Dataset Information

Landforms predict phylogenetic structure on one of the world's most ancient surfaces.

ABSTRACT:

Background

The iconic Pilbara in northwestern Australia is an ancient geological and biophysical region that is an important zone of biodiversity, endemism and refugia. It also is overlain by some of the oldest erosion surfaces on Earth, but very little is known about the patterns of biotic diversity within the Pilbara or how they relate to the landscape. We combined phylogenetic and spatial-autocorrelation genetic analyses of mitochondrial DNA data on populations of the gekkotan lizard Lucasium stenodactylum within the Pilbara with geological, distributional and habitat data to test the hypothesis that ancient surface geology predicts current clade-habitat associations in saxicoline animals.

Results

This is the first detailed phylogenetic examination of a vertebrate organism across the Pilbara region. Our phylogeny provides strong support for a deep and ancient phylogenetic split within L. stenodactylum that distinguishes populations within the Pilbara region from those outside the Pilbara. Within the Pilbara region itself, our phylogeny has identified five major clades whose distribution closely matches different surface geologies of this ancient landscape. Each clade shows strong affinities with particular terrain types and topographic regions, which are directly related to different geological bedrock.

Conclusion

Together our phylogenetic, distributional, geological and habitat data provide a clear example of ecological diversification across an ancient and heterogeneous landscape. Our favoured hypothesis is that ancestors of the Pilbara lineages radiated into the region at the onset of aridity in Australia approximately 5 mya and locally adapted to the various ancient and highly stable terrain types and the micro-habitats derived from them. In terms of specimen recovery and analysis, we are only beginning to reconstruct the biotic history of this ancient landscape. Our results show the geological history and the habitats derived from them will form an important part of this emerging story.

SUBMITTER: Pepper M

PROVIDER: S-EPMC2397392 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature

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Publications

Landforms predict phylogenetic structure on one of the world's most ancient surfaces.

Pepper Mitzy M Doughty Paul P Arculus Richard R Keogh J Scott JS

BMC evolutionary biology 20080519

<h4>Background</h4>The iconic Pilbara in northwestern Australia is an ancient geological and biophysical region that is an important zone of biodiversity, endemism and refugia. It also is overlain by some of the oldest erosion surfaces on Earth, but very little is known about the patterns of biotic diversity within the Pilbara or how they relate to the landscape. We combined phylogenetic and spatial-autocorrelation genetic analyses of mitochondrial DNA data on populations of the gekkotan lizard ...[more]

PMID: 18485245

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Project description:BackgroundPaedocypris, a highly developmentally truncated fish from peat swamp forests in Southeast Asia, comprises the world's smallest vertebrate. Although clearly a cyprinid fish, a hypothesis about its phylogenetic position among the subfamilies of this largest teleost family, with over 2400 species, does not exist. Here we present a phylogenetic analyses of 227 cypriniform taxa, including 213 cyprinids, based upon complete mitochondrial DNA cytochrome b nucleotide sequences in order to determine the phylogenetic position of Paedocypris and to study the evolution of miniaturization among cyprinids.ResultsOur analyses reveal a strongly supported sister group relationship (clade C) between Paedocypris and Sundadanio, another developmentally truncated miniature cyprinid. Clade C was resolved as sister group of a larger clade characterized by small rasborine taxa (clade D). We found that miniaturised taxa are more numerous in the rasborine clade A, formed by clades C and D, than in any other cyprinid clade. The consensus cytb in cyprinids includes 380 amino acids and an incomplete T-- stop codon. We noted that a few cyprinids mostly rasborine taxa placed within clade A had either a TAA or TAG stop codon, 376, 378, or 381 amino acids, and up to 10 base pairs (bp) of noncoding region before the 5' end of the tRNA-Thr. Our relaxed molecular clock estimates revealed high divergence times for the Sundadanio and Paedocypris clades and provide a first temporal framework for the evolution of miniaturization among cyprinids.ConclusionPaedocypris belongs to a clade (Rasborinae clade A) that shows recurrent miniaturization, including both taxa characterized by developmental truncation and by proportioned dwarfism. Its closest relative is another miniaturized taxon, the genus Sundadanio. We conclude that the miniaturized cyprinids with remarkable morphological novelties, like Paedocypris and Danionella, are at the same time the most developmentally truncated taxa. The miniaturized cyprinids with no or few developmental truncations like Boraras, Microrasbora, and Horadandia show no such evolutionary novelties.

Project description:BACKGROUND: The ferlin gene family possesses a rare and identifying feature consisting of multiple tandem C2 domains and a C-terminal transmembrane domain. Much currently remains unknown about the fundamental function of this gene family, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease. The availability of genome sequences from a wide range of species makes it possible to explore the evolution of the ferlin family, providing contextual insight into characteristic features that define the ferlin gene family in its present form in humans. RESULTS: Ferlin genes were detected from all species of representative phyla, with two ferlin subgroups partitioned within the ferlin phylogenetic tree based on the presence or absence of a DysF domain. Invertebrates generally possessed two ferlin genes (one with DysF and one without), with six ferlin genes in most vertebrates (three DysF, three non-DysF). Expansion of the ferlin gene family is evident between the divergence of lamprey (jawless vertebrates) and shark (cartilaginous fish). Common to almost all ferlins is an N-terminal C2-FerI-C2 sandwich, a FerB motif, and two C-terminal C2 domains (C2E and C2F) adjacent to the transmembrane domain. Preservation of these structural elements throughout eukaryotic evolution suggests a fundamental role of these motifs for ferlin function. In contrast, DysF, C2DE, and FerA are optional, giving rise to subtle differences in domain topologies of ferlin genes. Despite conservation of multiple C2 domains in all ferlins, the C-terminal C2 domains (C2E and C2F) displayed higher sequence conservation and greater conservation of putative calcium binding residues across paralogs and orthologs. Interestingly, the two most studied non-mammalian ferlins (Fer-1 and Misfire) in model organisms C. elegans and D. melanogaster, present as outgroups in the phylogenetic analysis, with results suggesting reproduction-related divergence and specialization of species-specific functions within their genus. CONCLUSIONS: Our phylogenetic studies provide evolutionary insight into the ferlin gene family. We highlight the existence of ferlin-like proteins throughout eukaryotic evolution, from unicellular phytoplankton and apicomplexan parasites, through to humans. We characterise the preservation of ferlin structural motifs, not only of C2 domains, but also the more poorly characterised ferlin-specific motifs representing the DysF, FerA and FerB domains. Our data suggest an ancient role of ferlin proteins, with lessons from vertebrate biology and human disease suggesting a role relating to vesicle fusion and plasma membrane specialization.

Dataset Information

Landforms predict phylogenetic structure on one of the world's most ancient surfaces.

Background

Results

Conclusion

Publications

Landforms predict phylogenetic structure on one of the world's most ancient surfaces.

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