Origins and early evolution of herbivory in tetrapods

The first herbivorous tetrapods date from the Late Carboniferous, about 300 million years ago. By the Late Permian, continental ecosystems of `modern' aspect had been established, with a vast standing crop of herbivores supporting relatively few carnivores. Processing of high-fibre plant material requires (1) structural modifications of the dentition, jaw apparatus and digestive tract and (2) the acquisition of microbial endosymbionts that produce the enzymes needed for fermentative digestion of cellulose, the principal compound of cell walls in plants. Recent phylogenetic analyses of tetrapods indicate that endosymbiotic cellulysis was acquired independently in a number of lineages during the late Palaeozoic.     

A genus-level supertree of the Dinosauria

One of the ultimate aims of systematics is the reconstruction of the tree of life. This is a huge undertaking that is inhibited by the existence of a computational limit to the inclusiveness of phylogenetic analyses. Supertree methods have been developed to overcome, or at least to go around this problem by combining smaller, partially overlapping cladograms. Here, we present a very inclusive generic-level supertree of Dinosauria (covering a total of 277 genera), which is remarkably well resolved and provides some clarity in many contentious areas of dinosaur systematics.     

Rise of the earliest tetrapods: an early Devonian origin from marine environment

Tetrapod fossil tracks are known from the Middle Devonian (Eifelian at ca. 397 million years ago--MYA), and their earliest bony remains from the Upper Devonian (Frasnian at 375-385 MYA). Tetrapods are now generally considered to have colonized land during the Carboniferous (i.e., after 359 MYA), which is considered to be one of the major events in the history of life. Our analysis on tetrapod evolution was performed using molecular data consisting of 13 proteins from 17 species and different paleontological data. The analysis on the molecular data was performed with the program TreeSAAP and the results were analyzed to see if they had implications on the paleontological data collected. The results have shown that tetrapods evolved from marine environments during times of higher oxygen levels. The change in environmental conditions played a major role in their evolution. According to our analysis this evolution occurred at about 397-416 MYA during the Early Devonian unlike previously thought. This idea is supported by various environmental factors such as sea levels and oxygen rate, and biotic factors such as biodiversity of arthropods and coral reefs. The molecular data also strongly supports lungfish as tetrapod's closest living relative.     

Temnospondyli bite club: ecomorphological patterns of the most diverse group of early tetrapods

Temnospondyls were a successful group of early tetrapods that lived during the Palaeozoic and Mesozoic periods. Different ecomorphotypes were present (terrestrial, amphibious and fully aquatic) with a wide range of lifestyles. Herein, we analysed several clades of temnospondyls using geometric morphometrics, Finite Element Analysis, and comparative phylogenetic analysis. Some temnospondyli clades were 'crocodilomorph' feeding analogues. The skull analysis reveals a concordance between form and feeding function, in amphibious and fully aquatic feeders. The form of terrestrial feeders could be consequences of adaptative or phylogenetical constraints. Basal temnospondyls, as edopoids, were able to leave the water and feed on land. Eryopids continued as terrestrial feeders, although some members showed a shift to increased aquatic feeding. The aquatic environment was especially occupied by archegosaurs during the Permian. After the Permo-Triassic extinction, trematosaurs and capitosaurs returned to the aquatic environment and their members were amphibious and fully aquatic feeders until their disappearance.     

A phylogenetic supertree of the fowls (Galloanserae, Aves)

The fowls (Anseriformes and Galliformes) comprise one of the major lineages of birds and occupy almost all biogeographical regions of the world. The group contains the most economically important of all bird species, each with a long history of domestication, and is an ideal model for studying ecological and evolutionary patterns. Yet, despite the relatively large amount of systematic attention fowls have attracted because of their socio‐economic and biological importance, the species‐level relationships within this clade remain controversial. Here we used the supertree method matrix representation with parsimony to generate a robust estimate of species‐level relationships of fowls. The supertree represents one of the most comprehensive estimates for the group to date, including 376 species (83.2% of all species; all 162 Anseriformes and 214 Galliformes) and all but one genera. The supertree was well‐resolved (81.1%) and supported the monophyly of both Anseriformes and Galliformes. The supertree supported the partitioning of Anseriformes into the three traditional families Anhimidae, Anseranatidae, and Anatidae, although it provided relatively poor resolution within Anatidae. For Galliformes, the majority‐rule supertree was largely consistent with the hypothesis of sequential sister‐group relationships between Megapodiidae, Cracidae, and the remaining Galliformes. However, our species‐level supertree indicated that more than 30% of the polytypic genera examined were not monophyletic, suggesting that results from genus‐level comparative studies using the average of the constituent species’ traits should be interpreted with caution until analogous species‐level comparative studies are available. Poorly resolved areas of the supertree reflect gaps or outstanding conflict within the existing phylogenetic database, highlighting areas in need of more study in addition to those species not present on the tree at all due to insufficient information. Even so, our supertree will provide a valuable foundation for understanding the diverse biology of fowls in a robust phylogenetic framework.     

Dermal bone in early tetrapods: a palaeophysiological hypothesis of adaptation for terrestrial acidosis

The dermal bone sculpture of early, basal tetrapods of the Permo-Carboniferous is unlike the bone surface of any living vertebrate, and its function has long been obscure. Drawing from physiological studies of extant tetrapods, where dermal bone or other calcified tissues aid in regulating acid-base balance relating to hypercapnia (excess blood carbon dioxide) and/or lactate acidosis, we propose a similar function for these sculptured dermal bones in early tetrapods. Unlike the condition in modern reptiles, which experience hypercapnia when submerged in water, these animals would have experienced hypercapnia on land, owing to likely inefficient means of eliminating carbon dioxide. The different patterns of dermal bone sculpture in these tetrapods largely correlates with levels of terrestriality: sculpture is reduced or lost in stem amniotes that likely had the more efficient lung ventilation mode of costal aspiration, and in small-sized stem amphibians that would have been able to use the skin for gas exchange.     

A phylogenetic supertree of oscine passerine birds (Aves: Passeri)

Oscine passerine birds make up almost half of all avian diversity. Relationships within the group, and its classification, have long been controversial. Over the last 10 years numerous molecular phylogenies have been published. We compiled source phylogenies from 99 published studies to construct an oscine supertree. We aimed to illustrate weak and strong parts of the phylogeny and set targets for future phylogenetic work and therefore preferred a heuristic approach where we judged the adequacy of taxon sampling and molecular method of each source tree instead of using matrices and automated tree-building programs. We present an estimate of the phylogenetic relationships of 1723 extant and one extinct species of oscine passerine birds (Aves: Passeri) — more than 37% of the total. We included 34/35 (97%) families, 38/39 (97%) subfamilies and 40/43 (93%) tribes. Overall resolution is 83% of a fully bifurcating tree. The basal lineages are all distributed in the Australo-Papuan region, but several more distal lineages dispersed out of this region and radiated in other parts of the world. However, taxa of the Australian region suffer from larger evolutionary gaps and the deep branches of the Sylvioidea and nine South American primaried oscines are still poorly resolved.     

A simulation study comparing supertree and combined analysis methods using SMIDGen

Background  

Supertree methods comprise one approach to reconstructing large molecular phylogenies given multi-marker datasets: trees are estimated on each marker and then combined into a tree (the "supertree") on the entire set of taxa. Supertrees can be constructed using various algorithmic techniques, with the most common being matrix representation with parsimony (MRP). When the data allow, the competing approach is a combined analysis (also known as a "supermatrix" or "total evidence" approach) whereby the different sequence data matrices for each of the different subsets of taxa are concatenated into a single supermatrix, and a tree is estimated on that supermatrix.     

SuperFine: fast and accurate supertree estimation

Many research groups are estimating trees containing anywhere from a few thousands to hundreds of thousands of species, toward the eventual goal of the estimation of a Tree of Life, containing perhaps as many as several million leaves. These phylogenetic estimations present enormous computational challenges, and current computational methods are likely to fail to run even on data sets in the low end of this range. One approach to estimate a large species tree is to use phylogenetic estimation methods (such as maximum likelihood) on a supermatrix produced by concatenating multiple sequence alignments for a collection of markers; however, the most accurate of these phylogenetic estimation methods are extremely computationally intensive for data sets with more than a few thousand sequences. Supertree methods, which assemble phylogenetic trees from a collection of trees on subsets of the taxa, are important tools for phylogeny estimation where phylogenetic analyses based upon maximum likelihood (ML) are infeasible. In this paper, we introduce SuperFine, a meta-method that utilizes a novel two-step procedure in order to improve the accuracy and scalability of supertree methods. Our study, using both simulated and empirical data, shows that SuperFine-boosted supertree methods produce more accurate trees than standard supertree methods, and run quickly on very large data sets with thousands of sequences. Furthermore, SuperFine-boosted matrix representation with parsimony (MRP, the most well-known supertree method) approaches the accuracy of ML methods on supermatrix data sets under realistic conditions.     

A fast algorithm to build a supertree with a set of gene trees

Important desired properties of an algorithm to construct a supertree (species tree) by reconciling input trees are its low complexity and applicability to large biological data. In its common statement the problem is proved to be NP-hard, i.e. to have an exponential complexity in practice. We propose a reformulation of the supertree building problem that allows a computationally effective solution. We introduce a biologically natural requirement that the supertree is sought for such that it does not contain clades incompatible with those existing in the input trees. The algorithm was tested with simulated and biological trees and was shown to possess an almost square complexity even if horizontal transfers are allowed. If HGTs are not assumed, the algorithm is mathematically correct and possesses the longest running time of n3 x[V0]3, where n is the number of input trees and [V0] is the total number of species. The authors are unaware of analogous solutions in published evidence. The corresponding inferring program, its usage examples and manual are freely available at http://lab6.iitp.ru/en/super3gl. The available program does not implement HGTs. The generalized case is described in the publication "A tree nearest in average to a set of trees" (Information Transmission Problems, 2011).     

Explosions and hot spots in supertree methods

In phylogenetic systematics a problem of great practical and theoretical interest is to construct one or more large phylogenies (evolutionary trees), i.e., supertrees, from a given set of small phylogenies with overlapping sets of leaf labels. Although the methods being used to solve this problem are usually given plausible biological or theoretical justifications, occasionally it is possible to see that the result of a supertree method (SM) is explosive, and therefore logically meaningless, in the sense that it has been inferred from logical propositions that are contradictory. This paper presents the basic ideas and issues of how explosions affect the inference of rooted trees by SMs. We define the relevant concepts, give examples, and show how sometimes it is possible to identify hot spots in the input from which an SM may make explosive inferences that cannot be logically justified.     

Temperature and hypoxia in ectothermic tetrapods

 

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Interactions between temperature and hypoxia in ectothermic tetrapods (reptiles and amphibians) are reviewed.     

Performance of flip supertree construction with a heuristic algorithm

Supertree methods are used to assemble separate phylogenetic trees with shared taxa into larger trees (supertrees) in an effort to construct more comprehensive phylogenetic hypotheses. In spite of much recent interest in supertrees, there are still few methods for supertree construction. The flip supertree problem is an error correction approach that seeks to find a minimum number of changes (flips) to the matrix representation of the set of input trees to resolve their incompatibilities. A previous flip supertree algorithm was limited to finding exact solutions and was only feasible for small input trees. We developed a heuristic algorithm for the flip supertree problem suitable for much larger input trees. We used a series of 48- and 96-taxon simulations to compare supertrees constructed with the flip supertree heuristic algorithm with supertrees constructed using other approaches, including MinCut (MC), modified MC (MMC), and matrix representation with parsimony (MRP). Flip supertrees are generally far more accurate than supertrees constructed using MC or MMC algorithms and are at least as accurate as supertrees built with MRP. The flip supertree method is therefore a viable alternative to other supertree methods when the number of taxa is large.     

Evolutionary patterns in early tetrapods. II. Differing constraints on available character space among clades

Radiations of large clades often accompany rapid morphological diversification. Evolutionary biologists debate the impact of external restrictions imposed by ecology, and intrinsic constraints imposed by development and genetics, on the rate at which morphological innovations are gained. These issues are particularly interesting for groups such as tetrapods, which evolved novel body plans relative to their piscine ancestors and which also invaded new ecosystems following terrestrialization. Prior studies have addressed these issues by looking at either ranges of morphological variation or rates of character change. Here, we address a related but distinct issue: the numbers of characters that freely vary within a clade. We modify techniques similar to those used by ecologists to infer species richnesses to estimate the number of potentially varying characters given the distributions of changes implied by a model phylogeny. Our results suggest both increasing constraints/restrictions and episodes of 'character release' (i.e. increasing the number of potentially varying characters). In particular, we show that stem lissamphibians had a restricted character space relative to that of stem amniotes, and that stem amniotes both had restrictions on some parts of character space but also invaded new character space that had been unavailable to stem tetrapods.     

Terrestrial tetrapods and the end Permian event: A comparison of analyses

Previous analyses of changes in diversity of Permo‐Triassic tetrapods are reviewed and compared. Biases inherent in such studies which distort the picture of diversity change are discussed. A new analysis of change in generic diversity of the tetrapods of the Karoo Basin, South Africa is presented. Various factors which could bias the results, namely, inconsistent taxonomy, insensitive stratigraphy, area of exposure per time interval, and differing intensity of collecting are addressed and corrections made for them. The results of the new analysis are compared to those of previous ones. In particular it is noted that, contrary to the results of other studies, large decreases in generic number are recorded not once, but twice in the Late Permian sediments, the second occurring in sediments dating from well before the close of that Period. It is concluded that stratigraphic sensitivity is the most important biasing factor in the present analysis and the implications of this for other diversity studies, and for explanations of diversity change, are emphasized.     

Heterochrony and the origin of tetrapods

Long, J. A. 1990 04 15: Heterochrony and the origin of tetrapods. Lethaia , Vol. 23, pp. 157–166. Oslo. ISSN 0024–1164.
Juveniles of the osteolepifonn fish Eusthenopteron show more features in common with primitive tetrapods than any other crossopterygian group. These similarities indicate that paedomorphosis may have played an important role directing anagenesis of cranial characters in the fish-tetrapod transition. The development of the tetrapod limb, however, probably resulted from peramorphosis. The first tetrapods may have originated in the East Gondwana vertebrate Province early in the Devonian, based on the oldest known tetrapod footprints from Australia. Furthermore, the biogeographic distribution of plesiomorphic osteichthyans indicates that the monophyletic group 'rhizodontiforms. osteolepiforms and tetrapods' most likely arose in east Gondwana.