COI Divergence Research Articles

High genetic connectivity among morphologically differentiated populations of the black sea urchin Arbacia lixula (Echinoidea: Arbacioida) across the central African Mediterranean coast

The present study represents the first population structure analysis of the black sea urchin Arbacia lixula across part of its African Mediterranean distribution range, the Tunisian coast. This location is appropriate for the study of biogeographical processes given the presence of a well-known discontinuous biogeographic area (the Siculo-Tunisian Strait). Patterns of morphological and genetic variation in this highly dispersive echinoid species were assessed among its populations from the western and eastern Mediterranean coasts of Tunisia. A total of 109 specimens from six sites were collected and examined for morphometric variability in seven morphometric traits. Concordant results, inferred from CDA analyses, pairwise NPMANOVA comparisons and MDS plot, showed significant inter-population differences in the measured traits among the studied populations. In addition, UPGMA clustering and discriminant/Hotelling analysis enabled the delineation of two morphologically differentiated groups assigned to the western and eastern Mediterranean basins. SIMPER analysis showed that total dry weight and test diameter were major contributors to the morphometric separation between locations and among groups. Despite the extensive morphological variation found in A. lixula, genetic analysis of the mitochondrial COI marker recovered only a single evolutionary lineage and showed a lack of population structure as inferred from the results of one-level AMOVA and pairwise comparisons of genetic differentiation. Possible explanations for this genetic pattern are discussed. Notably, the lack of COI divergence patterns, highlighted by shallow genealogy associated with high haplotype diversity and low nucleotide diversity, together with a recent demographic expansion event retrieved from mismatch distribution and BSP analysis could be considered a residual effect of a recent evolutionary history of the species in the Mediterranean.

Sequence-based species delineation and molecular phylogenetics of the transitional Nearctic–Neotropical grasshopper genus Taeniopoda (Orthoptera, Romaleidae)

Taeniopoda is a genus of grasshoppers currently represented by 12 species distributed from southern USA to Panama, with most of them occurring along the transitional Nearctic–Neotropical region in central and southern Mexico. Despite being a small group of conspicuous, colourful species, the systematics of Taeniopoda has been largely neglected, including its phylogenetic affinity with the morphologically similar, monotypic genus Romalea. Here, we assessed the species limits in 11 of the species of Teniopoda based on two mitochondrial (mt) markers (COI, cyt b). Phylogenetic relationships were reconstructed adding two nuclear gene markers (28S, H3). A relaxed molecular clock analysis was performed based on the mt markers. We detected nuclear mt paralogues (numts) and the probable introgression of T. tamaulipensis mtDNA in specimens of T. eques from central Mexico. Between six and 14 species of Taeniopoda were delimited by the sequence-based approaches performed (COI divergence with thresholds of 1 and 2%; General Mixed Yule-Coalescent (GMYC) model). The GMYC and 1% threshold analyses with COI were more congruent with the currently recognized morphology-based taxonomy with 10 and 11 putative species, respectively. Four of these species were regarded as ‘stable’, since they were supported by at least one of the molecular analyses and by diagnostic morphological features. The species-based phylogeny recovered Taeniopoda as paraphyletic with respect to the monotypic genus Romalea. Three morphologically and geographically congruent major clades were recovered, two with species having a considerably elevated pronotal crest and one with its members having it less elevated. The origin and subsequent diversification of Taeniopoda were estimated to occur from the mid and late Miocene to Pliocene, respectively. The current species diversity in Taeniopoda was estimated to occur during the Pleistocene, which was probably influenced by the climatic oscillations that occurred during this period and the uplift of mountain ranges in Central America.

Synalpheus pinkfloydi sp. nov., a new pistol shrimp from the tropical eastern Pacific (Decapoda: Alpheidae).

A new, conspicuously coloured species of the alpheid genus Synalpheus Spence Bate, 1888, is described based on material collected on the Pacific coast of Panama. Synalpheus pinkfloydi sp. nov. is closely related to the western Atlantic S. antillensis Coutière, 1909, the two taxa being transisthmian, cryptic sister species. Both species are characterised by the distal areas of their major and minor chelae coloured in an intense, almost glowing pink-red. The morphological differences between S. pinkfloydi sp. nov. and S. antillensis Coutière, 1909 are subtle, being limited to the slightly different proportions of the merus of both chelipeds, distodorsal armature of the major cheliped merus, relative length of the antennal scaphocerite, and body size. However, they are genetically different with a 10.2% sequence divergence in COI. Based on molecular clock estimates, these transisthmian taxa diverged around 6.8-7.8 mya, i.e. well before the final closure of the Isthmus of Panama 2.5-3 mya.

Taxonomy of Paraplatyarthrus Javidkar and King (Isopoda: Oniscidea: Paraplatyarthridae) with description of five new species from Western Australia, and comments on Australian Trichorhina Budde-Lunde, 1908 (Platyarthridae).

The oniscidean fauna of Australia is generally poorly known but recent sampling has revealed a new family, Paraplatyarthridae, found in both terrestrial and groundwater calcretes of central Western Australia. The family was initially described based on a new genus and species, Paraplatyarthrus subterraneus Javidkar and King, 2015. Here we describe an additional five Paraplatyarthrus species from the Yilgarn region of Western Australia, based on both morphological and molecular evidence (COI divergences). Four species are subterranean: P. crebesconiscus Javidkar and King sp. nov., P. cunyuensis Javidkar and King sp. nov., P. occidentoniscus Javidkar and King sp. nov., and P. pallidus Javidkar and King sp. nov., and one is a surface species, P. nahidae Javidkar and King sp. nov. A key to their identification is provided along with information on their distribution. In addition, type material of the two described Australian species of Platyarthridae, Trichorhina australiensis Wahrberg, 1922 from Western Australia and T. tropicalis Lewis, 1998 from Queensland, are examined. Morphological reassessment of type material shows T. australiensis belongs to Paraplatyarthrus (comb. nov.) and that T. tropicalis is correctly placed in Trichorhina, confirming that the genus and family Platyarthridae occur in Australia.

Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon).

Closely related marine species with large overlapping ranges provide opportunities to study mechanisms of speciation, particularly when there is evidence of gene flow between such lineages. Here, we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via restriction site-associated DNA sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister-species. On the other hand, complete lineage sorting was observed at the nuclear loci and most of the SNPs. Under neutral expectations, the smaller effective population size of mtDNA should lead to fixation of mutations faster than nDNA. Thus, these results suggest that hybridization in the recent past (0.174-0.263Ma) led to introgression of the mtDNA, with little effect on the nuclear genome. Analyses of the SNP data revealed 28 loci potentially under divergent selection between the two species. The combination of mtDNA introgression and limited nuclear DNA introgression provides a mechanism for the evolution of independent lineages despite recurrent hybridization events. This study adds to the growing body of research that exemplifies how genetic divergence can be maintained in the presence of gene flow between closely related species.

A new species of Amolops (Anura: Ranidae) from southern China.

A new species, Amolops albispinus sp. nov. is described based on a series of specimens collected from Mt. Wutong, Shenzhen, Guangdong Province, China. The new species can be distinguished from other known congeners by molecular divergence in the mitochondrial COI and 16S rRNA gene and morphological characters including presence of white conical spines on the lips, loreal and temporal regions, excluding the tympanum; small body, SVL 36.7-42.4 mm in adult males and 43.1-51.9 mm in adult females; very rough dorsal skin of body with numerous raised large warts; olive-brown dorsum with dark brown blotches; strongly developed vomerine teeth; absence of vocal sacs; absence of tarsal glands; absence of dorsolateral folds; presence of circummarginals groove on the disk of first finger; and absence of outer metatarsal tubercles. At present, the genus Amolops contains 51 species, of which 23 occur in China.

Gene flow between Atlantic and Pacific Ocean basins in three lineages of deep-sea clams (Bivalvia: Vesicomyidae: Pliocardiinae) and subsequent limited gene flow within the Atlantic

Pliocardiin (vesicomyid) clams rely on microbial symbionts for nutrition and are obligate inhabitants of deep-sea chemosynthetic ecosystems. Unlike many other invertebrate hosts of chemosynthetic microbes, pliocardiin clams are found in every ocean in a variety of reducing habitats, including hydrothermal vents, cold seeps, organic falls and deep-sea fans. The global distribution of pliocardiin clams suggests historical gene flow between ocean basins. We focus on 3 pliocardiin genera—‘Pliocardia’ I, Calyptogena and Abyssogena—each of which has a pair of sister clades in the Atlantic and Pacific. Our work tests the hypothesis that historical gene flow between the Atlantic and Pacific Oceans within these genera was interrupted by the closure of the Panamanian seaway and tests whether isolation between the ocean basins is the result of vicariance or past colonization. These questions are investigated in the context of fossil evidence, biogeography and phylogenetics. This study revealed a set of substitution rates consistent with other invertebrate studies (μ=0.8%/My/lineage), and a set consistent with much lower rates often attributed to deep-sea organisms (μ=0.3%/My/lineage). Among the Pacific/Atlantic sister pairs, ‘Pliocardia’ I COI divergence per lineage is intermediate (2.5%), Calyptogena is the highest (6.1%) and Abyssogena the lowest (0.8%). The substitution rates suggest that ‘Pliocardia’ I and Calyptogena have histories of at least 2.8My in the Atlantic, with Calyptogena likely older. The slower rate, however, is inconsistent with both the maximum age of the family and several well studied fossils: leaving the faster rate preferred. With the faster rate, the Abyssogena southwardae clade diverged from its Pacific sister clade around 1Mya, which likely post-dates the closure of the Isthmus of Panama and the opening of the Bering Strait. In light of this recent divergence, we test the previously proposed hypothesis that there is a high level of ongoing gene flow between Atlantic populations of A. southwardae. A. southwardae has colonized a broad geographic range of seep sites including the West Florida Escarpment, the Barbados Accretionary Prism, the Lobes of Congo, and the Mid-Atlantic Ridge north and south of the Romanche Transform Fault. Coalescent methods detect gene flow between Barbados and the Mid-Atlantic ridge; and between the West Florida Escarpment and the Lobes of Congo. All other comparisons failed to detect gene flow, contrary to prevailing interpretations of connectivity across the entire Atlantic Basin.

Morphological and taxonomic demarcation of Brachionus asplanchnoidis Charin within the Brachionus plicatilis cryptic species complex (Rotifera, Monogononta)

Three well-defined groups, consisting of 15 species, have recently been ascribed to organisms historically identified as the Brachionus plicatilis species complex. One of these groups, the large clade, is composed of two named species (Brachionus plicatilis s.s. and Brachionus manjavacas) and two species identifiers (B. ‘Nevada’ and B. ‘Austria’). B. ‘Austria’ has been confirmed to be B. asplanchnoidis. As no type specimen exists for this species, and the original taxonomic description is lacking in detail, we give a detailed account of this species using material from Obere Halbjochlacke in Austria where B. ‘Austria’ was first identified genetically. Our analysis of B. asplanchnoidis populations was of global scope, an approach that revealed a great degree of morphological variability. However, combining aspects of both the dorsal and ventral surfaces clearly discriminated B. asplanchnoidis from the rest of the large-type members. This approach may prove useful in taxonomic studies of other cryptic species with relatively few morphological features. We also observed a geographic pattern of genetic divergence within B. asplanchnoidis. Average uncorrected COI divergences for a 554-bp fragment of the COI gene ranged from 3.9% within species to 17.5% between species of the large clade and indicate deep divisions within the cryptic species complex.

DNA Barcoding of Metazoan Zooplankton Copepods from South Korea.

Copepods, small aquatic crustaceans, are the most abundant metazoan zooplankton and outnumber every other group of multicellular animals on earth. In spite of ecological and biological importance in aquatic environment, their morphological plasticity, originated from their various lifestyles and their incomparable capacity to adapt to a variety of environments, has made the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of cryptic or sibling species based on DNA sequence data. We examined sequence variation of a partial mitochondrial cytochrome C oxidase I gene (COI) from 133 copepod individuals collected from the Korean Peninsula, in order to identify and discriminate 94 copepod species covering six copepod orders of Calanoida, Cyclopoida, Harpacticoida, Monstrilloida, Poecilostomatoida and Siphonostomatoida. The results showed that there exists a clear gap with ca. 20 fold difference between the averages of within-specific sequence divergence (2.42%) and that of between-specific sequence divergence (42.79%) in COI, suggesting the plausible utility of this gene in delimitating copepod species. The results showed, with the COI barcoding data among 94 copepod species, that a copepod species could be distinguished from the others very clearly, only with four exceptions as followings: Mesocyclops dissimilis–Mesocyclops pehpeiensis (0.26% K2P distance in percent) and Oithona davisae–Oithona similis (1.1%) in Cyclopoida, Ostrincola japonica–Pseudomyicola spinosus (1.5%) in Poecilostomatoida, and Hatschekia japonica–Caligus quadratus (5.2%) in Siphonostomatoida. Thus, it strongly indicated that COI may be a useful tool in identifying various copepod species and make an initial progress toward the construction of a comprehensive DNA barcode database for copepods inhabiting the Korean Peninsula.

Strong genetic differentiation among populations of the freshwater shrimp Caridina cantonensis in Hong Kong: implications for conservation of freshwater fauna in urban areas

Freshwater organisms generally exhibit strong genetic structuring. Although understanding the level and spatial distribution of genetic diversity is crucial for conservation management planning, such information has received little attention until recently in highly developed cities where local extinction attributed to habitat destruction and urbanisation is intense. We compared the genetic divergence in mitochondrial COI of the freshwater shrimp Caridina cantonensis collected from 32 sites in Hong Kong, to determine the connectivity among populations and the levels of genetic diversity of the shrimp. We found that shrimp from different streams are genetically highly differentiated and each stream always has its own unique haplotype groups, even though some of the streams are separated only by a few kilometres, indicating very limited gene flow across streams. Moreover, genetic diversity within each stream is very low, usually with a single haplotype dominating the entire population, and genetic differentiation was observed among tributaries from the same drainage. The high genetic diversity of these species over short distances has significant conservation implications because a substantial amount of biodiversity may have already been lost as a result of past development. Careful conservation planning is essential for future development in Hong Kong and other cities.

A new genus of large hydrothermal vent-endemic gastropod (Neomphalina: Peltospiridae)

Recently discovered hydrothermal vent fields on the East Scotia Ridge (ESR, 56–60°S, 30°W), Southern Ocean, and the South West Indian Ridge (SWIR, 37°S 49°E), Indian Ocean, host two closely related new species of peltospirid gastropods. Morphological and molecular (mitochondrial cytochrome c oxidase subunit I, COI) characterization justify the erection of Gigantopelta gen. nov. within the Peltospiroidae with two new species, Gigantopelta chessoia sp. nov. from ESR and Gigantopelta aegis sp. nov. from SWIR. They attain an extremely large size for the clade Neomphalina, reaching 45.7?mm in shell diameter. The oesophageal gland of both species is markedly enlarged. Gigantopelta aegis has a thick sulphide coating on both the shell and the operculum of unknown function. The analysis of a 579-bp fragment of the COI gene resulted in 19–28% pairwise distance between Gigantopelta and six other genera in Peltospiridae, whereas the range amongst those six genera was 12–28%. The COI divergence between the two newly described species of Gigantopelta was 4.43%. Population genetics analyses using COI (370?bp) of 30 individuals of each species confirmed their genetic isolation and indicate recent rapid demographic expansion in both species.

Migration and isolation during the turbulent Ponto-Caspian Pleistocene create high diversity in the crustacean Paramysislacustris.

The Ponto-Caspian brackish-water fauna inhabits estuaries and rivers of the Black, Azov and Caspian seas and is fragmented by higher salinity waters and a major interbasin watershed. The fauna is known for the high levels of endemism, complex zoogeographic histories, and as a recent source of successful invasive species. It remains debated whether the Black and Azov Sea brackish-water populations survived unfavourable Pleistocene conditions in multiple separate refugia or whether the two seas were (repeatedly) recolonized from the Caspian. Using microsatellite and mtDNA markers, we demonstrate deep among- and within-basin subdivisions in a widespread Ponto-Caspian mysid crustacean Paramysislacustris. Five genetic clusters were identified, but their relationships did not reflect the geography of the region. The Azov cluster was the most distinct (4-5% COI divergence), despite its geographic position in the corridor between Black and Caspian seas, and may represent a new species. In the northern Black Sea area, the Dnieper cluster was closer to the Caspian cluster than to the neighbouring Danube-Dniester-Bug populations, suggesting separate colonizations of the Black Sea. Overall, the data implied a predominant gene flow from the east to the Black Sea and highlight the importance of Caspian Sea transgressions in facilitating dispersal. Yet, the presence of distinct lineages in the Black Sea points to the persistence of isolated refugial populations that have gained diagnostic differences under presumably high mutation rates and large population sizes. The unfavourable Pleistocene periods in the Black Sea therefore appear to have promoted diversification of the brackish-water lineages, rather than extirpated them.

Taxonomic status of the Columbia duskysnail (Truncatelloidea, Amnicolidae, Colligyrus).

Undescribed freshwater snails (Amnicolidae: Colligyrus) from the Mount Hood region (northwestern United States) identified as a new species (commonly known as the Columbia duskysnail) in grey literature have been provided federal protection under the “survey and manage” provisions of the Northwest Forest Plan and have been placed on conservation watch lists. However, there are no published studies of the identity of these snails aside from a molecular phylogenetic analysis which delineated a close relationship between the single sampled population and Colligyrus greggi, which is distributed more than 750 km to the east of the Mount Hood area. Here we examine the taxonomic status of the Columbia duskysnail based on additional molecular sampling of mitochondrial DNA sequences (COI) and morphological evidence. We found that the Columbia duskysnail is not a monophyletic group and forms a strongly supported clade with Colligyrus greggi. The COI divergence between these broadly disjunct groups (2.1%) was somewhat larger than that within Colligyrus greggi (1.0%) but considerably less than that among the three currently recognized species of Colligyrus (8.7–12.1%). Additionally we found that the Columbia duskysnail and Colligyrus greggi cannot be consistently differentiated by previously reported diagnostic characters (size and shape of shell spire, pigmentation of body and penis) and are closely similar in other aspects of morphology. Based on these results we conclude that the Columbia duskysnail is conspecific with Colligyrus greggi.

DNA barcoding of earthworms (Eisenia fetida/andrei complex) from 28 ecotoxicological test laboratories

Plenty of evidence indicates that the earthworms Eisenia fetida (Savigny, 1826) and Eisenia andreiBouché, 1972 (Lumbricidae) can be distinguished by morphological, physiological and molecular traits. However, the morphological differences alone do not allow to correctly identify these taxa. This may be a serious problem for the reliability of the standard ecotoxicological tests for which these worms are used. Recently, DNA barcoding (i.e., sequencing of a standard mtDNA COI gene fragment for identification purposes) has been proposed as a quick and simple method to identify species, including earthworms. In order to assess the practicability and reliability of this method, an international ring test was organized by the “Eisenia barcoding Initiative (EBI)”, a group of scientists from four public institutions and two contract laboratories. Coded samples of E. fetida,E. andrei, and Eisenia sp. were provided by 28 ecotoxicological laboratories from 15 countries on four continents. Five laboratories in Belgium, Canada, Germany, and Spain identified the specimen through DNA barcoding. All steps of the sample preparation were described by Standard Operating Procedures (SOP). The COI sequences (581bp) obtained were used to construct a neighbor-joining tree based on the uncorrected pairwise p-distance. This analysis revealed three distinct haplotype clusters: one including only E. andrei sequences (mean within-group p-distance 0.026±0.002) and two with only E. fetida sequences, referred to as E. fetida 1 and E. fetida 2. Each of the latter two in fact represented one single haplotype. The mean p-distance between E. fetida 1 and E. fetida 2 was 0.112, whereas the mean p-distances between these two taxa and E. andrei were 0.142 and 0.143, respectively. Such COI divergence levels are usually indicative of species level differentiation. Hence it is hypothesized that E. fetida 1 and E. fetida 2 refer to different cryptic species. Since the attribution of the individual worms to these three clusters was completely consistent among the five DNA barcoding laboratories the good applicability of DNA barcoding for the identification of these ecotoxicological test species is proven. Remarkably, specimens of the molecular E. fetida clusters were always identified morphologically as E. fetida. However, this was not true the other way round, i.e., some specimens of the molecular E. andrei cluster were identified morphologically as E. fetida. The results of this ring test are presented to standardization organizations (OECD, ISO) in order to improve the standardization and thus quality of ecotoxicological routine testing by using DNA barcoding.

Implications of hybridization, NUMTs, and overlooked diversity for DNA Barcoding of Eurasian ground squirrels.

The utility of DNA Barcoding for species identification and discovery has catalyzed a concerted effort to build the global reference library; however, many animal groups of economical or conservational importance remain poorly represented. This study aims to contribute DNA barcode records for all ground squirrel species (Xerinae, Sciuridae, Rodentia) inhabiting Eurasia and to test efficiency of this approach for species discrimination. Cytochrome c oxidase subunit 1 (COI) gene sequences were obtained for 97 individuals representing 16 ground squirrel species of which 12 were correctly identified. Taxonomic allocation of some specimens within four species was complicated by geographically restricted mtDNA introgression. Exclusion of individuals with introgressed mtDNA allowed reaching a 91.6% identification success rate. Significant COI divergence (3.5–4.4%) was observed within the most widespread ground squirrel species (Spermophilus erythrogenys, S. pygmaeus, S. suslicus, Urocitellus undulatus), suggesting the presence of cryptic species. A single putative NUMT (nuclear mitochondrial pseudogene) sequence was recovered during molecular analysis; mitochondrial COI from this sample was amplified following re-extraction of DNA. Our data show high discrimination ability of 100 bp COI fragments for Eurasian ground squirrels (84.3%) with no incorrect assessments, underscoring the potential utility of the existing reference librariy for the development of diagnostic ‘mini-barcodes’.

Taxonomy and DNA Sequencing ofCrematogaster coriariaMayr, 1872 (Hymenoptera: Formicidae), with Redescriptions of the Worker, Queen, and Male Castes

Crematogaster coriariaMayr, 1872, is revised based on the nest series samples. The following new synonymies are proposed:C. coriariaMayr, 1872 = C. coriaria fraudatrixForel, 1911syn. nov. = C. spengeliForel, 1912syn. nov. = C. spengeli taipingensisForel, 1913syn. nov.Worker, queen, and male castes ofC. coriariaMayr, 1872, are redescribed. The polymorphism ofC. coriariaMayr, 1872, was also discussed. DNA sequences were generated forC. coriariaMayr, 1872, using an amplification of second half region of the mitochondrial gene COI with a total of 711 bp. The interspecific COI divergence is 17.4% forC. coriariaMayr, 1872, andC. modiglianiiEmery, 1900.

Delimiting Evolutionarily Significant Units of the Fish, Piaractus brachypomus (Characiformes: Serrasalmidae), from the Orinoco and Amazon River Basins with Insight on Routes of Historical Connectivity.

The freshwater fish Piaractus brachypomus is an economically important for human consumption both in commercial fisheries and aquaculture in all South American countries where it occurs. In recent years the species has decreased in abundance due to heavy fishing pressure. The species occurs in the Amazon and Orinoco basins, but lack of meristic differences between fishes from the 2 basins, and extensive migration associated with reproduction, have resulted in P. brachypomus being considered a single panmictic species. Analysis of 7 nuclear microsatellites, mitochondrial DNA sequences (D-loop and COI), and body shape variables demonstrated that each river basin is populated by a distinct evolutionarily significant unit (ESU); the 2 groups had an average COI divergence of 3.5% and differed in body depth and relative head length. Historical connection between the 2 basins most probably occurred via the Rupununi portal rather than via the Casiquiare canal. The 2 ESUs will require independent fishery management, and translocation of fisheries stocks between basins should be avoided to prevent loss of local adaptations or extinction associated with outbreeding depression. Introductions of fishes from the Orinoco basin into the Putumayo River basin, an Amazon basin drainage, and evidence of hybridization between the 2 ESUs have already been detected.

Rebuttal to Koeda et al. (2014) on the Red Sea fishes of the perciform genus Pempheris.

Koeda et al. (2014) published a review of fishes of the genus Pempheris of the Red Sea. They concluded that there are four species: P. adusta Bleeker, P. mangula Cuvier, P. nesogallica Cuvier, and a new species, P. tominagai. We show that the first three species they cite are not present in the Red Sea, as follows. 1) P. adusta is a western Pacific species (type locality Ambon), described only from the holotype, and without a dark border on the anal fin. Koeda et al. (2014) mistakenly apply that name to P. flavicycla which is a widespread Indian Ocean species characterized by a prominent broad black border along the anal fin. Koeda et al. (2014) also redescribe P. adusta, using Indian Ocean specimens of P. flavicycla, despite the coloration difference and a 2.5% difference in the mtDNA sequence (COI) between Indian Ocean and W. Pacific populations. 2) P. mangula is a species from the east coast of India (type locality Visakhapatnam), clearly distinct in both gill-raker counts and a 1.1% sequence divergence in COI from its Red Sea relative P. rhomboidea. Pempheris mangula is not found west of India, and Koeda et al. (2014) mistakenly use DNA from Oman and Madagascar to represent P. mangula, instead of genetic material available from the type locality. 3) Pempheris nesogallica (type locality Mauritius) is unknown from the Red Sea. Koeda et al. (2014) separate P. nesogallica from P. rhomboidea (their "P. mangula") by eye size; we fail to find any difference (and they use their purported eye-size difference to erroneously rename one of the two syntypes of P. nesogallica as "P. mangula"). 4) Their new species P. tominagai is referred to as the Indian Ocean sister species of "P. schwenkii of the Pacific"; however, the type locality of P. schwenkii is the Batu Islands off the SW coast of Sumatra in the Indian Ocean. They mistakenly include specimens of a distant South African species as paratypes of P. tominagai. We have determined that P. tominagai is a valid species endemic to the Red Sea and Gulf of Aden. They misidentify one lot of P. rhomboidea in the collection of the Hebrew University of Jerusalem as their record of P. nesogallica from the Red Sea. They misidentify the specimen in their photograph of Fig. 1B as P. adusta and use it as material for their redescription of the species, but it is now shown to be a paratype of Pempheris bexillon Mooi & Randall, 2014. Additionally, they regard P. malabarica Cuvier as a junior synonym of P. molucca Cuvier, but the name P. molucca is based on a fanciful painting and is unavailable as a nomen dubium. They treat Pempheris russellii Day as a junior synonym of P. mangula; however, it is distinct in having longer pectoral fins, a larger eye, and more gill rakers. Their key to the species of Pempheris of the Red Sea is incorrect. We present a new key and conclude that only three species of Pempheris are presently known from the Red Sea: P. flavicycla, P. rhomboidea, and P. tominagai.

Evolutionary divergence of geographic subspecies within the scalloped spiny lobster Panulirus homarus (Linnaeus 1758).

Panulirus homarus is an economically important spiny lobster that is widespread through the Indo-West Pacific Region, but has an uncertain taxonomic status, with three or four geographic subspecies having been described. This study used mitochondrial (16S, COI and control region) and nuclear (18S, ITS-1) DNA sequences to examine specimens of all putative subspecies and forms from throughout their range, in order to determine their genetic validity, and understand the evolutionary history of this species. Despite the range of diversity present in the loci examined, the results were consistent across genes. P. h. rubellus from the SW Indian Ocean comprised the most divergent lineage that was reciprocally monophyletic with respect to all other P. homarus (approx. 9% divergence in COI), and has likely evolved reproductive barriers. The putative P. h. “Brown” subspecies from the Marquesas Is in the central Pacific also comprised a somewhat divergent monophyletic lineage (approx. 3% in COI), but may simply be an allopatric population. The widespread P. h. homarus was not diverged at all from the described P. h. megasculpta from the NW Indian Ocean. The degree of evolutionary divergence of populations at the extremes distribution of the species is somewhat surprising, given the long pelagic larval stage, but suggests that allopatric speciation has been an important driver in the evolution of the genus.

Cryptic diversity and phylogeography of the island‐associated barnacle Chthamalus moro in Asia

AbstractPleistocene glaciations were among the important historic events that shaped the population structures of marine organisms. Genetic studies of different marine fauna and flora have demonstrated the effect of Pleistocene glaciations on taxa that reside in marginal seas. However, how marine island species responded to Pleistocene glaciations remains relatively unstudied, especially in Asia. Genetic analyses based on the island‐associated barnacle Chthamalus moro collected from 14 sites in Asia reveal that C. moro comprises three distinct lineages, with COI divergence ranging from 3.9 to 8.3%. Population genetic analyses on respective lineages reveal signs of demographic expansion within the Pleistocene epoch at different times. The Ogasawara lineage, which has a more oceanic distribution, expanded the earliest, followed by the population expansion of the Ryukyu and Southern lineages that inhabit islands closer to the continent. The data suggest that the inhabitants of outer islands may have been less affected by Pleistocene glaciations than those that reside closer to the continent, as the former were able to maintain a large, stable, effective population size throughout the late Pleistocene.