Mitochondrial genome primers for Lake Malawi cichlids.

Resolving the evolutionary history of rapidly diversifying lineages like the Lake Malawi Cichlid Flock demands powerful phylogenetic tools. Although this clade of over 500 species of fish likely diversified in less than two million years, the availability of extensive sequence data sets, such as complete mitochondrial genomes, could help resolve evolutionary patterns in this group. Using a large number of newly developed primers, we generated whole mitochondrial genome sequences for 14 Lake Malawi cichlids. We compared sequence divergence across protein-coding regions of the mitochondrial genome and also compared divergence in the mitochondrial loci to divergence at two nuclear protein-coding loci, Mitfb and Dlx2. Despite the widespread sharing of haplotypes of identical sequences at individual loci, the combined use of all protein-coding mitochondrial loci provided a bifurcating phylogenetic hypothesis for the exemplars of major lineages within the Lake Malawi cichlid radiation. The primers presented here could have substantial utility for evolutionary analyses of mitochondrial evolution and hybridization within this diverse clade.

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates.

The uneven distribution of species richness is a fundamental and unexplained pattern of vertebrate biodiversity. Although species richness in groups like mammals, birds, or teleost fishes is often attributed to accelerated cladogenesis, we lack a quantitative conceptual framework for identifying and comparing the exceptional changes of tempo in vertebrate evolutionary history. We develop MEDUSA, a stepwise approach based upon the Akaike information criterion for detecting multiple shifts in birth and death rates on an incompletely resolved phylogeny. We apply MEDUSA incompletely to a diversity tree summarizing both evolutionary relationships and species richness of 44 major clades of jawed vertebrates. We identify 9 major changes in the tempo of gnathostome diversification; the most significant of these lies at the base of a clade that includes most of the coral-reef associated fishes as well as cichlids and perches. Rate increases also underlie several well recognized tetrapod radiations, including most modern birds, lizards and snakes, ostariophysan fishes, and most eutherian mammals. In addition, we find that large sections of the vertebrate tree exhibit nearly equal rates of origination and extinction, providing some of the first evidence from molecular data for the importance of faunal turnover in shaping biodiversity. Together, these results reveal living vertebrate biodiversity to be the product of volatile turnover punctuated by 6 accelerations responsible for >85% of all species as well as 3 slowdowns that have produced "living fossils." In addition, by revealing the timing of the exceptional pulses of vertebrate diversification as well as the clades that experience them, our diversity tree provides a framework for evaluating particular causal hypotheses of vertebrate radiations.

Osteology and skeletal development of Phyllomedusa vaillanti (Anura: Hylidae: Phyllomedusinae) and a comparison of this arboreal species with a terrestrial member of the genus.

Few descriptions of skeletal development and morphology exist for neobatrachians, despite their abundance and diversity. Herein, the adult morphologies of Phyllomedusa vaillanti and P. atelopoides are described and compared and the ontogeny of the larval skeleton of P. vaillanti is described and compared with those of Hyla lanciformis (the only hylid for which a detailed cranial and postcranial osteological ontogenesis has been described) and P. trinitatis (the only other member of this genus for which the larval skeleton has been described). These descriptions and comparisons are made on the basis of cleared and double-stained, dry skeletal, and alcohol-preserved specimens. In P. vaillanti, the first elements that ossify are the neural arches of the presacral vertebrae (Gosner Stage 34), followed by the parasphenoid, occipital condyles, exoccipitals, and prootics at Stage 38; many elements of the postcranial skeleton ossify contemporaneously with the first cranial elements. Major modifications of the chondrocranium begin at Stage 44. In adults, the skulls of P. vaillanti and P. atelopoides do not seem atypical of hylid frogs, and their elements are gracile and unornamented. Although P. atelopoides is a terrestrial species, the morphology of its hands and feet does not seem to differ dramatically from that of other phyllomedusines, which are arboreal; however, the relative lengths of the appendages and vertebral column are shorter and more robust than those of all other Phyllomedusa.