Molecular systematics of peppermint and cleaner shrimps: phylogeny and taxonomy of the genera Lysmata and Exhippolysmata (Crustacea: Caridea: Hippolytidae)

Shrimps from the ecologically diverse genera Lysmata and Exhippolysmata are rare among marine invertebrates because they are protandric simultaneous hermaphrodites: shrimps initially mature and reproduce solely as males, and later in life become functional simultaneous hermaphrodites. Considerable progress on the reproductive ecology of members from these two genera has been achieved during the last decade. However, several outstanding issues of systematic nature remain to be addressed. Here, a molecular phylogeny of these two genera was used to examine the overall evolutionary relationship within and between species and genera, and to answer various questions related to the systematic status of several species. The present phylogenetic analysis, including 53 sequences and 26 species of Lysmata and Exhippolysmata, indicates that semiterrestrial shrimps from the genus Merguia represent the sister group to a second natural clade composed by shrimps from the genera Lysmata and Exhippolysmata. Also, the phylogenetic analysis confirmed that the genus Lysmata is paraphyletic, and includes the genus Exhippolysmata, as noted in a preliminary study. The tree partially supports the separation of species with or without a developed accessory branch into two different genera or subgenera (i.e. Lysmata and Hippolysmata having a well‐developed accessory branch, or not, respectively). The genetic distance between the cleaner shrimps Lysmata amboinensis and Lysmata grabhami was smaller than has been observed between other sister species. On the other hand, the topology of the tree indicates that these two entities are reciprocally monophyletic. Thus, this latter result, together with minor but constant differences in the colour pattern reported for these two entities, indicates that there is no reason to stop treating them as different valid species. This study enabled the long overdue resolution of standing taxonomic questions in shrimps from the genera Lysmata and Exhippolysmata. In the future, this phylogeny will help to reveal the conditions favouring the origins of several behavioural and morphological novelties in these unique shrimps. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 254–265.     

Testing three models on the adaptive significance of protandric simultaneous hermaphroditism in a marine shrimp

Protandric simultaneous hermaphroditism, as reported for shrimps in the genus Lysmata, is a sexual system in which individuals invariably reproduce as males first and later in life as simultaneous hermaphrodites. I tested three models (i.e., sex-dependent energetic costs, sex-dependent mortality rates and sex-dependent time commitments) in an attempt to explain the adaptive value of protandric simultaneous hermaphroditism in the shrimp L. wurdemanni. Specific assumptions and predictions of each model were evaluated using manipulative experiments. In the laboratory, males grew faster than simultaneous hermaphrodites of the same size and age, an indication that the female function incurs higher energetic costs of reproduction than the male function. Also, large SHPs were more successful in monopolizing food than small males. The sex-dependent growth rate and size-dependent resource holding power agree with predictions of the sex-dependent energetic cost model. The time that simultaneous hermaphrodites required for replenishing their sperm reservoirs after mating as males was much shorter (2 days) than the time required to brood one clutch of embryos (11 days). Also, small simultaneous hermaphrodites experienced heavier mortality due to predatory fishes than large ones. The sex-dependent reproductive time commitment and size-dependent mortality agree with predictions of the sex-dependent time commitment model. Conversely, I found no evidence that the sex-dependent mortality model explains protandric simultaneous hermaphroditism in the studied species. In contrast to model predictions, mortality due to predatory fishes suffered by simultaneous hermaphrodites was not greater than that suffered by males of the same body size. In L. wurdemanni, the relationship between sex-specific investment and reproductive success seems to change during ontogeny in a way that is consistent with an adaptive adjustment of sex allocation to improve age-specific reproductive success.     

Protandric simultaneous hermaphroditism in the shrimps Lysmata bahia and Lysmata intermedia

Abstract. The sexual system of two peppermint shrimps, Lysmata bahia and Lysmata intermedia, inhabiting intertidal fossil coral terraces at Bocas del Toro, on the Caribbean coast of Panama, was examined. Dissections suggested that the population of each species consisted of functional males and functional simultaneous hermaphrodites. Males have cincinulli and appendices masculinae on the first and second pair of pleopods, respectively, gonopores located at the coxae of the third pair of walking legs, and ovotestes with a well‐developed male portion full of sperm, but an undeveloped female portion. Hermaphrodites lacked appendices masculinae and cincinulli. However, they have male gonopores and ovotestes with well‐developed ovaries full of mature oocytes and testes with sperm. When hermaphrodites were maintained in pairs, both molted and spawned eggs (to beneath abdomen) that continued developing after 3 d, demonstrating that hermaphrodites can reproduce as males and inseminate other hermaphrodites acting as females. The possibility of self‐fertilization or parthenogenetic reproduction was tested and disregarded, because hermaphrodites reared in isolation spawned oocytes that failed to develop, disappearing from the abdomen after 2 d. Males reared in pairs mature as hermaphrodites in <50 d, showing the ability of males to mature as hermaphrodites. These results demonstrate that L. bahia and L. intermedia are protandric simultaneous hermaphrodites, as reported for all species of this genus whose sexual system has been examined. However, the studied species featured a lifestyle, termed “tropical‐low abundance,” here not recognized previously for the genus; they occur in low abundances in tropical environments, they do not develop symbiotic associations with sessile invertebrates, and they are not conspicuously colored. Information on the sexual systems and lifestyles of more species needs to be examined before these observations can be placed into a comparative context within the genus.     

The evolutionary history of seahorses (Syngnathidae: Hippocampus): molecular data suggest a West Pacific origin and two invasions of the Atlantic Ocean

Sequence data derived from four markers (the nuclear RP1 and Aldolase and the mitochondrial 16S rRNA and cytochrome b genes) were used to determine the phylogenetic relationships among 32 species belonging to the genus Hippocampus. There were marked differences in the rate of evolution among these gene fragments, with Aldolase evolving the slowest and the mtDNA cytochrome b gene the fastest. The RP1 gene recovered the highest number of nodes supported by >70% bootstrap values from parsimony analysis and >95% posterior probabilities from Bayesian inference. The combined analysis based on 2317 nucleotides resulted in the most robust phylogeny. A distinct phylogenetic split was identified between the pygmy seahorse, Hippocampus bargibanti, and a clade including all other species. Three species from the western Pacific Ocean included in our study, namely H. bargibanti, H. breviceps, and H. abdominalis occupy basal positions in the phylogeny. This and the high species richness in the region suggests that the genus evolved somewhere in the West Pacific. There is also fairly strong molecular support for the remaining species being subdivided into three main evolutionary lineages: two West Pacific clades and a clade of species present in both the Indo-Pacific and the Atlantic Ocean. The phylogeny obtained herein suggests at least two independent colonization events of the Atlantic Ocean, once before the closure of the Tethyan seaway, and once afterwards.     

Phylogeny and species boundaries in the gobiid genus Gnatholepis (Teleostei: Perciformes)

Species of the goby genus Gnatholepis Bleeker, 1874, are common inhabitants of shallow tropical seas worldwide. In this study, mitochondrial DNA sequence (ND2 gene), from 349 Gnatholepis individuals sampled from across the South and Central Pacific and Caribbean, is used to infer phylogeny and determine species boundaries. Seven species of Gnatholepis are recognized: the Indo-Pacific G. anjerensis (Bleeker, 1851) [ G. cauerensis (Bleeker, 1853) is a synonym]; G. scapulostigma Herre, 1953; G. davaoensis Seale, 1910; G. knighti Jordan & Evermann, 1903; G. gymnocara Randall & Greenfield, 2001; G.  sp. Randall & Greenfield, 2001; and the Atlantic/Caribbean G. thompsoni Jordan, 1904. Results from the molecular phylogeny are compared with a previous morphology-based revision of the genus in order to establish which morphological characters diagnose species in correspondence with the molecular phylogeny.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 142 , 573–582.     

Species-level phylogeography and evolutionary history of the hyperdiverse marine gastropod genus Conus

Phylogenetic and paleontological analyses are combined to reveal patterns of species origination and divergence and to define the significance of potential and actual barriers to dispersal in Conus, a species-rich genus of predatory gastropods distributed throughout the world's tropical oceans. Species-level phylogenetic hypotheses are based on nucleotide sequences from the nuclear calmodulin and mitochondrial 16S rRNA genes of 138 Conus species from the Indo-Pacific, eastern Pacific, and Atlantic Ocean regions. Results indicate that extant species descend from two major lineages that diverged at least 33 mya. Their geographic distributions suggest that one clade originated in the Indo-Pacific and the other in the eastern Pacific + western Atlantic. Impediments to dispersal between the western Atlantic and Indian Oceans and the central and eastern Pacific Ocean may have promoted this early separation of Indo-Pacific and eastern Pacific + western Atlantic lineages of Conus. However, because both clades contain both Indo-Pacific and eastern Pacific + western Atlantic species, migrations must have occurred between these regions; at least four migration events took place between regions at different times. In at least three cases, incursions between regions appear to have crossed the East Pacific Barrier. The paleontological record illustrates that distinct sets of Conus species inhabited the Indo-Pacific, eastern Pacific + western Atlantic, and eastern Atlantic + former Tethys Realm in the Tertiary, as is the case today. The ranges of <1% of fossil species (N=841) spanned more than one of these regions throughout the evolutionary history of this group.     

Population distribution,host-switching,and chemical sensing in the symbiotic shrimp <Emphasis Type="Italic">Lysmata pederseni</Emphasis>: implications for its mating system in a changing reef seascape

Lysmata pederseni, a protandric simultaneously hermaphroditic shrimp that inhabits the tube sponge Callyspongia vaginalis, is monogamous in the central and southeastern Caribbean Sea. We tested the null hypothesis of monogamy in a northern Caribbean population. In the Florida Keys, shrimps did not inhabit host individuals in pairs with a frequency greater than expected by chance alone. Hermaphrodites inhabited sponges solitarily and often brooded embryos. Hermaphrodites do not store sperm and need to be inseminated shortly after molting to fertilize a new batch of eggs. Thus, males and/or other hermaphrodites are likely switching among host individuals in search of sexual partners. Field experiments demonstrated low shrimp host fidelity. Host residence time was ~2 times shorter for males than for hermaphrodites. We inferred a polygynandrous mating system in L. pederseni from the Florida Keys, with male-role and young hermaphrodites often moving among sponges in search of older, more sedentary, female-role hermaphrodites. We expected shrimps to use water-borne chemical cues originating from conspecifics or sponges to locate sexual partners. Experiments demonstrated that shrimps were attracted to water-borne cues originating from sponges but not conspecifics. We have described the mating system of a reef-associated shrimp in a fast-pace shifting seascape increasingly dominated by sponges and vanishing stony corals. In the central and southeastern Caribbean Sea, with greater coral cover and lower sponge abundance than in the Florida Keys, the same species is monogamous. Whether or not similar shifts in the social organization of other coral reef-dwelling marine organisms are occurring due to contemporary changes in seascapes is a relevant topic that deserves further attention.     

Observations on the sexual system and the natural history of the semi-terrestrial shrimp Merguia rhizophorae (Rathbun, 1900)

Abstract. The sexual system of the semi-terrestrial shrimp Merguia rhizophorae is described, along with natural history observations on this unusual caridean. Individuals of M. rhizophorae in the Bocas del Toro Archipelago, Panama, were found occupying fossilized coral terraces in the upper and mid-intertidal zones, inhabiting caves and crevices, in and out of water. These fossilized coral terraces represent a new habitat for this species, which was previously reported only from mangrove swamps. Males, which made up 65% of the studied population, were smaller than females on average. No small juvenile females were observed, but transitional individuals having the characteristics of both males (gonopores) and females (ovaries) were observed in the population. These data suggest that individuals of M. rhizophorae are protandric hermaphrodites. Logistic regression indicated that the carapace length at which 50% of the individuals change sex is 4.89 mm. The abundance of shrimps at the study site was low. Shrimps were usually solitary, but occasionally observed in groups of ≤5 individuals. Shrimps were commonly observed walking while out of water, and in some cases, emerged shrimps jumped vigorously, presumably to avoid capture by the researcher or by predatory crabs. Additional studies on the reproductive biology and the behavioral ecology of members of this genus and of members of the closely related families Barbouridae and Lysmatidae will aid in understanding the evolutionary origin and the adaptive value of gender expression patterns in shrimps.     

BREAKING UP AND GETTING TOGETHER: EVOLUTION OF SYMBIOSIS AND CLONING BY FISSION IN SEA ANEMONES (GENUS ANTHOPLEURA)

Abstract Clonal growth and symbiosis with photosynthetic zooxanthellae typify many genera of marine organisms, suggesting that these traits are usually conserved. However, some, such as Anthopleura , a genus of sea anemones, contain members lacking one or both of these traits. The evolutionary origins of these traits in 13 species of Anthopleura were inferred from a molecular phylogeny derived from 395 bp of the mitochondrial 16S rRNA gene and 410 bp of the mitochondrial cytochrome oxidase subunit III gene. Sequences from these genes were combined and analyzed by maximum-parsimony, maximum-likelihood, and neighbor-joining methods. Best trees from each method indicated a minimum of four changes in growth mode and that symbiosis with zooxanthellae has arisen independently in eastern and western Pacific species. Alternative trees in which species sharing growth modes or the symbiotic condition were constrained to be monophyletic were significantly worse than best trees. Although clade composition was mostly consistent with geographic sympatry, A. artemisia from California was included in the western Pacific clade. Likewise, A. midori from Japan was not placed in a clade containing only other Asian congeners. The history of Anthopleura includes repeated shifts between clonality and solitariness, repeated attainment of symbiosis with zooxanthellae, and intercontinental dispersal.     

Phylogenetics and morphological evolution of coral‐dwelling barnacles (Balanomorpha: Pyrgomatidae)

Pyrgomatid barnacles are a family of balanomorphs uniquely adapted to symbiosis on corals. The evolution of the coral‐dwelling barnacles is explored using a multi‐gene phylogeny (COI, 16S, 12S, 18S, and H3) and phenotypic trait‐mapping. We found that the hydrocoral associate Wanella should be excluded, while some archaeobalanids in the genus Armatobalanus should be included in the Pyrgomatidae. Three well supported clades were recovered: clade I is the largest group and is exclusively Indo‐West Pacific, clade II contains two plesiomorphic Indo‐West Pacific genera, while clade III is comprised of East and West Atlantic taxa. Some genera did not form reciprocally monophyletic groups, while the genus Trevathana was found to be paraphyletic and to include members of three other apomorphic genera/tribes. The highly unusual coral‐parasitic hoekiines appear to be of recent origin and rapidly evolving from Trevathana sensu lato. Pyrgomatids include six‐, four‐, and one‐plated forms, and exhibit convergent evolutionary tendencies towards skeletal reduction and fusion, loss of cirral armature, and increased host specificity. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 162–179.     

Orthodox and unorthodox phylogenetic relationships among tunas revealed by the nucleotide sequence analysis of the mitochondrial DNA control region

A phylogeny of all eight recognized taxa of the genus Thunnus was constructed from approximately 400 base pairs of sequence of the mitochondrial DNA (mtDNA) control region. The PCR-amplified control region I segment studied contained a total of 186 variable sites and 159 phylogenetically informative sites. Diagnostic sequences for every taxon were identified. Neighbour-joining phylogenies supported monophyletic origins of the temperate subgenus Thunnus and of the tropical subgenus Neothunnus . Similar results were obtained by maximum parsimony analyses except that there was no support for a monophyletic origin of the subgenus Thunnus . Bigeye tuna, which have been difficult to place in either subgenus using conventional morphological data, was identified as the sister species of Neothunnus . Within the subgenus Thunnus , the Atlantic bluefin and Southern bluefin tunas were shown to be sister taxa of the highly divergent monophyletic clade formed by the Pacific northern bluefin and the Albacore tunas. The conspecific Atlantic ( T. thynnus thynnus ) and Pacific ( T. t. orientalis ) northern bluefin tunas were more divergent (Tamura-Nei distance 0·145 ± 0·019) from each other than the average distance separating most species-pairs within the genus. Thus, a re-examination of their status as subspecies of T. thunnus is warranted.     

Same sexual system but variable sociobiology: evolution of protandric simultaneous hermaphroditism in Lysmata shrimps

The sexual system of the decapod (caridean) shrimp Lysmata isprotandric simultaneous hermaphroditism (PSH). Individuals firstmature as males (male phase = MP) and then when older (larger)change to the external phenotype of female carideans (femalephase = FP). However, unlike purely protandric carideans, LysmataFPs retain reduced male gonadal tissues and ducts, and are ableto mate nonreciprocally as males as well as to reproduce asfemales. Thus, FPs of Lysmata species are functional simultaneoushermaphrodites although most reproductive effort is devotedto embryo production and incubation. The question explored hereis, given the propensity of carideans to protandry, the apparentlow cost, and high reproductive advantage of PSH, why has notPSH evolved more frequently? The mating systems and sexual selectionof caridean shrimps, the original sex of protandric individuals,the cost of maleness, and sex allocation theory are discussedin relation to protandry and PSH. None of these factors adequatelyexplains the evolution of PSH of Lysmata species. Lysmata hasat least 2 species groups with very different sociobiologies;these groups do not appear to share current selective pressuresthat would explain PSH in both. A historical contingency hypothesis,testable in part with a phylogenetic analysis, may explain theevolution of PSH in Lysmata.     

Phylogeography and phyloecology of dorid nudibranchs (Mollusca, Gastropoda)

Dorid nudibranchs exhibit a number of anatomical and physiological adaptations that reflect a complex evolutionary history. The lack of a fossil record means that all available information on the evolution of this group comes from phylogenetic evidence. Deep imbalances in the phylogeny of dorid nudibranchs indicates that this group has probably undergone random extinction events and subsequent speciation of derived lineages. Sister-group relationships between eastern Pacific, Atlantic and tropical Indo-Pacific taxa [(eastern Pacific, Atlantic) Indo-Pacific], repeated throughout several lineages of dorid nudibranchs, provide solid evidence of two consecutive vicariant events: (1) the closure of communication between the tropical Indo-Pacific region and the Atlantic and eastern Pacific, which began during the Oligocene–Miocene transition and was completed with the formation of the East Pacific Barrier, and (2) the rise of the Panama isthmus. The absence of solid dates for the effective isolation of the eastern Pacific and the central Pacific does not allow estimations of the time of diversification of dorid nudibranchs. Phylogenetic evidence indicates that omnivorism and de novo synthesis of chemical defences are probably the plesiomorphic conditions in dorid nudibranchs. It is also likely that all sponge-feeding cryptobranch dorids have a common ancestor, but other cases of sponge feeding in phanerobranch dorids have arisen independently. The numerous instances in which de novo synthesis was replaced by sequestration of chemicals from the prey are evidence of a great metabolic versatility in dorid nudibranchs.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 551–559.     

Biodiversity hotspots: evolutionary origins of biodiversity in wrasses (Halichoeres: Labridae) in the Indo-Pacific and new world tropics

Halichoeres is a widely distributed coral reef fish genus with high levels of biodiversity in both the Indo-Pacific and New World tropics. This study employed molecular phylogenetic techniques and biogeographic analyses on 1700-1800 bp of mitochondrial CO1, 16s, and 12s to test competing hypotheses regarding the origins of biodiversity in this genus in these two biodiversity hotspots. Analyses indicate that Halichoeres is polyphyletic with distinct New World and Indo-Pacific Ocean components. The Halichoeres in the New World tropics formed a strongly supported clade (99% MP, 100% ML bootstrap values) that diverged 21.2-18.1 mya, suggesting that this lineage may represent a relictual fauna of the ancient Tethys Sea. The closure of the Isthmus of Panama contributed to the creation of Halichoeres biodiversity, but diversification across the Isthmus prior to its closure and within the W. Atlantic after the closure 3.1 mya were also important processes creating biodiversity in the New World tropics. Within the Indonesian Australian Archipelago (IAA) analysis of age vs. geographic distribution supported neither Center of Origin, Center of Accumulation or Center of Overlap hypotheses, and molecular clock estimates indicated that the role of Pleistocene sea level changes in the origins of IAA marine biodiversity may be less important than previously thought. Ancestral distribution reconstructions within the Indo-West Pacific (IWP) clade (99% ML bootstrap value) also failed to support these hypotheses as the reconstructions were highly sensitive to the inclusion of missing taxa. Results suggest plueralistic origins of biodiversity, but that vast amounts of habitat may favor the survival of biodiversity in the IAA biodiversity hotspot.     

Characterization of the sexual pattern of Parastacus varicosus (Crustacea: Decapoda: Parastacidae)

Abstract. Freshwater crayfishes of the genus Parastacus are intersex, i.e., show characteristics of both sexes in the same individual; also, intersexuality has been documented in hermaphroditic species. The aim of this study was to analyze the gonads of Parastacus varicosus , characterizing its sexual pattern. The animals were collected at Cova do Touro, Gravataí, Rio Grande do Sul, Brazil. Three sexual forms were identified: intersex females, intersex males, and transitional specimens showing an ovotestes gonad that could only be identified by means of histological analysis. All specimens had two pairs of gonopores and gonoducts. The oviduct had a wider diameter in females, whereas in males the vasa deferentia were more developed. Gonads were composed of two parallel structures located in the cephalothorax. Female gonads were classified into three stages. The presence of transitional specimens may indicate that sex change occurs, with protandric hermaphroditism, as observed in other species of Parastacus . Because previous studies had demonstrated that P. varicosus is a gonochoristic species in a population from Uruguay, the present study addressed the possibility that the sexual pattern depends on differences in environmental factors among populations. To improve understanding of evolution of hermaphroditism in these crustaceans, their reproductive dynamics should be studied, including identification of the factors stimulating male and female functions.     

基于线粒体基因组全序列的鲟形目鱼类(Pisces: Acipenseriformes)的分子系统发育重建

为厘清鲟形目鱼类的系统发育, 研究新测定了中华鲟(Acipenser sinensis)、长江鲟(A. dabryanus)、短吻鲟(A. brevirostrum)、纳氏鲟(A. naccarii)、鳇(Huso dauricus)和匙吻鲟(Polyodon spathula)共6种鲟类的线粒体全基因组序列。联合已测的17种鲟类的线粒体基因组数据, 利用最大似然法和贝叶斯法重建了鲟形目鱼类的分子系统发育关系, 并采用似然值检验对不同的树拓扑结构进行了评价。结果表明, 6种新测鲟类的线粒体基因组大小为16521—16766 bp, 编码13个蛋白质编码基因、22个转运RNA基因和2个核糖体基因, 与大多数已测的鲟类的线粒体基因组结构高度相似。基于23种鲟形目鱼类线粒体基因组数据, 系统发育分析的结果表明: (1)鲟形目的两个科, 匙吻鲟科(Polyodontidae)和鲟科(Acipenseridae)均为单系; (2)鲟科的内部亲缘关系复杂, 鲟属和鳇属的物种均不构成单系群。鲟科鱼类按分子系统发育重建结果可以分为3个类群: 尖吻鲟类(A. sturio - A. oxyrinchus clade)、大西洋鲟类(Atlantic clade)和太平洋鲟类(Pacific clade)。树拓扑结构的检验结果表明, 鲟科的系统发育关系为(尖吻鲟类(太平洋鲟类, 大西洋鲟类))。铲鲟属(Scaphirhynchus)是大西洋鲟类的基部类群。研究也说明线粒体基因组数据在鲟形目鱼类系统与进化研究方面具有重要应用价值。