http://orcid.org/0000-0002-5785-6841
Figures
Abstract
Lumbricidae taxonomy is vastly restricted by the morphological simplicity of earthworms and their lack of complex appendices. This has led to confusing results in the Lumbricidae classifications, which in turn, has hindered our ability to identify and assign new and cryptic species to the family. Here we propose the addition of a new Lumbricidae genus from the Zagros and Elburz Mountains of Iran, i.e. Philomontanus gen. nov, including three new species. Our taxonomic inferences were based on the phylogenetic analysis of two nuclear gene regions (28S rDNA and 18S rDNA) and 11 mitochondrial gene regions (16S rDNA, 12S rDNA, NADH dehydrogenase I, cytochrome oxidase subunits I and II and tRNAs Asn, Asp, Val, Leu, Ala and Ser). Philomontanus gen. nov comprises the earthworm species Philomontanus sarii sp. nov., Philomontanus mahmoudi sp. nov. and Philomontanus baloutchi sp. nov. These three species are morphologically similar to each other with only a few characters separating them (e.g. size, pigmentation and position of clitellum). Our findings support the adoption of an integrative approach including molecular information (e.g., DNA sequences) to aid earthworm classification and develop a robust taxonomy.
Citation: Bozorgi F, Seiedy M, Malek M, Aira M, Pérez-Losada M, Domínguez J (2019) Multigene phylogeny reveals a new Iranian earthworm genus (Lumbricidae: Philomontanus) with three new species. PLoS ONE 14(1): e0208904. https://doi.org/10.1371/journal.pone.0208904
Editor: Feng ZHANG, Nanjing Agricultural University, CHINA
Received: May 2, 2018; Accepted: November 22, 2018; Published: January 30, 2019
This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
Data Availability: All samples Deposited in earthworm collection of zoological museum at the University of Tehran with origin numbers 6572-6577 and are publicly accessible. The molecular data in this study are available on the GenBank repository with accession numbers LC427082-LC427098.
Funding: This study was funded by the Spanish Ministerio de Economía y Competitividad (projects CTM2013-42540-R and AGL2017-86813-R), the Xunta de Galicia (project ED431B-2016/043).
Competing interests: The authors have declared that no competing interests exist.
Introduction
Over the last years Iranian taxonomists have studied earthworms in different parts of Iran and published several studies [1, 2]. Those studies concluded that the Iranian earthworm fauna comprises at least 13 genera and 28 species, belonging to the families Lumbricidae, Megascolecidae and Acanthodrilidae [1, 2]. A recent survey by our group in two regions of Iran, the Zagros and Elburz Mountains, rendered 39 morphologically similar earthworm specimens that could be assigned to three morphotypes based on a few key characters (e.g., clitellum and tubercula pubertatis location and pigmentation). However, a comparative study of morphological diagnostic characters commonly used in earthworm taxonomy, was not sufficient to assign unequivocally these specimens to any known Lumbricidae genus. Delimitation of diagnostic morpho-anatomical features in earthworms has been hampered by high levels of homoplasy [3–6]. Recently, integrative approaches including molecular DNA sequences from multiple genes coupled with phylogenetic inference has been used to complement morphology-based taxonomic studies [4, 5, 7]. This approach has aided species delimitation, clarified taxonomic riddles and deciphered earthworm evolutionary relationships [4, 5, 7–16]. In the present study, we couple DNA sequences from multiple nuclear and mitochondrial gene regions and morphological evidence with phylogenetic analysis to determine the taxonomic position of three putative Lumbricidae earthworm species from two biologically diverse mountainous areas of Iran.
Material and methods
Taxon sampling
A total of 39 earthworm specimens were collected in June 2014 and July 2015 in two eco-regions of Iran, the Zagros and Elburz Mountains (Fig 1). The Elburz Mountains lie along the northern border of Iran at the southern shore of the Caspian Sea. Mountains dominate the landscape of this eco-region with mostly forest steppe [17]. We sampled the northern slopes, which have humid climate due to northerly airflow, enriched with moisture from the sea. This long mountain range forms a barrier between the Iran plateau (Northeast) and the Mesopotamian lowlands (Southwest), and also constitutes a corridor for the southward distribution of northern faunal elements [1]. Hence, the Elburz Mountains facilitate the distribution of species from northern to southern regions, and forms a barrier for species migration from eastern to western areas. The Zagros Mountains is part of the Alpine-Himalayan mountain range and begins in northwestern Iran and roughly spreads along the western border of the country [18]. The sampled Northern part of Zagros has sub-humid continental climate and winter precipitation.
Red, Type locality of Philomontanus sarii sp. nov, Elburz Mountains. Green, Type locality of Philomontanus mahmoudi sp. nov, Zagros Mountains. Blue, Type locality of Philomontanus baloutchi sp. nov, Zagros Mountains.
We collected 23 earthworms in Mazandaran, Abbasabad, in the Elburz Mountains (36°36'29"N 51°07'38"E), and 10 and 6 specimens in Kurdistan, Baneh (36°02'15"N 45°56'50"E) and Kurdistan, Kamyaran (35°04'23"N 46°35'50"E), respectively, in the Zagros Mountains. Adult earthworms were collected by digging very small areas (<1 m2) and hand sorting, and then transferred to the laboratory. Earthworms were rinsed in water, anaesthetized in diluted ethanol, fixed in a mixture (1:1 v/v) of 90º ethanol and formaldehyde (4%) and placed in glass tubes containing 4% formaldehyde. Specimens and tissues collected for DNA extraction were preserved in absolute ethanol and stored at -20ºC. The species descriptions were made by external and internal visual examination using taxonomic identification keys [19–26]. Internal morphological examination was conducted by dorsal dissection under a stereomicroscope (Nikon SMZ1500). Body color was described in living specimens, whereas body dimensions were measured in fixed material. The following external and internal standard earthworm taxonomic characters were compared: size, number of body segments, body pigmentation, type of prostomium, arrangement of setae, presence and position of the first dorsal pore, nephridiopores, location and size of the male pores, type, start and end number of segments of clitellum, length and shape of tubercula pubertatis, segment and position of glandular tumescences, number and segment of testes, number of seminal vesicles, number of spermathecae, presence, location and extension of the gizzard and crop, segment and shape of typhlosole, segment of last pair of heart, extraoesophageals, excretory system, shape of nephridial bladder, shape of longitudinal muscle and presence of calciferous glands.
Ethics statement.
None of the locations from which samples were collected required specific permissions. None of the earthworms collected in this study are listed as endangered or protected. All of the specimens included in this study are archived in the earthworm collection of the zoological museum at the University of Tehran with numbers 6572–6577 and are publicly accessible. The molecular data in this study are submitted into genbank with accession numbers LC427082-LC427098 and are publicly availbe.
DNA extraction and phylogenetic analyses
Using the morphological characters above, we were able to split the collected specimens into three groups based on their geographic distribution and the following morphological differences: i) the Abbasabad group (23 specimens) from the Elburz Mountains: red violet, epilobic prostomium, size from 43–53 mm, 101–114 number of segments, clitellum in segments 25–30, tubercula pubertatis in segments 25–29; ii) the Baneh group (10 specimens) from the Zagros Mountains: totally pale, tanylobic prostomium, size from 25–31 mm, 51–70 number of segments, clitellum in segments 24–29, tubercula pubertatis in segments 25-28/29 and iii) the Kamyaran group (6 specimens) from the Zagros Mountains: red violet, epilobic prostomium, size from 57–68 mm, 123–140 number of segments, clitellum in segments 24–30, tubercula pubertatis in segments 26–29. We sequenced one specimen from each group.
One earthworm exemplar from each of the three morphological groups was used for the molecular and phylogenetic analyses. Total genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen). Two nuclear gene regions (18S rDNA and 28S rDNA) and 11 mitochondrial gene regions (16S rRNA, 12S rRNA, NADH dehydrogenase (ND1), cytochrome oxidase subunit I and II (COI and COII) and tRNA Asn, Asp, Val, Leu, Ala and Ser) were amplified using the polymerase chain reaction (PCR), as previously described [4, 5, 7]. PCR products were purified using a MultiScreen PCRμ96 (Millipore) kit and sequenced bidirectionally using an Applied Biosystems (ABI) 377XL automated sequencer. The ABI Big-dye Ready-Reaction kit was used following the standard cycle sequencing protocol, but with a 16th of the suggested reaction size. DNA sequences were deposited in GenBank under Accession Numbers LC427082-LC427098. To determine the phylogenetic position of the Iranian taxa within the Lumbricidae, we performed a phylogenetic analysis of the new taxa and other available earthworm species in Domínguez et al. [7] and Pérez-Losada et al. [9]. This dataset included 89 ingroup species (Lumbricidae) and three outgroup (Hormogastridae and Criodrilidae) species (see Fig 2). Nucleotide sequences for each gene region (all tRNAs were combined into a single gene region) were aligned using MAFFT v6 [27, 28] under the global (G-INS-i) algorithm and default settings. Phylogenetic congruence among gene regions (COI: 658 bp, COII: 688 bp, 12S: 350 bp, 16S: 1408 bp, 18S: 781 bp, ND1: 929 bp, tRNAs: 708 bp, and 28S: 964 bp) was assessed using the protocol developed by Wiens [29]. No areas of strongly supported incongruence between gene trees were observed. Gene regions were analyzed in multiple concatenated partitions as in Domínguez et al. [7]. JModelTest v1.0.1 [30] was used to determine the best evolutionary model for each DNA partition under the Akaike Information Criterion (AIC) [31]. The general time reversible model [32], with invariable sites and gamma distribution, was selected for all partitions (GTR+G+I). Maximum likelihood analysis of the concatenated partitions was performed in RAxML v7.2.0 [33] with 1,000 replicates. Clade support was assessed using the non-parametric bootstrap procedure [34] with 5,000 bootstrap replicates. Bayesian analysis coupled with Markov chain Monte Carlo (BMCMC) inference was performed in Mr. Bayes v3.1.2 [35]. Four independent BMCMC analyses were run in the CIPRES Science Gateway portal [36], each consisting of four chains. Each Markov chain was started from a random tree and run for 2x107 cycles, sampling every 1,000th generation. Evolutionary model parameters were estimated independently for each data partition starting as unknown variables with uniform default priors. Convergence and mixing were monitored using Tracer v1.5 [37]. All sample points prior to reaching stationary levels were discarded as burn-in. The posterior probabilities for individual clades obtained from separate analyses were compared for congruence and then combined and summarized on a 50% majority-rule consensus tree.
Bootstrap proportions (if P>70%) and Bayesian posterior probabilities (if P>95%) are shown above and below the branches, respectively. The Philomontanus exemplars from each of the three morphological groups are shown in red.
Nomenclatural acts.
The electronic edition of this article conforms to the requirements of the amended International Code of Zoological Nomenclature, and hence the new names contained herein are available under that Code from the electronic edition of this article. This published work and the nomenclatural acts it contains have been registered in ZooBank, the online registration system for the ICZN. The ZooBank LSIDs (Life Science Identifiers) can be resolved and the associated information viewed through any standard web browser by appending the LSID to the prefix "http://zoobank.org/". The LSID for this publication is: urn:lsid:zoobank.org:pub:C9F380AF-B080-4CFE-A99A-F2539FC169B1. The electronic edition of this work was published in a journal with an ISSN, and has been archived and is available from the following digital repositories: PubMed Central, LOCKSS.
Results
Phylogenetic inference
To determine the phylogenetic position of Iranian earthworms from Zagros and Elburz Mountains as well as their closest relatives we conducted a molecular phylogenetic analysis of a wide range of lumbricids and three non-Lumbricidae species (outgroup). Iranian earthworms fell in a well-supported clade within the Lumbricidae tree, depicted as (Aporrectodea georgii, Aporrectodea jassyensis, (Philomontanus mahmoudi, (P. baloutchi, (P. sarii)))) (Fig 2)–although formal descriptions are presented later in the paper, here we use the taxonomic names of the new taxa for clarity of interpretations. The Iranian clade was sister to a larger clade including the monophyletic lumbricid genera Lumbricus, Scherotheca, Eiseniona, Eisenia and Eiseniodes (Fig 2). The ML and Bayesian phylogenetic analyses showed strong support for the clade including the three Iranian species (bp = 100 and pP = 1.0), with the two species from Zagros Mountains forming a paraphyletic assemblage. The sister species to the Iranian clade, Aporrectodea. jassyensis and A. georgii, were collected in Turkey (Diyarbakir) and Serbia (Goc Mountains), respectively, suggesting a potential phylogeographic pattern of dispersion.
Morphological differential diagnosis
The three new Philomontanus species are morphologically very similar with only some differences in size, pigmentation, type of prostomium, and length and position of clitellum and tubercula pubertatis (Table 1). Their main differences with their sister species, A. georgii and A. jassyensis, are: 1) the type of clitellum, which is saddle shaped for the two Aporrectodea species, 2) the setal arrangement, which is closely paired for two Aporrectodea species and 3) the shape of the nephridial bladders, which is J shape for two Aporrectodea species. Considering that the Iranian species formed a well-supported clade and were geographically separated and morphologically distinct from their closest relatives, i.e. A. georgii and A. jassyensis, we have adopted an inclusive taxonomic approach to revise the current Lumbricidae classification. Hence, we propose that the three Iranian earthworm species should be placed in a new genus Philomontanus (including P. sarii, P. mahmoudi and P. baloutchi). Further sampling and phylogenetic analyses of earthworms from these contiguous geographical areas may suggest new splits, but at this point, we opt for a more conservative approach.
* = Morphological differences.
Taxonomy
Phylum Annelida Lamarck, [38]
Class Oligochaeta Grube, [39]/ Clitellata Michaelsen, [40]
Order Megadrilli Benham, [41] /Haplotaxida Michaelsen, [42]
Family Lumbricidae Rafinesque-Schmaltz, 1815[43]
Genus Philomontanus gen.nov.urn:lsid:zoobank.org:act: 95F2ACE7-5D0E-4691-BFD5-A455D85214BB
Diagnosis: Setae widely distant. Pigmentation variable, red-violet or totally pale. Prostomium epi- or tanylobous. First dorsal pore around 7/8. Male pore on 15 very small, on setal line bc. Clitellum annular. Spermathecae, which are small and round shaped present, frequently empty in 9/10–10/11 and open in setal line cd. Tubercula pubertatis ribbon shape. Nephridiopores aligned in setal bc. Two pairs of testes and funnels in segments 10–11, not iridescent. Four pairs of seminal vesicles in 9–12, those in 11 and 12 are slightly smaller than others. Two pairs of small, roundly shaped and almost empty spermathecae in 9/10 and 10/11 and open in setae line cd. Calciferous glands in segments 11 with hardly recognizable diverticula. Excretory system holoic, nephridial bladders ocarina shape. Typhlosole simple lamelliform, the cross-section of longitudinal muscle layer is of pinnate type. Since the morphological characters above are not sufficient to pinpoint the taxonomic position of Philomontanus in the Lumbricidae, we have used phylogenetic analysis of DNA sequences to determine its taxonomic position and closest relatives.
Type species: Philomontanus sarii sp. nov. by original designation herein.
Included species: Philomontanus sarii sp. nov., P. mahmoudi sp. nov. and P. baloutchi sp. nov.
Etymology. Philomontanus is composed of Philo (Greek prefix means liking for specified thing) and montanus (Latin noun means mountains). This name has been chosen as new genus and its three species have been found in mountains.
Remarks. The closest genus based on morphological evidence is Dendrobaena [44], but with distinguishable differences in pigmentation (reddish vs. both reddish and pale), size and number of body segments (small to medium sized species vs. larger range of size), shape of clitellum (saddle shape vs. annular shape) and shape of tubercles (different shapes observed; nob shape, ribbon shape and etc. vs. ribbon shape). However, according to morphological descriptions in several references, it is obvious that Dendrobaena is very heterogeneous [45–47], not monophyletic and needs taxonomic revision [7, 16]. The annular clitellum could relate Philomontanus to Eiseniona albolineata or to Bimastos, although our phylogenetic analyses showed otherwise. According to their morphological features and characteristics of the habitat where they were sampled, the Phylomontanus species could be considered epigeic earthworms.
Philomontanus sarii Bozorgi & Malek sp. nov. urn:lsid:zoobank.org:act:2F35B21F-9764-4AFA-8EBB-75DDD54147FD. Figs 3 and 4
Arrows point to tubercula pubertatis A. Philomontanus sarii sp. nov. B. Philomontanus mahmoudi sp. nov. C. Philomontanus baloutchi sp. nov..
Yellow, Spermathecae Blue, Male pore Brown, Clitellum Green, Tubercula pubertatis Orange, Variation of Tubercula pubertatis.
Etymology. The new species name was chosen to honor Dr. Alireza Sari, who has done extensive research on various aspects of Iranian fauna.
Sampling site. Oak (Quercus sp.) forest near mountain hillside, semi humid brown soil, covering in decaying plants and rotting logs on the forest floor. Plants present: Juniperus sp., Pistacia sp. and Acer sp. (Fig 5).
(A1, A2) Mazandaran, Abbasabad (36.72 o N; 51.11o E), Elburz Mountains, sampling site of Philomontanus sarii sp. nov. (B1, B2) Kurdistan, Kamyaran (35.49o N; 46.35o E), Zagros Mountains, sampling site of Philomontanus baloutchi sp. nov. (C1, C2) Kurdistan, Baneh (35.99o N; 45.88o E), Zagros Mountains, sampling site of Philomontanus mahmoudi sp.nov.
Type material. Holotype, ZUTC/ 6572, Abbasabad, Mazandaran, Elburz mountains, Iran (36°36'29"N 51°07'38"E). Leg. F. Bozorgi and A. Kazemi, 02.06.2014. Deposited in the earthworm collection of the Zoological Museum, University of Tehran. Paratypes, ZUTC/ 6573, 22 ex., Same locality and collection date as the Holotype. Leg. F. Bozorgi and A. Kazemi. Deposited in earthworm collection of Zoological Museum, University of Tehran.
Diagnosis. Body length 45–53 mm, diameter 2.8–3.1 mm. Color red-violet (Fig 3). Prostomium epilobous, first dorsal pore in 7/8. Setae widely distant, glandular tumescences visible in 9–11,ab. Clitellum annular, on segments 25–30. Male pores hardly seen on 15. Nephridiopores hardly seen between b and c. Septa visible and strengthened in 6/7,8/9 and 11/12. Calciferous glands in segment 11 with no diverticula. Excretory system holoic. Nephridial bladders ocarina shape. Typhlosole simple lamelliform, the cross-section of longitudinal muscle layer is of pinnate type.
Description. Length of the holotype 53 mm, diameter just after the clitellum 3.1 mm. Number of segments 114. Paratypes 43–53 mm long and 2.8–3.1 mm wide. Number of segments 101–114. Color preserved dorsal red violet pigmented, less dense of pigmentation ventrally (Fig 3). Prostomium epilobous. First dorsal pore in the intersegmental furrow 7/8. Setae widely distant. Setal formula at segment 20; aa:ab:bc:cd:dd = 1.50:1.25:1.11:1:2.3. Male pores hardly seen, in very small size on the segment 15 between setae bc. Nephridiopores hardly seen aligned in setal line bc. Clitellum on 25–30 annular. Tubercula pubertatis ribbon shape on 25–29. Glandular tumescences on segments 9–11ab. Septa thickened in 6/7, 8/9 and 11/12. Two pairs of testes and funnels in segments 10–11, not iridescent. Four pairs of seminal vesicles in 9–12, those in 11 and 12 are slightly smaller than others. Two pairs of small, roundly shaped and almost empty spermathecae in 9/10 and 10/11 and open in setae line cd. Calciferous glands in11. Last pair of hearts in 11. Excretory system holonephridial. Nephridial bladders ocarina- shaped with an intangible bump at the end. Crop in 15–16, gizzard in 17–18. Typhlosole simple lamelliform, quiet large. Longitudinal muscle layer of pinnate type.
Remarks. This new species is morphological similar to Dendrobaena byblica (Rosa, 1893), but with slight differences in size (22-42mm vs. 43-53mm), segment of clitellum (23/24-29 vs. 25–30), shape of tubercula pubertatis (verity shapes vs. ribbon shape) and position of tubercula pubertatis (25–27 vs. 25–29).
Philomontanus mahmoudi Bozorgi & Malek sp. nov. urn:lsid:zoobank.org:act:B3BF1AEB-D20C-43B5-84AB-E42C4C83125F. Figs 3 and 4
Etymology. The new species is named in memory of coauthor Masoumeh Malek’s father.
Sampling site: Walnut (Juglans regia) forest near mountain slope, semi humid soil with carious plants and gravel developed over slate. Plants present: Crataegus sp., Pistacia sp. and Quercus sp. (Fig 5).
Type material. Holotype, ZUTC/ 6574, Baneh, Kurdistan, Zagros Mountains, Iran (36°02'15"N 45°56'50"E). Leg. F. Bozorgi, 13.07.2015. Deposited in the earthworm collection of the Zoological Museum, University of Tehran. Paratypes, ZUTC/ 6575, 9 ex., Same locality and collection date as the Holotype. Leg. F. Bozorgi. Deposited in earthworm collection of Zoological Museum, University of Tehran.
Diagnosis. Body length 25–31 mm, diameter 2.1–2.5 mm. Color totally pale (Fig 3). Prostomium tanylobous, first dorsal pore in 7/8. Setae widely distant, glandular tumescences visible in 9–11,ab. Clitellum annular, on segments 24–29. Male pores hardly seen on 15, nephridiopores visible between b and c. Septa visible with no recognizable strengthened. Calciferous glands in segment 11 with slight diverticula. Excretory system holoic. Nephridial bladders ocarina shape. Typhlosole simple lamelliform, quiet large, the cross-section of longitudinal muscle layer is of pinnate type.
Description. Length of the holotype 27 mm, diameter just after the clitellum 2.4 mm. Number of segments 67. Paratypes 25–31 mm long and 2.1–2.5 mm wide. Number of segments 51–70. Color totally pale without any pigmented parts all over the body (Fig 3). Prostomium tanylobous. First dorsal pore in the intersegmental furrow 7/8. Setae widely distant. Setal formula at segment 20; aa:ab:bc:cd:dd = 1.20:1.12:1:1.05:1.5. Male pores hardly seen, in very small size facing ventral on the segment 15 between setae bc. Nephridiopores aligned in setal line bc. Clitellum on 24–29 annular. Tubercula pubertatis ribbon shape with more swelling in some individual on 25–28/29. Glandular tumescences on segments 9–11ab. Septa seen but there were no recognizable difference for thickness between segments. Two pairs of testes and funnels in segments 10–11, not iridescent. Four pairs of seminal vesicles in 9–12, those in 11 and 12 are slightly smaller than others. Two pairs of small, roundly shaped and almost empty spermathecae in 9/10 and 10/11 and open in setae line cd. Calciferous glands in 11. Last pair of hearts in 11. Excretory system holonephridial. Nephridial bladders ocarina- shaped with little more elongation. Crop in 15–16 and gizzard in 17–18. Typhlosole simple lamelliform, quiet large. Longitudinal muscle layer of pinnate type.
Remarks. This new species has also morphological resemblance with P. sarii but differences in size (43–53mm vs. 25–31 mm), pigmentation (red violet vs. pale), position of clitellum (25–30 vs. 24–29) and position of gizzard (17–18 vs. 16–17).
Philomontanus baloutchi Bozorgi & Malek sp. nov. urn:lsid:zoobank.org:act:473B8329-9E95-44CA-8A22-4CA20F4E2F2B. Figs 3 and 4
Etymology. The new species is named in memory of Dr. Mohammad Baloutch, who was a prominent zoology professor in Iran.
Sampling site: Walnut (Juglans regia) forest near mountain springs with cool slow flowing water, in the steep slope of valleys with permanent slow water, humid loam soil covered with carious plants. Plants present: Crataegus sp., Pistacia sp. and Quercus sp. (Fig5).
Type material. Holotype, ZUTC/ 6576, Kamyaran, Kurdistan, Zagros Mountains, Iran (35°04'23"N 46°35'50"E). Leg. F. Bozorgi, 23.07.2015. Deposited in the earthworm collection of the Zoological Museum, University of Tehran. Paratypes, ZUTC/ 6577, 5 ex., Same locality and collection date as the Holotype. Leg. F. Bozorgi. Deposited in earthworm collection of Zoological Museum, University of Tehran.
Diagnosis. Body length 57–68 mm, diameter 3.8–4.7 mm. Color red-violet (Fig 3). Prostomium epilobous, first dorsal pore in 7/8. Setae widely distant, glandular tumescences visible in 9–11, ab. Clitellum annular, on segments 24–30. Male pores hardly seen on segment 15, nephridiopores visible between b and c. Septa visible, strengthened in 7/8, 9/10 and 14/15. Calciferous glands in segment 11. Excretory system holoic. Nephridial bladders ocarina shape. Typhlosole simple lamelliform, large, the cross-section of longitudinal muscle layer is of pinnate type.
Description. Length of the holotype 67 mm, diameter just after the clitellum 4.2 mm. Number of segments 136. Paratypes 57–68 mm long and 3.8–4.7 mm wide. Number of segments 123–140. Red violet pigmented, less dense pigmentation ventrally especially on primary segments. (Fig 3). Prostomium epilobous. First dorsal pore in the intersegmental furrow 7/8. Setae widely distant. Setal formula at segment 20; aa:ab:bc:cd:dd = 1.21:1.14:1:1.03:1.5. Male pores hardly seen, in very small size on the segment 15 between setae bc. Nephridiopores aligned in setal line bc. Clitellum on 24–30 annular. Tubercula pubertatis ribbon shape on 26–29. Glandular tumescences on segments 9–11ab. Septa visible, strengthened in 7/8, 9/10 and 14/15. Two pairs of testes and funnels in segments 10–11, not iridescent. Four pairs of seminal vesicles in 9–12, those in 11 and 12 are slightly smaller than others. Two pairs of small, roundly shaped and almost empty spermathecae in 9/10 and 10/11 and open in setae line cd. Calciferous glands in 11. Last pair of hearts in 11. Excretory system holonephridial. Nephridial bladders ocarina- shaped. Crop in 15–16. gizzard in 17–18. Typhlosole simple lamelliform, large. Longitudinal muscle layer of pinnate type.
Remarks. This new species also has some morphological similarity to D. byblica (Rosa, 1893), but with differences in size (22–42 mm vs. 57–68mm), position of clitellum (23/24-29 vs. 24–30), shape of tubercles (verity shapes vs. just ribbon shape) and position of tubercles (25–27 vs. 26–29). This new species differs from P. sarii in size (43-53mm vs. 57-68mm), position of clitellum (25–30 vs. 24–30) and position of tubercles (25–29 vs. 26–29). It also differs from P. mahmoudi in size (25–31 mm vs. 57–68mm), pigmentation (pale vs. red violet), position of clitellum (24–29 vs. 24–30), position of tubercles (25–28/29 vs. 26–29) and position of gizzard (16–17 vs. 17–18).
Discussion
The accurate delimitation of species boundaries is essential to numerous areas of biological research, especially for the belowground fauna, a major component of global biodiversity [47]. The classification of earthworms at the genus level in the family Lumbricidae has always been puzzling and varies according to different authors, with proposals ranging from 6 to 45 genera [7]. Moreover, those classifications are based on lists of diagnostic morphological characters that are mostly simple structures and can vary and overlap among taxa [4]. Phylogenetic analysis of DNA sequences is a powerful systematic tool to assess biodiversity, identify new species and untangle cryptic diversity [48]. Hence, using molecular-based phylogenies to investigate earthworm systematics has become common practice for researches nowadays [49]. In this study, multilocus phylogenetic inference and morphological evidence were used to identify and describe three new earthworm species from the Elburz and Zagros Mountains in Iran. The 39 collected specimens were morphologically similar but could be confidently assigned to three different morphotypes based on differences in a few characters (like clitellum and tubercula pubertatis position and pigmentation). The standard diagnostic characters used in earthworm taxonomy were similar to those seen in several Lumbricidae genera, hence it was impossible to unequivocally assign them to any known Lumbricidae genus. Our phylogenetic analyses of three Iranian exemplars showed, however, three divergent lineages in a clade clearly separated from the other Lumbricidae genera and well-supported by our bootstrap (BP> 70%) and Bayesian (PP> 0.95) analyses. This, hence, suggests that the Iranian specimens correspond to three new congeneric species and should be included in a new Lumbricidae genus, Philomontanus gen. nov. Our phylogenetic analysis also indicates that the sister taxa to Philomontanus spp. are A. jassyensis and A.georgii. According to Domínguez et al. [7], A. jassyensis and A.georgii are not valid species within the Aporrectodea genus and need to be re-classified within the Lumbricidae. Qiu and Bouché [19] created the genus Koinodrilus for K. georgi, K. jasseyensis as well as other earthworm species. However, Czusdi and Zicsi [25] and Blakemore [26] clearly indicated that Koinodrilus is a synonymous of Aporrectodea. Therefore, the external diagnosis of the genus Aporrectodea is setae closely paired, pigmentation lacking and prostomium epilobic. These morphological features are not seen in Philomontanus, which includes small and medium-sized reddish or pale lumbricids, with prostomium type epilobic or tanylobic and widely distant setae. Hence, given all this evidence, we consider that Phylomontanus is a valid genus morphologically distinct from Aporrectodea or the obsolete Koinodrilus genus.
Previous earthworm species collected in Iran were not preserved adequately to carry out molecular systematics comparisons, hence their evolutionary relatedness to the new genus described here could not be assessed. Additionally, no previous studies exist describing the phylogenetic radiation of Iranian lumbricids.
Earthworm systematics and taxonomy can benefit greatly from the integration of morphological and molecular lines of evidence. Preliminary morphology-based taxon identifications in the field or laboratory can be then re-evaluated using DNA barcoding genes (COI) or multigene phylogenies. In many earthworm groups, species boundaries are blurred, which makes global estimates of diversity difficult and sometimes unrealistic [50, 51]. Additionally, conservation efforts aiming at preserving the evolutionary potential of a species, can greatly benefit from this integrative approach by assessing the phylogenetic diversity of the species under consideration [52]. We encourage earthworm taxonomists to combine morphological and molecular evidence with available ecological and geographical information to investigate Lumbricidae systematics. Such an integrative approach will most certainly provide a powerful tool for identifying new and cryptic earthworm species and will lead to a better understanding of their diversity and the processes maintaining it.
Acknowledgments
We would like to thank the Research Affairs of the University of Tehran for their financial support. We gratefully acknowledge Mr. Kazemi, Mohammadi and Alizadeh for helping in collecting and processing samples. We thank our colleagues Dr. Ahmad Reza Katouzian, who provided insight and expertise that greatly assisted the research.
References
- 1. Farhadi Z, Malek M, Elahi E. Review of the earthworm fauna of Iran with emphasis on Kohgiluyeh & Boyer-Ahmad Province. Zootaxa. 2013;3670(4):440–8.
- 2. Latif R, Malek M, Csuzdi C. New earthworm records from the Central Zagros Mountain, Iran with description of a new species. North-Western Journal of Zoology. 2017;13(2).
- 3. Pérez-Losada M, Høeg JT, Crandall KA. Unraveling the evolutionary radiation of the thoracican barnacles using molecular and morphological evidence: a comparison of several divergence time estimation approaches. Systematic Biology. 2004;53(2):244–64. pmid:15205051
- 4. Pérez-Losada M, Ricoy M, Marshall JC, Domínguez J. Phylogenetic assessment of the earthworm Aporrectodea caliginosa species complex (Oligochaeta: Lumbricidae) based on mitochondrial and nuclear DNA sequences. Molecular phylogenetics and evolution. 2009;52(2):293–302. pmid:19364539
- 5. Pérez-Losada M, Breinholt JW, Porto PG, Aira M, Domínguez J. An earthworm riddle: systematics and phylogeography of the Spanish lumbricid Postandrilus. PLoS One. 2011;6(11):e28153. pmid:22140529
- 6. Novo M, Almodóvar A, Fernández R, Trigo D, DÍAZ‐COSÍN DJ, Giribet G. Appearances can be deceptive: different diversification patterns within a group of Mediterranean earthworms (Oligochaeta, Hormogastridae). Molecular ecology. 2012;21(15):3776–93. pmid:22805584
- 7. Domínguez J, Aira M, Breinholt JW, Stojanovic M, James SW, Pérez-Losada M. Underground evolution: new roots for the old tree of lumbricid earthworms. Molecular phylogenetics and evolution. 2015;83:7–19. pmid:25463017
- 8. Domínguez J, Aira M, Porto PG, Díaz Cosín DJ, Pérez-Losada M. Multigene phylogeny reveals two new isolated and relic earthworm genera (Oligochaeta: Lumbricidae). Zoological Journal of the Linnean Society. 2017;182(2):258–74.
- 9. Pérez-Losada M, Breinholt JW, Aira M, Domínguez J. An updated multilocus phylogeny of the Lumbricidae (Annelida: Clitellata: Oligochaeta) earthworms. Journal of Phylogenetics & Evolutionary Biology. 2015;2015.
- 10. Dupont L, Lazrek F, Porco D, King RA, Rougerie R, Symondson WOC, et al. New insight into the genetic structure of the Allolobophora chlorotica aggregate in Europe using microsatellite and mitochondrial data. Pedobiologia. 2011;54(4):217–24.
- 11. Fernández R, Almodóvar A, Novo M, Gutiérrez M, Cosín DJD. A vagrant clone in a peregrine species: phylogeography, high clonal diversity and geographical distribution in the earthworm Aporrectodea trapezoides (Dugès, 1828). Soil Biology and Biochemistry. 2011;43(10):2085–93.
- 12. King RA, Tibble AL, Symondson WO. Opening a can of worms: unprecedented sympatric cryptic diversity within British lumbricid earthworms. Molecular ecology. 2008;17(21):4684–98. pmid:18992008
- 13. Novo M, Almodóvar A, Díaz‐Cosín DJ. High genetic divergence of hormogastrid earthworms (Annelida, Oligochaeta) in the central Iberian Peninsula: evolutionary and demographic implications. Zoologica scripta. 2009;38(5):537–52.
- 14. Novo M, Almodóvar A, Fernández R, Trigo D, Cosín DJD. Cryptic speciation of hormogastrid earthworms revealed by mitochondrial and nuclear data. Molecular Phylogenetics and Evolution. 2010;56(1):507–12. pmid:20398776
- 15. Marchán DF, Fernández R, de Sosa I, Sánchez N, Cosín DJD, Novo M. Integrative systematic revision of a Mediterranean earthworm family: Hormogastridae (Annelida, Oligochaeta). Invertebrate Systematics. 2018;32(3):652–71.
- 16. Szederjesi T, Pop VV, Pavlíček T, Márton O, Krízsik V, Csuzdi C. Integrated taxonomy reveals multiple species in the Dendrobaena byblica (Rosa, 1893) complex (Oligochaeta: Lumbricidae). Zoological Journal of the Linnean Society. 2017;182(3):500–16.
- 17. Hollingsworth J, Fattahi M, Walker R, Talebian M, Bahroudi A, Bolourchi MJ, et al. Oroclinal bending, distributed thrust and strike-slip faulting, and the accommodation of Arabia–Eurasia convergence in NE Iran since the Oligocene. Geophysical Journal International. 2010;181(3):1214–46.
- 18. Khadivi S, Mouthereau F, Larrasoaña JC, Vergés J, Lacombe O, Khademi E, et al. Magnetochronology of synorogenic Miocene foreland sediments in the Fars arc of the Zagros Folded Belt (SW Iran). Basin Research. 2010;22(6):918–32.
- 19. Qiu J, Bouché M. Révision des taxons supraspécifiques de Lumbricoidea. Documents pédozoologiques et intégrologiques. 1998;3:179–216.
- 20. Qiu J, Bouché M. Liste classée des taxons valides de Lombriciens (Oligochaeta: Lumbricoidea) apres l’etude des trios cinquieme d’entre-eux. Documents pédozoologiques et intégrologiques. 1998;4:181–200.
- 21. Qiu J, Bouché M. Hydrilus, un remarquable nouveau genre de Lumbricidae (Annelida: Oligochaeta). Documents Pédozoologiques et Intégrologiques. 1998;4:17–9.
- 22. Qiu J, Bouché M. Heraclescolex, un nouveau genre de Lumbricidae (Annelida: Oligochaeta). Documents Pédozoologiques et Intégrologiques. 1998;4:140–52.
- 23. Qiu J, Bouché M. La decouverte de Postandrilus ge. Nov(Oligochaeta: Lumbricidae) et remarques sur la reproduction des lombriciens Doc pedozoologiq integrologiq, Dijon. 1998;4:65–72.
- 24.
Sims RW, Gerard BM. Earthworms: Keys and Notes for the Identification and Study of the Species: Brill Archive; 1985.
- 25.
Csuzdi C, Zicsi A. Earthworms of Hungary: Annelida: Oligochaeta, Lumbricidae: Hungarian Natural History Museum; 2003.
- 26.
Blakemore R. Cosmopolitan Earthworms-An Eco-Taxonomic Guide to the Peregrine Species of the World. VermEcology. Japan; 2006.
- 27. Katoh K, Kuma K-i, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic acids research. 2005;33(2):511–8. pmid:15661851
- 28. Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Briefings in bioinformatics. 2008;9(4):286–98. pmid:18372315
- 29. Wiens JJ. Combining data sets with different phylogenetic histories. Systematic Biology. 1998;47(4):568–81. pmid:12066302
- 30.
Posada D. Selection of M odels of DNA Evolution with jM odelT est. Bioinformatics for DNA sequence analysis: Springer; 2009. p. 93–112.
- 31. Posada D, Buckley TR. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic biology. 2004;53(5):793–808. pmid:15545256
- 32. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on mathematics in the life sciences. 1986;17(2):57–86.
- 33. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Systematic biology. 2008;57(5):758–71. pmid:18853362
- 34. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39(4):783–91. pmid:28561359
- 35. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003;19(12):1572–4. pmid:12912839
- 36.
Miller MA, Pfeiffer W, Schwartz T, editors. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE), 2010; 2010: Ieee.
- 37.
Rambaut A, Suchard M, Drummond A. Tracer ver. 1.5. tree. bio. ed. ac. uk/software/tracer. Accessed; 2009.
- 38.
de Lamarck J-BdM. Hydrogeologie: Agasse; 1802.
- 39.
Grube AE. Die familien der Anneliden1850.
- 40. Michaelsen W. Über die Beziehungen der Hirudineen zu den Oligochaeten. Mitteilungen aus dem Naturhistorischen Museum Hamburg. 1919;36:131–53.
- 41.
Benham W. An attempt to classify earthworms: QJ Science; 1890.
- 42.
Michaelsen W. Das Tierreich, 10: Vermes, Oligochaeta. Friedländer & Sohn, Berlin, 575 pp. 1900.
- 43.
Rafinesque CS. Analyse de la nature, ou tableau de l'univers et des corps organisés: Aux dépens de l'auteur; 1815.
- 44. Eisen G. Om Skandinaviens Lumbricider. Öfversigt af Kongliga Vetenskaps-Akademiens Förhandligar. 1873;30(8):43–56.
- 45. Szederjesi T, PAVLÍČEK T, COŞKUN Y, Csuzdi C. New earthworm records from Turkey, with description of three new species (Oligochaeta: Lumbricidae). Zootaxa. 2014;3764(5):555–70.
- 46. Szederjesi T, Pop VV, Csuzdi C. New and little known earthworm species from peripheral areas of the Romanian Carpathians (Oligochaeta, Lumbricidae). ACTA ZOOLOGICA HUNGARICA. 2014;60(2):85–107.
- 47. Rosa D. Viaggio del Dr. E. Festa in Palestina, nel Libano e regioni vicine. II. Lumbricidi. Bollettino dei Musei di Zoologia ed Anatomia comparata della R Università di Torino. 1893;8(160):1–14.
- 48. Proudlove G, Wood PJ. The blind leading the blind: cryptic subterranean species and DNA taxonomy. Trends in Ecology & Evolution. 2003;18(6):272–3.
- 49. Giska I, Sechi P, Babik W. Deeply divergent sympatric mitochondrial lineages of the earthworm Lumbricus rubellus are not reproductively isolated. BMC evolutionary biology. 2015;15(1):217.
- 50. Appeltans W, Ahyong ST, Anderson G, Angel MV, Artois T, et al. (2012) The magnitude of global marine species diversity. Current biology 22: 2189–202. pmid:23159596
- 51. Costello MJ, May RM, Stork NE (2013) Can we name Earth’s species before they go extinct? Science (New York, NY) 339: 413–6.
- 52. Moritz C (2002) Strategies to protect biological diversity and the evolutionary processes that sustain it. Systematic biology 51: 238–54. pmid:12028731