Homology and homoeomorphy in ostracod limbs

The functional modifications of myodocopan and podocopan ostracod limbs constitute a rich data set with which to carry out phylogenetic analyses, but efforts are hindered by lack of consensus on homologies. Homoeomorphy presents particular difficulties; for example, the furca is post-anal in Myodocopa but pre-anal in Podocopa, suggesting homoeomorphy, not homology. Homoeomorphies also exist between ostracod appendages and those of other Crustacea, for example the oral cone and styliform mandibulae of Paradoxostomatidae (Ostracoda) and Siphonostomatoida (Copepoda), both adaptations to commensal or parasitic lifestyles. Such clear manifestations of homoeomorphy, arising independently in different lineages as a result of similar functional requirements imposed on plesiomorphic appendage structures, warn of the possibility of more subtle examples which, if unrecognized, would lead to misinterpretations of character states used in phylogenetic analysis. For instance, the branchial plates found on third, fourth and fifth limbs of podocopans may not be homologous with the branchial plates on the fifth and sixth limbs of myodocopans. Limb homologies of podocopan ostracods (primarily as represented by various podocopid taxa) are investigated. Evidence is presented, based on studies of morphology and musculature, that podocopid branchial plates are exopodites (arising from the basis), while those of myodocopans are epipodites (arising from the coxa or precoxa). In Podocopida, moreover, the protopodites of post-mandibular limbs appear to be undifferentiated, comprising only a basis, while those of Myodocopa clearly exhibit a basis, coxa and often a precoxa. These differences argue against monophyly of the Ostracoda. The absence of epipodites, combined with the lack of a coxa in post-mandibular limbs, is potentially indicative of closer affinities between podocopans and Cambrian stem-group crustaceans (including Phosphatocopida) than between podocopans and myodocopans. The possible derivation of podocopid third, fourth and fifth limbs from a stem-group crustacean limb is demonstrated. The hypothesis is advanced that podocopan ostracods (represented today by Podocopida, Platycopida and Palaeocopida) are derived from much nearer the base of the crown-group Crustacea than myodocopans.     

介形纲丽足目和速足目及相关类群18S rDNA分子系统发育的研究

文中分析现生介形类 (Ostracoda) 4目 2 1科 2 9属的 18SrDNA部分序列 ,采用最大似然法 (ML)、邻接法 (NJ)和最大简约法 (MP) ,尝试构建介形类的分子系统树 ;结合介形类的形态特征和化石记录 ,主要对速足目(Podocopida)、丽足目 (Myodocopida)及其超科级分类阶元的系统发生关系进行探讨。 3种分析方法均支持形态学上Podocopida ,Myodocopida和海萤超科 (Cypridinacea)的界定 ;但对Podocopida目土菱介超科 (Bairdiacea)的系统地位提出质疑 ,该类群可能不是单系发生的自然类群。上述分析显示 ,Podocopida,Myodocopida,Platycopida和Halo cypridina组成一个单系群 ;介形类在目、超科、科和属的水平上可能发生过多次辐射分化     

A revised classification of the higher taxa of the Ostracoda (Crustacea)

Focusing on palaeontological data from the literature of the last four decades, a new classification of the Ostracoda is outlined. The superorder Podocopomorpha is accepted as a mantle term for the ‘P-orders’ Palaeocopida, Punciocopida, Platycopida and Podocopida; its counterpart are the Myodocopomorpha (Cypridinida, Halocypridida and ? Leperditicopida). The Podocopida comprise the suborders Bairdiocopina, Cytherocopina, Sigilliocopina, Cypridocopina, Darwinulocopina and Healdiocopina (n.;=Metacopina s.s.). The non-calcifying ostracodomorph arthropods (Archaeocopida and Phosphatocopida) of the Early Palaeozoic, now excluded from the Ostracoda by many authors, are also considered briefly.     

Functional morphology of Palaeozoic ostracods: phylogenetic implications

Recent discussions of ostracod systematics have focused on soft anatomy, both as seen in extant groups and as recorded by rare examples of special fossil preservation. The position of the fossil Palaeocopina and Leperditicopida, for which no substantial soft part evidence has yet been found, remains in the view of post-Palaeozoic workers uncertain, with some doubt as to whether they should be retained within the Ostracoda. The evolution of carapace bauplans (e.g. the development of brood pouches and lobal structures in palaeocopids as well as the development of adductor muscle scar patterns, calcified inner lamellae and carapace incisures in podocopines) is discussed in relation to presumed soft anatomy. It seems possible to distinguish between plesiomorphic (ancestral, simple) and apomorphic (derived, advanced) characters and consider their significance in ostracod systematics. Although the presumed ‘protostracod’ is not known, the combination of soft anatomy, carapace architecture and behaviour (feeding techniques, brood care) provide evidence of a general body plan which appeared (at the latest) during the Ordovician and continuously evolved towards the anatomy of modern ostracods. In parallel lineages, plesiomorphic forms have died out (leperditicopids and most palaeocopines as well as metacopines), while apomorphic lineages (‘drepanellid archetype’ of palaeocopines; resistant platycopines, podocopines and myodocopines) have survived all extinction events. The evidence supports the retention of the Palaeocopina (and probably the Leperditicopida) in the Ostracoda.     

介形类系统分类与起源演化的形态、分子和化石证据

介形类(Ostracoda)因其丰富的化石记录和广布的海陆现生代表类群,而被认为是进化生物学中研究生物多样性产生机制和演变历程的颇具潜力的重要模式生物。介形类在甲壳亚门中的谱系发生位置、起源及其内部各类群间的系统关系还存在诸多争议。基于其体制构造的形态学特征,介形类被归入甲壳亚门下的颚足纲(Maxillopoda),但来自18S rDNA序列数据分析却显示Maxillopoda不是单系群。基于化石记录和壳体形态特征,高肌虫(Bradoriida)长期以来被认为是介形类的一个祖先类群,但保存有软躯体的早寒武世化石的研究表明,Bradoriida不是介形类甚至可能也不属于甲壳类。不同的研究者所强调的壳体和肢体形态特征各异,导致介形类最大的现生类群速足目(Podocopida)的四个超科之间的关系也存在诸多推测。壳体和肢体特征在系统演化意义上的不兼容,需要分子生物学等证据的介入。分子、形态和化石证据的积累及各种信息整合是系统演化研究的必然趋势。     

First record of preserved soft parts in a Palaeozoic podocopid (Metacopina) ostracod, Cytherellina submagna: phylogenetic implications

The metacopines represent one of the oldest and most important extinct groups of ostracods, with a fossil record from the Mid-Ordovician to the Early Jurassic. Herein, we report the discovery of a representative of the group with three-dimensionally preserved soft parts. The specimen--a male of Cytherellina submagna--was found in the Early Devonian (416 Ma) of Podolia, Ukraine. A branchial plate (Bp) of the cephalic maxillula (Mx), a pair of thoracic appendages (walking legs), a presumed furca (Fu) and a copulatory organ are preserved. The material also includes phosphatized steinkerns with exceptionally preserved marginal pore canals and muscle scars. The morphology of the preserved limbs and valves of C. submagna suggests its relationship with extant Podocopida, particularly with the superfamilies Darwinuloidea and Sigillioidea, which have many similar characteristic features, including a large Bp on the Mx, the morphology of walking legs, Fu with two terminal claws, internal stop-teeth in the left valve, adductor muscle scar pattern, and a very narrow fused zone along the anterior and posterior margins. More precise determination of affinities will depend on the soft-part morphology of the cephalic segment, which has not been revealed in the present material.     

Origin of the Ostracoda and their maxillopodan and hexapodan affinities

There are Cambrian fossils attributed to the Ostracoda but the extant subclasses Podocopa and Myodocopa do not appear until the Ordovician. At this time the morphologically similar, free-living ancestors of the now sedentary Thecostraca (Ascothoracida, Acrothoracica and Cirripedia) may have still been extant, and from an ecological point of view it seems likely that, by and large, ostracods replaced them. However, living ostracods have an abbreviated, direct development, and some key aspects of their morphology, such as the nature of the maxillary segment and abdomen, are conjectural. Thus the affinities between these and related taxa remain uncertain; e.g., while some contemporary carcinologists place Ostracoda as a taxon coordinate with the Branchiopoda, Remipedia, Cephalocarida, Maxillopoda, Malacostraca, others tentatively or unequivocally ally them with the Maxillopoda (generally Mystacocarida, Copepoda, Tantulocarida and Thecostraca, and sometimes Branchiura and Pentastomida). Others, largely involved with fossils, have stretched the definition of the Maxillopoda even further, to the point where it seems even less likely a monophyletic taxon. Until recently cladistic analyses utilizing genetic (largely 18S rDNA) as well traditional morphological characteristics have given confusing results regarding the affinities between these taxa, and an important one suggested the Ostracoda might even be diphyletic. Furthermore, a very recent genetic study utilizing protein encoding genes places a podocopine ostracod among the most primitive of the extant crustaceans (Branchiopoda, Cephalocarida Remipedia and Mystacocarida), and then generally at the base of a lineage leading to the Malacostraca, a lineage giving rise to copepods and cirripeds along the way. This indicates these so-called maxillopodan taxa evolved independently from a malacostracan-like ancestor, and if so they are convergent. And finally, from genetic studies it is not only becoming well documented the Crustacea rather than Myriapoda gave rise to the Hexapoda, but it appears the Hexapoda stem from among the lower rather than the higher crustaceans, possibly even from the Ostracoda. Whether there were terrestrial ostracods at the time hexapods appeared in the Lower Ordovician is unknown, but the modest diversity of terrestrial ostracods today are podocopines which also first appeared in the Lower Ordovician. Thus, if current interpretations of living ostracodan and fossil hexapodan body plans are largely correct, it can be hypothesized the Ostracoda are close to the ancestor of the Hexapoda.     

The ontogeny of the platycopid Keijcyoidea infralittoralis (Ostracoda: Podocopa)

Platycopid ostracods such as the genus Keijcyoidea Malz, 1981 (Family Cytherellidae) have a unique body plan and are regarded as a phylogenetically ancient lineage. Their ontogeny, which is important in considering phylogenetical relationships, is very poorly known except for the growth of the carapace; there are nine instars including the adult, as in other podocopan groups. All appendages in all immature instars (A-8 to A-1) of Keijcyoidea infralittoralis Tsukagoshi, Okada & Horne, 2006 are described and illustrated here. The anlagen of the copulatory organs and the sexual dimorphism of carapace size appear in the sixth (A-3) instar, whereas sexual dimorphism in both the fifth and the sixth limbs, a distinctive feature of adults, is not clearly evident until the eighth (A-1) instar. Appendages are added at the moults between the second (A-7) and third (A-6), and between the fifth (A-4) and sixth (A-3) instars. The seventh limb, which platycopid ostracods have lost in the adult stage, is observed as an anlage in the sixth (A-3) and seventh (A-2) instars. During the other moults, there are no significant changes to the body plan. The ontogeny of the Platycopida is compared with that of the Podocopida, and strongly suggests that the phylogenetic position of the Platycopida is as an end-member of the Podocopa. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 213–237.     

Phosphatocopina – ostracode-like sister group of Eucrustacea

The Phosphatocopina were long considered as the oldest, Cambrian, record of ostracode Crustacea. However, our detailed analysis of more than 2,500 specimens from the Upper Cambrian ‘Orsten’ of Sweden reveals that Phosphatocopina are neither Ostracoda nor Eucrustacea. The antenna and mandible of the phosphatocopines investigated consist of a prominent limb stem which carries a two-segmented endopod and multi-annulated exopod. This stem portion is now recognised as the fusion product of the coxa and basipod during ontogeny. Phosphatocopina share features, such as the coxa and basipod on antennae and mandibles, as well as ventral body structures such as the prominent pre-oral labrum and a single post-oral cephalic plate, the sternum (with paragnaths on the mandibular sternal portion), exclusively with the Eucrustacea. As a plesiomorphy, the ontogeny of Phosphatocopina starts with a ‘head larva’ with four pairs of limbs, a larva type found in the ground pattern of the Euarthropoda as well as the Crustacea. In contrast, eucrustacean ontogeny begins with a nauplius with three pairs of limbs, a ‘short-head larva’ or orthonauplius. Again, the post-mandibular limbs of phosphatocopines retain the plesiomorphic limb design of a basipod with a setiferous ‘ proximal endite’, whereas Eucrustacea, including the Ostracoda, have their first post-mandibular limb differentiated into a ‘ mouthpart’, the maxillula. Autapomorphies of Phosphatocopina include the small antennula with few terminal setae, a bivalved shield with interdorsum, and the fused coxa and basipod on antenna and mandible. We therefore consider the Phosphatocopina to be the sister group of the Eucrustacea. The respective phosphatocopine species of the Upper Cambrian of southern Sweden are restricted to a particular time zone and may be useful as stratigraphic markers.     

Occurrence of Hemocyanin in Ostracod Crustaceans

Hemocyanin is a copper-containing protein that transports O₂ in the hemolymph of many arthropod species. Within the crustaceans, hemocyanin appeared to be restricted to Malacostraca but has recently been identified in Remipedia. Here, we report the occurrence of hemocyanin in ostracods, indicating that this respiratory protein is more widespread within crustaceans than previously thought. By analyses of expressed sequence tags and by RT-PCR, we obtained four full length and nine partial hemocyanin sequences from six of ten investigated ostracod species. Hemocyanin was identified in Myodocopida (Actinoseta jonesi, Cypridininae sp., Euphilomedes morini, Skogsbergia lerneri, Vargula tsujii) and Platycopida (Cytherelloidea californica) but not in Podocopida. We found no evidence for the presence of hemoglobin in any of these ostracod species. Like in other arthropods, we identified multiple hemocyanin subunits (up to six) to occur in a single ostracod species. Bayesian phylogenetic analyses showed that ostracod hemocyanin subunit diversity evolved independently from that of other crustaceans. Ostracod hemocyanin subunits were found paraphyletic, with myodocopid and platycopid subunits forming distinct clades within those of the crustaceans. This pattern suggests that ostracod hemocyanins originated from distinct subunits in the pancrustacean stemline.     

Pliocene coastal palaeomorphology and ostracod faunas of the Bass Strait hinterland,southeast Australia

Early to late Pliocene sedimentary strata present across the northern Bass Strait hinterland, southeastern Australia yield extensive fossil proxy data relevant to the interpretation of high sea level coastal palaeomorphology. Within the Pliocene Whalers Bluff Formation exposed in coastal cliffs near the township of Portland, Victoria, marine microfossil faunas delineate two broad cycles of deposition. Both these sedimentary cycles are bound below by unconformity surfaces. Within the lower sedimentary cycle, a basal stress-tolerant (low diversity) marginal marine microfossil fauna devoid of ostracods and suggestive of bottom-water hypoxia, is succeeded by a diverse shallow marine ostracod fauna dominated by stenohaline species indicative of a sheltered (but open) oceanic embayment. This lower sedimentary cycle has an early Pliocene (Zanclean) age. Equivalent shallow marine (e.g. coastal embayment) deposits occur broadly across the coastal hinterland of southeastern Australia—reflecting the generally higher global sea levels of this time. The upper cycle in the cliff exposures at Portland is late Pliocene (Piacenzian) in age. Equivalent deposits across the Bass Strait hinterland are restricted to former incised river valley settings. Euryhaline estuarine/coastal lagoon Ostracoda are present throughout the upper cycle in the Portland cliffs. These are associated with a low diversity microfauna at the base of the upper cycle and a high diversity microfauna towards the top of the cycle. Early Pliocene coastal marine deposits can be distinguished from late Pliocene coastal marine deposits across the northern Bass Strait hinterland on the basis of the presence or absence of certain open marine (‘stenohaline’) ostracod species.     

An Overview of the Introns-First Theory

We review the introns-first hypothesis a decade after it was first proposed. It is that exons emerged from non-coding regions interspersed between RNA genes in an early RNA world, and is a subcomponent of a more general ‘RNA-continuity’ hypothesis. The latter is that some RNA-based systems, especially in RNA processing, are ‘relics’ that can be traced back either to the RNA world that preceded both DNA and encoded protein synthesis or to the later ribonucleoprotein (RNP) world (before DNA took over the main coding role). RNA-continuity is based on independent evidence—in particular, the relative inefficiency of RNA catalysis compared with protein catalysis—and leads to a wide range of predictions, ranging from the origin of the ribosome, the spliceosome, small nucleolar RNAs, RNases P and MRP, and mRNA, and it is consistent with the wide involvement of RNA-processing and regulation of RNA in modern eukaryotes. While there may still be cause to withhold judgement on intron origins, there is strong evidence against introns being uncommon in the last eukaryotic common ancestor (LECA), and expanding only within extant eukaryotic groups—the ‘very-late’ intron invasion model. Similarly, it is clear that there are selective forces on numbers and positions of introns; their existence may not always be neutral. There is still a range of viable alternatives, including introns first, early, and ‘latish’ (i.e. well established in LECA), and regardless of which is ultimately correct, it pays to separate out various questions and to focus on testing the predictions of sub-theories.     

Anchialine podocopid Ostracoda of the Galapagos Islands

Water-filled fissures and lava tubes on Isla Santa Cruz and Isla Isabela provide anchialine habitats for 11 species of podocopid and platycopid Ostracoda, most with Atlantic and West Indian affinities. Their ancestors may have been carried to earlier islands in the Galapagos system by trans-Isthmian currents, on vegetation or larger animals, or by migrating waterfowl. None are derived from present-day Pacific coastal faunas of North, Central or South America. Two species of Cytheracea, a new species of Anchistrocheles (Bairdiacea), and one of Cytherella (Platycopida) are described.     

Ventrale Inzisuren bei paläozoischen Podocopida (Ostracoda) und ihre funktionelle Deutung

Ventral incisures, till now not really functionally interpreted, are described in three genera of the Family Pachydomellidae (Podocopida, Ostracoda). The functional meaning of these structures (respiration and locomotion when the carapace is closed, special behavior of reproduction or brood care, etc.) and resulting taxonomic conclusions are discussed in detail. All specimens were found in basinal faciès.     

Neuronal Network Models of Phase Separation Between Limb CPGs of Digging Sand Crabs

Ordinary differential equations are used to model a peculiar motor behaviour in the anomuran decapod crustacean Emerita analoga. Little is known about the neural circuitry that permits E. analoga to control the phase relationships between movements of the fourth legs and pair of uropods as it digs into sand, so mathematical models might aid in identifying features of the neural structures involved. The geometric arrangement of segmental ganglia controlling the movements of each limb provides an intuitive framework for modelling. Specifically, due to the rhythmic nature of movement, the network controlling the fourth legs and uropods is viewed as three coupled identical oscillators, one dedicated to the control of each fourth leg and one for the pair of uropods, which always move in bilateral synchrony. Systems of Morris–Lecar equations describe the voltage and ion channel dynamics of neurons. Each central pattern generator for a limb is first modelled as a single neuron and then, more realistically as a multi-neuron oscillator. This process results in high-dimensional systems of equations that are difficult to analyse. In either case, reduction to phase equations by averaging yields a two-dimensional system of equations where variables describe only each oscillator’s phase along its limit cycle. The behaviour observed in the reduced equations approximates that of the original system. Results suggest that the phase response function in the two dimensional system, together with minimal input from asymmetric bilateral coupling parameters, is sufficient to account for the observed behaviour.     

Single base errors in PCR products from avian museum specimens and their effect on estimates of historical genetic diversity

Conservation genetic studies often employ DNA extracts from museum specimens for comparisons with extant populations to monitor temporal changes in genetic diversity. Here, we report on artifact base changes in mitochondrial DNA sequences amplified from relatively recent (≤ 35 years) museum specimens of indigobirds (Vidua spp.). Single base errors were confirmed by replicate sequencing and included both double peaks and artifact substitutions at rates of ∼3 × 10⁻⁴ and ∼1 × 10⁻⁴ per base-pair, respectively, resulting in one or more errors or ambiguities in an 1100 base pair sequence in 21% of 219 samples. Most errors involved C→T changes on the L-strand, presumably due to deamination of cytosine in the template. The error rates encountered here bias comparisons of haplotype number between historical and extant populations, such that the ‘loss’ of artifact haplotypes present in a historical sample could be incorrectly attributed to a population decline or bottleneck. Sequencing errors due to miscoding lesions in template DNA have so far been reported only from ancient and formalin-fixed tissue, but they may also affect relatively recent museum samples, as shown here, and perhaps also non-invasive samples that typically yield low-quality DNA.     

Strict paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in intraspecific crosses of kiwifruit

 Previous studies have established that chloroplasts are inherited paternally in Actinidia interspecific crosses. However, fertilisation problems in interspecific crosses may affect the transmission of organelles. Six female clones, i.e. ‘Abbott’, ‘Bruno’, ‘Greensill’, ‘Hayward’, ‘Jones’, ‘Monty’, and four male clones were used to identify cpDNA polymorphisms within the cultivated kiwifruit species A. deliciosa. The restriction patterns by HpaII of a chloroplast fragment amplified by PCR with a pair of universal primers revealed a polymorphism at the intraspecific level. The inheritance of cpDNA in 143 seedlings from three intraspecific crosses in kiwifruit (Actinidia deliciosa) was studied. All offspring displayed the restriction pattern of the paternal parent, indicating that maternal inheritance of cpDNA in kiwifruit is rare at best. Strict maternal inheritance of mtDNA was confirmed in the same crosses used to investigate cpDNA transmission. Studies of cytoplasmic inheritance in the Actinidia genus represent to date the best documented report of differential organelle inheritance of cpDNA and mtDNA in angiosperms. Received: 10 November 1998 / Accepted: 14 December 1998     

The evolutionary pathway of light emission in myodocopid Ostracoda

The evolutionary history of bioluminescence and iridescence in myodocopid ostracods was estimated by phylogenetic analysis of mitochondrial 16S ribosomal RNA sequences. The inferred phylogeny of the myodocopids suggests that the common ancestor of Myodocopida evaluated in this study exhibits iridescence. This type of light emission was once lost and recaptured independently in the descendant lineages. Bioluminescent species also evolved from non-luminous ancestral species. In the suborder Myodocopina, all the bioluminescent species form a monophyletic group, suggesting that bioluminescence evolved only once. Structural differences between two bioluminescent groups in the order Myodocopida suggests independent origins for bioluminescence.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 449–455.     

Species of <Emphasis Type="Italic">Neohaliotrema</Emphasis> Yamaguti, 1965 (Monogenea: Ancyrocephalidae) from the pomacentrid <Emphasis Type="Italic">Abudefduf vaigensis</Emphasis> (Quoy &; Gaimard) off Pulau Langkawi,Malaysia, with a revised diagnosis of the genus and a key to its species

Four new and one unidentified species of Neohaliotrema Yamaguti, 1965 were obtained from the gills of the Indo-Pacific sergeant Abudefduf vaigensis (Quoy & Gaimard) off Pulau Langkawi, Malaysia. The five species, N. malayense n. sp., N. bombini n. sp., N. andamanense n. sp., N. parvum n. sp. and an unidentified Neohaliotrema sp. (similar to N. macracanthum Zhukov, 1976), are described and distinguished based mainly on features of the haptor. Species of this genus are divisible into two groups, the ‘maomao group’, with two pairs of morphometrically modified ‘marginal’ hooks and a fenestrated haptor, and the ‘gracile group’, with morphologically similar marginal hooks and an entire haptor. With the exception of N. bombini n. sp., the species described fit within the ‘maomao group’. It is suggested that the more complex Neohaliotrema species of the ‘maomao group’ have modified hooks 1 and 2 on a haptoral ‘isthmus’ between two large apertures, i.e. ‘windows’, whereas the less complex species lacking these features are those of the ‘gracile group’. Neohaliotrema spp. have only a single pair of pigmented eye-spots. A fenestrated haptor is unique to the Neohaliotrema spp. of the ‘maomao group’. The generic diagnosis of Neohaliotrema is amended to include new data and a key to its known species is presented.