Variable Nucleotide Sites Research Articles

Identification of Cotylophoron cotylophorum (Fischoeder, 1901) in cattle on St. Kitts, West Indies and its relationship with African and Asian populations

There is limited information about the species of rumen fluke (Family Paramphistomidae) in the Caribbean. However, knowledge of species distribution is needed to better understand disease risk and epidemiology. Morphological identification is challenging with more recent DNA sequencing enabling a better understanding of rumen fluke distribution. In this study, rumen fluke specimens, collected between 2015 and 2016 from cattle on the island of St. Kitts, West Indies, were analysed. The ribosomal internal transcribed spacer 2 (ITS-2) region of rDNA was amplified using generic trematode primers. Results from Sanger sequencing were compared to reference sequences in GenBank and indicated the species was Cotylophoron cotylophorum with 100% sequence identity and 91% query cover. The ITS2 sequences were then compared to previously published ITS2 sequences for the Cotylophoron genus. When all the St. Kitts C. cotylophorum ITS2 sequences were compared with all other Cotylophoron sequences from India, Kenya, and Zimbabwe, three variable nucleotide sites, resulting in five unique haplotypes, were identified. Nine ITS2 sequences shared haplotype 1, which included all those from St. Kitts and single representatives from India and Kenya, potentially indicating global movement of this species.

Molecular identification and phylogenetics of local pearl millet cultivars using internal-transcribed spacers of nuclear ribosomal DNA

AbstractLocal cultivars of pearl millet in Saudi Arabia are known to tolerate extreme heat and drought stress. In the current study, the sequences of internal-transcribed spacers (ITSs) of six pearl millet cultivars were sequenced and analysed to investigate the genetic diversity among the local cultivars. The nucleotide polymorphism, secondary structures and phylogenetics were analysed for ITS sequences of the six local cultivars. The obtained sequences were 772–774 base pairs (bp) in length, including complete sequences of the ITS1–5.8S–ITS2 region and partial sequences of 18S and 26S rRNA. The nucleotide diversity among cultivars was higher in ITS2 sequences than ITS1 sequences. The ITS2 had four variable nucleotide sites in three native cultivars, whereas the ITS1 contained one base insertion. The secondary structures of the ITS1 and 5.8S region were highly conserved among the six cultivars and contained some motifs that are conserved across Viridiplantae. However, the ITS2 secondary structure for the two native cultivars, Sayah and Jazan, was distinct from the other cultivars, which confirms the applicability of the ITS2 sequence in distinguishing between genetically close taxa. Additionally, the phylogenetic analysis of the six investigated cultivars and 31 pearl millet accessions from the NCBI database showed close relationships between the local accessions and NCBI accessions from India and France. However, the local cultivar Sayah appeared to be distinct from the other cultivars in the phylogenetic trees. This study provides insights into the polymorphism within local pearl millet cultivars which is important for the identification and conservation of these cultivars.

Remarkably low genetic diversity and shallow population structure detected of the spiny eel (Sinobdella sinensis) in Eastern China.

The spiny eel (Sinobdella sinensis) is a small subtropical fish endemic to China, Vietnam, and Laos. It has disappeared in many rivers and lakes due to anthropogenic stressors. The aim of this study was to investigate the genetic diversity and population structure and to provide pertinent information of the evolutionary history and conservation of S. sinensis. Mitochondrial DNA (mtDNA) cytochrome c oxidase I (COI) sequences of 144 individuals from five lakes in the Jiangsu Province of Eastern China were sequenced. A total of 17 haplotypes were defined by 20 variable nucleotide sites. Remarkably low haplotype and nucleotide diversity was observed in all sampled populations. The AMOVA analyses revealed that 96.44% of the genetic variation occurred within the populations. Significant genetic differentiation was detected among populations (P < 0.05), but no large-scale regional differences were detected. Analysis of neutral evolution and mismatch distribution suggests population expansion. Low genetic diversity and shallow population structure based on COI sequences were also confirmed. The wild resource of S. sinensis in Eastern China has sharply declined. Low genetic diversity and shallow population structure based on COI sequences were confirmed. Fishing management and resource conservation of this species should be taken urgently.

Genetic analysis of Cryptozona siamensis (Stylommatophora, Ariophantidae) populations in Thailand using the mitochondrial 16S rRNA and COI sequences.

Cryptozona siamensis, one of the most widespread land snails, is native to Thailand, and plays a key role as an agricultural pest and intermediate host for Angiostrongylus spp. However, its genetic diversity and population structure has not yet been investigated, and are poorly understood. Therefore, a genetic analysis of the C. siamensis population in Thailand was conducted, based mitochondrial 16S rRNA (402 bp) and COI (602 bp) gene fragment sequences. Cryptozona siamensis randomly collected from 17 locations in four populations across Thailand, between May 2017 and July 2018. Fifty-eight snails were used to examine the phylogeny, genetic diversity, and genetic structure. The maximum likelihood tree based on the 16S rRNA and COI fragment sequences revealed two main clades. A total of 14 haplotypes with 44 nucleotide variable sites were found in the 16S rRNA sequences, while 14 haplotypes with 57 nucleotide variable sites were found in the COI sequences. The genetic diversity of C. siamensis in term of the number of haplotypes and haplotype diversity, was found to be high but the nucleotide diversity showed low levels of genetic differentiation for the COI sequence as also noted with the 16S rRNA sequence. The population genetic structure of C. siamensis revealed genetic difference in most populations in Thailand. However, low genetic difference in some populations may be due to high gene flow. This study provides novel insights into the basic molecular genetics of C. siamensis.

Interspecific hybridization in North American Polygala (Polygalaceae)

As a part of ongoing systematic and phylogenetic studies in Polygalaceae, field collections of two pairs of North American species (Polygala balduinii and P. ramosa, and P. lutea and P. rugelii) had morphologically intermediate forms and grew sympatrically, and so were suspected to be interspecific hybrids. Although hybrids among plants are often invoked in taxonomic and floristic literature based on morphologic intermediacy, they are rarely documented and substantiated using molecular tools. We found that the morphologically intermediate individuals within intermixed populations of both species pairs did indeed share all of the variable nucleotide sites in nrITS among the parent species. Likewise, using plastid sequence data (trnL-F), we determined that in both species pairs, the parentage was bidirectional. Although some DNA inheritance phenomena (e.g. incomplete lineage sorting) can result in similar polymorphic DNA sequence data, the intermediacy in both morphology and sequence data within sympatric populations is more indicative of interspecific hybridization.

Intron sequence variation of the echinostomes (Trematoda; Echinostomatidae): implications for genetic investigations of the 37 collar-spined, Echinostoma miyagawai Ischii, 1932 and E. revolutum (Fröelich, 1802).

Echinostomes are a diverse group of digenetic trematodes that are difficult to classify by predominantly traditional techniques and contain many cryptic species. Application of contemporary genetic/molecular markers can provide an alternative choice for comprehensive classification or systematic analysis. In this study, we successfully characterized the intron 5 of domain 1 of the taurocyamine kinase gene (TkD1Int5) of Artyfechinostomum malayanum and the other two species of the 37 collar-spined group, Echinostoma revolutum and Echinostoma miyagawai, whereas TkD1Int5 of Hypoderaeum conoideum cannot be amplified. High levels of nucleotide polymorphism were detected in TkD1Int5 within E. revolutum and E. miyagawai, but not in A. malayanum. Thus, TkD1Int5 can be potentially used as genetic marker for genetic investigation of E. miyagawai and E. revolutum. We therefore used TkD1Int5 to explore genetic variation within and genetic differentiation between 58 samples of E. miyagawai and five samples of E. revolutum. Heterozygosity was observed in 17 and two samples with 16 and three insertion/deletion (indel) patterns in E. miyagawai and E. revolutum, respectively. Heterozygous samples were then cloned and nucleotide sequence was performed revealing the combined haplotypes in a particular sample. Based on nucleotide variable sites (excluding indels), the 72 E. miyagawai and seven E. revolutum haplotypes were subsequently classified. The haplotype network revealed clear genetic differentiation between E. miyagawai and E. revolutum haplogroups, but no genetic structure correlated with geographical localities was detected. High polymorphism and heterogeneity of the TkD1Int5 sequence found in our study suggest that it can be used in subsequent studies as an alternate independent potential genetic marker to investigate the population genetics, genetic structure, and possible hybridization of the other echinostomes, especially the 37 collar-spined group distributed worldwide.

Species discrimination of mountain garlic based on the nrDNA ITS region sequence

Mountain garlic is an edible perennial herb widely distributed in Asian, European, and Siberian regions, referring to a class of Allium species. In South Korea, mountain garlic mainly consists of two Allium species, Allium ochotense Prokh. and A. microdictyon Prokh. Due to having spicy garlic odor and nutrition contents, mountain garlic is used as a vegetable and traditional medicine in South Korea, Japan, and China. However, the genetic relationship between A. ochotense and A. microdictyon belonging to the subgenus Anguinum is still unclear. To understand the genetic diversity and phylogenetic relationships of mountain garlic populations in South Korea, we collected 25 mountain garlic materials from 8 geographical areas and analyzed their genetic diversity and relationships based on sequence variations of the nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) region. The DNA alignment result showed that A. ochotense and A. microdictyon were clearly divided into two groups, sharing 11 respective, particular nucleotide variable sites. It suggested that the nrDNA ITS region could be used to discriminate among Allium intraspecies. This species identification method would be utilized to distinguish unclear mountain garlic materials. This work not only provides more sequence resources of mountain garlic, but also validates the efficiency of the molecular discrimination method based on the nrDNA ITS region sequence.

Population diversity of Cistopus indicus inferred from mitochondrial DNA (Cytochrome b) variation from China and Vietnam

ABSTRACTThe octopus Cistopus indicus is an important target of cephalopod fisheries in China. It is widely distributed in the South Pacific and tropical Indian Ocean, from the South China Sea, the Philippines, Malaysia, to Indian and Pakistan seas. We collected specimens from five sites in China and Vietnam (Zhoushan, Wenzhou, Shacheng, Zhanjiang and Mangjie). A fragment of 675bp of cytochrome b (Cytb) was amplified from 95 individuals. A total of 27 haplotypes and 78 variable nucleotide sites was observed. High haplotype diversity and low nucleotide diversity were observed in all populations. The phylogenetic analysis separated these populations into two clades; one was composed of three populations (Zhoushan, Wenzhou and Shacheng), the other of two (Zhanjiang, Mangjie). AMOVA analysis detected that 4.67% of the genetic variation occurred within populations and 95.33% occurred among populations. FST values ranged from 0.014 to 0.993, highlighting the high genetic variation among the populations. Assuming a molecular clock with a rate of 2.15–2.6%/Ma for the Cytb gene, the two clades may have diverged 2.88–3.49 million years ago (Pliocene). Neutral evolution tests and mismatch distribution analysis suggested recent population expansion. The present results revealed valuable information for genetic assessment, management and conservation of this species.

Germplasm differences among three species of genus Erythroculter based on morphological characters and gene sequences of mitochondrial CO I and Cyt b

Fish of genus Erythroculter (Cypriniformes, Cyprinidae, Abramidinae) are important commercial freshwater species in China. In this work, morphological characters and gene sequences of mitochondrial CO I and Cyt b were analysed to investigate the germplasm differences among E. mongolicus, E. dabryi and E. ilishaeformis. Results demonstrated that about countable trait, there were six traits (scale in/ above/ below lateral line, gill‐raker in first left gill‐arch and branched fin‐ray in anal/ pectoral fin) showed significant differences. Gene fragments of CO I and Cyt b was 905 bps and 1,142 bps respectively. In CO I, there were 54.3% base content of A + T, 14 haplotypes and 84 nucleotide variable sites. As to Cyt b, there were 56.3% base content of A + T, 20 haplotypes and 142 nucleotide variable sites. In both CO I and Cyt b, the highest and lowest nucleotide diversity was detected in E. ilishaeformis and E. mongolicus respectively. According to morphological distance, genetic distance, genetic differentiation coefficient (Fst) and gene flow, E. dabryi was grouped together with E. ilishaeformis firstly, and then clustered with E. mongolicus. These results might be useful in the conservation and management of fishery resources of these three species.

Highly polymorphic mitochondrial DNA and deceiving haplotypic differentiation: implications for assessing population genetic differentiation and connectivity

BackgroundHyperdiverse mtDNA with more than 5% of variable synonymous nucleotide sites can lead to erroneous interpretations of population genetic differentiation patterns and parameters (φST, DEST). We illustrate this by using hyperdiverse mtDNA markers to infer population genetic differentiation and connectivity in Melarhaphe neritoides, a NE Atlantic (NEA) gastropod with a high dispersal potential. We also provide a recent literature example of how mtDNA hyperdiversity may have misguided the interpretation of genetic connectivity in the crab Opecarcinus hypostegus.ResultsmtDNA variation surveyed throughout the NEA showed that nearly all M. neritoides specimens had haplotypes private to populations, suggesting at first glance a lack of gene flow and thus a strong population genetic differentiation. Yet, the bush-like haplotype network, though visually misleading, showed no signs of phylogeographic or other haplotype structuring. Coalescent-based gene flow estimates were high throughout the NEA, irrespective of whether or not mtDNA hyperdiversity was reduced by removing hypervariable sites.ConclusionsMelarhaphe neritoides seems to be panmictic over the entire NEA, which is consistent with its long-lived pelagic larval stage. With hyperdiverse mtDNA, the apparent lack of shared haplotypes among populations does not necessarily reflect a lack of gene flow and/or population genetic differentiation by fixation of alternative haplotypes (DEST ≈ 1 does not a fortiori imply φST ≈ 1), but may be due to (1) a too low sampling effort to detect shared haplotypes and/or (2) a very high mutation rate that may conceal the signal of gene flow. Hyperdiverse mtDNA can be used to assess connectivity by coalescent-based methods. Yet, the combined use of φST and DEST can provide a reasonable inference of connectivity patterns from hyperdiverse mtDNA, too.

Population structuring of Channa striata from Indian waters using control region of mtDNA

Striped snakehead (Channa striata) is a freshwater species of early Miocene period belonging to family Channidae. The genetic variability of the snakehead populations in India was not well known. Present study was undertaken using 149 sequences of control region of mitochondrial DNA from seven geographically distinct populations of Indian water, which resulted in 46 haplotypes with 137 variable nucleotide sites (60 singletons and 77 parsimony informative) and the nucleotide frequencies was: A = 33.0, T = 28.1, G = 15.4, and C = 23.5%. The presence of low-frequency of younger haplotypes with a large number of singletons indicates the absence of dominant haplotype. Hierarchical AMOVA showed highly significant genetic differentiation (FST = 0.56, p < .00) among the populations. The pattern of genetic differentiation was not consistent with geographical distributions. AMOVA identified three genetically heterogeneous clades. The significant finding of Imphal and Chaliyar was that they were found genetically close to each other, but geographically much isolated from each other. The inference of the study suggests that the hypothesis of the single panmictic population of C. striata in Indian waters is rejected.

Phylogeography of the red-bellied lizard, Darevskia parvula in Turkey

The groups of red-bellied lizards had a small distribution area in the Pontic zone. The several studies performed on these lizard groups are based on taxonomy and systematics. Although there were several taxonomic or systematic researches on some species of this group, the phylogeographical pattern and species disturbing boundaries of this group is still not clear. In the present study, we aimed to resolve the taxonomic and phylogenetic relationships of the red-bellied lizards in Turkey, based on two combined mitochondrial gene fragments and one protein-coding nuclear gene (rag1). Also, we evaluated ecological niches differentiations among red-bellied lizard groups. The mitochondrial DNA genes were found to be highly polymorphic in this group. One hundred and one variable nucleotide sites were detected on the combined gene sequences. According to phylogenetic trees based on the maximum likelihood (ML) and Bayesian inference (BI), the red-bellied lizards group have three species groups; Darevskia parvula, D. adjarica and unnamed Darevskia sp. (candidate species for Darevskia genus). This situation was supported by high bootstrap and posterior probability values in the trees of mitochondrial DNA gene fragments. However, no genetic variation was detected according to nuclear DNA (rag1) sequence. Because the species groups have no overlaps in terms of their ecological niches, ecological niche modelling (ENM) results revealed differences among the groups of D. parvula, D. adjarica, and unnamed Darevskia sp. Besides, we detected no geographical overlaps among three species groups, since there were geographical isolation zones among the species groups of red-bellied lizard.

Unexpected rDNA divergence between two morphologically minimalistic nematodes with description of a new species (Tylenchomorpha: Tylenchidae)

Summary Species of the family Tylenchidae are encountered in large numbers in soils. The genus Labrys was recently described characterised by a remarkable lip pattern that differs from all other known Tylenchidae genera. Here we describe a curious new species, Labrys fujianensis sp. n., that morphologically fits the genus Labrys but which is genetically divergent. The phylogeny was inferred based on 18S and 28S rDNA and light and scanning electron microscopy were used to extract detailed morphologies. The phylogenetic position of this species and its phenotypic convergence are discussed. The possibility of a long-branch attraction artefact was inspected both by removal of variable nucleotide sites and monophyletic testing of topologies. The results confirmed the divergent positioning of the presented species and it is demonstrated that the genetic diversity in Tylenchidae may be much higher than expected due to morphological homoplasy.

Genetic Structure of &amp;lt;i&amp;gt;Spinibarbus caldwelli&amp;lt;/i&amp;gt; Based on mtDNA D-Loop

Spinibarbus caldwelli was an endemic species to China, and its germplasm protection and resources utilization had become more and more concerned. To know its genetic diversity and differentiation, the mitochondrial DNA D-loop was amplified and sequenced for 148 individuals from four regions of Pearl River and Yangtze River Basin. Altogether 9 variable nucleotide sites existed among the aligned sequences of 748 bp, and 8 haplotypes were found within 148 individuals. The average nucleotide diversity (Pi) was high 0.00297, while haplotype diversity (Hd) was 0.706. The average genetic distance was 0.00298, most value occurred between LJ and CL populations, and small value occurred between HJ and QZ populations.

Detection and analysis of new psittacine beak and feather disease virus (PBFDv) nucleotide sequences

Psittacine beak and feather disease (PBFD) affects a large number of Psittaciformes species. In this study, five White Cockatoo parrots (Cacatua alba) with clinical signs of PBFD were examined. After euthanasia, a full necropsy of parrots was performed and organs with macroscopic changes were sampled for routine histopathological evaluation. To confirm the presence of psittacine beak and feather disease virus (PBFDv), feather samples were analyzed with the PCR method. Sequence analysis of the obtained PCR products indicated their close relationship (99%) to other PBFDv isolates. Six variable nucleotide sites were discovered, two missense and four silent mutations. This paper presents the evidence of new PBFDv sequence in Cockatoo species.

Genetic Variations of Candida glabrata Clinical Isolates from Korea using Multilocus Sequence Typing

Background: Although Candida albicans is considered to be the major fungal pathogen of candidemia, severe infections by non-albicans Candida (NAC) spp. have been on the increase in recent years. Among NAC spp., C. glabrata has emerged as the second most common pathogen. Unlike other Candida spp., it is often resistant to various azole antifungal agents, such as fluconazole. However, few studies have been conducted to investigate its structure, epidemiology, and basic biology. Recently, multi-locus sequence typing (MLST) has been developed as a highly useful and portable molecular biology technique. Methods: In the present study, MLST was performed with a total of 102 C. glabrata clinical isolates that were isolated from various types of clinical specimens. The present study was performed with a total of 102 C. glabrata clinical isolates that were isolated from various types of clinical specimens. The fungal internal transcribed spacer (ITS) gene wad amplified and sequenced to identify and confirm C. glabrata clinical isolates. For MLST, six housekeeping genes including 1,3-beta-glucan synthase (FKS), 3-isopropylmalate dehydrogenase (LEU2),myristoyl-CoA, protein Nmyristoyltransferase (NMT1), phosphoribosyl-anthranilate isomerase (TRP1), UTP-glucose-1-phosphate uridylyltransferase (UGP1), and orotidine-5'-phosphate decarboxylase (URA3) were amplified and sequenced. The results were analyzed by using the C. glabrata database. Results: Of a total of 3,345 base-pair DNA sequences, 49 (1.5%) variable nucleotide sites were found and the results showed that a total of 12 different sequence types (STs) were identified from the 102 clinical isolates. As classified by STs, The ST138 was the most predominant sequence type (ST) in this study as a result of 52.9% (54/102), and the following most predominant ST was the ST63 as a result of 23.5% (24/102). Conclusion: In conclusion, this data demonstrated that the ST138 was the most predominant ST in Korea. Further, we found eight undetermined STs (USTs) and then seven STs among these STs were given the number by PubMLST database. The data from this study might provide a fundamental database for further studies on C. glabrata, including its epidemiology, and evolution. Furthermore, the data might also contribute to the development of novel antifungal agents and diagnostic tests.

A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history

BackgroundMaximum compatibility is a method of phylogenetic reconstruction that is seldom applied to molecular sequences. It may be ideal for certain applications, such as reconstructing phylogenies of closely-related bacteria on the basis of whole-genome sequencing.ResultsHere I present an algorithm that rapidly computes phylogenies according to a compatibility criterion. Although based on solutions to the maximum clique problem, this algorithm deals properly with ambiguities in the data. The algorithm is applied to bacterial data sets containing up to nearly 2000 genomes with several thousand variable nucleotide sites. Run times are several seconds or less. Computational experiments show that maximum compatibility is less sensitive than maximum parsimony to the inclusion of nucleotide data that, though derived from actual sequence reads, has been identified as likely to be misleading.ConclusionsMaximum compatibility is a useful tool for certain phylogenetic problems, such as inferring the relationships among closely-related bacteria from whole-genome sequence data. The algorithm presented here rapidly solves fairly large problems of this type, and provides robustness against misleading characters than can pollute large-scale sequencing data.

SEQUENCE ANALYSIS OF THE CYTOCHROME OXIDASE I GENE IN AEDES ALBOPICTUS ISOLATED FROM TAMAN BUKIT KINRARA AND PJS7, SELANGOR

Aedes albopictus is one of the most invasive mosquitoes in the world that harbors and can transmit many arboviruses, most notably dengue and chikungunya virus. In recent time, Ae. aegypti has gained more attention during dengue outbreaks compared to its counter parts, obscuring the role of Ae. albopictus as a vector. Moreover, existing data regarding Ae. albopictus is also currently limited in Malaysia. Hence, the present study was conducted to determine the genetic diversity of Ae. albopictus using molecular techniques from two dengue infested areas in Subang Jaya, Selangor, namely Taman Bukit Kinrara (TBK) and PJS7. Cytochrome oxidase 1 (CO1) gene from field collected mosquitoes were analyzed and compared to the USM laboratory strain (F135) together with sequences from the GenBank. Results from this study revealed that the field collected mosquitoes from TBK and PJS7 are genetically similar with each other. However, the samples exhibited polymorphism with the laboratory strain by 47 variable nucleotide sites. Our local samples are related with the Ae. albopictus populations from India, probably due to its migration across these two regions via several human activities. This study shows that the CO1 gene is a valuable marker for the detection of Ae. albopictus and can be utilized to study its worldwide geographical distribution. Further analysis is strongly recommended using larger sample size and different localities to validate and substantiate our findings.

Genetic Diversity and Phylogenetic Relationships between Chinese Cabbages [B. campestris (syn. rapa) L.] and Cabbages (B. oleracea L.) in Korea

Members of the genus Brassica, which are known as oil crops or cruciferous vegetables, are widely cultivated in Canada, Australia, Asian and Europe. Because Brassica species have high yields, are well adapted to their environments, and are self-incompatible, the germplasm is abundant. Previous studies have reported abundant genetic diversity even within Brassica subspecies. In Korea, fresh cabbage leaves are eaten with roast meat, and to meet the current popular demand, new varieties are being increasingly bred. To determine the genetic diversity and relationships among the cabbage vegetables in Korea, we evaluated the genetic variation of 18 accessions based on 5S and 18S ribosomal RNA (rRNA) gene sequences. We detected many variable nucleotide sites, especially in the 5S rRNA gene sequences. Because the length of the 18S rRNA gene might influence the dissimilarity rate statistics, we used both the 5S and 18S sequences to analyze the phylogenetic relationships. S7 (B. oleracea) showed the most distant phylogenetic relationship with the other Brassica species. Interestingly, B2 (B. oleracea), B15, and B18 (B. campestris) have three different types of leaf profiles, and were divided into one group, and the other Brassica species formed another group. Statistical analysis of interspecies and intraspecies genetic distances revealed that B. campestris L. showed higher genetic diversity than B. oleracea L. This work provides additional data that facilitates the evaluation of the genetic variation and relationships among Brassica species. The results could be used in functional plant breeding programs to improve Brassica crops.

Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water.

Antarctic krill (Euphausiasuperba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limited number of markers and have covered only part of their circum-Antarctic range. We used mitochondrial DNA and restriction site-associated DNA sequencing (RAD-seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD-seq methodology, we obtained over a billion sequences from >140krill, and thousands of variable nucleotides were identified at hundreds of loci. However, downstream analysis found that markers with sufficient coverage were primarily from multicopy genomic regions. Careful examination of these data highlights the complexity of the RAD-seq approach in organisms with very large genomes. To characterize the multicopy markers, we recorded sequence counts from variable nucleotide sites rather than the derived genotypes; we also examined a small number of manually curated genotypes. Although these analyses effectively fingerprinted individuals, and uncovered a minor laboratory batch effect, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill's enormous population size creates substantial panmictic inertia, so genetic differentiation may not occur on an ecologically relevant timescale even if demographically separate populations exist.