics ,25 , 2078–2079.
Lindgren, A. R., & Anderson, F. E. (2018). Assessing the utility of
transcriptome data for inferring phylogenetic relationships among
coleoid cephalopods. Molecular Phylogenetics and Evolution ,118 , 330–342. doi: 10.1016/j.ympev.2017.10.004
Lu, X. T., Gu, Q. Y., Limpanont, Y., Song, L. G., Wu, Z. D., Okanurak,
K., & Lv, Z. Y. (2018). Snail-borne parasitic diseases: An update on
global epidemiological distribution, transmission interruption and
control methods. Infectious Diseases of Poverty , 7 (1),
1–16. doi: 10.1186/s40249-018-0414-7
Lunter, & Goodson. (2011). Stampy: a statistical algorithm for
sensitive and fast mapping of Illumina sequence reads. Genome
Research , 21 , 936–939.
Lydeard, C., & Cummings, K. S. (2019). Freshwater mollusks of the
world (C. Lydeard & K. S. Cummings, Eds.). Baltimore, MD: Johns
Hopkins University Press.
Malaquias, M. A. E., Berecibar, E., & Reid, D. G. (2009). Reassessment
of the trophic position of Bullidae (Gastropoda: Cephalaspidea) and the
importance of diet in the evolution of cephalaspidean gastropods.Journal of Zoology , 277 (2002), 88–97. doi:
10.1111/j.1469-7998.2008.00516.x
Malaquias, M. A. E., Mackenzie-Dodds, J., Bouchet, P., Gosliner, T., &
Reid, D. G. (2009). A molecular phylogeny of the Cephalaspideasensu lato (Gastropoda: Euthyneura): Architectibranchia redefined
and Runcinacea reinstated. Zoologica Scripta , 38 (1),
23–41. doi: 10.1111/j.1463-6409.2008.00354.x
McArthur, A. G., & Harasewych, M. G. (2003). Molecular systematics of
the major lineages of the Gastropoda. In C. Lydeard & D. Lindberg
(Eds.), Molecular Systematics and Phylogeography of Mollusks (pp.
140–160). Washington, D.C.: Smithsonian Books.
McCormack, J. E., Faircloth, B. C., Crawford, N. G., Gowaty, P. A.,
Brumfield, R. T., & Glenn, T. C. (2012). Ultraconserved elements are
novel phylogenomic markers that resolve placental mammal phylogeny when
combined with species-tree analysis. Genome Research ,22 (4), 746–754. doi: 10.1101/gr.125864.111.746
Medina, M., Lal, S., Vallès, Y., Takaoka, T. L., Dayrat, B. A., Boore,
J. L., & Gosliner, T. (2011). Crawling through time: transition of
snails to slugs dating back to the Paleozoic, based on mitochondrial
phylogenomics. Marine Genomics , 4 (1), 51–59. doi:
10.1016/j.margen.2010.12.006
Minh, B. Q., Nguyen, M. A. T., & Haeseler, A. von. (2013). Ultrafast
approximation for phylogenetic bootstrap. Molecular Biology and
Evolution , 30 , 1188–1195. doi:
http://dx.doi.org/10.1093/molbev/mst024
Moles, J., Avila, C., & Malaquias, M. A. E. (2019). Unmasking Antarctic
mollusc lineages: novel evidence from philinoid snails (Gastropoda:
Cephalaspidea). Cladistics , 35 (5), 487–513. doi:
10.1111/cla.12364
Neusser, T. P., Jörger, K. M., Lodde-Bensch, E., Strong, E. E., &
Schrödl, M. (2016). The unique deep sea—land connection: interactive
3D visualization and molecular phylogeny of Bathyhedyle bouchetin. sp. (Bathyhedylidae n. fam.)—the first panpulmonate slug from
bathyal zones. PeerJ , 4 , e2738. doi: 10.7717/peerj.2738
Nguyen, L. T., Schmidt, H. A., Von Haeseler, A., & Minh, B. Q. (2015).
IQ-TREE: A fast and effective stochastic algorithm for estimating
maximum-likelihood phylogenies. Molecular Biology and Evolution ,32 (1), 268–274. doi: 10.1093/molbev/msu300
Oskars, T. R., Bouchet, P., & Malaquias, M. A. E. (2015). A new
phylogeny of the Cephalaspidea (Gastropoda: Heterobranchia) based on
expanded taxon sampling and gene markers. Molecular Phylogenetics
and Evolution , 89 , 130–150. doi: 10.1016/j.ympev.2015.04.011
Oskars, T. R., Too, C. C., Rees, D., Mikkelsen, P. M., Willassen, E., &
Malaquias, M. A. E. (2019). A molecular phylogeny of the gastropod
family Haminoeidae sensu lato (Heterobranchia: Cephalaspidea): a
generic revision. Invertebrate Systematics , 33 , 426–472.
Pabst, E. A., & Kocot, K. M. (2018). Phylogenomics confirms monophyly
of Nudipleura (Gastropoda: Heterobranchia). Journal of Molluscan
Studies , 84 (3), 259–265. doi: 10.1093/mollus/eyy013
Padula, V., Bahia, J., Stöger, I., Camacho-García, Y., António, M.,
Malaquias, E., … Schrödl, M. (2016). A test of color-based
taxonomy in nudibranchs: Molecular phylogeny and species delimitation of
the Felimida clenchi (Mollusca: Chromodorididae) species complex.Molecular Phylogenetics and Evolution , 103 , 215–229. doi:
10.1016/j.ympev.2016.07.019
Passamaneck, Y. J., Schander, C., & Halanych, K. M. (2004).
Investigation of molluscan phylogeny using large-subunit and
small-subunit nuclear rRNA sequences. Molecular Phylogenetics and
Evolution , 32 , 25–38. doi: 10.1016/j.ympev.2003.12.016
Peijnenburg, K. T. C. A., Janssen, A. W., Wall-palmer, D., Goetze, E.,
Maas, A., Todd, J. A., & Marlétaz, F. (2019). The origin and
diversification of pteropods predate past perturbations in the Earth’s
carbon cycle. BioRxiv . doi: https://doi.org/10.1101/813386
Quinlan, A. R., & Hall, I. M. (2010). BEDTools: a flexible suite of
utilities for comparing genomic features. Bioinformatics ,26 , 841–842.
Rambaut, A. (2014). Figtree, a graphical viewer of phylogenetic
trees . Retrieved from https://github.com/rambaut/figtree
Rohland, N., & Reich, D. (2012). Cost-effective, high-throughput DNA
sequencing libraries for multiplexed target capture. Genome
Research , 22 (5), 939–946. doi: 10.1101/gr.128124.111
Schrödl, M., Jörger, K. M., Klussmann-Kolb, A., & Wilson, N. G. (2011).
Bye bye “Opisthobranchia”! a review on the contribution of mesopsammic
sea slugs to euthyneuran systematics. Thalassas , 27 (2),
101–112.
Sharma, P., & Giribet, G. (2009). Sandokanid phylogeny based on eight
molecular markers-The evolution of a southeast Asian endemic family of
Laniatores (Arachnida, Opiliones). Molecular Phylogenetics and
Evolution , 52 (2), 432–447. doi: 10.1016/j.ympev.2009.03.013
Smith, S. A., Wilson, N. G., Goetz, F. E., Feehery, C., Andrade, S. C.
S., Rouse, G. W., … Dunn, C. W. (2011). Resolving the
evolutionary relationships of molluscs with phylogenomic tools.Nature , 480 (7377), 364–367. doi: 10.1038/nature10526
Song, L., & Florea, L. (2015). Rcorrector: Efficient and accurate error
correction for Illumina RNA-seq reads. GigaScience , 4 (1),
1–8. doi: 10.1186/s13742-015-0089-y
Talavera, G., & Castresana, J. (2007). Improvement of phylogenies after
removing divergent and ambiguously aligned blocks from protein sequence
alignments. Systematic Biology , 56 , 564–577.
Tanner, A. R., Fuchs, D., Winkelmann, I. E., Gilbert, M. T. P., Pankey,
M. S., Ribeiro, Â. M., … Vinther, J. (2017). Molecular clocks
indicate turnover and diversification of modern coleoid cephalopods
during the Mesozoic Marine Revolution. Proceedings of the Royal
Society B: Biological Sciences , 284 (1850), 20162818. doi:
10.1098/rspb.2016.2818
Tavaré, S. (1986). Some probabilistic and statistical problems in the
analysis of DNA sequences. Lectures on Mathematics in the Life
Sciences , 17 , 57–86.
Tin, M. M. Y., Economo, E. P., & Mikheyev, A. S. (2014). Sequencing
degraded DNA from non-destructively sampled museum specimens for
RAD-tagging and low-coverage shotgun phylogenetics. PLoS ONE ,9 (5), e96793. doi: 10.1371/journal.pone.0096793
Vonnemann, V., Schrödl, M., Klussmann-Kolb, A., & Wägele, H. (2005).
Reconstruction of the phylogeny of the Opisthobranchia (Mollusca:
Gastropoda) by means of 18S and 28S rRNA gene sequences. Journal
of Molluscan Studies , 71 (2), 113–125. doi:
10.1093/mollus/eyi014
Wägele, H., Deusch, O., Händeler, K., Martin, R., Schmitt, V., Christa,
G., … Martin, W. (2011). Transcriptomic evidence that longevity
of acquired plastids in the photosynthetic slugs Elysia timidaand Plakobranchus ocellatus does not entail lateral transfer of
algal nuclear genes. Molecular Biology and Evolution ,28 (1), 699–706. doi: 10.1093/molbev/msq239
Wägele, H., & Klussmann-Kolb, A. (2005). Opisthobranchia (Mollusca,
Gastropoda) - more than just slimy slugs. Shell reduction and its
implications on defence and foraging. Frontiers in Zoology ,2 (3), 1–18. doi: 10.1186/1742-9994-2-3
Wägele, H., Klussmann-Kolb, A., Verbeek, E., & Schrödl, M. (2014).
Flashback and foreshadowing—a review of the taxon Opisthobranchia.Organisms Diversity & Evolution , 14 , 133–149. doi:
10.1007/s13127-013-0151-5
Wägele, H., & Willan, R. C. (2000). Phylogeny of the Nudibranchia.Zoological Journal of the Linnean Society , 130 , 83–181.
doi: 10.1006/zjls
Winnepenninckx, B., Backeljau, T., & De Wachter, R. (1996).
Investigation of molluscan phylogeny on the basis of 18S rRNA sequences.Molecular Biology and Evolution , 13 (10), 1306–1317. doi:
10.1093/oxfordjournals.molbev.a025577
WoRMS Editorial Board. (2020). World Register of Marine Species.
Available from. doi: 10.14284/170
Zaharias, P., Pante, E., Gey, D., Fedosov, A. E., & Puillandre, N.
(2020). Data, time and money: evaluating the best compromise for
inferring molecular phylogenies of non-model animal taxa.Molecular Phylogenetics and Evolution , 142 , 106660. doi:
10.1016/j.ympev.2019.106660
Zapata, F., Wilson, N. G., Howison, M., Andrade, S. C. S., Jörger, K.
M., Schrödl, M., … Dunn, C. W. (2014). Phylogenomic analyses of
deep gastropod relationships reject Orthogastropoda. Proceedings
of the Royal Society B: Biological Sciences , 281 , 20141739.
Zerbino, D. R., & Birney, E. (2008). Velvet: algorithms for de novo
short read assembly using de Bruijn graphs. Genome Research ,
821–829. doi: 10.1101/gr.074492.107