Mitochondrial phylogenomics reveals insights into taxonomy and evolution of Penaeoidea (Crustacea: Decapoda)

The taxonomy and phylogeny of Penaeoidea have long been fraught with controversy. Here, we carried out the first mitochondrial phylogenomic analysis on all the penaeoid families and tribes, including nine newly sequenced and 14 published mitogenomes, towards elucidating the phylogeny and evolutionary history of Penaeoidea. All these nine mitogenomes exhibit the pancrustacean ground pattern, except that Benthonectes filipes contains two additional clusters of tRNA^Ala, tRNA^Arg and tRNA^Asn and an uncommon noncoding region. The resulted phylogenetic tree is generally well resolved with Benthesicymidae sister to Aristeidae, forming a clade with Solenoceridae. Contrary to traditional classification, this clade has a sister relationship with the tribe Penaeini of the family Penaeidae. The family Sicyoniidae is deeply nested within the penaeid tribe Trachypenaeini which forms a sister clade with the remaining penaeid tribe, Parapenaeini. As the family Penaeidae is recovered to be polyphyletic, the three tribes in Penaeidae are all elevated to familial status. On the other hand, the family Sicyoniidae is retained to accommodate Trachypenaeini because they are now synonyms and the former name is more senior. This work is the first molecular analysis concurring with the latest findings in fossil assessments showing that Parapeaneini is the most primitive in Penaeoidae. Our results also illustrate a shallow‐water origin and an onshore–offshore evolutionary shift in penaeoid shrimps.     

Spermatozoal ultrastructure in three Atlantic solenocerid shrimps (Decapoda, Dendrobranchiata)

The spermatozoal ultrastructure in three solenocerid shrimps (Solenocera membranacea, S. africana, and Pleoticus muelleri) from different Atlantic locations was examined with the aim of increasing understanding of the phylogenetic relationships in the Dendrobranchiata. A considerable structural similarity between the sperm of these species and those of penaeid shrimps supports a close affinity between the Penaeidae and Solenoceridae. However, significant differences in the sperm morphology of the previously investigated sicyoniids (namely, a greater complexity of the acrosomal complex) suggest evolutionary separation of the Sicyoniidae from the assemblage Penaeidae-Solenoceridae. Two ultrastructural features distinguish the spermatozoa of the three studied solenocerids from penaeid sperm: 1) separation of the plasma and acrosome membranes at the base of the spike and anterior region of the cap, and 2) asymmetry of the acrosomal cap, which appears to be a synapomorphy of the group. No striking ultrastructural differences were found between the spermatozoa of the closely related species S. membranacea and S. africana, whereas a great number of morphological differences separate the spermatozoa of Pleoticus from those of Solenocera (e.g., shape of the acrosomal cap, structural arrangement of the contents of the whole acrosome vesicle, thickness and distribution of the cytoplasm, and external shape of the spike).     

Molecular phylogeny and diversity of penaeid shrimps (Crustacea: Decapoda) from South-East Asian waters

The decapod family Penaeidae comprises most of the economically important marine shrimp species. Its members are widespread throughout the world, with its highest species diversity centred in the Indo-West Pacific region. Despite this importance, their taxonomy, classification and phylogeny are not yet settled due in part to incongruence among hypotheses proposed from molecular versus morphological studies. In this study, using a thorough taxonomic sampling of especially the South-East Asian species, we aim to (a) utilize a reconstructed phylogeny to test the monophyly of the Penaeidae and its currently recognized genera and (b) explore its species diversity in South-East Asian waters. To infer the phylogeny, a combined gene data set (including 109 ingroup and six outgroup taxa) of mitochondrial genes, COI and 16S rRNA, and two nuclear genes, NaK and PEPCK, was utilized. To explore its diversity, another data set that included 371 COI gene sequences (231 newly generated and 140 retrieved from public sources) was compiled and subsequently analysed with two different tools (ABGD and bPTP) for species delimitation. Other than supporting the non-monophyly of the Penaeidae with the Sicyoniidae nested within the penaeid tribe Trachypenaeini, the genera Penaeus, Mierspenaeopsis and Parapenaeopsis were also revealed to be polyphyletic. Our species delimitation analysis inferred that 94 putative species actually existed within the 71 morphospecies reviewed, indicating an underestimated biodiversity in this family and the potential presence of new species within the following morphospecies: Kishinouyepenaeopsis cornuta, K. incisa, Mierspenaeopsis sculptilis, M hardwicki, Parapenaeopsis coromandelica and Penaeus monodon.     

Phylogeny of penaeoid shrimps (Decapoda: Penaeoidea) inferred from nuclear protein-coding genes

Penaeoidea is a diverse group of economically important marine shrimps. Attention to the evolutionary history of the penaeoids has been raised since studies using mitochondrial DNA markers and sperm ultrastructure contradict classification of the penaeoid families based on morphology and hence challenge the long standing taxonomy of this superfamily. In this study, DNA sequences of two nuclear protein-coding genes, phosphoenolpyruvate carboxykinase and sodium–potassium ATPase α-subunit, were determined from 37 penaeoid genera to reconstruct the evolutionary relationships and to estimate divergence ages of the penaeoid shrimps. Phylogenetic analyses using maximum likelihood and Bayesian approaches strongly support the monophyly of Solenoceridae, Aristeidae and Benthesicymidae, but find Sicyoniidae nested within Penaeidae, making this family paraphyletic. Penaeoidea comprises two lineages: the former three families in one while the latter two in another. The diversification of these lineages may be related to bathymetry. The penaeid-like lineage diversified in the Triassic, earlier than the aristeid-like lineage with an origin in the Jurassic. Taxonomic revisions within Penaeoidea are also proposed for further investigation. Due to the paraphyly of Penaeidae and the high genetic divergence among the three penaeid tribes of Burkenroad [Burkenroad, M.D., 1983. Natural classification of Dendrobranchiata, with a key to recent genera. In: Schram, F.R. (Ed.), Crustacean Issues I. Crustacean Phylogeny. A.A. Balkema, Rotterdam, pp. 279–290], these tribes should be treated as having the same taxonomic rank as Sicyoniidae, while the family ranking of Benthesicymidae has to be re-considered owing to the low genetic divergence between the benthesicymids and the aristeids.     

Ultrastructure of the spermatozoa of Aristaeopsis edwardsiana and Aristeus varidens (Crustacea, Dendrobranchiata, Aristeidae)

The acrosome-less spermatozoon of Aristaeopsis edwardsiana (Crustacea, Aristeidae), which consists of a central non-membrane bound nuclear region surrounded by a thin peripheral cytoplasm, much resembles that of the previously studied aristeid Aristaeomorpha foliacea. The marked spermatozoal similarities between these two species appear to indicate a close phylogenetic proximity. A considerably different spermatozoal pattern is observed in aristeids from the genus Aristeus (A. varidens and A. antennatus), whose spermatozoa possess an anterior spherical acrosome, lacking a spike, and partially embedded in (instead of capping) the main sperm body. The two distinct sperm types found in the Aristeidae differ significantly from the spiked sperm typically found in most penaeoids (Penaeidae, Solenoceridae and Sicyoniidae), thus suggesting a phylogenetic separation of the Aristeidae from the remaining Penaeoidea.     

Evolutionary patterns of two major reproduction candidate genes (Zp2 and Zp3) reveal no contribution to reproductive isolation between bovine species

Background  

It has been established that mammalian egg zona pellucida (ZP) glycoproteins are responsible for species-restricted binding of sperm to unfertilized eggs, inducing the sperm acrosome reaction, and preventing polyspermy. In mammals, ZP apparently represents a barrier to heterospecific fertilization and thus probably contributes to reproductive isolation between species. The evolutionary relationships between some members of the tribe Bovini are complex and highly debatable, particularly, those involving Bos and Bison species for which interspecific hybridization is extensively documented. Because reproductive isolation is known to be a major precursor of species divergence, testing evolutionary patterns of ZP glycoproteins may shed some light into the speciation process of these species. To this end, we have examined intraspecific and interspecific genetic variation of two ZP genes (Zp2 and Zp3) for seven representative species (111 individuals) from the Bovini tribe, including five species from Bos and Bison, and two species each from genera Bubalus and Syncerus.     

Comparative sperm ultrastructure in Nemertea

Although the monophyly of Nemertea is strongly supported by unique morphological characters and results of molecular phylogenetic studies, their ingroup relationships are largely unresolved. To contribute solving this problem we studied sperm ultrastructure of 12 nemertean species that belong to different subtaxa representing the commonly recognized major monophyletic groups. The study yielded a set of 26 characters with an unexpected variation among species of the same genus (Tubulanus and Procephalothrix species), whereas other species varied in metric values or only one character state (Ramphogordius). In some species, the sperm nucleus has grooves (Zygonemertes virescens, Amphiporus imparispinosus) that may be twisted and give a spiral shape to the sperm head (Paranemertes peregrina, Emplectonema gracile). To make the characters from sperm ultrastructure accessible for further phylogenetic analyses, they were coded in a character matrix. Published data for eight species turned out to be sufficiently detailed to be included. Comparative evaluation of available information on the sperm ultrastructure suggests that subtaxa of Heteronemertea and Hoplonemertea are supported as monophyletic by sperm morphology. However, the data do not provide information on the existing contradictions regarding the internal relationships of “Palaeonemertea.” Nevertheless, our study provides evidence that sperm ultrastructure yields numerous potentially informative characters that will be included in upcoming phylogenetic analyses. J. Morphol. 2010. © 2010 Wiley‐Liss, Inc.     

Microsatellite primers for three Western Atlantic Farfantepenaeus prawn species

Microsatellite loci were identified for three closely related penaeid species, Farfantepenaeus subtilis, F. paulensis and F. sp., from genomic libraries enriched for CA repeats. Seven out of nine highly polymorphic loci detected were amplified across all three species. Between four and 64 alleles were recorded per locus (average = 36). The average observed heterozygosity ranged from 0.094 to 0.897 (mean = 0.613), while the expected heterozygosity ranged from 0.091 to 0.985 (mean = 0.822).     

Morphological observations on the gills of dendrobranchiate shrimps

Gill morphology, traditionally, has played an important role in attempts to reconstruct the phylogenetic history of the Crustacea Decapoda. We examined the gills of dendrobranchiate shrimps (Crustacea, Decapoda, Dendrobranchiata) to test the assumption that all members of the clade have gills that are “dendrobranchiate” (highly branching) in form, from whence the taxon name Dendrobranchiata comes. Currently, the Dendrobranchiata consists of two superfamilies and seven families. Specimens from two genera in each of the known families were examined using light and scanning electron microscopy. Members of the family Luciferidae, all of which lack gills as adults, were not examined. Only one genus was examined for the Penaeidae (because they have been the subject of numerous previous studies) and Sicyoniidae (a monogeneric family). All gills examined have secondary branches that are further subdivided, conforming to existing and rather broad definitions of dendrobranchiate gills. Families with “typical” dendrobranchiate gills, which consist of curved secondary branches that in turn bear branched (dendritic) tubular tertiary elements on their distal surfaces, include the Penaeidae, Aristeidae, and Solenoceridae. In other families, secondary and tertiary gill elements are sometimes quite flattened, and the tertiary elements are not dendritic, giving the gill a distinctly non-dendrobranchiate appearance. Flattened biserial secondary branches and their flattened tertiary elements are particularly obvious in gills of the monogeneric family Sicyoniidae (Sicyonia). Within the family Sergestidae, gills of the genus Sergestes are unusual in having secondary branches that arise from the main gill axis in an alternating pattern; these gills also have distinctly oval tertiary elements that are not further subdivided and are directed basally rather than distally. Another sergestid genus, Petalidium, displays gills that differ from those of Sergestes; in Petalidium the secondary branches also come off the main gill axis in an alternating pattern, but these branches are more widely spaced and have relatively larger and broader tertiary elements when compared with gills of Sergestes. The family Benthesicyemidae also contains species with different gill types; Gennadas is shown to have flattened, plate-like tertiary elements, whereas Benthesicyemus has more typical dendrobranchiate gills. The significance of this variation in gill morphology within families and within the Dendrobranchiata as a whole is unclear at this point; rearrangements of the currently accepted phylogeny and resulting classification based solely on gill morphology are not recommended at this time.     

Isolation and characterization of new microsatellite loci in the Pacific white shrimp Litopenaeus vannamei and cross‐species amplification in other penaeid species

The goal of the present study was to obtain valuable microsatellite markers useful in genetic approaches of the shrimp Litopenaeus vannamei, an important aquaculture species of the world. Eight loci produced suitable polymorphic patterns with allele number ranging from two to 12 and expected heterozygosity from 0.18 to 0.89. Cross‐species amplification was successfully performed in five other penaeid species (Litopenaeus schmitti, Farfantepenaeus brasiliensis, Farfantepenaeus paulensis, Xiphopenaeus kroyeri and Rimapenaeus constrictus), indicating that some these loci can be useful in studies of other related species.     

Molecular species identification of commercially important penaeid shrimp from the Gulf of Mexico using a multiplex haplotype-specific PCR assay

This study describes a multiplex PCR assay based on the 16S rRNA mitochondrial gene to identify the penaeid shrimp Farfantepenaeus aztecus, Farfantepenaeus duorarum, Farfantepenaeus brasiliensis and Litopenaeus setiferus, all native to the Gulf of Mexico, and the exotic Litopenaeus vannamei. The assay was validated using positively identified adult shrimp and confirmed by direct sequencing. Samples of postlarvae and early juveniles collected in the eastern and western Gulf of Mexico were tested yielding 119 F. aztecus, 78 F. duorarum and five L. setiferus. Reliable identification of the morphologically similar early life stages of F. aztecus and F. duorarum has important implications for management and conservation. Similarly, the ability to identify L. vannamei is relevant as early detection could help minimize the ecological impact if this species escapes to the wild.     

Morphology and ecology of Pacific sturgeons

The six North Pacific members of the genus Acipenser have generally similar environmental requirements and share several specific morphological features. This Pacific group consists of green sturgeon, Acipenser medirostris, Sakhalin sturgeon, A. mikadoi, white sturgeon, A. transmontanus, Chinese sturgeon, A. sinensis, Dabry’s sturgeon, A. dabryanus and Amur sturgeon, A. schrenkii. A qualitative morphological examination of these species revealed synapomorphic characters that suggest close phyolgenetic relationships resulting from common ancestry of eastern and western species within the Pacific Rim. An evolutionary taxonomic approach, considering a reduction of characters from east to west, would suggest an Asian ancestry for all Pacific sturgeons. In contrast however, a phylogenetic approach using derived character states suggests a North American ancestry. Besides a common ancestry for Chinese and American sturgeons, the taxonomic status of A. mikadoi is discussed.     

Isolation and characterization of microsatellites in three overexploited penaeid shrimp species along the Brazilian coastline

Most Brazilian commercial species of penaeid shrimp are currently overexploited. Thirteen polymorphic microsatellite loci herein isolated and characterized in Farfantepenaeus brasiliensis, Rimapenaeus constrictus and Xiphopenaeus kroyeri could be very useful for population studies on these penaeid species and proved to be potentially functional in cross-amplification with other species of shrimp. These microsatellites may be very helpful tools for research programs aimed at the sustainable management and conservation of these important fishery resources.     

Molecular phylogeny of western Atlantic Farfantepenaeus and Litopenaeus shrimp based on mitochondrial 16S partial sequences

Partial sequences for the 16S rRNA mitochondrial gene were obtained from 10 penaeid shrimp species: Farfantepenaeus paulensis, F. brasiliensis, F. subtilis, F. duorarum, F. aztecus, Litopenaeus schmitti, L. setiferus, and Xiphopenaeus kroyeri from the western Atlantic and L. vannamei and L. stylirostris from the eastern Pacific. Sequences were also obtained from an undescribed morphotype of pink shrimp (morphotype II) usually identified as F. subtilis. The phylogeny resulting from the 16S partial sequences showed that these species form two well-supported monophyletic clades consistent with the two genera proposed in a recent systematic review of the suborder Dendrobranchiata. This contrasted with conclusions drawn from recent molecular phylogenetic work on penaeid shrimps based on partial sequences of the mitochondrial COI region that failed to support recent revisions of the Dendrobranchiata based on morphological analysis. Consistent differences observed in the sequences for morphotype II, coupled with previous allozyme data, support the conclusion that this is a previously undescribed species of Farfantepenaeus.     

Sperm morphology and phylogeny of lagriids (Coleoptera,Tenebrionidae)

The systematics of tenebrionids remain unclear, principally at the subfamily level, as is the case of the Lagriinae. Considering that sperm morphology has contributed to the various insect group phylogenies, in this work we describe the structure and ultrastructure of these cells in Lagria villosa. Sperm in this species exhibit a strong morphological similarity to those of Tenebrio molitor and Tribolium castaneum, the only two species of Tenebrionidae with previously described sperm. In tenebrionids, the flagellar components offer good diagnostic characters, e.g. the symmetry of mitochondrial derivatives in L. villosa differentiates sperm of this species from those of Te. molitor and Tr. castaneum. However, the lateral association of the nucleus with flagellar components, the form of accessory bodies, and the presence of material connecting the axoneme to the accessory bodies and mitochondrial derivatives indicate that the three species form a sister group. Therefore, the sperm morphology of L. villosa support lagriid beetles as a subfamily (Lagriinae) of Tenebrionidae.     

Helmet‐shaped Body of Entodiniomorphid Ciliates (Ciliophora,Entodiniomorphida), a Synapomorphy or a Homoplasy?

Triadinium was created to include Triadinium caudatum. Further, four other species were included, T. minimum, T. galea, T. elongatum, and T. magnum, all sharing a characteristic helmet‐shaped body. Wolska and Grain argued that the inclusion of T. minimum and T. galea into Triadinium was done based on superficial morphological aspects, and established two new genera to accommodate these species: Circodinium and Gassovskiella. Although the phylogenetic relationships within Entodiniomorphida have been investigated by multiple authors, none of them discussed the evolutionary relationship of helmet‐shaped entodiniomorphids. We performed molecular phylogenetics and revisited old literature digging for morphological data to explain our results. According to our analyses, the helmet‐shaped body is homoplastic and may have evolved from at least three different entodiniomorphid ancestors. Circodinium minimum is phylogenetically related to members of Blepharocorythidae, T. caudatum emerged within Spirodiniidae and G. galea within Polydiniellidae. This phylogenetic hypothesis is partially supported by information on infraciliature and ultrastructure of C. minimum and T. caudatum. However, such morphological information is not available for polydiniellids. In order to shed some light into the evolution of the helmet‐shaped ciliates, future works should focus to collect information on the infraciliature and the ultrastructure of Polydiniella mysorea and of other Triadinium species.     

Structure and ultrastructure of spermatozoon in six species of Drosophilidae (Diptera)

The Drosophilidae family is formed by Brachycera Diptera distributed widely across different regions of the planet. It is composed of about 4000 species, 304 of which are found in Brazil. The objective of this work was to characterize morphologically the structure of the male internal reproductive apparatus and the ultrastructure of the spermatozoon in four Neotropical (Drosophila cardini, D. mercatorum, D. nebulosa and D. sturtevanti) and two invasive (D. simulans and Zaprionus indianus) species of drosophilids. The structural aspect of the internal reproductive apparatus corresponds with that described for other drosophilids; however, there are differences in the size and coloration of the structures, such as the testes, in each species analyzed. The spermatozoon of these species was seen to be long and fine, presenting morphological variation. The ultrastructure of the spermatozoon revealed that the morphological pattern is similar to that found in the majority of insects. The head region presents a nucleus with condensed chromatin and the acrosome positioned laterally to the nucleus. In the tail region, the axoneme presents the 9 + 9 + 2 pattern commonly described for other species of Diptera. The species presented differences regarding the shape and size of the mitochondrial derivatives. Cytochemical analysis using EPTA also revealed differences in terms of the location of the basic proteins in the mitochondrial derivates. The results obtained contribute to expanding the database for the Drosophilidae family, providing information that may contribute to intra- and inter-specific identification and supplying phylogenetic analyses.     

Unistellate spermatozoa of decapods: comparative evaluation and evolution of the morphology

Decapod unistellate spermatozoa are primarily characterized by the presence of a single appendage (spike) extending from the acrosome. Among decapods, this type of spermatozoon is found only in shrimps of the families Sicyoniidae, Penaeidae, and Solenoceridae (suborder Dendrobranchiata) and of the infraorder Caridea (suborder Pleocyemata). This review comparatively discusses the morphological diversity of unistellate spermatozoal ultrastructure among these decapods, as well as the role of the primary structures involved in the fertilization and spermatozoal capacitation. Furthermore, the use of the unistellate spermatozoal ultrastructure to support phylogenetic relationships and of the current phylogenetic evidences to investigate the evolution of spermatozoa of decapods is discussed. Morphologically, the main differences between caridean and dendrobranchiate unistellate spermatozoa are the shape of the main body (inverted cup-shaped, and spherical, bulged or elongate, respectively) and complexity of the acrosomal region. The latter is directly related to the type of fertilization. For example, dendrobranchiates have more complex acrosomal regions than that carideans, and fertilization involves a visible acrosome reaction, which is not observed in carideans. Ultrastructural changes of spermatozoa throughout capacitation are unknown in carideans, but for dendrobranchiates generally occur in the acrosomal vesicle and subacrosomal region throughout attachment of the spermatophore to the thelycum, enabling fertilization by the spermatozoa. Comparative evaluation of spermatozoal morphology and current phylogenetic evidences corroborates the hypothesis that the spermatozoal spike of carideans and dendrobranchiates is the result of convergent evolution.     

Refuting the six‐genus classification of Penaeus s.l. (Dendrobranchiata,Penaeidae): a combined analysis of mitochondrial and nuclear genes

Ma, K. Y., Chan, T. ‐Y & Chu, K. H. (2011). Refuting the six‐genus classification of Penaeus s.l. (Dendrobranchiata, Penaeidae): a combined analysis of mitochondrial and nuclear genes. —Zoologica Scripta, 40, 498–508. The taxonomic revision in 1997 of the shrimps formerly classified in Penaeus s.l. has been one of the most controversial issues on systematics of the decapods in recent years. Since Pérez Farfante & Kensley (Penaeoid and Sergestoid Shrimps and Prawns of the World, 1997) split this long‐accepted taxon into six genera, much debate has been devoted to their proposed new classification scheme; this has taken place because there are serious doubts whether the said scheme could reflect the evolutionary relationships among the 29 Penaeus s.l. species. Although these shrimps can be easily separated into several groups morphologically, whether these subdivisions are truly monophyletic and warrant a generic rank continues to be hotly debated among taxonomists. This study examined a total of 2425 bp sequences from three nuclear protein genes (enolase, phosphoenolpyruvate carboxykinase and sodium–potassium ATPase α‐subunit), and the mitochondrial 16S and 12S rRNA gene of 18 Penaeus s.l. shrimps and 13 other species in the family Penaeidae. Our phylogenetic analyses strongly support the monophyly of Penaeus s.l. and, concurring with previous studies that used the mitochondrial genes alone, the paraphyly of both Penaeus s.s. (sensu Pérez Farfante & Kensley, Penaeoid and Sergestoid Shrimps and Prawns of the World, 1997) and Melicertus, rendering them non‐natural groupings. Our study reveals two lineages: Penaeus s.s. + Fenneropenaeus + Litopenaeus + Farfantepenaeus and Melicertus + Marsupenaeus, which exhibit genetic divergences comparable with those among other penaeid genera. However, all the morphological characters, which are emphasized by Pérez Farfante and Kensley and used to separate Penaeus s.l., do not correlate with the grouping revealed by the present, perhaps decisive, phylogenetic result. Such disparity may arise from selection on the morphology of genitalia and convergent evolution. Our molecular data clearly refute the six‐genus classification, and we advocate the restoration of the old Penaeus genus (=Penaeus s.l.) definition which is the only classification scheme with both the morphological and the molecular data being in agreement.