Biodiversity Data Journal :
Research Article
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Corresponding author: Ani Bikashvili (ani.bikashvili.1@iliauni.edu.ge)
Academic editor: Alexander Weigand
Received: 04 Apr 2022 | Accepted: 29 Jul 2022 | Published: 13 Sep 2022
© 2022 Ani Bikashvili, Nino Kachlishvili, Bella Japoshvili, Levan Mumladze
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Bikashvili A, Kachlishvili N, Japoshvili B, Mumladze L (2022) Species diversity and DNA barcode library of freshwater Molluscs of South Caucasus. Biodiversity Data Journal 10: e84887. https://doi.org/10.3897/BDJ.10.e84887
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This study provides the first attempt to investigate the molecular diversity of South Caucasian freshwater molluscs (Mollusca, Gastropoda) and lay down the first bricks to build up a DNA-barcode library. In total, 289 COI barcode sequences were obtained from 33 morpho-species belonging to 24 molluscan genera and 10 families that represent nearly 30% of known freshwater molluscan diversity of the South Caucasus region. DNA barcodes were analysed by means of the Barcode Index Number (BIN) and the other tools available in BOLD Systems. Results showed that the knowledge of freshwater molluscs diversity in the South Caucasus is far from comprehensive. For the studied 33 morpho-species, 289 barcodes were clustered into 40 BINs, from which unique BINs were defined for 12 species and five species were characterised with more than a single BIN. From the studied taxa, 60% were characterised larger than 2.2% sequence divergence indicating high genetic variation or cryptic diversity. Within our limited taxonomic coverage, we found one new species for the Republic of Georgia (Galba schirazensis) and at least three undescribed species belonging to the genera Stagnicola, Segmentina and Anisus. Uniqueness and high molecular diversity of the studied species emphasise the need for further intensive morphological and molecular investigations of the South Caucasian freshwater molluscan fauna.
South Caucasus, DNA barcode library
Under increasing anthropogenic pressure, the conservation of freshwater biodiversity and maintaining freshwater ecosystem functioning remain two of the most critical challenges for the 21st century’s world (
Recent developments of DNA barcoding technology helped significantly to revive and advance the biodiversity inventory and monitoring at an unprecedented rate (
Sample collection campaigns were carried out from 2015 to 2021 across the various regions of Georgia (and also, to a lesser extent, in Armenia and Azerbaijan during 2019) (Fig.
Map of collection localities for freshwater molluscs in the present study. The red dots correspond to the localities from where one or more specimens/species were submitted to barcoding, while the yellow dots correspond to localities from where the specimens are still waiting for genetic investigation.
One to ten specimens per morphologically defined species were selected for barcoding. In cases of genera - Radix and Ancylus for which the systematics of Caucasian taxa is not yet well understood, we took a larger number of specimens for each morpho-species. All selected specimens were first photographed according to BOLD standards (
Collected materials/vouchers are deposited in the collection of the Institute of Zoology of Ilia State University, Tbilisi under the respective CaBOL identification numbers given in Suppl. material
Genomic DNA was extracted from tissue samples using the Quick-DNA™ Miniprep Plus Kit (Zymo Research) (for 25 mg tissue), Quick-DNA™ Miniprep Plus Kit (Zymo Research) (for 5 mg tissue) DNeasy Blood & Tissue Kits (Qiagen, Germany) according to the manufacturer’s instructions and the protocol proposed by
Sequences were edited in Geneious Pro v.7 (
Barcode Index Numbers (BIN) (
In total, 289 COI barcode sequences were obtained and uploaded in the “GEOFM” BOLD project, representing 33 species from 24 molluscan genera from 10 families. Prior to the present study, there were 47 freshwater molluscs COI barcode sequences available in the BOLD Systems (from the study area) including 11 sequences from an unpublished project within the “DNAqua-Net” COST Action (
The average fragment length of COI barcodes in the “DS-FMOL” dataset (combining “GEOFM” project plus pre-existing barcodes) was 534 bp (min: 409 bp and max: 658 bp). Nucleotide base frequencies were: A-25.4%, G-18.4, C-14.4%, T-41.8%) - similar to reported frequencies for molluscs (e.g.
The families Planorbidae and Lymnaeidae are represented by the highest number of barcodes (116 and 99, respectively). The two families Unionidae and Neritidae are represented each with 19 and 12 barcodes, respectively. The two families Cyrenidae and Sphaeriidae are represented by an equal number of barcodes (each with 11 barcodes). The two families Physidae and Viviparidae are represented each with 10 and 5 barcodes, respectively and the family Melanopsidae and Acroloxidae by the lowest number of barcodes (three barcodes each). The most common genus was Ancylus, for which 93 barcodes (two species) were generated, followed by Radix and Unio (73 and 16 barcodes, respectively and three species for each of them). The 18 genera were represented by a single species, two genera with two species and a single genus by the four species. Of all species obtained, two species Ancylus sp. 2 and Radix auricularia were represented the highest number of barcodes (each with 89 and 52 , respectively), followed by Radix euphratica, Lymnaea stagnalis, Theodoxus fluviatilis, Corbicula fluminalis, Unio crassus and Physella acuta (each with 21, 14, 12, 11, 13 and 10 barcodes, respectively). Most of the species are represented with less than 10 barcodes, including six species, with a single barcode (Fig.
The BIN and RESL analyses resulted in 41 BINs united into 40 OTUs. In addition, 13 OTUs were also formed for 23 sequences (all belonging to Hydrobiidae and mined from GenBank) for which no BINs had been defined due to the small barcode size (less than 500 bp (
Average within species divergence were 0.69 ± 0.0% (ranged from 0% to 4.1%) followed with divergence of 6.4 ± 0.0% within genera (ranged from 0 to 16.7%) and 17.8 ± 0.0% divergence within families (ranged from 10.42% to 21.9%).
In most cases, morphologically determined specimens (comprising 28 species) were matched with a single OTU/BIN cluster with intraspecific (or within BIN) sequence divergence of less than 2.2%. More than one BIN were found in five species-level taxa - Planorbis planorbis (2 BINs), Physella acuta (2 BINs), Lymnaea stagnalis (2 BINs), Radix auricularia (2 BINs) and Radix euphratica (4 BINs) (Table
BOLD summary data of barcoded Freshwater Molluscs with mean and maximum intraspecific and nearest neighbour (K2P) distances. Country Codes: AT = Austria, ALB = Albania, ARG = Argentina, AZR = Azerbaijan, ARM = Armenia, ALB = Albania, AU = Australia, BY = Belarus, BG = Bulgaria, BIH = Bosnia and Herzegovina, CH = China, CO = Colombia, CU = Cuba, CA = Canada, HR = Croatia, CZ = Czech Republic, ECUA = Ecuador, FI = Finland, FR = France, DE = Germany, GE = Georgia, GR = Greece, HU = Hungary, IT = Italy, IR = Iran, IQ = Iraq, IN = India, JP = Japan, KZ = Kazakhstan, KE = Kenya, LT = Lithuania, MA = Morocco, MX = Mexico, MLO = Moldova, ME = Montenegro, MT = Malta, MY - Malaysia, MM = Myanmar, NZ = New Zeland, NP = Nepal, NL = Netherlands, MK = North Macedonia, PL = Poland, PT = Portugal, PE = Peru, RU = Russia, RO = Romania, RS = Serbia, SE = Sweden, SI = Slovenia, SK = Slovakia, ESP = Spain, CH = Switzerland, SG = Singapore, TH = Thailand, TR = Turkey, UKR = Ukraine, UK = United Kingdom, UZB = Uzbekistan, US = United States VE = Venezuela. n = BIN member count.
Species | BIN | n | MeanISD | MaxISD | Country | Nearest BIN/ species | Distance to NN |
Ancylus sp. 1 | BOLD:AEN7656 | 12 | 0.19 | 0.55 | GE | BOLD:AAD2028 | 4.95 |
Ancylus sp. 2 | BOLD:AAD2028 | 185 | 1.49 | 3.39 | TR, GR, MK, SI, IT, RO, ALB, GE, ME, AT, FR, ARM, AZR | BOLD:ACZ3241 | 3.3 |
Bathyomphalus contortus | BOLD:AAK0034 | 20 | 0.75 | 1.61 | DE, NL, AT, PL, GE | BOLD:ADR9065 | 9.45 |
Gyraulus albus | BOLD:AAN4112 | 19 | 1.16 | 3.02 | DE, ME, AT, PL, RS, CZ, GE | BOLD:AEB5660 | 7.55 |
Segmentina sp. | BOLD:AEN3217 | 3 | 0.22 | 0.32 | GE | BOLD:AAN3912 | 11.89 |
Anisus sp. | BOLD:AEC8114 | 6 | 0.43 | 0.81 | GE | BOLD:AAR3430 | 8.58 |
Planorbis planorbis | BOLD:AED0778 | 5 | 0.39 | 0.97 | GE | BOLD:ACS1294 | 3.4 |
Planorbis planorbis | BOLD:ADJ5964 | 4 | 0.28 | 0.5 | IR, GE | BOLD:ACS1294 | 2.1 |
Ferrissia californica | BOLD:AEJ3761 | 3 | 0 | 0 | GE | BOLD:AAE6642 | 3.06 |
Ampullaceana sp. | BOLD:AEN6567 | 2 | 0 | 0 | GE | BOLD:ACI0501 | 4.97 |
Radix euphratica | BOLD:ADJ8863 | 53 | 1.34 | 2.96 | IQ, IR, GE, USB, RU | BOLD:AEI7975 | 2.82 |
Radix euphratica | BOLD:ADK5204 | 5 | 0.96 | 1.7 | IQ, GE | BOLD:ADJ8863 | 3.37 |
Radix euphratica | BOLD:ADK6106 | 3 | 0.32 | 0.48 | IQ, GE | BOLD:ADR3052 | 1.92 |
Radix euphratica | BOLD:ADR3052 | 3 | 0.11 | 0.16 | IQ, GE | BOLD:ADK6106 | 1.92 |
Radix auricularia | BOLD:ACI2007 | 14 | 0.46 | 0.84 | ARM, GE | BOLD:AAD6712 | 2.88 |
Radix auricularia | BOLD:AAD6712 | 153 | 0.91 | 2.99 | DE, PL, ME, HR, GR, MK, RU, ARM, CA, FR, ESP, CH, AT, US, GE | BOLD:ACI2007 | 2.88 |
Peregriana peregra | BOLD:AAD0368 | 74 | 2.03 | 4.92 | ALB, FR, RS, GR, MK, ME, DE, SK, RU, AT, IR, GE | BOLD:AEN6567 | 10.14 |
Lymnaea stagnalis | BOLD:AEM9638 | 6 | 0 | 0 | GE | BOLD:ACQ2679 | 2.12 |
Lymnaea stagnalis | BOLD:AEN6037 | 9 | 0.73 | 1.4 | GE, DE | BOLD:ACQ0092 | 2.43 |
Galba truncatula | BOLD:ABA2623 | 50 | 0.99 | 2.74 | FR, VE, IR, NP, SI, GR, RU, ME, ALB, GE | BOLD:AAI7214 | 4.03 |
Galba schirazensis | BOLD:AAY4012 | 64 | 0.42 | 0.02 | CA, VE, PE, ECUA, MX, IR, FR, US, CO, JP, GE | BOLD:ADR2784 | 7.84 |
Stagnicola sp. | BOLD:AEN6388 | 2 | 0.16 | 0.16 | GE | BOLD:ACV7473 | 4.83 |
Acroloxus lacustris | BOLD:AAS0589 | 29 | 1.44 | 2.92 | DE, TR, MK,GR, RS, AT, ALB, UKR | BOLD:ADK8211 | 2.9 |
Physella acuta | BOLD:AAB6433 | 50 | 0.67 | 3.86 | FR, US, GR, MK, IR, JP, MT, UKR, AZR, GE | BOLD:AEM0595 | 2.03 |
Physella acuta | BOLD:AEM0595 | 358 | 1.72 | 6.35 | US, FR, NL, CU, AU, CA, IN, ARG, GR, MK, TH, SG, MY, NZ, MM, IR, CN, JP, AT, IQ, KE, ESP, MT, ME, DE, UKR, AZR, PE, GE | BOLD:AAB6433 | 2.03 |
Viviparus costae | BOLD:AEE7831 | 4 | 0.67 | 1.33 | GE | BOLD:ADI2641 | 0.44 |
Bithynia tentaculata | BOLD:AAN3084 | 55 | 1.32 | 3.73 | DE, US, AT, GE, RU, KZ, BY, UKR, RO | BOLD:AAF5645 | 7.77 |
Melanopsis mingrelica | BOLD:AEB5510 | 4 | 0.16 | 0.32 | GE | BOLD:AEB0981 | 3.85 |
Theodoxus fluviatilis | 291 | 1.8 | 7.25 | DE, FI, AT, HR, HU, BIH, UKR, ME, ALB, MK,GR, RU, TR, BG, GE, MLD, FR, RO, PT, ESP, LT, GB, MA, IT, SK | BOLD:ACF4500 | 5.08 | |
Corbicula fluminalis | BOLD:ACF4380 | 64 | 0.15 | 3.07 | FR, ARG, HU, IN, RU, GE, AZR | BOLD:ACF5867 | 1.92 |
Anodonta anatina | BOLD:AAB7495 | 897 | 1.93 | 5 | PO, SE, PT, IT, ESP, FR, HR, RU, HU, CZ, UKR, AT, BG, MA, TR, DE, KZ, GE | BOLD:AAF6127 | 10.81 |
Anodonta cygnea | BOLD:AAF0516 | 110 | 0.28 | 2.1 | SE, PT, DE, PL, FR, IT, CZ, GB, HU, AT, TR, RU, GE | BOLD:AEE8900 | 8.73 |
Unio crassus | BOLD:AAF5083 | 175 | 0.52 | 2.17 | AT, UKR, TR, DE, GE | BOLD:ADR4461 | 2.28 |
Unio pictorum | BOLD:AAD9208 | 232 | 0.36 | 2.68 | AT, PL, GB, UKR, RU, IR, GR, SK, FR, TR, DE, GE, MLD | BOLD:ADR3328 | 2.38 |
Unio tumidus | BOLD:AAF0052 | 78 | 0.22 | 1.28 | SE, PL, UKR, AT, DE, GB, RU, SK, GE, MLD | BOLD:ADR6944 | 9.39 |
Sphaerium sp. | BOLD:ACQ8004 | 4 | 0.73 | 1.47 | GE, GB | BOLD:ABU6190 | 3.85 |
Musculium lacustre | BOLD:AEE5622 | 4 | 0.18 | 0.36 | ESP, GE | BOLD:ACQ4690 | 1.6 |
Euglesa sp. 1 | BOLD:AEN6788 | 3 | 1.12 | 1.44 | GE | BOLD:ACQ0055 | 5.13 |
Euglesa sp. 2 | BOLD:AEN0712 | 1 | N/A | N/A | GE | BOLD:ACQ0055 | 3.08 |
Euglesa sp. 3 | BOLD:ACQ7011 | 4 | 1.03 | 1.71 | ALB, GR, DE, GE | BOLD:AAG0350 | 1.92 |
Euglesa subtruncata | BOLD:ACQ3092 | 7 | 0.77 | 1.61 | GE, IT, MK, AT, US | BOLD:ACQ6136 | 3.09 |
South Caucasian freshwater molluscs (and all invertebrates in general) are still poorly known (
Within the current project, we were able to generate 298 new barcodes corresponding to 33 freshwater mollusc species-level taxa. Roughly, this is no more than 30% of the expected species number in the South Caucasus (based on
Pond snails of the family Lymnaeidae are distributed worldwide (
Amphipepleinae represents one of the most species-rich and taxonomically challenging groups. Morphologically identified species - Ampullaceana lagotis formed the unique BIN BOLD:AEN6567 with the divergence of 4.97% to the nearest neighbour (NN) BIN BOLD:ACI0501 that includes specimens of yet unresolved “Radix zazurnensis” from Russia (3) and China (32) (
The genus Radix turned out to be the most complex within the family Lymnaeidae. Based on morphology alone, we were able to confidently identify only R. auricularia, barcodes of which formed two separate BINs: 12 specimens were allocated to BIN BOLD:ACI2007 (with 2.88% divergence to NN, BOLD:AAD6712) and 40 specimens were formed under BIN BOLD:AAD6712 (2.88% divergence to NN BOLD: ACI2007). Both BINs seem to characterise geographically variable R. auricularia populations. Other unidentified specimens of Radix (22 in total) formed four unique BINs, including 17 Georgian specimens that were classified under the BIN BOLD:ADJ8863. With our specimens, this BIN includes specimens from Iraq, Iran, Uzbekistan and Russia and represents species R. euphratica (with NN BIN BOLD:AEI7975 (2.82% divergence) representing a single specimen of R. euphratica from Iran). Five other specimens of Radix sp. formed three different BINs, BOLD:ADK5204 (with 3.37% divergence to NN BIN, BOLD:ADJ8863), BOLD:ADK6106 (with 1.92% divergence to NN BIN BOLD:ADR3052) and BOLD:ADR3052 (with 1.92% divergence to NN, BIN BOLD:ADK6106). Due to its small within-BIN distances, specimens can be named as R. euphratica which was first mentioned from the Tbilisi Reservoir (voucher number Mlym68 (Russian Museum of Biodiversity Hotspots, Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, Arkhangelsk, Russia) (
Subfamily Lymnaeinae includes three representative genera in South Caucasus each with a single species. Galba is characterised by high phenotypic plasticity and extremely uniform anatomical traits, which are often the reasons for species misidentification (
From the genus Lymnaea a single species – L. stagnalis is known. Our specimens of L. stagnalis formed two BINs. Eight specimens matched with BIN BOLD:AEN6037, for which only a single barcode was available from Ukraine. The NN BIN is BOLD:ACQ0092 with 2.43% divergence, includes specimens also belonging to L. stagnalis. The remaining six specimens formed the unique BIN (BOLD:AEM9638) with the NN BIN - BOLD:ACQ2679 (with 2.12% divergence) comprising specimens of L. stagnalis. Thus, in South Caucasus, at least two haplotypes of L. stagnalis occur, both in a mountainous Javakheti region (southern Georgia). The last genera in this subfamily is Stagnicola which is also represented with a single species (S. palustris) in South Caucasus. Only two specimens of Stagnicola were represented in our dataset forming the unique BIN - BOLD:AEN6388 which were diverged by 4.83% from NN BIN BOLD:ACV7473, representing the specimens of S. turricula from Poland. Most probably the genus Stagnicola in Georgia (and in South Caucasus) is not a S. palustris or the genus is represented with more than one species in the region. Thus, additional sampling and taxonomic investigation are required.
The Ramshorn snails of the family Planorbidae is the most diverse group of freshwater pulmonates inhabiting a wide range of freshwater habitats (
Seven specimens of Planorbis planorbis formed two BINs - BOLD:AED0778 and BOLD:ADJ5964 diverged both from the same NN BIN (BOLD:ACS1294) with 3.4% and 2.1%, respectively. All three BINs are considered as P. planorbis in BOLD systems comprising the specimens from different regions of Europe and Middle East.
The genus Segmentina is taxonomically understudied. Some authors consider only a single S. nitida species within the genus (
Two representatives of the genus Anisus is known for South Caucasus (A. leucostoma and A. spirorbis) (
The taxonomy of the genus of Ancylus is far from being resolved. For the Caucasus region, six species are indicated (
The remaining Planorbidae species – Ferrissia californica, Gyraulus albus and Bathyomphalus contortus all matched exactly within the conspecific representatives from the wide areas of western Palearctic. An exception is the F. californica which formed a unique BIN BOLD:AEJ3761 with 3.06% divergence from NN BIN BOLD:AAE6642 (includes specimens under the name of F. fragilis (synonym of F. califonica)).
The freshwater clams (family Sphaeriidae) are a cosmopolitan group inhabiting all types of freshwater habitats (
Another genus of clams with a complicated genetic structure is Euglesa. Specimens submitted to a barcoding pipeline were morphologically identified as either E. casertana (five specimens) or E. subtruncata (two specimens). The only specimen of putative E. subtruncata was validated under BIN: BOLD:ACQ3092, while the rest of the specimens formed unique genetic clusters with no clear systematic position. As an example, BIN BOLD:ACQ7011 contains specimens from Greece, Albania, Germany and one specimen from Georgia with a maximum intra-specific divergence of 1.71%. The closest NN BIN BOLD:AAG0350 (an unnamed clade) diverged with 1.92%. The remaining five specimens all turned out to belong to a yet unknown species under BINs BOLD:AEN6788 (5.13% divergence to NN) and BOLD:AEN0712 (3.8% divergence to NN BIN). Similar to Sphaerium, this genus is also difficult to classify, based on shell morphology alone due to limitations in taxonomically meaningful characters (
One more specious family in the study area is the bivalve family Unionidae that includes at least five valid species occurring in South Caucasus, including Unio crassus, U. tumidus, U. pictorum, Anodonta cygnea and A. anatina (
Our results clearly showed the insufficiency of the current knowledge of freshwater molluscs diversity in the South Caucasus region. In spite of the limited taxon coverage, nearly half of the studied taxa turned out to be in need of substantial taxonomic investigation/revision. In particular, nearly all genera with more than one known species are represented with regionally unique radiation and the species level taxonomy is inadequate. The South Caucasus region is considered a Plio-Pleistocene refugium and occurrence of unique or endemic lineages are not a surprise. However, a good understanding of its biodiversity is necessary to apply effective monitoring and conservation measures. In addition, the knowledge of the origin and phylogeography of most of the South Caucasian freshwater molluscs are generally missing (but see rare exception by
We would like to thank our colleagues, Zhaneta Shubitidze, Ekaterine Pankvelashvili, Giorgi Bananashvili, Giorgi Epitashvili, Tatia Kuljanishvili, Lela Arabuli, Nika Paposhvili, D. Copilac-Ciocianu and M. Berch for their help during the fieldwork. This study (fieldwork and molecular genetic analyses) was supported by the Shota Rustaveli National Science Foundation Ph.D. Grant to A.B. (Grant Number PHDF-18–1649; “Biodiversity and Phylogeography of family Lymnaeide distributed in Georgia“). We would like to thank to the CaBOL (Caucasus Barcode of Life https://ggbc.eu/) lab team for their support. We also would like to thank Katrin Schniebs, Christian Albrecht, the anonymous reviewer and the editor, Alexander Weigand, for their valuable comments and suggestions.
Details on barcoded freshwater molluscs from Georgia, Armenia and Azerbaijan.