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An integrative taxonomic approach to the identification of three new New Zealand endemic earthworm species (Acanthodrilidae, Octochaetidae: Oligochaeta)

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This work adds three new species to the ca. 200 currently known from New Zealand. In Acanthodrilidae is Maoridrilus felix and in Octochaetidae are Deinodrilus gorgon and Octochaetus kenleei. All three are endemics that often have restrict-ed ranges; however, little is yet known of their distribution, ecology nor conservation status. DNA barcoding was conduct-ed, which is the first time that New Zealand endemic holotypes have been so characterized. The barcoding region COI (cytochrome c oxidase subunit 1) as well as the 16S rDNA region were sequenced using tissue from the holotype specimen to provide indisputable uniqueness of the species. These DNA sequences are publically available on GenBank to allow accurate cross checking to verify the identification of other specimens or even to identify specimens on the basis of their DNA sequences alone. Based on their 16S rDNA sequences, the position of the three newly described species in the phy-logeny of New Zealand earthworms was discussed. The description of new species using this approach is encouraged, to provide a user-friendly identification tool for ecologists studying diverse endemic faunas of poorly known earthworm species.
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Accepted by B. Sket: 28 Jun. 2011; published: 12 Aug. 2011
ZOOTAXA
ISSN 1175-5326 (print edition)
ISSN 1175-5334 (online edition)
Copyright © 2011 · Magnolia Press
Zootaxa 2994: 2132 (2011)
www.mapress.com/zootaxa/Article
21
An integrative taxonomic approach to the identification of
three new New Zealand endemic earthworm species
(Acanthodrilidae, Octochaetidae: Oligochaeta)
STEPHANE BOYER1,3, ROBERT J. BLAKEMORE2 & STEVE D. WRATTEN1
1Bio-Protection Research Centre, Lincoln University, New Zealand
2National Museum of Science and Nature in Tokyo, Japan
3Corresponding author. E-mail: stephane.boyer@lincoln.ac.nz
Abstract
This work adds three new species to the ca. 200 currently known from New Zealand. In Acanthodrilidae is Maoridrilus
felix and in Octochaetidae are Deinodrilus gorgon and Octochaetus kenleei. All three are endemics that often have restrict-
ed ranges; however, little is yet known of their distribution, ecology nor conservation status. DNA barcoding was conduct-
ed, which is the first time that New Zealand endemic holotypes have been so characterized. The barcoding region COI
(cytochrome c oxidase subunit 1) as well as the 16S rDNA region were sequenced using tissue from the holotype specimen
to provide indisputable uniqueness of the species. These DNA sequences are publically available on GenBank to allow
accurate cross checking to verify the identification of other specimens or even to identify specimens on the basis of their
DNA sequences alone. Based on their 16S rDNA sequences, the position of the three newly described species in the phy-
logeny of New Zealand earthworms was discussed.
The description of new species using this approach is encouraged, to provide a user-friendly identification tool for
ecologists studying diverse endemic faunas of poorly known earthworm species.
Key words: Morphological description, DNA barcoding, phylogeny, COI, 16S rDNA
Introduction
The definitive study of New Zealand earthworms by Ken Lee (1959) was updated and checklisted by Blakemore
(2004, 2006) as modified by Blakemore in Lee et al., (2000). While the enduring work by Lee (1959) listed
approximately 193 species, the current list has about 200 taxa with natives now given separate family status in
either Acanthodrilidae, Octochaetidae or Megascolecidae sensu Blakemore (2000).
Because of this high diversity, ecological studies focusing on New Zealand earthworms require the expertise of
a taxonomist for accurate identification of the species. Indeed, earthworm taxonomy is based on complexe and
variable morphological diagnostic characters, which require a high level of expertise (Pop et al., 2007).
Modern molecular-based species identification is a promising way for researchers with basic molecular knowl-
edge to identify earthworm species using barcoding regions of the genome (Pop et al., 2007). However, this
requires a comprehensive database of earthworm DNA sequences. More than 6,000 species of earthworm have
been named to date and this figure is continuously growing as illustrated in the current study. At the same time, the
Genbank database (http://www.ncbi.nlm.nih.gov/genbank/) contains barcoding sequences (COI) for only earth-
worm 600 taxa (i.e., 10% of the species), and for most of these (~400) the DNA description is not associated with
any morphological taxonomic description and no valid species name is provided.
Although thousands of described species are still requiring DNA barcoding, molecular ecologists are releasing
many barcoding sequences for new undescribed species, with little or no taxonomic support. Because of this imbal-
ance between the taxonomically described species and the ‘DNA barcoded’ species, earthworm DNA barcoding
can rarely be used for its original purpose: identifying species (Hebert et al., 2003). In ecological studies it is often
BOYER ET AL.
22 · Zootaxa 2994 © 2011 Magnolia Press
restricted to the determination of species richness in particular areas (e.g., Boyer & Wratten, 2010b), or the so-
called discovery of cryptic species (e.g., King et al., 2008 cf. Blakemore et al., 2010). However, this does not pro-
vide species names, so interpretation and comparison to other ecological studies is difficult.
This paper aims at combining morphological description and DNA barcoding techniques to achieve a better
taxonomic description of earthworm species. Such approach, using multiple and complementary perspectives to
delimit the units of life’s diversity is known as integrative taxonomy (Dayrat 2004). The adoption of integrative
taxonomy will allow ecologists to identify earthworm species with standard molecular techniques. Because DNA
analyses are directly conducted on the type specimen, this integrative approach also circumvents the release of spe-
cies DNA codes originating from mis-identified non-type specimens (Blakemore et al., 2010). In addition, by
inferring evolutionary history from DNA sequences, one can confirm that the taxonomical diagnostic on a new spe-
cies matches with its position in the phylogeny.
Classification follows Blakemore (2000); nomenclature follows ICZN (1999). In addition to the barcoding
region of COI, molecular analyses were also conducted on the 16S rDNA region, which has complementary taxo-
nomic value at genus and species level for earthworms (Pop et al., 2003). These two markers have been often used
in earthworm molecular ecology, protocols are easily accessible in the literature (e.g., Pop et al., 2003; Chang and
Chen, 2005; Huang et al., 2007; Pop et al., 2007; Chang et al., 2008; Blakemore et al., 2010; Boyer and Wratten
2010b). The 16S rDNA region was also chosen by Buckley et al. (2011) in their recent phylogenetic analysis of
New Zealand endemic earthworms. Because this study provides the only comprehensive dataset of DNA sequences
for New Zealand earthworms, it was necessary to use the same molecular marker to permit phylogenetic analysis of
the specimens described here.
Material and methods
Earthworms were collected by excavation and hand sorting of soil samples (20×20 ×20 cm) from the tussock grass-
land of ‘Happy Valley’ in the Upper Waimangaroa Valley, Buller Region, West Coast, New Zealand), on the ‘foot-
print’ of the proposed Cypress coal mine. Specimens were sketched, dissected and described under low power
microscope using the techniques and conventions noted in Blakemore (2002, 2008). Small tissue samples (muscu-
lar body wall) were taken from behind the clitellar region and placed in 98% ethanol for molecular analyses.
Genomic DNA was extracted using the DNeasy® Tissue Isolation Kit from Qiagen. Universal invertebrate 16S
mitochondrial DNA primers (LR-J-12887 and LR-N-13398, Simon et al. 1994) were used to amplify a ~500 base
pair fragment of DNA. Universal invertebrate COI mitochondrial DNA primers (LC01490 and HC02198, Folmer
et al. 1994) were used to amplify a ~650 base pair fragment of DNA.
The 25µl polymerase chain reaction (PCR) contained 5µl Qiagen Q solution, 2.5µl 10X buffer (Invitrogen),
2.5µl dNTPs [2.5mM], 1µl MgCl2 [25mM], 1µl Bovine Serum Albumin [10mg/ml], 0.5µl forward and 0.5µl
reverse primers [10µM], 0.3µl Invitrogen Taq DNA polymerase [5unit/µl], 1µl DNA template and 10.7µl nanopure
water. The thermocycler protocol consisted of an initial denaturation at 95°C (4 min), 35 cycles of denaturation at
94°C (1 m) annealation at 51°C (1 m) and elongation at 72°C (1.5 m), followed by a final elongation at 72°C (10
min). PCR products were purified (Qiagen Qiaquick© PCR purification kit), and sequenced using Big Dye Termi-
nator Cycle Sequencing Kit according to the manufacturers’ protocol (Applied Biosystems, CA, USA). DNA
sequences were submitted to the GenBank database (see accession numbers in results).
The 16S rDNA sequences obtained for the three newly described species were compared to similar sequences
obtained by Buckley et al. (2011). One representative for each major clade of New Zealand endemic earthworms
was included in the analysis (see Buckley et al. 2011). The evolutionary history was inferred using the Neighbor-
Joining method (Saitou & Mei 1987). The evolutionary distances were computed using the Maximum Composite
Likelihood method (Tamura et al. 2004) and are in the units of the number of base substitutions per site. Phyloge-
netic analyses were conducted in MEGA4 (Tamura et al. 2007).
Zootaxa 2994 © 2011 Magnolia Press · 23
INTEGRATIVE TAXONOMY FOR THREE NEW EARTHWORMS
Results
Acanthodrilidae Claus, 1880
Maoridrilus felix Blakemore sp. nov.
Material examined. Museum of New Zealand Te Papa Tongarewa W.002908 (Holotype). From the tussock grass-
land of ‘Happy Valley’ (Upper Waimangaroa Valley, Buller Region, West Coast, New Zealand). Collected by S.
Boyer, 2010. Mature, complete, fixed in ethanol 98% and placed in propylene glycol.
Etymology. Adjectival Latin for “Happy”, after the location name.
External characters. Body circular in anterior, squaring off in mid-body and dorsally canaliculate in the pos-
terior 50 or so segments. Pigment dark, especially dorsum chocolate brown with darker mid-dorsal stripe. Length
170 mm with 199 segments. Prostomium tanylobous. Setae lumbricine. Clitellum faintly marked 15-19,½20. Dor-
sal pores wanting. Nephropores, after the first few segments, alternate regularly between c and b lines with anterior
segmental distributions: 3–7c, 8 c or b, 9–10c, 11b, 12c, 13b, etc. Spermathecal pores in mid-ab lines in 7/8 and 8/
9. Female pores faint, just anterior to b setae on 14. Prostatic pores approximately in a lines on 17 and 19 with pro-
tuberant penial setae. Male pores not located within concave seminal grooves, although likely central between
retained ab setae. Genital markings absent, but setae ab on 16 with slight pale tumescence as on 20lhs. Genital
setae absent; penial setae longish, curving with spoon-shaped tips [one of their functions, if not primary function, is
to scrape out or disrupt any prior semen from spermathecal diverticula that often correspond in depth to the setal
length (see Blakemore 2000)].
Internal morphology. Pharyngeal mass anterior to 4/5. Septa mostly thin and translucent. Proventriculus wide
and S-shaped in 5. Gizzard muscular in 6. Dorsal blood vessel single thoughout. Heart paired in 10–13. Nephridia
holoic with long, sausage-shaped vesicles. Spermathecae in 8 and 9 each with a multiloculate diverticulum (insem-
inated) transcending anterior septum. Testes free, posterio-ventrally in 10 and 11. Seminal vesicles saccular, ante-
rio-dorsally in 11 and 12. Ovaries compact sheets in 13 with large oviducts; ovisacs not found. Prostates tubular in
17 and 19 exiting through muscular ducts with ectal penial setal sheathes and tendons. Vasa deferentia seen to 18.
Oesophagus dilated in 11–15 with blood vessels attaching dorsally but not saccular and not construed as calciferous
glands. Intestinal origin in 18. Typhlosole not detected to about 26. Gut contains colloidal organic matter.
Ecology: Lack of dorsal pores is more usually associated with a semi-aquatic habitat. Unidentified nematodes
were found near the prostates (cf. Yeates et al., 1985). Specimen was found under 10 to 20 cm of soil. Dark colou-
ration on the dorsum suggests at least partial surface exposure on topsoil, gut content suggests topsoil geophagy.
This species is likely to be anecic.
Remarks. Quintessentially Maoridrilus due to its alternating nephridiopores, this species appears unique in its
lack of dorsal pores (although more information is needed on several other congeners), gizzard in 6, lack of
oesophageal glands, and genital marking absence. Multiloculate spermathecae appear characteristic of the genus
and in the current species their form is almost identical to Maoridrilus thomsoni Benham, 1919: fig. 4 from
D’Urville Island in Cook Strait. Lee (1959) held this species, along with similar M. intermedius Michaelsen, 1923
and M. mauiensis Benham, 1904, as incertae sedis because original descriptions were inadequate. Permanence of
the name M. felix depends on redescription of M. thomsoni, however, the manifestly larger penial setae and lack of
oesophageal glands in 14–16 seem to separate the current species. Maoridrilus nelsoni Lee, 1959 differs in its pro-
static pores in b lines, and its prominent tuberculae pubertatis ventrally on segments 10 and 16. Maoridrilus uligi-
nosus (Hutton, 1877) differs, not least, in its paired dorsal blood vessel.
DNA sequences
COI, GenBank accession number HQ529282 (submitted 01 November 2010)
AAGATATTGGAACTCTATATTTCATTTTAGGTGTTTGGGCCGGTATAATTGGAGCTGGGATAAGATTATT
AATTCGAATTGAATTAAGACAGCCTGGTGCTTTTCTAGGGAGTGATCAACTATATAATACTATTGTCACT
GCCCACGCTTTTTTAATAATCTTTTTCTTAGTGATACCAGTATTTATCGGAGGATTCGGAAATTGGTTAC
TACCCCTAATACTTGGAGCACCTGACATGGCTTTTCCACGATTAAACAATATAAGATTTTGATTACTGCC
CCCATCTCTTATTCTCCTAGTTTCTTCCGCAGCCGTAGAAAAGGGGGCTGGAACAGGGTGAACTGTAT
BOYER ET AL.
24 · Zootaxa 2994 © 2011 Magnolia Press
ACCCCCCCTTAGCAAGCAATCTAGCTCATGCTGGACCCTCTGTAGATCTTGCAATCTTCTCCCTCCACC
TAGCTGGTGCCTCATCAATTTTAGGTGCTATTAATTTTATTACAACCGTTATTAATATGCGGTCAGTTGG
ATTACGGTTAGAGCGAGTACCACTATTCGTTTGAGCGGTATTAATTACAGTAGTATTACTACTCTTGTCC
CTACCAGTATTAGCCGGTGCTATCACCATATTACTAACAGACCGAAATTTAAATACATCATTTTTTGACC
CGTCAGGAGGGGGTGACCCAATTCTATATCAACACTTATTCTGATTTTTTG
16S, GenBank accession number HQ529285 (submitted 01 November 2010)
CAAAAACATTGCTTTTTGAATAACTATAAAAAGTAATTTCCTGCCCAGTGACAAAGTTAAACGGCCGC
GGAACCCTAACCGTGCAAAGGTAGCATAATCACTTGCCTATTAATTGTAGGCTAGAATGAACGGATGA
ACGAAATAGAGACTGTCTCAGTCAGCTCACTAAAAATTAACACATGCATGAAGAGTTGCAAATAAAGT
CGAAGGACAAGAAGACCCTATAGAGCTTTATTTTAACTATAGATACAACTATACAAAAATTCGGTTGGG
GCGACCAAGGACATAGAGAATATCAACCTAAACAAAAATGATAAATTAATCTATAAACTGACCCTTATA
AAGAACATAAAAATAAGCTACCTTAGGGATAACAGGCTAATCCTATTTGAGAGTCCATATCTACAATAG
GGTTTGGCACCTCGATGTTGGCTTAGGGTATCAATATGGCGCAAAAGTTGTATGAAGATGGTTTGTTCA
ACCAGTAACTCCCTACATGAGCTGA
Octochaetidae Michaelsen, 1900 sensu Blakemore, 2000
Deinodrilus gorgon Blakemore sp. nov.
Material examined. Museum of New Zealand Te Papa Tongarewa W.002909 (Holotype). From the tussock grass-
land of “Happy Valley” (Upper Waimangaroa Valley, Buller Region, West Coast, New Zealand). Collected by S.
Boyer, 2010. Mature, posterior amputee, fixed in ethanol 98% and placed in propylene glycol.
Etymology. Noun alluding to Greek mythical monsters with sharp fangs, staring eyes and, similar perhaps to
the ring of diverticula on each spermatheca – a belt of serpents.
External characters. Body circular in anterior. Pigment dark, especially dorsum with paler setal auriolae; cli-
tellum and male field white. Length 55+ mm with 73+ segments (amputee). Prostomium tanylobous. Setae per-
ichaetine, 12 per segment, evenly spaced. Clitellum pale, tumid 13–16. Dorsal pores from 10/11. Nephropores
not found. Spermathecal pores in b lines in 7/8 and 8/9, small but gaping. Female pores anterio-ventral to a setae on
14 in common field. Prostatic pores at b on 17 and 19. Male pores within concave seminal grooves lateral to b.
Genital markings as large eye-shaped papillae paired on 10; with smaller markings on 13rhs, 16 rhs and two addi-
tional pairs on 18 as figured. Genital and penial setae not found.
Internal morphology. Pharyngeal mass anterior to 4/5. Septa 8/9–10/11 with some thickening. Gizzard mus-
cular in 6 (weak septum 6/7 can be carefully teased off to base). Dorsal blood vessel doubled. Heart paired in 10–
13. Nephridia meroic; equatorial forests especially obvious around clitellar segments. Spermathecae in 8 and 9
each with a thin duct to multiple, finger-like diverticula, five per spermatheca (inseminated) surrounding duct from
where it thickens before reaching yellowish, knob-like ampulla. Testes free, posterio-ventrally in 10 and 11. Semi-
nal vesicles small saccular in 9 (vestigial?) and larger racemose anterio-dorsally in 11 and 12. Ovaries fan-shaped
in 13 with several strings of largish eggs; ovisacs vestigial in 14. Prostates compacted tubular in 17 and 19 exiting
through muscular ducts. Vasa deferentia seen to exit unceremoniously in 18. Oesophagus dilated in 15–17 but lack-
ing internal lamellae and thus not construed as calciferous glands. Intestinal origin in 18. Typhlosole thin, lamellar
becoming deeper from 19. Gut contains colloidal soil and organic matter.
Ecology. Specimen was found under 10 to 20 cm of soil. Dark colouration suggests at least partial surface
exposure on topsoil, gut content suggests topsoil geophagy. This species is likely to be anecic.
Remarks. Of the eight currently known Deinodrilus species, only two have tanylobous prostomia: D. gracilis
Ude, 1905 from Stephen Island and D. parvus Lee, 1959 from Mangamuku Range. Both also have 5 or 6 spermath-
ecal diverticula however, D. gracilis has copulatory setae, oesophageal glands and intestine from 19; while D. par-
vus has a saddle-shaped clitellum in 12–16, and all its reproductive pores are in a or ab. Further, their gizzards are
in 6–7 and 5, respectively, rather than single in 6 as in the current species. D. montanus Lee, 1959 from Rimutaka
Range is similar to D. parvus and differs for similar reasons. The current species appears unique in the distribution
of its eye-like genital markings that are especially noticeable on segment 10.
Zootaxa 2994 © 2011 Magnolia Press · 25
INTEGRATIVE TAXONOMY FOR THREE NEW EARTHWORMS
FIGURE 1. Maoridrilus felix Holotype showing dorsal view of prostomium and pygidium, and ventral view of body with sper-
mathecae and prostates in situ; nephridium of 6lhs is as seen from dorsal dissection; enlarged penial seta 19rhs.
BOYER ET AL.
26 · Zootaxa 2994 © 2011 Magnolia Press
FIGURE 2. Deinodrilus gorgon Holotype showing dorsal view of prostomium and ventral view of body with spermathecae
and prostates in situ; gizzard is in 6.
Zootaxa 2994 © 2011 Magnolia Press · 27
INTEGRATIVE TAXONOMY FOR THREE NEW EARTHWORMS
DNA sequences:
COI, GenBank accession number HQ529284 (submitted 01 November 2010)
AAAGATATTGGAACACTATATTTTATCTTAGGAGTTTGAGCAGGTATGATCGGAGCCGGAATAAGACTA
TTAATCCGAATCGAATTGAGCCAACCTGGAGCCTTCCTAGGAAGCGATCAATTATATAATACAATTGTT
ACAGCACACGCATTTCTAATAATCTTCTTTTTAGTAATACCAGTATTTATTGGGGGGTTTGGAAACTGAC
TACTTCCATTAATACTAGGAGCACCAGACATAGCATTTCCACGACTTAATAATATAAGATTCTGATTGTT
GCCCCCATCTCTAATTCTTCTAGTATCCTCTGCAGCCGTCGAAAAAGGAGCTGGAACAGGATGAACAG
TATATCCTCCCCTAGCTAGAAATATTGCCCATGCTGGTCCATCAGTAGATCTAGCAATTTTCTCACTCCA
TCTAGCAGGTGCATCATCTATTTTAGGAGCAATCAACTTTATTACAACTGTAATTAATATGCGATGAACA
GGTCTACGACTAGAGCGAGTTCCTTTATTTGTATGAGCTGTATTAATTACAGTAGTACTTCTTCTTCTAT
CCTTACCAGTACTAGCTGGTGCCATTACCATACTCCTTACAGACCGAAATCTAAATACCTCATTCTTTGA
TCCCTCAGGAGGGGGAGATCCCATTCTATATCAACACTTATTTTGATTTTTTG
16S, GenBank accession number HQ529287 (submitted 01 November 2010)
AAAAACATTGCTTTATGAAAAACCATATAAAGTAATTCCTGCCCAGTGACAACTGTTCAACGGCCGCG
GTATCCTAACCGTGCAAAGGTAGCATAATAACTTGCCTATTAATTGTAGGCTAGAATGAACGGATAAAC
GAAATAAAAGCTGTCTCAGTCAGCAATCCTAAAAATTAATATCTACACGAAGAATTGTAGATAAAGTC
GAAGGACAAGAAGACCCTATAGAGCTTTATTTAAAATCTAGATACTCTAGACAAAAATTCGGTTGGGG
CGACCAAGGGCACTATAAAACACCCTGAAAAAAAAAGATATATTAATCTACATGAATGACCCTAATAA
GATCACAAGATCAAGCTACCTTAGGGATAACAGGCTAATCCTATTTAAGAGTCCATATCAATAATAGGG
TTTGGCACCTCGATGTTGGCTTAGGGTATCGATATAGCGCAAAAGTTATACATGGATGGTTTGTTCAAC
CAATAATACCCTACATGAGCTG
Octochaetus kenleei Blakemore sp. nov.
Material examined. Museum of New Zealand Te Papa Tongarewa W.002910 (Holotype). From the tussock grass-
land of “Happy Valley” (Upper Waimangaroa Valley, Buller Region, West Coast, New Zealand). Collected by S.
Boyer, 2010. Mature, complete, fixed in ethanol 98% and placed in propylene glycol.
Etymology. In patronymic tribute to the foremost earthworm eco-taxonomist of New Zealand, Dr Kenneth
Earnest Lee (1927–2007).
External characters. Body circular but posterior slightly square. Pigment lacking and generally fair. Length
220 mm with 270 segments. Prostomium prolobous. Setae lumbricine, 8 per segment, evenly spaced. Clitellum not
well marked, perhaps in some or all of 14–20. Dorsal pores from 14/15, small. Nephropores not clear, some possi-
bly in c and d lines or rather irregular. Spermathecal pores segmental, lateral to b lines on 8 and 9 on small mounds.
Female pores just anterior to setae a on 14. Prostatic pores at b on 17 and 19. Male pores within concave seminal
grooves lateral to b. Genital markings as small lens-shaped hollows paired in 8/9 and 9/10 near b lines and in 15/16
in a lines with a unilateral marking in 18/19lhs; area bb in 19/20–22/23 tumid. Genital and penial setae not found.
Internal morphology. Pharyngeal mass anterior to 4/5. Septa 8/9–10/11 with some thickening. Gizzards mus-
cular in 5 and 6. Dorsal blood vessel appears single on gizzards but is doubled from 7 posteriorly. Heart paired in
10–13. Nephridia meroic as a few (ca. 4 per side) small tufted clusters in each segment. Spermathecae in 8 and 9
saccular each with small discrete and interlocular diverticula (inseminated) ringing exit. Testes free, posterio-ven-
trally in 10 and 11. Seminal vesicles large finely racemose anterio-dorsally in 11 and 12. Ovaries composed of sev-
eral strings of largish eggs in 13; ovisacs absent. Prostates tubular in 17 and 19 exiting through narrow ducts. Vasa
deferentia exits in 18. Oesophagus dilated as annular calciferous gland in 17 with several internal lamellae but not
especially vascularized. Intestinal origin in 20 (valval in 19). Typhlosole large inverted T-shape developing from
21. Gut contains colloidal soil with a few quartz grits and woody fragments.
Ecology. Specimen was found under 10 to 20 cm of soil. Large size, pale colouration and gut contents suggest
subsoil geophagy. This species is likely to be endogeic.
Remarks. The current species is compared to Octochaetus thomasi Beddard, 1892, widespread in the Canter-
bury Plains, that is the only other congener known to have gizzards in 5–6. As with all other members, it has sper-
mathecal pores in 7/8/9 and on this character alone the current species is differentiated. Neodrilus
campestris(Hutton, 1877) from Dunedin has segmental spermathecal pores (on 8) but differs, not least, by qualify-
ing for inclusion in Acanthodrilidae due to its holoic nephridia.
BOYER ET AL.
28 · Zootaxa 2994 © 2011 Magnolia Press
FIGURE 3. Octochaetus kenleei Holotype showing dorsal view of prostomium and pygidium, and ventral view of body with
spermathecae and prostates in situ; gizzards are in 5 and 6 and calciferous gland is in 17; enlarged 9rhs spermatheca shows
nephridia on either side.
Zootaxa 2994 © 2011 Magnolia Press · 29
INTEGRATIVE TAXONOMY FOR THREE NEW EARTHWORMS
DNA sequences
COI, GenBank accession number HQ529283 (submitted 01 November 2010)
AAAGATATTGGAACCCTTTACTTCATTCTAGGAGTCTGAGCAGGAATAATCGGTGCAGGAATAAGACT
TCTTATTCGTATCGAGCTCAGCCAACCTGGAGCCTTTTTAGGAAGAGACCAACTATATAATACAATCGT
AACCGCTCATGCATTTTTAATAATTTTCTTTCTAGTAATACCAGTATTTATTGGAGGATTTGGAAACTGA
TTACTACCTTTAATACTAGGAGCCCCCGACATAGCTTTTCCACGACTAAATAATATAAGATTCTGACTAT
TACCGCCATCATTAATCTTACTAGTCTCTTCCGCGGCCGTTGAAAAAGGTGCTGGAACAGGATGAACA
GTATATCCACCTCTTGCTAGAAATATGGCACATGCAGGACCATCAGTAGATCTCGCAATTTTTTCATTAC
ATTTAGCAGGTGCCTCATCAATTTTAGGGGCCATCAACTTTATTACAACTGTAATTAATATACGATGAGC
AGGATTACGACTAGAACGAGTACCACTATTTGTATGAGCTGTTGTAATTACGGTAGTTCTTCTATTATTA
TCCTTACCAGTTCTAGCAGGAGCTATTACTATACTTTTAACAGATCGAAACCTCAATACTTCATTCTTTG
ACCCATCTGGAGGAGGAGATCCAATTTTATATCAACATCTATTTTGATTTTT
16S, GenBank accession number HQ529286 (submitted 01 November 2010)
AAAACATTGCTTTCTGAAATTTTATAGAAAGTAATTCCTGCCCAGTGACAACTGTTCAACGGCCGCGG
TATCCTAACCGTGCAAAGGTAGCATAATAACTTGCCTATTAATTGTAGGCTAGAATGAACGGGTAAACG
AAATAAGAACTGTCTCAATCAGTTAATATAAAAATTAATATCTGTACGAAGAATTACAGATACAGTTGA
AGGACAAGAAGACCCTATAGAGCTTTATTTTAAACATATATTAAAATATGTAAAAATTCGGTTGGGGCG
ACCCAGGAATTTATAAAACATCCTAAAAAACAAAGATCTATAAATCTATTAAATGACCCTTATTAAGATC
AAAAGACAAAGCTACCTTAGGGATAACAGGCTAATCCTATTTAAGAGTCCATATCAATAATAGGGTTTG
GCACCTCGATGTTGGCTTAGGGTATCAATATAGCGCAAAAGTTATATAAAGATGGTTTGTTCAACCAAT
TATTCCCTACATGAGCTGA
Phylogeny
Taxonomical diagnostic for the three newly described species matches with the main clades in the phylogeny of
New Zealand earthworms. The phylogenetic tree in Fig. 4 was built using the DNA sequence of one specimen for
each of the main New Zealand clades (Buckley et al. 2011). Within the clades of interest, specimens that were most
closely related to the species described here were selected.
D. gorgon was very close to a specimen of D. montanus (~2% of difference on the 16S NJ tree). This specimen
of D. montanus was collected from the Denniston area, about 10km South-West from Happy Valley (Buckley et al.
2011). Important geographical and DNA proximity between D. gorgon and D. montanus could indicate a potential
synonymy. However, the fact that D. gorgon is tanylobous and the presence of eye-like genital markings on seg-
ment 10 are sufficient to consider it as a new species. Direct morphological comparison between these two speci-
mens and the holotype of D. montanus (Lee 1959) could help confirming these results.
Among the specimens sequenced by Buckley at al. (2011) the one closest to O. kenleei was Octhochaetus n.
sp., collected from the Okarito region (about 220 km South-West of Happy Valley). Genetic distance between those
two specimens was less than 2%. They are therefore likely to be the same species.
M. felix was genetically quite different to any of the species sequenced by Buckley et al. (2011). The specimen
that was closest to M. felix was M. parkeri, collected from the Chinamans Bluff (about 430 km South-West from
Happy Valley).
Discussion
In this study, morphology-based taxonomy and molecular techniques were used to describe in a taxonomically inte-
grated way three new species of earthworms from the West Coast of New Zealand’s South Island. The barcoding
region COI and the 16S rDNA region were sequenced using tissue from the holotype specimens to provide indis-
putable uniqueness of the species. Morphological identification of new specimens can now be verified using the
DNA sequences publically available on GeneBank. In addition, when morphological identification cannot be used
(i.e., for juveniles, pieces of earthworms or environmental samples), species are still identifiable on the sole basis
of their DNA sequences. Further DNA analyses targeting different markers are also possible since type specimens
were all fixed in ethanol 98% and preserved in propylene glycol. This conforms to the ‘genetype’ concept sug-
gested by other authors (e.g., Tautz et al., 2003; Chackrabarty 2010).
BOYER ET AL.
30 · Zootaxa 2994 © 2011 Magnolia Press
FIGURE 4. Simplified phylogeny of New Zealand earthworms including the three newly described species M. felix, D. gorgon
and O. kenleei (NJ tree based on 16S rDNA). The 16S rDNA sequences obtained for the three newly described species were
compared to similar sequences obtained by Buckley et al. (2011). One representative for each major clade of New Zealand
endemic earthworms was included in the analysis (see Buckley et al. 2011). The tree is drawn to scale, with branch lengths in
the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were com-
puted using the Maximum Composite Likelihood method (Tamura et al. 2004) and are in the units of the number of base substi-
tutions per site. There were a total of 441 positions in the final dataset.
The DNA sequencing of holotypes helps the description of a new species by confirming that the taxonomical
diagnostic matches with its position in the phylogeny. In addition, potential incongruence and synonymies are eas-
ily detectable on a phylogenetic tree.
Earthworm taxonomists and ecologists are encouraged to use this procedure for future species description and
to apply DNA barcoding methods to type specimens of previously described species.
The generalization of this approach for earthworm species descriptions would provide a valuable tool for ecol-
ogists wanting rapidly to compare what they suspect to be undescribed species, new populations, or species in syn-
onymy. Also, such database could serve to resolve questions about the taxonomic identity of juvenile specimens
(Richard et al., 2010) or for identification of earthworm DNA in environmental samples (e.g., Boyer et al., unpub-
lished).
An integrative taxonomic description, combining morphological description, DNA barcoding and phylogeny is
particularly useful when working on highly diverse endemic faunas. These faunas are usually poorly known and
only a few internationally recognized taxonomists can identify them. Yet many endemic earthworm species, which
often represent high diversity (e.g., Blakemore, 2000; Chang et al., 2008), substantial biomass (e.g., Brockie and
Moeed, 1986), and have crucial roles in the functioning of native ecosystem (Boyer & Wratten 2010a), are likely to
be threatened with extinction.
In New Zealand, most endemic earthworm species have been rarely recorded or studied and only few speci-
mens have been found. Therefore, only three species are listed as New Zealand’s threatened invertebrates
(McGuinness, 2001) while 167 species are qualified as ‘data deficient’ (Hitchmough et al., 2005).
Some of the new species described here could be under threat as opencast coal mining is about to begin in
‘Happy Valley’. Their conservation may rely on the environmentally-driven habitat management and specific eco-
logical rehabilitation measures conducted by the mining company Solid Energy New Zealand Limited (Boyer et
al., unpublished). For other species in New Zealand, further studies such as those of Springett & Grey (1998) are
needed.
Zootaxa 2994 © 2011 Magnolia Press · 31
INTEGRATIVE TAXONOMY FOR THREE NEW EARTHWORMS
Acknowledgements
Collection and molecular analyses are by S. Boyer and S. Wratten. All taxonomic decisions and nomenclatural acts
are by R. Blakemore. This study was funded by Solid Energy New Zealand Limited as part of their work on mine
rehabilitation, the Department of Conservation as part of the Conservation Management Unit Fund and the Bio-
Protection Research Centre.
References (For brevity, not all earlier taxonomic citations are provided here).
Blakemore, R.J. (2000) Tasmanian Earthworms with Review of World Families. CD-ROM Monograph, VermEcology, Can-
berra, Australia.
Blakemore, R.J. (2002) Cosmopolitan Earthworms – an Eco-Taxonomic Guide to the Peregrine Species of the World. VermE-
cology, Kippax, ACT, Australia.
Blakemore, R.J. (2004) Checklist of New Zealand Earthworms updated from Lee (1959). In: Moreno, A.G., Borges, S. (Eds.)
Avances en taxonomia de lombrices de tierra / Advances in earthworm taxonomy (Annelida: Oligochaeta). Editorial Com-
plutense, Universidad Complutense, Madrid, Spain, pp. 175–185.
Blakemore, R.J., 2006. A review of New Zealand earthworms after Lee (1959). In: Kaneko, N. & Ito, M.T. (Eds.), A Series of
Searchable Texts on Earthworm Biodiversity, Ecology and Systematics from Various Regions of the World. CD-ROM pub-
lication by Soil Ecology Research Group, Yokohama National University, Tokiwadai, Yokohama, Japan.
Blakemore, R.J. (2008) Cosmopolitan earthworms – an Eco-Taxonomic Guide to the Species (3rd Edition). VermEcology,
Yokohama, Japan.
Blakemore, R.J., Kupriyanova, E.K. & Grygier, M.J. (2010) Neotypification of Drawida hattamimizu Hatai, 1930 (Annelida,
Oligochaeta, Megadrili, Moniligastridae) as a model linking mt DNA (COI) sequences to an earthworm type, with a
response to the ’Can of Worms’ theory of cryptic species. Zookeys, 41, 1–29.
Boyer, S. & Wratten, S.D. (2010a). The potential of earthworms to restore ecosystem services after opencast mining - A review.
Basic and Applied Ecology, 11, 196–203.
Boyer, S. & Wratten, S.D. (2010b). Using molecular tools to identify New Zealand endemic earthworms in a mine restoration
project (Oligochaeta: Acanthodrilidae, Lumbricidae, Megascolecidae). Zoology in the Middle East Supplementum, 2, 31–
40.
Brockie, R.E. & Moeed, A. (1986) Animal biomass in a New Zealand forest compared with other parts of the world. Oecolo-
gia, 70, 24–34.
Chakrabarty, P. (2010) Genetypes: a concept to help integrate molecular phylogenetics and taxonomy. Zootaxa, 2632, 67–68.
Chang, C.H. & Chen, J.H. (2005) Taxonomic status and intraspecific phylogeography of two sibling species of Metaphire (Oli-
gochaeta : Megascolecidae) in Taiwan. Pedobiologia, 49, 591–600.
Chang, C.H., Lin, S.M. & Chen, J.H. (2008) Molecular systematics and phylogeography of the gigantic earthworms of the
Metaphire formosae species group (Clitellata, Megascolecidae). Molecular Phylogenetic and Evolution, 49, 958–968.
Dayrat, B. (2005) Towards integrative taxonomy. Biological Journal Of The Linnean Society, 85, 407–415.
Folmer, O., Black, M., Hoeh, W., Lutz, R., Vrijenhoek, R. (1994) DNA primers for amplification of mitochondrial cytochrome
c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294–297.
Hebert, P.D.N., Ratnasingham, S. & deWaard, J.R. (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences
among closely related species. Proceedings of the Royal Society B: Biological Sciences, 270, S96–S99.
Hitchmough, R., Bull, L. & Cromarty, P. (2007) New Zealand threat classification system lists. Science and Technical Publish-
ing, Department of Conservation, Wellington, New Zealand.
Huang, J., Xu, Q., Sun, Z.J., Tang, G.L. & Su, Z.Y. (2007) Identifying earthworms through DNA barcodes. Pedobiologia, 51,
301–309.
King, R.A., Read, D.S., Traugott, M. & Symondson, W.O.C. (2008) Molecular analysis of predation: a review of best practice
for DNA-based approaches. Molecular Ecology, 17, 947–963.
Lee, K.E., Blakemore, R.J. & Fraser, P. (2000) Noke a Aotearoa - The Earthworms of New Zealand. The New Zealand Inven-
tory of Biodiversity: A Species 2000 Symposium Review. Te Papa Museum, Wellington, New Zealand.
Lee, K.E. (1959) The earthworm fauna of New Zealand. Department of Scientific and Industrial Research Bulletin 130, Wel-
lington, New Zealand.
Lee, K.E. (1985) Earthworms: their Ecology and Relationships with Soils and Plant Growth. Academic Press, Sydney, Austra-
lia.
McGuiness, C.A. (2001) The conservation requirements of New Zealand's nationally threatened invertebrates. Department of
Conservation, Wellington, New Zealand.
Michaelsen, W. (1900) Das Tierreich. Vol. 10: Oligochaeta. Friedländer & Sohn, Berlin.
Pop, A.A., Cech, G., Wink, M., Csuzdi, C. & Pop, V.V. (2007) Application of 16S, 18S rDNA and COI sequences in the molec-
ular systematics of the earthworm family Lumbricidae (Annelida, Oligochaeta). European Journal of Soil Biology, 43,
S43–S52.
BOYER ET AL.
32 · Zootaxa 2994 © 2011 Magnolia Press
Pop, A.A., Wink, M. & Pop, V.V. (2003) Use of 18S, 16S rDNA and cytochrome C oxidase sequences in earthworm taxonomy
(Oligochaeta, Lumbricidae). Pedobiologia, 47, 428–433.
Richard, B., Decaens, T., Rougerie, R., James, S.W., Porco, D. & Hebert, P.D.N. (2010) Re-integrating earthworm juveniles
into soil biodiversity studies: species identification through DNA barcoding. Molecular Ecology Resources,10, 606–614.
Saitou N. & Nei M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biol-
ogy and Evolution, 4, 406–425.
Simon, C., Frati, F., Beckenbach, A., Crespi, B., Liu, H. & Flook, P. (1994) Evolution, weighting, and phylogenetic utility of
mitochondrial gene-sequences and a compilation of conserved polymerase chain-reaction primers. Annals of the Entomo-
logical Society of America, 87, 651–701.
Springett, J.A., Gray, R.A.J., Barker, D.J., Lambert, M.G., Mackay, A. & Thomas, V.J. (1998) Population density and distribu-
tion of the New Zealand indigenous earthworm Octochaetus multiporus (Megascolecidae : Oligochaeta) in hill pastures.
New Zealand Journal of Ecology, 22, 87–93.
Tamura K., Nei M. & Kumar S. (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method.
Proceedings of the National Academy of Sciences (USA), 101, 11030–11035.
Tamura K., Dudley J., Nei M. & Kumar S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software ver-
sion 4.0. Molecular Biology and Evolution, 24, 1596–1599.
Tautz, D., Arctander, P., Minelli, A., Thomas, R.H. & Vogler, A.P. (2003) A plea for DNA taxonomy. Trends in Ecology and
Evolution, 18, 70–74.
Yeates, G.W., Spiridonov, S.E. & Blakemore, R.J. (1998) Plesioungella kathleenae gen. n. et sp. n. (Nematoda: Drilonema-
toidea) from the Australian endemic megascolecid earthworm Fletcherodrilus unicus (Fletcher, 1889). New Zealand Jour-
nal of Zoology, 25, 205–212.
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