Fine‐scale phylogeography reveals cryptic biodiversity in Pederson's cleaner shrimp,Ancylomenes pedersoni (Crustacea: Caridea: Palaemonidae), along the Florida Reef Tract

Populations of continuously distributed marine organisms that disperse via pelagic larvae are often assumed to exist in a state of genetic panmixia because of their potential ability for long‐distance dispersal. However, obligate symbionts may have more restricted gene flow due to recruitment limitations, making host specificity an important potential driver of biodiversity. To explore the tension between broad dispersal ability and limited recruitment potential, we used sequences of mtDNA cytochrome c oxidase subunit I (COI) to assess the fine‐scale phylogeography of the cleaner shrimp, Ancylomenes pedersoni, an obligate symbiont of sea anemones, along 300 km of the Florida Reef Tract (FRT). The results indicate high genetic diversity within A. pedersoni populations along the FRT. Pair‐wise ?_ST values indicate significant genetic structuring between northern (Fort Lauderdale and Upper Keys) and southwestern (Lower Keys) populations, with significant isolation by distance. Two divergent COI haplotype lineages were detected through statistical parsimony analysis: one evenly distributed across the entire FRT (Clade 1) and one found primarily in two sample localities in the Lower Keys (Clade 2). Phylogenetic analyses using 16S‐rDNA indicates that this genetic diversity is of paraphyletic origin, and possibly the result of multiple colonization events. These results reveal a complex demographic and evolutionary history for A. pedersoni populations and provide the first evidence of highly divergent intra‐specific lineages independently colonizing the FRT. Because the FRT is a highly impacted coral reef system, understanding phylogeographic patterns along it has value beyond documentation of the factors that generate genetic diversity in tropical reef systems: these data are critical for creating scientifically based management strategies.     

Genetic difference of Chinese horseshoe crab (Tachypleus tridentatus) in southeast coast of China based on mitochondrial COI gene analysis

Population genetic structure and historical demography of Chinese horseshoe crab (T. tridentatus) along southeast coast of China were inferred from the sequence data of mitochondrial cytochrome c oxidase subunit I (COI) fragment. The sequence analysis for 964 bp COI fragment was conducted in 28 individuals collected from five localities: Ninghai in Zhejiang Province, Meizhou and Zhangpu in Fujian Province, Beihai of Guangxi Zhuang Autonomous Region and Danzhou of Hainan Province. Sequence variation was relatively low with a total of seven transitions observed. In all localities, Haplotype H3 was the dominant type observed among eight haplotypes defined previously, and was at the center of radiation in Median-Joining network. The prolonged star-like network suggests a signature of population expansions. The level of diversity was low in total, with haplotype diversity (H_d) being equal to 0.765 and nucleotide diversity (π) being equal to 0.001 18, respectively. The genetic structure analysis revealed the significant genetic difference between Ninghai and Danzhou populations. Both mismatch distribution analysis and Fu's F_s test provided consistent inference of historic population expansion. The low genetic diversity of horseshoe crab observed along China coast indicated that urgent measures should be taken to protect this rare marine animal.     

Mitochondrial DNA variation reveals distinct lineages in Penaeus semisulcatus (Decapoda,Penaeidae) from the Indo‐West Pacific Ocean

Penaeus semisulcatus, the green tiger prawn, is an ecologically and economically important penaeid shrimp in the Indo‐West Pacific region, especially in rice‐shrimp farming and capture fisheries in Bangladesh and Sri Lanka, respectively. Genetic variation and phylogeography of samples of this species from Bangladesh and Sri Lanka were studied utilizing different mitochondrial DNA markers, i.e. cytochrome oxidase subunit 1 (CO1), control region (CR) and 16S rRNA genes. No evidence of population structure was observed in Bangladesh, but distinct variations were found among the Sri Lankan samples (Φ_ST = 0.04, p = .002; F_ST = 0.07, p = .001), with the western sample differing from the northwestern and southern samples. The Bangladesh population had lower genetic diversity than two of the three Sri Lanka populations. The phylogeography of P. semisulcatus revealed two distinct mitochondrial DNA (mtDNA) lineages, one in the Western Pacific Ocean and second in the Indian Ocean. The Bangladesh samples showed highest levels of similarity with samples from Sri Lanka, India and Malaysia, with the Bangladesh and Sri Lanka populations sharing the most common recent ancestry. Among the Indian Ocean samples, high levels of variation were observed in the samples from Iran, indicating admixture of two distinct mtDNA lineages, one shared by the populations from the Bay of Bengal and the other possibly originating from Eastern Africa. The genetic and phylogeographic information obtained in this study will be useful in appropriate planning for management and conservation of shrimp fisheries in Bangladesh and Sri Lanka, and in the Indo‐West Pacific region.     

6种帘蛤科贝类及4个地理种群文蛤线粒体COI基因片段序列分析

对文蛤(Meretrix meretrix L.,1758)、青蛤(Cyclina sinensis G.,1791)、硬壳蛤(Mercenaria mercenaria L.,1758)、江户布目蛤(Protothaca jedoensis L.,1874)、薄片镜蛤(Dosinia corrugata R.,1850)和菲律宾蛤仔(Ruditapes philippinarum A.,1850)6种帘蛤科贝类和4个地理种群文蛤(大连、连云港、湛江、防城港)的细胞色素c氧化酶亚基I(COI)基因片段的核苷酸序列进行了分析,以探讨这一序列在种质鉴定、种群遗传结构和分子系统发生研究中的应用价值.测序结果表明,所有物种扩增片段长度均为709 bp,序列A+T含量(62.2%~67.6%)明显高于GC含量.物种间共有变异位点311个,其中简约信息位点202个;文蛤4个地理种群间共有变异位点46个,其中简约信息位点2个.此区段共编码235个氨基酸,种间共有氨基酸变异位点85个;文蛤种群间只有1个氨基酸变异位点.以COI基因片段序列为标记,用大竹蛏(Solen grandis)作外群,构建了帘蛤科贝类的系统发生树,其拓扑结构显示4个地理种群文蛤首先聚为1个单元,然后与青蛤聚在一起,最后所有帘蛤科物种聚为一枝,与外群相区别,其结果与传统形态分类基本一致,说明COI基因适合作为该科贝类种群遗传结构和系统发生研究的分子标记.     

Size at first maturity in females of the spiny lobster jasus verreauxi (Crustacea: Decapoda: Palinuridae)

The carapace length and total length size at first maturity in females of Jasus verreauxi (H. Milne Edwards, 1851) has been investigated by a detailed study of (a) the detection of the smallest size class with external eggs, and (b) the incidence of egg‐carrying females per size‐class interval. For the study 834 females were measured and examined at Spirits Bay, New Zealand, during mid October and late December 1966. The specimens ranged in carapace length from 12.0 cm to 23.9 cm, and in total length from 29.0 cm to 56.9 cm.

The results of the study show clearly that the females reach first maturity at a carapace length or a total length larger than the present minimum legal size, i.e. a carapace length of 10.2 cm (4.02 in.), or a total length of 25.4 cm (10.0 in.). No mature females were found less than 13.5 cm carapace length, or 32.0 cm total length. First maturity was attained by the majority (50% or more) of the J verreauxi females at a carapace length of 15.3 cm or larger, or at a total length of 38.0 cm or larger.

No undersized (smaller than the minimum legal size) females were present in the collections—yet 10.3% of the specimens were found to be immature. Immature females ranged in carapace length from 12.0 cm to 16.9 cm, or in total length from 29.0 cm to 41.9 cm. Being larger than the minimum legal size, all of the immature specimens examined were “harvested"—without having reached first maturity. It appears therefore that the stocks of small, immature female J. verreauxi are not protected by the present New Zealand minimum size regulation.     

Phylogeography of Ophryotrocha labronica (Polychaeta,Dorvilleidae) along the Italian coasts

Species of the genus Ophryotrocha are a well‐studied group of organisms but, despite the relatively large body of biological studies, little is known about their intra‐specific patterns of genetic diversity. In the present study, we analysed the patterns of genetic variation in samples of Ophryotrocha labronica (Polychaeta, Dorvilleidae) collected along the Italian coasts within three regions with different thermal regimes: the Northern Adriatic Sea (NAS), the Ligurian Sea (LS), and the South/Southeast Sicilian Sea (SS). A partial sequence of the cytochrome c oxidase subunit I (COI) gene was used as a genetic marker. An analysis of molecular variance (AMOVA) showed significant genetic differentiation between the NAS and the other regions. Conversely, little or no genetic structuring was found between the LS and the SS or amongst locations within a given region. A Bayesian phylogenetic tree and a median‐joining network provided evidence for the occurrence of two highly divergent genetic lineages characterized by a high average sequence divergence (17.2%, Kimura two‐parameter distance). The spatial patterns of genetic variation found in O. labronica may reflect the signature of past expansion events of the two genetic lineages. Although the high sequence divergence suggested that cryptic speciation within O. labronica may have occurred, other traits such as the absence of reproductive isolation, pattern of phenotypic variation and habitat specificity prompted us to regard the two groups as distinct COI lineages of O. labronica.     

Phylogeography of the mud crab (Scylla serrata) in the Indo‐West Pacific reappraised from mitochondrial molecular and oceanographic clues: transoceanic dispersal and coastal sequential colonization

The widespread mud crab, Scylla serrata, of the Indo‐West Pacific is an excellent model species to demonstrate how the colonization history of a species can be influenced by complex oceanographic conditions. Through the combination of ecological data (fossil records and paleo‐oceanographic conditions) and molecular data (coalescent simulations, network analysis, and nucleotide diversity tests), the phylogeographic history of S. serrata was re‐analyzed. Based on the analysis of mtDNA cytochrome oxidase I sequences, two major clades were identified for S. serrata, including a widespread clade (Clade I) with three disjunct geographic clusters (IA, IB and IC) and an endemic Northwest Australian clade (Clade II). Moreover, a significant phylogeographic structure corresponding to four subpopulations was revealed: Northwest Australia, West Indian Ocean, Red Sea‐South China Sea and West Pacific. A colonization history of a Northwest Australia origin for S. serrata followed by westward transmarine dispersal across the Indian Ocean for Clade I and sequential colonization from the West Indian Ocean to Red Sea‐South China Sea and West Pacific was corroborated. The Pleistocene fluctuations of paleo‐oceanographic conditions including surface circulations and physical topography in the Indo‐West Pacific might be responsible for the wide distribution, colonization history and genetic divergence of this species.     

A pilot study of genetic differentiation between two phenotypes of a Mediterranean population of the bivalve Cerastoderma glaucum and genetic discrimination with other Cerastoderma glaucum and Cerastoderma edule populations outside the Mediterranean

The internal transcribed spacer 1 (ITS1) region of 29 individuals of Cerastoderma glaucum (from the Mediterranean Sea, the Atlantic and the North Sea) and 18 individuals of Cerastoderma edule (from the Atlantic and the North Sea) and the cytochrome c oxidase subunit I (COI) region of 43 individuals of C. glaucum (from the Mediterranean Sea, the Atlantic and the North Sea) and 9 individuals of C. edule (from the Atlantic and the North Sea) were PCR amplified and sequenced. The ITS1 sequences led us to describe 27 genetic haplotypes, while 21 genetic haplotypes were determined via the COI sequences. The ITS1 and the COI sequences revealed an important genetic variability within the Mediterranean population of C. glaucum, which contained two different phenotypes: orange foot and yellow foot. A genetic differentiation between the two phenotypes was revealed by the nucleotide diversity index (π) and is strengthened by the AMOVA analysis. This result leads us to suspect the presence of two different groups in the same population of C. glaucum. Nevertheless to be confirmed this hypothesis requires further studies using more locations and a larger number of sample sizes.     

Distribution and abundance patterns of two parapagurid hermit crabs (Crustacea: Decapoda: Anomura) along the west and south coasts of South Africa

A series of over 6 000 research-trawl samples collected along the west and south coasts of South Africa between 1987 and 2014 were analysed for the presence and biomass of two parapagurid hermit crabs, Sympagurus dimorphus and Parapagurus bouvieri. The percentage of trawls that landed S. dimorphus and P. bouvieri and the mean caught biomass were higher on the west than on the south coast for both the more-abundant S. dimorphus (30.59 vs 5.81% success and 287.88 vs 31.37 kg km^–2, respectively) and for the less-abundant P. bouvieri (13.76 vs 3.58% success and 38.56 vs 16.32 kg km^–2, respectively). Very few parapagurids were caught shallower than 150 m; thereafter, the proportion of trawls containing hermit crabs increased, peaking over the depth range 201–250 m for S. dimorphus (54%) and 401–450 m for P. bouvieri (51%), and declining steadily thereafter. On the west coast, the relative caught biomass of S. dimorphus increased significantly from north to south, but there was no apparent latitudinal trend in relative biomass for P. bouvieri. Similarly, there was a significant decline in caught biomass of S. dimorphus with increasing longitude along the south coast, but no apparent trend for P. bouvieri. Although this represents by far the most comprehensive global analyses of distribution and abundance patterns for parapagurids to date, extremely little remains known about the biology and ecological relationships of these species, or indeed of other members of the group.     

Phylogeny of the cuttlefishes (Mollusca: Cephalopoda) based on mitochondrial COI and 16S rRNA gene sequence data

To clarify cuttlefish phylogeny, mitochondrial cytochrome c oxidase subunit I (COI) gene and partial 16S rRNA gene are sequenced for 13 cephalopod species. Phylogenetic trees are constructed, with the neighbor-joining method. Coleoids are divided into two main lineages, Decabrachia and Octobrachia. The monophyly of the order Sepioidea, which includes the families Sepiidae, Sepiolidae and Idiosepiidae, is not supported. From the two families of Sepioidea examined, the Sepiolidae are polyphyletic and are excluded from the order. On the basis of 16S rRNA and amino acid of COI gene sequences data, the two genera (Sepiella and Sepia) from the Sepiidae can be distinguished, but do not have a visible boundary using COI gene sequences. The reason is explained. This suggests that the 16S rDNA of cephalopods is a precious tool to analyze taxonomic relationships at the genus level, and COI gene is fitter at a higher taxonomic level (i.e., family).     

Distribution of Phyllosoma Larvae (Crustacea: Decapoda: Palinuridae,Scyllaridae and Synaxidae) in the Western North Pacific

Phyllosoma larvae were identified and their distribution was examined, based on the larvae in ichthyoplankton samples collected in the Japanese Eel Expedition to the spawning area of A. japonica in the western North Pacific from August 30 to September 13, 1986 (Leg. 1), and from September 22 to 25, 1986 (Leg. 2), on board the R/V Hakuho-maru. Phyllosoma larvae belonged to 3 families (Scyllaridae, Palinuridae and Synaxidae) representing 6 genera and 14 species. A total of 336 palinurid and synaxid phyllosoma larvae were collected, of which 233 larvae (about 70%) were identical with P. longipes s. l, while a total of 362 scyllarid phyllosoma larvae were collected, of which 274 larvae (about 76%) were identical with S. cultrifer. Phyllosoma larvae of P. longipes s. l and S. cultrifer showed a similar distribution to each other. The larvae were abundant in the water close to Mariana Islands, although late stage examples were abundant in waters of Luzon and eastern Taiwan. Distributions of these larvae may be related intimately with the North Equatorial Current existing along 15°N. The North Equatorial Current approaches the eastern coast of the Philippines and then separates into two branches of northward and southward flows. The northward flow contributes to generating the Kuroshio Current while the southward flow goes to generate the Mindanao Current. Judging from distributions of phyllosoma larvae in the present study, it is assumed that the larvae of the above two species may have been released in Mariana Islands and transported westward from there through the North Equatorial Current. These larvae may then be transported to eastern Taiwanese waters.     

Genetic diversity and population structure of three dominant myctophid fishes (<Emphasis Type="Italic">Diaphus theta,Stenobrachius leucopsarus</Emphasis>, and <Emphasis Type="Italic">S. nannochir</Emphasis>) in the North Pacific Ocean

We compared the genetic diversity of three dominant myctophid fishes in the North Pacific Ocean that have different diel vertical migration patterns on the basis of the nucleotide sequences of the mitochondrial gene for cytochrome b. No genetic structure was detected for each of these three species. The genetic diversity progressively increased for Diaphus theta, a diel migrant species showing clear diel vertical migration; Stenobrachius leucopsarus, a semi-diel migrant, in which only part of the population migrates vertically; S. nannochir, a non-diel migrant. All three species were suggested to have experienced a recent, sudden population expansion. Interspecific differences in genetic diversity might be attributable to differences in the degree of population size reduction during the glacial periods; this degree in turn corresponds to the energy demand of the fishes.