A daphniid ephippium (Branchiopoda: Anomopoda) of Cretaceous age

An anomopod ephippium from the Lower Cretaceous of Australia, remarkably similar to that of Simocephalus , shows that daphniids whose ephippia at least were very similar to those of extant species, existed about 120 million years ago. The family clearly originated in pre-Cretaceous times, and the Anomopoda considerably early than this.     

Study of the late embryogenesis of Daphnia (Anomopoda, ‘Cladocera’, Branchiopoda) and a comparison of development in Anomopoda and Ctenopoda

The embryonic development of Daphnia galeata and D. hyalina (`Cladocera', Anomopoda, Daphniidae) has been investigated by observing living embryos removed from female brood pouches. The sequence of morphological changes was analysed, as was the time at which the activity of certain organs began. The timing of these events at 22 °C is documented for both species.These data were compared with similar information, previously obtained for two representatives of the Ctenopoda (Kotov & Boikova, 1998). The sequence of events is basically similar in the two groups during early and late phases of their development, but the time of shedding of the embryonic membranes is different in the Anomopoda and Ctenopoda. The ctenopod embryo hatching from the second egg membrane is covered by the third membrane, which will be cast some hours later. The anomopod embryo hatches from the second egg membrane approximately simultaneously with the shedding of the third membrane, and it is covered already by the fourth membrane after the shedding of the second egg membrane.Earlier (Kotov & Boikova, 1998), we determined four embryonic instars in the course of the development of the Ctenopoda. Two of them are passed within the egg membranes, the next two instars occur after the shedding the egg membranes within the mother's brood pouch. However, in anomopods, one of the latter (the third) occurs within the second egg membrane, one is incorporated into the egg. Thus, the development of the Anomopoda is more embryonized in comparison with that of the Ctenopoda.     

Morphology and the classification of the so-called Cladocera

The validity as a monophyletic taxon of the group of branchiopod crustaceans long regarded as constituting the Cladocera is questioned. This seems in fact to be a heterogeneous assemblage whose members probably merit assignment to four separate orders. The Onychopoda and Haplopoda (the so-called Gymnomera) clearly stand apart from the Ctenopoda and Anomopoda (the so-called Calyptomera) and differ in important respects from each other. While sharing several characters, some doubtless indicative of distant ancestral similarities, others probably convergent, the Ctenopoda and Anomopoda differ in many respects, have clearly evolved along different lines, and are probably much less closely related than is generally assumed.     

Notothrix halsei gen. n., sp. n., representative of a new family of freshwater cladocerans (Branchiopoda, Anomopoda) from SW Australia, with a discussion of ancestral traits and a preliminary molecular phylogeny of the order

The parthenogenetic female of a new anomopod crustacean, Notothrix halsei gen. n. et sp. n., is described from Lake Angove and found in five other sites in SW Australia. Although macrotrichid-like at first glance, a detailed morphological study including thoracic appendages revealed a set of primitive characters and similarities with primitive families, in particular with the Eurycercidae and Acantholeberidae. Ancestral traits of Notothrix gen. n. comprise: (i) a single large head pore; (ii) second maxilla; (iii) incomplete dorsal merger of valves; (iv) second antenna with a three- and a four-segmented branch; (v) six trunk limbs; (vi) two setae on a sixth endite in the first limb, vs. complete row of posterior setae on the second limb; (vii) large number of setae on exopodites III–V; (viii) well-developed gnathobase V; and (ix) massive postabdomen with wide, telson-like terminus between end-claws that show complex spinulation but no basal spine. Analysis of the complete 18S (SSU) rRNA gene sequence including taxa from all but four anomopod families and using Ctenopoda as an outgroup, confirms our separation of the new taxon, the Nototrichidae fam. n. Although different alignments resulted in different trees, the analyses confirm an isolated position of Notothrix , which has the shortest SSU rRNA gene length known for anomopods. However, the phylogenies derived from a comparison of 18S rRNA gene sequences between families of the order Anomopoda, does not resolve the descent of the various family groups.     

Chromosomal phylogeny and evolution of gibbons (Hylobatidae)

Although human and gibbons are classified in the same primate superfamily (Hominoidae), their karyotypes differ by extensive chromosome reshuffling. To date, there is still limited understanding of the events that shaped extant gibbon karyotypes. Further, the phylogeny and evolution of the twelve or more extant gibbon species (lesser apes, Hylobatidae) is poorly understood, and conflicting phylogenies have been published. We present a comprehensive analysis of gibbon chromosome rearrangements and a phylogenetic reconstruction of the four recognized subgenera based on molecular cytogenetics data. We have used two different approaches to interpret our data: (1) a cladistic reconstruction based on the identification of ancestral versus derived chromosome forms observed in extant gibbon species; (2) an approach in which adjacent homologous segments that have been changed by translocations and intra-chromosomal rearrangements are treated as discrete characters in a parsimony analysis (PAUP). The orangutan serves as an "outgroup", since it has a karyotype that is supposed to be most similar to the ancestral form of all humans and apes. Both approaches place the subgenus Bunopithecus as the most basal group of the Hylobatidae, followed by Hylobates, with Symphalangus and Nomascus as the last to diverge. Since most chromosome rearrangements observed in gibbons are either ancestral to all four subgenera or specific for individual species and only a few common derived rearrangements at subsequent branching points have been recorded, all extant gibbons may have diverged within relatively short evolutionary time. In general, chromosomal rearrangements produce changes that should be considered as unique landmarks at the divergence nodes. Thus, molecular cytogenetics could be an important tool to elucidate phylogenies in other species in which speciation may have occurred over very short evolutionary time with not enough genetic (DNA sequence) and other biological divergence to be picked up.Electronic Supplementary Material Supplementary material is available in the online version of this article at     

Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record

A recent molecular phylogeny of the mammalian order Carnivora implied large body size as the ancestral condition for the caniform subclade Arctoidea using the distribution of species mean body sizes among living taxa. "Extant taxa-only" approaches such as these discount character state observations for fossil members of living clades and completely ignore data from extinct lineages. To more rigorously reconstruct body sizes of ancestral forms within the Caniformia, body size and first appearance data were collected for 149 extant and 367 extinct taxa. Body sizes were reconstructed for four ancestral nodes using weighted squared-change parsimony on log-transformed body mass data. Reconstructions based on extant taxa alone favored large body sizes (on the order of 10 to 50 kg) for the last common ancestors of both the Caniformia and Arctoidea. In contrast, reconstructions incorporating fossil data support small body sizes (< 5 kg) for the ancestors of those clades. When the temporal information associated with fossil data was discarded, body size reconstructions became ambiguous, demonstrating that incorporating both character state and temporal information from fossil taxa unambiguously supports a small ancestral body size, thereby falsifying hypotheses derived from extant taxa alone. Body size reconstructions for Caniformia, Arctoidea, and Musteloidea were not sensitive to potential errors introduced by uncertainty in the position of extinct lineages relative to the molecular topology, or to missing body size data for extinct members of an entire major clade (the aquatic Pinnipedia). Incorporating character state observations and temporal information from the fossil record into hypothesis testing has a significant impact on the ability to reconstruct ancestral characters and constrains the range of potential hypotheses of character evolution. Fossil data here provide the evidence to reliably document trends of both increasing and decreasing body size in several caniform clades. More generally, including fossils in such analyses incorporates evidence of directional trends, thereby yielding more reliable ancestral character state reconstructions.     

INFERRING THE RATES OF BRANCHING AND EXTINCTION FROM MOLECULAR PHYLOGENIES

Molecular techniques provide ancestral phylogenies of extant taxa with estimated branching times. Here we studied the pattern of ancestral phylogeny of extant taxa produced by branching (or cladogenesis) and extinction of taxa, assuming branching processes with time-dependent rates. (1) If the branching rate b and extinction rate c are constant, the semilog plot of the number of ancestral lineages over time is not a straight line but is curvilinear, with increasing slope toward the end, implying that ancestral phylogeny shows apparent increase in the branching rate near the present. The estimate of b and c based on nonlinear fitting is examined by computer simulation. The estimate of branching rate can be usable for a large phylogeny if b is greater than c, but the estimate of extinction rate c is unreliable because of large bias and variance. (2) Gradual decrease in the slope of the semilog plot of the number of ancestral lineages over time, as was observed in a phylogeny of bird families based on DNA hybridization data, can be explained equally well by either the decreasing branching rate or the increasing extinction rate. Infinitely many pairs of branching and extinction rates as functions of time can produce the same ancestral phylogeny. (3) An explosive branching event in the past would appear as a quick increase in the number of ancestral lineages. In contrast, mass extinction occurring in a brief period, if not accompanied by an increase in branching rate, does not produce any rapid change in the number of ancestral lineages at the time. (4) The condition in which the number of ancestral lineages of extant species changes in parallel with the actual number of species in the past is derived.     

Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves

The level of DNA polymorphism in the ancestral species at the time of speciation can be estimated using DNA sequences from many loci sampled from 2 or more extant species. The comparison between ancestral and extant polymorphism can be informative about the population genetics of speciation. In this study, we collected and analyzed DNA sequences of approximately 60 genes from 4 species of Sonneratia, a common genus of mangroves on the Indo-Pacific coasts. We found that the 3 ancestral species were comparable to each other in terms of level of polymorphism. However, the ancestral species at the time of speciation were substantially more polymorphic than the extant geographical populations. This ancestral polymorphism is in fact larger than, or at least equal to, the level of polymorphism of the entire species across extant geographical populations. The observations are not fully compatible with speciation by strict allopatry. We suggest that, at the time of speciation, the ancestral species consisted of interconnected but strongly divided geographical populations. This population structure would give rise to high level of polymorphism across species range. This approach of studying the speciation history by genomic means should be applicable to nonmodel organisms.     

Evolution of ossification sequences in salamanders and urodele origins assessed through event-pairing and new methods

SUMMARY Ossification sequences of the skull in extant Urodela and in Permo‐Carboniferous Branchiosauridae have already been used to study the origin of lissamphibians. But most of these studies did not consider some recent methods developed to analyze the developmental sequences within a phylogenetic framework. Here, we analyze the ossification sequences of 24 cranial bones of 23 extant species of salamanders using the event‐pairing method. This reveals new developmental synapomorphies for several extant salamander taxa and ancestral sequences for Urodela under four alternative reference phylogenies. An analysis with the 12 bones for which ossification sequence data are available in urodeles and in the branchiosaurid Apateon is also performed in order to compare the ancestral condition of the crown‐group of Urodela to the sequence of Apateon. This reveals far more incompatibilities than previously suggested. The similarities observed between some extant salamanders and branchiosaurids may result from extensive homoplasy, as the extreme variation observed in extant Urodela suggests, or be plesiomorphic, as the conservation of some ossification patterns observed in other remotely related vertebrates like actinopterygians suggests. We propose a new, simpler method based on squared‐change optimization to estimate the relative timing of ossification of various bones of hypothetical ancestors, and use independent‐contrasts analysis to estimate the confidence intervals around these times. Our results show that the uncertainty of the ancestral ossification sequence of Urodela is much greater than event‐pairing suggests. The developmental data do not allow to conclude that branchiosaurids are closely related to salamanders and their limited taxonomic distribution in Paleozoic taxa precludes testing hypotheses about lissamphibian origins. This is true regardless of the analytical method used (event‐pairing or our new method based on squared‐change parsimony). Simulations show that the new analytical method is generally more powerful to detect evolutionary shifts in developmental timing, and has lower Type I error rate than event‐pairing. It also makes fewer errors in ancestral character value or state assignment than event‐pairing.     

Fossil mushrooms from Miocene and Cretaceous ambers and the evolution of Homobasidiomycetes

Two species of fossil mushrooms that are similar to extant Tricholomataceae are described from Cretaceous and Miocene ambers. Archaeomarasmius leggetti gen. et sp. nov., from mid-Cretaceous amber of New Jersey, resembles the extant genera Marasmius and Marasmiellus. Two fruiting bodies of Archaeomarasmius were found. One consists of a complete pileus with stipe, and the other consists of a fragment of a pileus. The latter was accidentally exposed, and zxsubsequently was used for molecular systematics studies (attempts to amplify ribosomal DNA were unsuccessful) and electron microscopy. The spores are smooth and broadly elliptic with a distinct hilar appendage. Protomycena electra gen. et sp. nov., which is represented by a single complete fruiting body from Miocene amber of the Dominican Republic, is similar to the extant genus Mycena. Based on comparison to extant Marasmieae and Myceneae, Archaeomarasmius and Protomycena were probably saprophytes of leaf litter or wood debris. The poor phylogenetic resolution for extant homobasidiomycetes limits the inferences about divergence times of homobasidiomycete clades that can be drawn from Archaeomarasmius and Protomycena. The ages of these fossils lend support to hypotheses that the cosmopolitan distributions of certain mushroom taxa could be due to fragmentation of ancestral ranges via continental drift. Anatomical and molecular studies have suggested that there has been extensive convergence and parallelism in the evolution of homobasidiomycete fruiting body form. Nevertheless, the striking similarity of these fossils to extant forms suggests that in certain lineages homobasidiomycete macroevolution has also involved long periods during which there has been little morphological change.     

A genomewide survey of developmentally relevant genes in Ciona intestinalis. X. Genes for cell junctions and extracellular matrix

Cell junctions and the extracellular matrix (ECM) are crucial components in intercellular communication. These systems are thought to have become highly diversified during the course of vertebrate evolution. In the present study, we have examined whether the ancestral chordate already had such vertebrate systems for intercellular communication, for which we have searched the genome of the ascidian Ciona intestinalis. From this molecular perspective, the Ciona genome contains genes that encode protein components of tight junctions, hemidesmosomes and connexin-based gap junctions, as well as of adherens junctions and focal adhesions, but it does not have those for desmosomes. The latter omission is curious, and the ascidian type-I cadherins may represent an ancestral form of the vertebrate type-I cadherins and desmosomal cadherins, while Ci-Plakin may represent an ancestral protein of the vertebrate desmoplakins and plectins. If this is the case, then ascidians may have retained ancestral desmosome-like structures, as suggested by previous electron-microscopic observations. In addition, ECM genes that have been regarded as vertebrate-specific were also found in the Ciona genome. These results suggest that the last common ancestor shared by ascidians and vertebrates, the ancestor of the entire chordate clade, had essentially the same systems of cell junctions as those in extant vertebrates. However, the number of such genes for each family in the Ciona genome is far smaller than that in vertebrate genomes. In vertebrates these ancestral cell junctions appear to have evolved into more diverse, and possibly more complex, forms, compared with those in their urochordate siblings.     

Separation of two Neotropical species: Macrothrix superaculeata (Smirnov, 1982) versus M. elegans Sars, 1901 (Macrothricidae, Anomopoda, Cladocera)

The morphology of two Neotropical taxa, Macrothrix elegans Sars, 1901 and M. superaculeata (Smirnov, 1982) (Macrothricidae, Anomopoda, Cladocera) was redescribed, based on type materials (a lectotype of M. elegans was selected here), and additional samples from the Americas. Previous conclusion about synonymy of both species was erroneous, because it was based on limited material from South America. M. superaculeata differs from M. elegans in the presence of a sharp spine at postero-dorsal angle of valves; a more fine ring around dorsal head pore; thinner hexagonal reticulation of valves; the presence of setules on basal segment of postabdominal seta; armature of exopod on antenna II, and some features of thoracic limbs. Previously, the discriminative features of the two species were not formulated accurately, and it was a reason of several misidentifications. Actually, M. superaculeata is found only in a limited set of localities from the Amazon basin, while M. elegans is one of the most common anomopod species in all Neotropics, from Argentina to Mexico.     

Contrasting phylogenetic signals and evolutionary rates in floral traits of Neotropical lianas

The diversity of floral forms has long been considered a prime example of radiation through natural selection. However, little is still known about the evolution of floral traits, a critical piece of evidence for the understanding of the processes that may have driven flower evolution. We studied the pattern of evolution of quantitative floral traits in a group of Neotropical lianas (Bignonieae, Bignoniaceae) and used a time‐calibrated phylogeny as basis to: (1) test for phylogenetic signal in 16 continuous floral traits; (2) evaluate the rate of evolution in those traits; and (3) reconstruct the ancestral state of the individual traits. Variation in floral traits among extant species of Bignonieae was highly explained by their phylogenetic history. However, opposite signals were found in floral traits associated with the attraction of pollinators (calyx and corolla) and pollen transfer (androecium and gynoecium), suggesting a differential role of selection in different floral whorls. Phylogenetic independent contrasts indicate that traits evolved at different rates, whereas ancestral character state reconstructions indicate that the ancestral size of most flower traits was larger than the mean observed sizes of the same traits in extant species. The implications of these patterns for the reproductive biology of Bignonieae are discussed. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 378–390.     

Cambrian anemones with preserved soft tissue from the Chengjiang biota, China

The group Cnidaria includes 'jellyfish', soft-bodied anemone and anemone-like forms and calcified corals. These diploblastic organisms have a fossil record extending back to the earliest metazoans of the Neoproterozoic; however certain cnidarians of the subclass Zoantharia, characterized by soft-bodied anemone-like forms, are absent or poorly represented in the fossil record. Despite the paucity of fossils, it is thought that calcification by soft anemone-like animals was responsible for producing the skeleton that allowed the preservation of the first corals. We report discovery of an abundant assemblage of in situ soft-bodied polyps with tissues. They are preserved in exquisite detail and come from the well-known Lower Cambrian Chengjiang biota of Yunnan, China. The soft-bodied polyps display a simple anatomy that is comparable to some extant anemones of the order Actinaria. The new fossils are assigned to Archisaccophyllia kunmingensis n. gen. et n. sp. Their simple and conservative form suggests that these fossils may represent some kind of ancestral rootstock. The preserved life assemblage provides a unique snapshot of Lower Cambrian anemone life and provides clues for relationships with extant actiniarians as well as calcified corals.     

The feeding mechanisms of the Daphniidae (Crustacea: Cladocera): recent suggestions and neglected considerations

While the importance of grazing by anomopod cladocerans of thefamily Daphniidae on crops of planktonic algae and bacteria,and on detritus, is widely recognized, and although many calculationshave been made on the filtering rate of these crustaceans, thefeeding mechanisms involved in these processes have frequendybeen misinterpreted by ecologists. Recent accounts that purportto describe the feeding mechanism of Daphnia are based on misinterpretationsof morphology and are completely erroneous. The ancestors ofdaphniids were probably benthic, littoral animals, similar invarious respects to primitive represcritatives of extant chydoridsand macrothricids. The feeding mechanisms of the latter giveuseful indications of the kind of device from which that ofthe daphniids probably arose. The daphniid mechanism was derivedby restricting particle abstraction to trunk limbs 3 and 4.Contraiy to recent claims, mink limbs 1 and 2 are not involvedin this element of the feeding process. Comparative studieson many anomopods reveal invariable correlations. Species employingcurrents to cany food particles have filter plates bearing filtratorysetules. Species that, for whatever reason, do not employ currents,except sometimes for respiration, have homologous structuresthat lack filtratory setules, even when, as is often the case,they feed on particulate matter. Comparisons with other branchiopodsare also helpful.     

A molecular mechanism for the origin of a key evolutionary innovation,the bird beak and palate,revealed by an integrative approach to major transitions in vertebrate history

The avian beak is a key evolutionary innovation whose flexibility has permitted birds to diversify into a range of disparate ecological niches. We approached the problem of the mechanism behind this innovation using an approach bridging paleontology, comparative anatomy, and experimental developmental biology. First, we used fossil and extant data to show the beak is distinctive in consisting of fused premaxillae that are geometrically distinct from those of ancestral archosaurs. To elucidate underlying developmental mechanisms, we examined candidate gene expression domains in the embryonic face: the earlier frontonasal ectodermal zone (FEZ) and the later midfacial WNT‐responsive region, in birds and several reptiles. This permitted the identification of an autapomorphic median gene expression region in Aves. To test the mechanism, we used inhibitors of both pathways to replicate in chicken the ancestral amniote expression. Altering the FEZ altered later WNT responsiveness to the ancestral pattern. Skeletal phenotypes from both types of experiments had premaxillae that clustered geometrically with ancestral fossil forms instead of beaked birds. The palatal region was also altered to a more ancestral phenotype. This is consistent with the fossil record and with the tight functional association of avian premaxillae and palate in forming a kinetic beak.     

Holocene thecideide brachiopods from the north‐western Pacific Ocean: Systematics,life habits and ontogeny

Abstract

A new species of the lacazelline brachiopod genus Ospreyella is described from shallow cryptic habitats in Palau, western Caroline Islands and Arnd Atoll, Pohnpei, eastern Caroline Islands, north‐western Pacific Ocean. This new taxon, here named Ospreyella palauensis, and representing the third discovery of a species of Ospreyella from the Indo‐Pacific region, is compared with the other two recently described extant species of the genus, O. depressa Lüter from the Great Barrier Reef, Australia, and O. maldiviana Logan from the Maldive Islands, northern Indian Ocean. An ontogenetic sequence is described for the new species and compared with those previously described for other Holocene lacazellines. Additionally, a study of ontogenetic stages in Thecidellina congregata from Saipan in the Northern Mariana Islands shows early‐stage similarities to those of the new species and other lacazellines. These observations on development in extant forms provide important analogies for comparison with ontogenetic stages in ancestral fossil forms and information which may be useful in reconstructing thecideide phylogenetic history.     

Phenetic relationships and probable ways of morphological diversification of the African large barbs (<Emphasis Type="Italic">Barbus intermedius</Emphasis> complex) in Lake Tana (Ethiopia)

29 quantitative and 18 qualitative skull characters were studied in the African large barbs (Barbus intermedius complex) from Lake Tana (Ethiopia). Based on results of principle components analysis phenetic relationships of 12 morphotypes were assessed. External features diagnostic of the morphotypes were found in individuals substantially different in the skull characters. The obtained data along with the data on morphological diversity of large barbs from Ethiopia beyond the Lake Tana basin suggest origination of the Lake Tana complex of forms from a complex of forms that existed in the upper reaches of the Blue Nile before the lake came into being, and the extant morphotypes of the Lake Tana barbs originated from three or four forms that composed the ancestral riverine local complex.     

Testing phylogenetic implications of eggshell characters in side-necked turtles (Testudines: Pleurodira)

Amniote egg and eggshell morphology is a rich source of characters to link aspects of reproductive biology with systematics. Extensive work concerning both anatomy and phylogenetic assignability has been done on fossil bird and dinosaur eggs, but little is known for extant sauropsids. The utility of eggshell characters for phylogenetic analyses is tested and discussed for extant side-necked turtles (Pleurodira), and the diversity of egg ultrastructure is examined in several species. Egg gross morphology and eggshell ultrastructure of 12 species of extant side-necked turtles was documented using scanning electron microscopy. Thirteen eggshell characters were scored and mapped on a composite phylogeny and ancestral character states were reconstructed. Many of the characters do not show a phylogenetic signal according to a test comparing the number of steps on the chosen phylogeny with that on randomly generated trees. The presence of conservative, clade-supporting features could be demonstrated, and the following clades are supported by several characters: the Elseya-Emydura entity, short-necked Australasian chelids, is backed by two characters, and two additional characters could potentially support this group. Three characters support the monophyly of South American chelids, whereas two characters argue for the exclusion of Hydromedusa, a long-necked form resembling Australian chelids rather than South American forms, from this clade.     

A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes

The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a general methodological framework for reconstructing ancestral genome segments from conserved syntenies in extant genomes. We show that this problem, from a computational point of view, is naturally related to physical mapping of chromosomes and benefits from using combinatorial tools developed in this scope. We develop this framework into a new reconstruction method considering conserved gene clusters with similar gene content, mimicking principles used in most cytogenetic studies, although on a different kind of data. We implement and apply it to datasets of mammalian genomes. We perform intensive theoretical and experimental comparisons with other bioinformatics methods for ancestral genome segments reconstruction. We show that the method that we propose is stable and reliable: it gives convergent results using several kinds of data at different levels of resolution, and all predicted ancestral regions are well supported. The results come eventually very close to cytogenetics studies. It suggests that the comparison of methods for ancestral genome reconstruction should include the algorithmic aspects of the methods as well as the disciplinary differences in data aquisition.