Phylogeny of Serpulidae (Annelida, Polychaeta) Inferred from Morphology and DNA Sequences, with a New Classification
Abstract
:1. Introduction
2. Materials and Methods
2.1. Taxa Used in This Study and Morphological Matrix
2.2. DNA Extraction, Amplification, and Sequencing
2.3. Phylogenetic Analyses
2.3.1. Morphology Only Dataset
2.3.2. Molecular Dataset
2.3.3. Molecular + Morphology Dataset
3. Results
3.1. Morphology Only Dataset
3.2. Molecular Only Dataset
3.3. Molecular + Morphology Dataset
3.4. Transformations
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
- Body symmetry: symmetrical—0, asymmetrical—1.
- Chaetal inversion: complete—0, incomplete—1.
- Radiolar lobes: fused—0, separate—1.
- Inter-radiolar membrane: absent—0, present —1.
- Radiolar eyespots: absent—0, present—1.
- Arrangements of radioles: in semi-circles—0, pectinately—1, in spiral—2.
- Radiolar stylodes: present—0, absent—1.
- Tube material: mucous—0, calcareous—1.
- Tube keels: absent—0, present—1.
- Tube (semi)circular in cross-section: no—0, yes—1.
- Tube triangular in cross-section: no—0, yes—1.
- Tube trapezoid in cross-section: no—0, yes—1.
- Tube quadrangular in cross-section: no—0, yes—1.
- Granular overlay: absent—0, present—1.
- Tube wall transparency: completely opaque—0, with outer hyaline and inner opaque layer—1, completely hyaline—2.
- Tube coiling: straight or irregular—1, spirally coiled—2.
- Colonies due to asexual budding: absent—0, present—1.
- Adult tube attachment: attached—0, unattached—1.
- Internal tube structures: absent—0, present—1.
- Tabulae: absent—0, present—1.
- Colour of opaque tubes: white opaque—0, coloured—2.
- Operculum: absent—0, present—1.
- Pseudoperculum: absent—0, present—1.
- Pseudoperculum: borne on pinnulated radiole—0, borne on smooth short radiole—1.
- Opercular reinforcement: absent—0, present—1.
- Chitinous reinforcement: absent—0, present—1.
- Calcareous reinforcement: absent—0, present—1.
- Thickened cuticle: absent—0, present—1.
- Chitinous opercular reinforcement: without spines—0, with spines—1.
- Chitinous endplate: flat opercular plate or concave—0, elongated opercular cap—1, multi-tiered structure—2.
- Basal processes below operculum: absent—0, present—1.
- Serpula-type operculum: absent—0, present—1.
- Verticil on Serpula-type operculum: absent—0; present—1
- Type of calcareous opercular reinforcement: operculum infested with calcareous flakes—1, calcareous deposits forming distal plate—2, entirely calcified operculum—3.
- Calcareous opercular spines: absent—0, non-movable—1, movable—2.
- Calcareous opercular talon: absent—0, short, embedded in opercular ampulla—1, long, continues into opercular peduncle—2.
- Opercular constriction: operculum gradually merges into peduncle without constriction—0, operculum separated from the peduncle by a constriction—1.
- Ontogeny of operculum: indirect—0, direct—1.
- The operculum-bearing radiole is not different from all other radioles—0, operculum-bearing radiole is modified into a thickened peduncle—1.
- Peduncle smooth, without pinnules—0, peduncle with pinnules—1.
- Distal peduncular wings: absent—0, present—1.
- Proximal peduncular wings: absent—0, present—1.
- Insertion of the opercular peduncle: as second dorsal radiole—0, as the first radiole—1, at the base of radiolar crown, median insertion covering several opercular radioles—2.
- Peduncle cross-section: circular—0, triangular—1, flattened—2.
- Peduncle width: as wide as normal radioles—0, wider than normal radioles—1, much wider than normal radioles—2.
- Peduncle surface texture: smooth—0, wrinkled—1.
- Collar: unlobed—0, trilobed—1.
- Collar tonguelets: absent—0, present—1.
- Chaetae on the collar segment (collar chaetae): absent—0, present—1.
- Special collar chaetae: absent—0, with basal modification—1, with distal modification—2.
- Special fin-and-blade collar chaetae: absent—0, present—1
- Special bayonet collar chaetae: absent—0, present—1.
- Special Spirobranchus collar chaetae: absent—0, present—1.
- Thoracic membranes: absent—0, present—1.
- Thoracic membranes end: short, second segment—0, mid-thorax—1, end of thorax—2, form apron—3.
- Thoracic Apomatus chaetae: absent—0, present—1.
- Thoracic uncini rasp-shaped: absent—0, present—1.
- Thoracic uncini saw-to-rasp: absent—0, present—1.
- Thoracic uncini saw-shaped: absent—0, present—1.
- Anterior tooth of thoracic uncini pointed: absent—0, present—1.
- Anterior tooth of thoracic uncini blunt elongated, with rows of teeth implanted over almost entire length of peg (Protula type): absent—0, present—1.
- Anterior tooth of thoracic uncini blunt rounded: absent—0, present—1.
- Anterior tooth of thoracic uncini blunt flattened, often gouged underneath: absent—0, present—1.
- Number of teeth in thoracic uncini in profile: < 8–0; 8–19–1; > 20–2.
- Number of uncinigerous thoracic segments: seven—0, six—1, five—2, four—3, three—4.
- Variable number of thoracic uncinigerous chaetigers: no—0, yes—1.
- Ventral arrangement of thoracic uncini: parallel, not forming triangular depression—0, converging posteriorly forming triangular depression—1, fused—2.
- Achaetous region in the beginning of abdomen: absent—0, present—1.
- Abdominal chaetae capillary: no—0, yes—1.
- Abdominal chaetae flat trumpet-shaped: no—0, yes—1.
- Abdominal chaetae true trumpet shaped: no—0, yes—1.
- Abdominal chaetae flat geniculate: no—0, yes—1.
- Abdominal chaetae acicular: no—0, yes—1.
- Posterior glandular pad: absent—0, present—1.
- Long capillary chaetae in posterior abdominal segments: absent—0, present—1.
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Species | Vouchers | 28S | 18S | Histone H3 | Cytochrome b |
---|---|---|---|---|---|
Apomatus globifer | ZMA V.Pol. 5250 | EU195362 | EU195378 | OQ397982 | OQ427448 |
Apomatus sp. | FMNH 5201 | OQ389662 | OQ379428 | OQ397983 | OQ427449 |
Apomatus voightae | FMNH 6217 | OQ389663 | GU441856 | - | OQ427450 |
Bathyditrupa hovei | ZMA V.Pol 5325 | - | - | - | - |
Bathyvermilia eliasoni | FMNH 6189 | - | GU441857 | - | - |
Chitinopoma serrula | SAM E3524 | EU195350 | DQ317112 | OQ397984 | - |
Chitinopomoides wilsoni | ZMA V.Pol. 3166 | - | - | - | - |
Crucigera inconstans | SAM E3525 | EU184071 | DQ317113 | - | EU190464 |
Crucigera tricornis | SAM E3587 | EU184067 | EU184056 | - | EU190474 |
Crucigera zygophora | SAM E3503 | DQ242577 | DQ242543 | EF192929 | EU190470 |
Dasynema chrysogyrus | AM W.45087 | OQ397664 | OQ379429 | - | - |
Ditrupa arietina | SAM E3527 | EU195351 | DQ317114 | EF192933 | - |
Ficopomatus enigmaticus | SAM E3356 | EU195373 | DQ317115 | OQ427487 | OQ427451 |
Ficopomatus macrodon | SAM E3618 | EU167535 | EU167532 | OQ412612 | KP863778 |
Ficopomatus miamiensis | SAM E3617 | EU167534 | EU167531 | OQ397989 | KP863779 |
Filograna implexa | SAM E3528 | EU195347 | DQ317116 | - | OQ427452 |
Filogranella elatensis | SAM E3661 | EU195370 | EU195385 | - | - |
Filogranula stellata | SAM E3606 | EU195358 | EU195374 | OQ397985 | - |
Floriprotis sabiuraensis | SAM E3659 | EU195371 | EU195386 | - | OQ427453 |
Floriprotis sabiuraensis | SAM E7192 | OQ389665 | OQ379430 | - | OQ427454 |
Galeolaria caespitosa | SAM E3529 | OQ389666 | OQ379431 | OQ412631 | EU184054 |
Galeolaria hystrix | SAM E3526 | EU256550 | DQ314839 | OQ397988 | EU200441 |
Helicosiphon biscoeensis | SIO-BIC A4000 | OQ392408 | OQ379432 | OQ412613 | - |
Hyalopomatus mironovi | SAM E3728 | OQ651975 | GU063862 | MT468421 | MT468442 |
Hydroides elegans | SAM E3616 | EU195369 | EU195384 | OQ412614 | OQ427455 |
Hydroides ezoensis | SAM E3584 | EU184077 | EU184062 | - | OQ427456 |
Hydroides nikae | SAM E3530 | EU184072 | DQ317117 | - | EU190466 |
Hydroides minax | SAM E3597 | EU184074 | EU184063 | - | EU190475 |
Hydroides pseudouncinata | ZMA V.Pol. 5240 | EU184075 | DQ140403 | - | EU190467 |
Hydroides sanctaecrucis | SAM E3625 | EU184076 | EU184061 | - | - |
Hydroides trivesiculosa | SAM E3601 | EU184073 | EU184060 | OQ397992 | EU190476 |
Hydroides tuberculata | SAM E3596 | OQ389667 | EU184059 | - | EU190473 |
Janita fimbriata | AM W.42388 | OQ389668 | OQ379433 | - | OQ427457 |
Josephella marenzelleri | SAM E3620 | EU195359 | EU195375 | - | OQ427458 |
Laminatubus alvini | SAM E3531 | EU195355 | DQ317118 | OQ412616 | OQ427459 |
Marifugia cavatica | SAM E3612 | EU167533 | EU167530 | OQ397990 | OQ427460 |
Metavermilia acanthophora | SAM E3533 | EU195352 | DQ317119 | - | OQ427461 |
Microprotula ovicellata | ZMA V.Pol. 4046 | - | - | - | - |
Neomicrorbis azoricus | ZMA V.Pol. 3905 | - | - | - | - |
Neovermilia globula | SAM E3586 | EU195363 | EU195379 | - | - |
Spirodiscus grimaldii | ZMA V.Pol. 3906 | - | - | - | - |
Omphalopomopsis langerhansii | NHMWAN14552.2054 | - | - | - | - |
Paraprotis dendrova | SAM E3591 | EU195361 | EU195377 | - | - |
Paraprotis pulchra | SAM E3665 | OQ389669 | OQ379434 | OQ412629 | OQ427462 |
Paumotella takemoana | USNM 19432 | - | - | - | - |
Placostegus sp. | SAM E3589 | OQ397665 | OQ379435 | OQ412628 | - |
Placostegus tridentatus | SAM E3585 | EU195364 | OQ379436 | OQ412622 | - |
Pomatostegus actinoceras | AM W.42378 | OQ389670 | OQ379437 | - | - |
Pomatostegus stellatus | SAM E3607 | EU195367 | EU195382 | - | - |
Protis hydrothermica | SAM E3541 | EU195356 | DQ317122 | - | - |
Protis sp. | SAM E3727 | OQ389671 | OQ379438 | - | OQ427463 |
Protula bispiralis | SAM E3657 | OQ389672 | OQ379439 | OQ412609 | OQ427464 |
Protula tubularia | SAM E3542 | EU195349 | DQ317123 | EF192934 | OQ427465 |
Pseudochitinopoma occidentalis | SAM E3501 | DQ242575 | DQ242542 | OQ412626 | OQ427466 |
Pseudochitinopoma pavimentata | SAM E3660 | OQ397666 | OQ379440 | OQ412627 | OQ427467 |
Pseudovermilia occidentalis | SAM E3613 | EU195368 | EU195383 | - | OQ427468 |
Pyrgopolon ctenactis | SIO-BIC A25451 | OQ389673 | OQ379441 | OQ412625 | - |
Rhodopsis pusilla | SAM E3621 | EU195360 | EU195376 | OQ397987 | OQ427469 |
Salmacina sp. | SAM E3499 | EU256545 | DQ317126 | - | OQ427470 |
Semivermilia annehoggettae | SAM E3628 | OQ389674 | OQ379442 | - | OQ427471 |
Semivermilia elliptica | SAM E3664 | EU195372 | EU195387 | OQ397986 | OQ427472 |
Semivermilia lylevaili | SAM E3629 | OQ397667 | OQ389601 | - | - |
Serpula columbiana | SAM E3505 | DQ242576 | DQ317127 | - | EU190469 |
Serpula concharum | ZMA V.Pol. 5245 | EU184066 | DQ140408 | - | EU190468 |
Serpula jukesii | SAM E3536 | EU184069 | DQ317129 | - | EU190465 |
Serpula narconensis | SIO-BIC A3469 | OQ389676 | OQ379443 | OQ397991 | - |
Serpula uschakovi | SAM E3593 | EU184078 | EU184065 | - | EU190477 |
Serpula vermicularis | SAM E3537 | EU184070 | DQ317128 | - | EU190479 |
Serpula vittata | SAM E3594 | EU184079 | EU184064 | - | EU190471 |
Serpula watsoni | SAM E3595 | EU184068 | EU184057 | - | EU190472 |
Spiraserpula iugoconvexa | AM W.42093 | OQ389680 | OQ379444 | - | OQ427473 |
Spirobranchus akitsushima | ZMA V.Pol. 3201 | EU195365 | EU195380 | - | OQ427474 |
Spirobranchus corniculatus | ZMA V.Pol. 5247 | OQ389677 | OQ379446 | - | OQ427475 |
Spirobranchus corniculatus | SAM E3608 | EU195366 | EU195381 | - | OQ427476 |
Spirobranchus coronatus | SAM E3609 | OQ389678 | OQ379445 | OQ412624 | OQ427477 |
Spirobranchus kraussii | AM W.49977 | OQ397668 | MK308673 | OQ412619 | MK308658 |
Spirobranchus lima | SAM E3538 | EU256547 | DQ317130 | EF192930 | OQ427478 |
Spirobranchus richardsmithi | SAM E3610 | OQ389679 | OQ379447 | - | OQ427479 |
Spirobranchus taeniatus | SAM E3532 | EU195353 | DQ317120 | OQ412618 | OQ427480 |
Spirobranchus triqueter | SAM E3534 | EU195348 | DQ317121 | EF192932 | OQ427481 |
Tanturia zibrowii | ZMA V.Pol. 4668 | - | - | - | - |
Turbocavus secretus | USNM 251863 | - | OQ379448 | OQ412611 | OQ427483 |
Vermiliopsis infundibulum | ZMA V.Pol. 5248 | OQ389681 | DQ140411 | - | OQ427484 |
Vermiliopsis labiata | SAM E3543 | EU256549 | DQ317131 | - | OQ427485 |
Vermiliopsis pygidialis | SAM E3544 | EU256546 | DQ317132 | - | - |
Vermiliopsis striaticeps | SAM E3545 | EU256548 | DQ317133 | EF192931 | OQ427486 |
Vitreotubus digeronimoi | ZMA V.Pol.3907 | - | - | - | - |
Zibrovermilia zibrowii | AM W.46387 | - | - | - | - |
Protolaeospira tricostalis | SAM E3487 | DQ242606 | DQ318587 | EF192936 | - |
Romanchella quadricostalis | SAM E3491 | DQ242608 | DQ242559 | EF192935 | - |
Spirorbis tridentatus | SAM E3477 | DQ242602 | DQ242573 | OQ412623 | - |
Manayunkia athalassia | SAM E3518 | DQ209245 | EF116202 | EF192917 | - |
Schizobranchia insignis | GenBank | AY732225 | AY732222 | - | - |
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Kupriyanova, E.; ten Hove, H.A.; Rouse, G.W. Phylogeny of Serpulidae (Annelida, Polychaeta) Inferred from Morphology and DNA Sequences, with a New Classification. Diversity 2023, 15, 398. https://doi.org/10.3390/d15030398
Kupriyanova E, ten Hove HA, Rouse GW. Phylogeny of Serpulidae (Annelida, Polychaeta) Inferred from Morphology and DNA Sequences, with a New Classification. Diversity. 2023; 15(3):398. https://doi.org/10.3390/d15030398
Chicago/Turabian StyleKupriyanova, Elena, Harry A. ten Hove, and Greg W. Rouse. 2023. "Phylogeny of Serpulidae (Annelida, Polychaeta) Inferred from Morphology and DNA Sequences, with a New Classification" Diversity 15, no. 3: 398. https://doi.org/10.3390/d15030398