Héctor Botella

Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

BackgroundSequencing projects have allowed diverse retroviruses and LTR retrotransposons from different eukaryotic organisms to be characterized. It is known that retroviruses and other retro-transcribing viruses evolve from LTR retrotransposons and that this whole system clusters into five families: Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao and Caulimoviridae. Phylogenetic analyses usually show that these split into multiple distinct lineages but what is yet to be understood is how deep evolution occurred in this system.ResultsWe combined phylogenetic and graph analyses to investigate the history of LTR retroelements both as a tree and as a network. We used 268 non-redundant LTR retroelements, many of them introduced for the first time in this work, to elucidate all possible LTR retroelement phylogenetic patterns. These were superimposed over the tree of eukaryotes to investigate the dynamics of the system, at distinct evolutionary times. Next, we investigated phenotypic features such as duplication and variability of amino acid motifs, and several differences in genomic ORF organization. Using this information we characterized eight reticulate evolution markers to construct phenotypic network models.ConclusionThe evolutionary history of LTR retroelements can be traced as a time-evolving network that depends on phylogenetic patterns, epigenetic host-factors and phenotypic plasticity. The Ty1/Copia and the Ty3/Gypsy families represent the oldest patterns in this network that we found mimics eukaryotic macroevolution. The emergence of the Bel/Pao, Retroviridae and Caulimoviridae families in this network can be related with distinct inflations of the Ty3/Gypsy family, at distinct evolutionary times. This suggests that Ty3/Gypsy ancestors diversified much more than their Ty1/Copia counterparts, at distinct geological eras. Consistent with the principle of preferential attachment, the connectivities among phenotypic markers, taken as network-represented combinations, are power-law distributed. This evidences an inflationary mode of evolution where the system diversity; 1) expands continuously alternating vertical and gradual processes of phylogenetic divergence with episodes of modular, saltatory and reticulate evolution; 2) is governed by the intrinsic capability of distinct LTR retroelement host-communities to self-organize their phenotypes according to emergent laws characteristic of complex systems.ReviewersThis article was reviewed by Eugene V. Koonin, Eric Bapteste, and Enmanuelle Lerat (nominated by King Jordan)

Jaws and teeth of the earliest bony fishes

Extant jawed vertebrates, or gnathostomes, fall into two major monophyletic groups, namely chondrichthyans (cartilaginous fishes) and osteichthyans (bony fishes and tetrapods). Fossil representatives of the osteichthyan crown group are known from the latest Silurian period, 418 million years (Myr) ago, to the present. By contrast, stem chondrichthyans and stem osteichthyans are still largely unknown. Two extinct Palaeozoic groups, the acanthodians and placoderms, may fall into these stem groups or the common stem group of gnathostomes, but their relationships and monophyletic status are both debated. Here we report unambiguous evidence for osteichthyan characters in jaw bones referred to the late Silurian (423–416-Myr-old) fishes Andreolepis hedei and Lophosteus superbus, long known from isolated bone fragments, scales and teeth, and whose affinities to, or within, osteichthyans have been debated. The bones are a characteristic osteichthyan maxillary and dentary, but the organization of the tooth-like denticles they bear differs from the large, conical teeth of crown-group osteichthyans, indicating that they can be assigned to the stem group. Andreolepis and Lophosteus are thus not only the oldest but also the most phylogenetically basal securely identified osteichthyans known so far.

Grist for Riedl's mill: a network model perspective on the integration and modularity of the human skull.

Riedls concept of burden neatly links development and evolution by ascertaining that structures that show a high degree of developmental co-dependencies with other structures are more constrained in evolution. The human skull can be precisely modeled as an articulated complex system of bones connected by sutures, forming a network of structural co-dependencies. We present a quantitative analysis of the morphological integration, modularity, and hierarchical organization of this human skull network model. Our overall results show that the human skull is a small-world network, with two well-delimited connectivity modules: one facial organized around the ethmoid bone, and one cranial organized around the sphenoid bone. Geometric morphometrics further support this two-module division, stressing the direct relationship between the developmental information enclosed in connectivity patterns and skull shape. Whereas the facial module shows a hierarchy of clustered blocks of bones, the bones of the cranial modules show a regular pattern of connections. We analyze the significance of these arrangements by hypothesizing specific structural roles for the most important bones involved in the formation of both modules, in the context of Riedls burden. We conclude that it is the morphological integration of each group of bones that defines the semi-hierarchical organization of the human skull, reflecting fundamental differences in the ontogenetic patterns of growth and the structural constraints that generate each module. Our study also demonstrates the adequacy of network analysis as an innovative tool to understand the morphological complexity of anatomical systems.

Structural Constraints in the Evolution of the Tetrapod Skull Complexity: Williston’s Law Revisited Using Network Models

Ever since the appearance of the first land vertebrates, the skull has undergone a simplification by loss and fusion of bones in all major groups. This well-documented evolutionary trend is known as “Williston’s Law”. Both loss and fusion of bones are developmental events that generate, at large evolutionary scales, a net reduction in the number of skull bones. We reassess this evolutionary trend by analyzing the patterns of skull organization captured in network models in which nodes represent bones and links represent suture joints. We also evaluate the compensatory process of anisomerism (bone specialization) suggested to occur as a result of this reduction by quantifying the heterogeneity and the ratio of unpaired bones in real skulls. Finally, we perform simulations to test the differential effect of bone losses in skull evolution. We show that the reduction in bone number during evolution is accompanied by a trend toward a more complex organization, rather than toward simplification. Our results indicate that the processes by which bones are lost or fused during development are central to explain the evolution of the morphology of the skull. Our simulations suggest that the evolutionary trend of increasing morphological complexity can be caused as a result of a structural constraint, the systematic loss of less connected bones during development.

Pseudodalatias henarejensis nov. sp. A New Pseudodalatiid (Elasmobranchii) from the Middle Triassic of Spain

ABSTRACT Pseudodalatiids, a chondrichthyan family of uncertain phylogenetic affinities, have been hitherto exclusively known from the tooth-based species Pseudodalatias barnstonensis (Sykes, 1971), which has a stratigraphic range restricted to the Upper Triassic of Europe. Pseudodalatias presents a characteristic dentition which allows it to hold and cut its prey, showing a neoselachian design, but lacking the triple-layered enameloid microstructure of neoselachian teeth. The discovery of Pseudodalatias henarejensis nov. sp. in the Ladinian of Spain extends the stratigraphical range and the palaeogeographical distribution of this family. This new species also demonstrates that a cutting-clutching dentition evolved progressively in the family Pseudodalatidiidae. Pseudodalatiids are likely to represent stem-batoids or stemneoselachians rather than aberrant hybodonts.

Network Models in Anatomical Systems

Network theory has been extensively used to model the underlying structure of biological processes. From genetics to ecology, network thinking is changing our understanding of complex systems, specifically how their internal structure determines their overall behavior. Concepts such as hubs, scale-free or small-world networks, common in the complexity literature, are now used more and more in sociology, neurosciences, as well as other anthropological fields. Even though the use of network models is nowadays so widely applied, few attempts have been carried out to enrich our understanding in the classical morphological sciences such as in comparative anatomy or physical anthropology. The purpose of this article is to introduce the usage of network tools in morphology; specifically by building anatomical networks, dealing with the most common analyses and problems, and interpreting their outcome.

Testing models of dental development in the earliest bony vertebrates, Andreolepis and Lophosteus

Theories on the development and evolution of teeth have long been biased by the fallacy that chondrichthyans reflect the ancestral condition for jawed vertebrates. However, correctly resolving the nature of the primitive vertebrate dentition is challenged by a dearth of evidence on dental development in primitive osteichthyans. Jaw elements from the Silurian–Devonian stem-osteichthyans Lophosteus and Andreolepis have been described to bear a dentition arranged in longitudinal rows and vertical files, reminiscent of a pattern of successional development. We tested this inference, using synchrotron radiation X-ray tomographic microscopy (SRXTM) to reveal the pattern of skeletal development preserved in the sclerochronology of the mineralized tissues. The tooth-like tubercles represent focal elaborations of dentine within otherwise continuous sheets of the dermal skeleton, present in at least three stacked generations. Thus, the tubercles are not discrete modular teeth and their arrangement into rows and files is a feature of the dermal ornamentation that does not reflect a polarity of development or linear succession. These fossil remains have no bearing on the nature of the dentition in osteichthyans and, indeed, our results raise questions concerning the homologies of these bones and the phylogenetic classification of Andreolepis and Lophosteus.

New data on the Lower Devonian chondrichthyan fauna from Celtiberia (Spain)

CARLOS MARTINEZ-PEREZ,1 VINCENT DUPRET,2 ESTHER MANZANARES,1 and HECTOR BOTELLA*1; department of Geology, University of Valencia, C/ Doctor Moliner, 50. CP. 46100, Burjassot, Valencia, Spain, Carlos.Martinez-PerezC^uv.es; Hector.Botella@uv.es; Esther.Manzanares@uv.es; 2Subdepartment of Evolutionary Organismal Biology, Department of Physiology and Developmental Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18A 752 36, Uppsala, Sweden, vincent.dupret@ebc.uu.se

New insights into the diversity dynamics of Triassic conodonts

In this paper, we examine the diversity trends and the evolutionary patterns of Triassic conodonts through a newly powered large-scale data-set compiled directly from the primary literature. Paleodiversity dynamics analyses have been undertaken by working at the species level and using a system of time units based on biozone subdivisions for a fine temporal level resolution. The role of heterogeneous duration of taxa in diversity estimates has been evaluated through the probabilistic profiles. Results reveal three different stages in the diversity behaviour of Triassic conodonts from standing metrics delimited by two inflections at the mid-Anisian and mid-Carnian. Survivorship analysis supports this pattern. Origination–extinction metrics report a diversification pattern characterised by important fluctuations during the Lopingian–Induan (earliest Triassic), the early-middle Olenekian (Early Triassic) and the Anisian–Ladinian transitions (Middle Triassic), as well as in the early Late Triassic. In addition, two clear diversification peaks are observed in the late Carnian and in the end-Norian. Reported patterns are interpreted in the context of deep extinction and environmental instability by documenting the biological signal of the main diversification and turnover patterns observed from such records. This study emphasises the singularity behaviour of diversity trends derived from the conodont record.

Machaeracanthus goujeti n. sp. (Acanthodii) from the Lower Devonian of Spain and northwest France, with special reference to spine histology

ABSTRACT We describe here a new machaeracanthid acanthodian (Machaeracanthus goujeti n. sp.), based on isolated spines, scales and scapulocoracoids from the Lower Devonian (Lochkovian-Pragian) of the Nogueras Formation, Celtiberia, Spain. The new taxon also includes a fragmentary spine and isolated scales from the Lower Devonian of northern Spain (Palencia and Cantabrian Mountains) and western France (Saint-Céneré) originally assigned to Machaeracanthus sp. The spines of M. goujeti n. sp. comprise two morphotypes in agreement with the morphofunctional model of a pair of pectoral spines articulating with the pectoral girdle already indicated for M. hunsrueckianum Südkamp & Burrow, 2007, M. longaevus Eastman, 1907, and M. sulcatus Newberry, 1857. The morphology and size of the spines distinguish M. goujeti n. sp. from the coeval species M. bohemicus Barrande, 1872; the new species most closely resembles the younger species M. peracutus Newberry, 1857. The spines of M. goujeti n. sp. consist of trabecular and lamellar dentine layers which form the wall of the central axis (pierced by a longitudinal pulp cavity) and lateral expansions. The most superficial layer of dentine is centrifugally deposited in the complete spine; this condition is found in fin spines of some chondrichthyans and contrasts with that observed in typical acanthodian fin spines where the exserted portion is ornamented with ribs of centripetally growing dentine. Very small spines and scapulocoracoids of M. goujeti n. sp. described here, are the first report of juvenile specimens of a species of Machaeracanthus Newberry, 1857. The distal part of the juvenile spine lacks lateral expansions (keel and wing) and demonstrates the first stage in the development of the spine.