Evolution and phylogenetic significance of cardioidean shell microstructure (Mollusca, Bivalvia)

2001 ◽  
Vol 75 (3) ◽  
pp. 607-643 ◽  
Author(s):  
Jay A. Schneider ◽  
Joseph G. Carter
Keyword(s):  
Phylogenetic Relationships ◽  
Outer Shell ◽  
Data Sets ◽  
Shell Layer ◽  
Shell Microstructure ◽  
Data Set ◽  
Fracture Control ◽  
Selection For ◽  
Morphologic Data ◽  
Combined Data

The shell microstructure of Carboniferous and Triassic permophorids; Triassic and Recent carditids; Devonian, Carboniferous, and Triassic crassatelloideans; and Jurassic through Recent cardioideans is examined in a phylogenetic context, using separate microstructural and morphologic data sets, as well as a combined data set. The microstructural and morphologic data sets are significantly incongruent, but the combined data set suggests that modiomorphoideans (modiomorphids and permophorids) are basal to crassatelloideans; crassatelloideans are basal to carditids (includingSeptocardia), and carditids are basal to cardiids. On the other hand, the possibility of direct permophorid ancestry for the carditid-cardiid clade cannot be excluded, as suggested by the retention of permophorid-like matted (transitional nacreous-porcelaneous) structure in some early carditids and cardiids. In the absence of stratigraphic data and other evidence for phylogenetic relationships, shell microstructure offers limited potential for assessing subfamily-level phylogenetic relationships within the Cardioidea. This is because of microstructural convergences reflecting biomechanical adaptations for fracture control and abrasion resistance, and possibly also selection for metabolic economy of secretion in tropical, oligotrophic habitats. General evolutionary trends in cardiid shell microstructure are nevertheless apparent: Cretaceous cardiids completely replaced an ancestral laminar, matted structure in their inner shell layer with non-laminar porcelaneous structures; evolved better defined CL structure, stronger reflection of the shell margins, and increased thickness or secondary loss of the ancestral prismatic outer shell layer; and, inProtocardia(Pachycardium)stantoni, added inductural deposition. Some Cenozoic cardiids then evolved wider first-order crossed lamellae, non-denticular composite prisms, composite fibrous prisms, ontogenetic submergence of a juvenile non-denticular composite prismatic outer shell layer into the CL middle shell layer, or ontogenetic submergence of the inner part of a juvenile fibrous prismatic outer shell layer into the CL middle shell layer.The shell microstructure ofHemidonax donaciformisis unusual for a cardioidean, and suggests closer affinities with the superfamily Tellinoidea than with the superfamily Cardioidea.Extensive inductural deposits inProtocardia(Pachycardium)stantoniraise the possibility that photosymbiosis evolved among some Mesozoic members of the Protocardiinae, thereby increasing the likelihood that this feature has evolved several times independently in the Cardiidae.Cemented, calcareous periostracal granules or spines are known to occur in modiolopsoideans, mytiloideans, modiomorphids, permophorids, trigonioids, astartids, cardiids, myoids, pholadomyoids, and septibranchoids. Consequently, the presence of these structures is not necessarily indicative of close anomalodesmatan affinities.

Taxonomy and phylogeny of the Triassic bivalve families Mysidiellidae Cox, 1964 and Healeyidae new family

2008 ◽  
Vol 82 (3) ◽  
pp. 555-564 ◽  
Author(s):  
M. Hautmann
Keyword(s):  
Outer Shell ◽  
Junior Synonym ◽  
Late Triassic ◽  
Late Paleozoic ◽  
Great Similarity ◽  
Shell Layer ◽  
Shell Microstructure ◽  
General Shape ◽  
New Family

The Mysidiellidae are morphologically isolated among Triassic bivalves but share important characters with Late Paleozoic Ambonychioidea. Apart from a great similarity in the general shape of the shell, the most primitive mysidiellid genus Promysidiella resembles ambonychioids in the presence of a duplivincular-opisthodetic ligament system. Within the Mysidiellidae, this ligament type evolved into the transitional ligament system that characterizes Late Triassic Mysidiella. The phyletic polarity indicates that this evolution probably took place by paedomorphosis. New examinations of the shell microstructure of Mysidiella demonstrate the presence of simple prismatic and possibly foliated structures in the calcitic outer shell layer, which further supports an ambonychioid affinity. Therefore, the Mysidiellidae are removed from the Mytiloidea and assigned to the Ambonychioidea. The poorly known genus Protopis, which was originally included in the Mysidiellidae, probably had a parivincular ligament system and was hence a member of the Heteroconchia. Joannina, which was previously considered a junior synonym of Protopis, is re-established. The hinge margin of Joannina carries a well developed nymph but lacks teeth. These characters as well as its modioliform shape, anterior shell lobe, and pronounced diagonal carina link Joannina with the Late Triassic genus Healeya (Modiomorphoidea). Both taxa are herein placed in the new family Healeyidae, which differs from the morphologically similar Kalenteridae in the absence of elaborated hinge teeth. Protopis, as well as the recently described genera Leidapoconcha, Waijiaoella, and Qingyaniola, are tentatively assigned to the Healeyidae.

Links between shell chemistry and microstructure – A case study using Arctica islandica

2020 ◽  
Author(s):  
Ellen Schnabel ◽  
Kotaro Shirai ◽  
Naoko Murakami-Sugihara ◽  
Klaus Peter Jochum ◽  
Nils Höche ◽  
...  
Keyword(s):  
Environmental Control ◽  
Formation Rate ◽  
Strong Relationship ◽  
Outer Shell ◽  
Ventral Margin ◽  
Shell Layer ◽  
Shell Microstructure ◽  
Arctica Islandica ◽  
Growth Increments ◽  
Strong Control

<p>Bivalves offer outstanding potential as environmental archives. However, vital effects exert a strong control on the incorporation of many trace and minor elements into the shell so that their use as environmental proxies is currently limited. Furthermore, Sr and Mg show a strong relationship to the micrometer-sized shell architecture (shell microstructure), i.e., near growth lines, which are typically dominated by irregular simple/spherulitic prismatic microstructures, the concentrations of these elements are significantly higher than in portions between growth lines (= growth increments, which are microstructurally more complex). In contrast, Ba is uncoupled from the prevailing shell microstructure. To shed more light on these issues, we conducted a combined element chemical (in-situ analysis by means of LA-ICP-MS) and microstructural analyses (using SEM) of shells of <em>Arctica islandica</em> collected alive in NE Iceland.</p><p>According to our findings, (1) contemporaneous shell portions in the hinge and ventral margin (both belonging to the outer shell layer) within individual specimens showed nearly identical Sr/Ca and Mg/Ca values, but Ba/Ca was 1.5 – 2.5 times higher in the ventral margin than in the hinge. (2) In agreement with previous studies, Sr and Mg were strongly elevated near annual growth lines. (3) Along an isochronous transect from the inner portion of the outer shell layer near the myostracum toward the outer shell surface (in the ventral margin), Si/Ca values increased, on average, by 75% ± 11%, whereas Na/Ca values decreased by 7% ± 1%. Along this transect, the shell microstructure gradually changed from crossed-acicular to homogeneous suggesting that Si and Na are linked to the prevailing nanometer-sized shell architecture or underlying physicochemical processes controlling their formation. (4) In the hinge, Ba/Ca, Sr/Ca, Mn/Ca and Mg/Ca attained highest values along the axis of maximum growth, but gradually decreased in slower growing (contemporaneous) shell portions away from that axis. (5) In contemporaneous shell portions (in either the hinge or the ventral margin), the concentration of some elements varied significantly among specimens, whereas others showed little variability. For example, in similar and contemporaneous shell portions of different specimens, Na/Ca values exhibited only little variation (17.4 – 23.7 mmol/mol), whereas Sr/Ca and B/Ca differed more severely (0.3 – 1.6 mmol/mol and 0.04 – 0.07 mmol/mol, respectively; both within growth increments). Despite these inter-specimen chemical differences, the shell microstructure remained largely invariant.</p><p>Our findings firstly suggest that the extrapallial fluid, if it exists at all, is chemically inhomogeneous. This could result from differences in the efficiency of transmembrane ion transport or to differences in shell formation rate along the growing margin (e.g., faster growth in the outer portion of the outer shell layer than in portions closer to the myostracum). Secondly, chemical differences among specimens may be attributed to physiological differences. Thirdly, some elements such as Ba are uncoupled to microstructural properties, but co-vary strongly among specimens suggesting an environmental control on the uptake and incorporation of this element into the shell.</p>

Combining cross-crystal averaging and MRSAD to phase a 4354-amino-acid structure

2016 ◽  
Vol 72 (2) ◽  
pp. 182-191
Author(s):  
Jason Nicholas Busby ◽  
J. Shaun Lott ◽  
Santosh Panjikar
Keyword(s):  
Radiation Damage ◽  
Model Building ◽  
Data Sets ◽  
Low Resolution ◽  
Data Set ◽  
C Protein ◽  
Large Size ◽  
Anomalous Signal ◽  
Difference Fourier ◽  
Combined Data

The B and C proteins from the ABC toxin complex ofYersinia entomophagaform a large heterodimer that cleaves and encapsulates the C-terminal toxin domain of the C protein. Determining the structure of the complex formed by B and the N-terminal region of C was challenging owing to its large size, the non-isomorphism of different crystals and their sensitivity to radiation damage. A native data set was collected to 2.5 Å resolution and a non-isomorphous Ta6Br12-derivative data set was collected that showed strong anomalous signal at low resolution. The tantalum-cluster sites could be found, but the anomalous signal did not extend to a high enough resolution to allow model building. Selenomethionine (SeMet)-derivatized protein crystals were produced, but the high number (60) of SeMet sites and the sensitivity of the crystals to radiation damage made phasing using the SAD or MAD methods difficult. Multiple SeMet data sets were combined to provide 30-fold multiplicity, and the low-resolution phase information from the Ta6Br12data set was transferred to this combined data set by cross-crystal averaging. This allowed the Se atoms to be located in an anomalous difference Fourier map; they were then used inAuto-Rickshawfor multiple rounds of autobuilding and MRSAD.

Assessing the usefulness of histone H3, U2 snRNA and 28S rDNA in analyses of polychaete relationships

1999 ◽  
Vol 47 (5) ◽  
pp. 499 ◽  
Author(s):  
S. Brown ◽  
G. Rouse ◽  
P. Hutchings ◽  
D. Colgan
Keyword(s):  
Maximum Parsimony ◽  
Sequence Data ◽  
Histone H3 ◽  
28S Rdna ◽  
Maximum Parsimony Analysis ◽  
Data Sets ◽  
Data Set ◽  
U2 Snrna ◽  
Dna Sequence Data ◽  
Combined Data

DNA sequence data from for histone H3 (34 species), U2 snRNA (34 species) and two segments (D1 and D9–10 expansion regions) of 28S rDNA (28 and 26 species, respectively) have been collected to investigate the relationships of polychaetes. Representatives of all of the major morphologically identified clades were used, as well as members of the Sipuncula, Echiura, Turbellaria, Clitellata and Siboglinidae (formerly the phyla Pogonophora and Vestimentifera). Maximum parsimony analyses of the separate data sets gave conflicting results and none conformed closely to previous results based on morphology. Instead each data set provided corroboration of a few of the morphological groupings, usually pairing, though inconsistently, members of the same family. Higher groupings proposed on morphological grounds were rarely recovered. Maximum parsimony analysis of the combined data, excluding areas of uncertain alignment, recovered some morphological groupings such as Cirratulidae, Terebellidae, scale worms and eunicimorphs, and did not significantly contradict others. However, some expected groupings were not recovered. Surprisingly, the fanworms (Sabellidae and Serpulidae) were not shown as sister taxa, and monophyly of Phyllodocida, a morphologically well corroborated clade, required four more steps than most parsimonious trees. Aciculata was not seen in our analyses, although it was the most strongly supported large clade in Rouse and Fauchald (1997, Cladistics and polychaetes. Zoologica Scripta 26, 138–204). Trees constrained to show Aciculata as monophyletic were 18 steps longer than the most parsimonious trees. If trees are rooted on sipunculans rather than the nematode, Aciculata is nearly recovered, being rendered paraphyletic by the inclusion of the sister-pair of Oweniidae and Chaetopteridae. As suggested by some recent morphological and molecular analyses, Siboglinidae and Clitellata may well have sister groups among polychaetes. The morphologically aberrant Sternaspidae are closest to members of Terebellida in the present analyses, supporting the placement of Rouse and Fauchald. Interesting results deserving further assessment concern the placement of Chaetopteridae, Oweniidae and Sipuncula.

Phylogenetic relationships and placement of the Empidoidea (Diptera: Brachycera) based on 28S rDNA and EF-1α sequences

2002 ◽  
Vol 33 (4) ◽  
pp. 421-444 ◽  
Author(s):  
Kenneth P. Collins ◽  
Brian M. Wiegmann
Keyword(s):  
Phylogenetic Relationships ◽  
Elongation Factor ◽  
Sister Group ◽  
Morphological Data ◽  
Sister Group Relationship ◽  
Data Set ◽  
Molecular Phylogenetic ◽  
Data Partitions ◽  
28S Ribosomal Dna ◽  
Combined Data

AbstractThe phylogenetic relationships within the Eremoneura (Empidoidea + Cyclorrhapha) have been controversial. The monophyly of the Empidoidea, as well as the position and rank of higher-level empidoid clades remains unresolved despite numerous analyses using morphological data. In addition, the origin of the Cyclorrhapha and their relationship to the Empidoidea continues to be debated. We present the results of a molecular phylogenetic analysis using nucleotide sequences collected from 28S ribosomal DNA (rDNA) and elongation factor-1α (EF-1α) genes. All currently recognized empidoid families and subfamilies, many lower cyclorrhaphan families (including Opetiidae), and several asiloid outgroups are represented in this study. Unweighted and weighted parsimony, as well as maximum likelihood analyses were applied to individual data partitions and a combined data set. Our results support the monophyly of both Empidoidea and Cyclorrhapha (including Opetia), as well as their sister-group relationship. Within Empidoidea we find support for the following: 1) Chvála's (1983) proposal to divide Empidoidea into five families; 2) Atelestidae as the basal empidoid lineage; and 3) monophyly of Microphoridae + Dolichopodidae.

scholarly journals Retrieval of ozone profiles from OMPS limb scattering observations

2017 ◽  
Author(s):  
Carlo Arosio ◽  
Alexei Rozanov ◽  
Elizaveta Malinina ◽  
Kai-Uwe Eichmann ◽  
Thomas von Clarmann ◽  
...  
Keyword(s):  
Visible Spectral Range ◽  
Retrieval Algorithm ◽  
Tropical Region ◽  
Data Sets ◽  
Absorption Bands ◽  
Data Set ◽  
Northern Latitudes ◽  
The University ◽  
Combined Data ◽  
Good Agreement

Abstract. This study describes a retrieval algorithm developed at the University of Bremen to retrieve vertical profiles of ozone from limb observations performed by the Ozone Mapper and Profiler Suite (OMPS). This algorithm was originally developed for use with data from the SCIAMACHY instrument. As both instruments make limb measurements of the scattered solar radiation in the ultraviolet and visible spectral range, an overarching objective of the study is to facilitate the provision of consolidated and consistent ozone profiles from the two satellites and to produce a combined data set. The optimization of the retrieval algorithm for OMPS takes into account the instrument-specific spectral coverage by exploiting information from spectral windows in the Hartley, Huggins and Chappuis ozone absorption bands. Thereby, ozone concentrations in the 12–60 km altitude range can be retrieved. Observations at altitudes where the measurements are contaminated by clouds are rejected by applying a cloud filter. An independent aerosol retrieval is performed beforehand and its results are used to account for the aerosol load in the stratosphere during the ozone retrieval. Results for seven months of data (July 2016–January 2017) are compared and validated against independent data sets from both satellite-based and balloon-borne measurements, indicating a good agreement. Between 20 and 50 km, the OMPS ozone profiles typically agree with the MLS v4.2 results within 5–10 %, with the exception of high northern latitudes (> 70° N above 40 km) and the tropical lower stratosphere. The comparison of OMPS profiles with those from ozonesondes shows an agreement within ±5 % between 14 and 30 km at northern mid-latitudes. At southern mid-latitudes, an agreement within 5–10 % is achieved, although these results are less reliable because of a limited number of available coincidences. An unexpected bias of approximately 10 % is detected in the tropical region at all altitudes. The processing of the 2013 data set using the same retrieval settings and its validation against ozonesondes reveals a much smaller bias; possible reasons are under investigation.

scholarly journals Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dario Karmeinski ◽  
Karen Meusemann ◽  
Jessica A. Goodheart ◽  
Michael Schroedl ◽  
Alexander Martynov ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Set Covering ◽  
Phylogenetic Position ◽  
Data Sets ◽  
Transcriptome Data ◽  
Data Set ◽  
Sea Slugs ◽  
History Of

Abstract Background The soft-bodied cladobranch sea slugs represent roughly half of the biodiversity of marine nudibranch molluscs on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as targets for drug discovery), the evolutionary history of cladobranch sea slugs is not yet fully understood. Results To enlarge the current knowledge on the phylogenetic relationships, we generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa (Berthella plumula and Polycera quadrilineata). We complemented our taxon sampling with previously published transcriptome data, resulting in a final data set covering 56 species from all but one accepted cladobranch superfamilies. We assembled all transcriptomes using six different assemblers, selecting those assemblies that provided the largest amount of potentially phylogenetically informative sites. Quality-driven compilation of data sets resulted in four different supermatrices: two with full coverage of genes per species (446 and 335 single-copy protein-coding genes, respectively) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximal statistical support for all major splits and phylogenetic relationships at the family level. Besides the questionable position of Noumeaella rubrofasciata, rendering the Facelinidae as polyphyletic, the only notable discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal. Conclusions Our data matrices and the inferred trees can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The placement of E. pulchra, however, proves challenging, even with large data sets and various optimization strategies. Moreover, quartet mapping results show that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.

Testing the plateau: a reexamination of disparity and morphologic constraints in early Paleozoic crinoids

Paleobiology ◽  
2011 ◽  
Vol 37 (2) ◽  
pp. 214-236 ◽  
Author(s):  
Bradley Deline ◽  
William I. Ausich
Keyword(s):  
Current Data ◽  
Rapid Expansion ◽  
Data Sets ◽  
Early Paleozoic ◽  
Data Set ◽  
Middle Ordovician ◽  
Early Ordovician ◽  
Class Level ◽  
Significant Difference ◽  
Morphologic Data

Studies of crinoid morphology have been pivotal in understanding the constraints on the range of morphology within a clade as well as the patterns of disparity throughout the Phanerozoic. Newly discovered and described faunas and recent study of early Paleozoic crinoid diversity provide an ideal opportunity to reanalyze Ordovician through Early Silurian crinoid disparity with more complete taxonomic coverage and finer stratigraphic resolution. Using the coarse stratigraphic binning of Foote (1999), the updated morphologic data set has a similar disparity pattern to those previously reported for the early Paleozoic. However, with the more resolved stratigraphic binning used by Peters and Ausich (2008), a significant difference exists between the original and current data sets. Both data sets have a pronounced disparity high during the late Middle Ordovician. However, the updated disparity curve has a much higher initial disparity during the Early Ordovician and a pronounced rise in disparity during the Silurian recovery. Examination of differential sampling, proportions of the crinoid orders through time, and methods of coding characters indicate these factors have little effect on the pattern of crinoid disparity. The Silurian morphospace expansion occurs primarily within disparids and coincides with the origination of the myelodactylids. These findings corroborate the rapid expansion of morphospace during the Ordovician. However, crinoid disparity did not remain static and, although less frequent than during the initial radiation, new body plans evolved following the Ordovician Extinction (e.g., the myelodactylids). These results are consistent with the hypothesis of ecology constraining the limits on morphologic disparity at the class level.

Integration of morphological and molecular data sets in estimating fungal phytogenies

1995 ◽  
Vol 73 (S1) ◽  
pp. 649-659 ◽  
Author(s):  
François Lutzoni ◽  
Rytas Vilgalys
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Molecular Data ◽  
Morphological Data ◽  
Homogeneity Test ◽  
Data Sets ◽  
Data Set ◽  
Sampling Statistics ◽  
Combined Data

To provide a clearer picture of fungal species relationships, increased efforts are being made to include both molecular and morphological data sets in phylogenetic studies. This general practice in systematics has raised many unresolved questions and controversies regarding how to best integrate the phylogenetic information revealed by morphological and molecular characters. This is because phylogenetic trees derived using different data sets are rarely identical. Such discrepancies can be due to sampling error, to the use of an inappropriate evolutionary model for a given data set, or to different phylogenetic histories between the organisms and the molecule. Methods have been developed recently to test for heterogeneity among data sets, although none of these methods have been subjected to simulation studies. In this paper we compare three tests: a protocol described by Rodrigo et al., an adapted version of Faith's T-PTP test, and Kishino and Hasegawa's likelihood test. These tests were empirically compared using seven lichenized and nonlichenized Omphalina species and the related species Arrhenia lobata (Basidiomycota, Agaricales) for which nrDNA large subunit sequences and morphological data were gathered. The results of these three tests were inconsistent, Rodrigo's test being the only one suggesting that the two data sets could be combined. One of the three most parsimonious trees obtained from the combined data set with eight species is totally congruent with the relationships among the same eight species in an analysis restricted to the same portion of the nrDNA large subunit but extended to 26 species of Omphalina and related genera. Therefore, the results from phylogenetic analyses of this large molecular data set converged on one of the three most parsimonious topologies generated by the combined data set analysis. This topology was not recovered from either data set when analysed separately. This suggests that Rodrigo's homogeneity test might be better suited than the two other tests for determining if trees obtained from different data sets are sampling statistics of the same phylogenetic history. Key words: data sets heterogeneity, homogeneity test, lichen phylogeny, Omphalina, ribosomal DNA.

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