Functional similarity and molecular divergence of a novel reproductive transcriptome in two male-pregnant Syngnathus pipefish species.

Evolutionary studies have revealed that reproductive proteins in animals and plants often evolve more rapidly than the genome-wide average. The causes of this pattern, which may include relaxed purifying selection, sexual selection, sexual conflict, pathogen resistance, reinforcement, or gene duplication, remain elusive. Investigative expansions to additional taxa and reproductive tissues have the potential to shed new light on this unresolved problem. Here, we embark on such an expansion, in a comparison of the brood-pouch transcriptome between two male-pregnant species of the pipefish genus Syngnathus. Male brooding tissues in syngnathid fishes represent a novel, nonurogenital reproductive trait, heretofore mostly uncharacterized from a molecular perspective. We leveraged next-generation sequencing (Roche 454 pyrosequencing) to compare transcript abundance in the male brooding tissues of pregnant with nonpregnant samples from Gulf (S. scovelli) and dusky (S. floridae) pipefish. A core set of protein-coding genes, including multiple members of astacin metalloprotease and c-type lectin gene families, is consistent between species in both the direction and magnitude of expression bias. As predicted, coding DNA sequence analysis of these putative "male pregnancy proteins" suggests rapid evolution relative to nondifferentially expressed genes and reflects signatures of adaptation similar in magnitude to those reported from Drosophila male accessory gland proteins. Although the precise drivers of male pregnancy protein divergence remain unknown, we argue that the male pregnancy transcriptome in syngnathid fishes, a clade diverse with respect to brooding morphology and mating system, represents a unique and promising object of study for understanding the perplexing evolutionary nature of reproductive molecules.

Multi-locus phylogeography of the dusky dolphin (Lagenorhynchus obscurus): passive dispersal via the west-wind drift or response to prey species and climate change?

BACKGROUND: The dusky dolphin (Lagenorhynchus obscurus) is distributed along temperate, coastal regions of New Zealand, South Africa, Argentina, and Peru where it feeds on schooling anchovy, sardines, and other small fishes and squid tightly associated with temperate ocean sea surface temperatures. Previous studies have suggested that the dusky dolphin dispersed in the Southern Hemisphere eastward from Peru via a linear, temperate dispersal corridor provided by the circumpolar west-wind drift. With new mitochondrial and nuclear DNA sequence data, we propose an alternative phylogeographic history for the dusky dolphin that was structured by paleoceanographic conditions that repeatedly altered the distribution of its temperate prey species during the Plio-Pleistocene. RESULTS: In contrast to the west-wind drift hypothesis, phylogenetic analyses support a Pacific/Indian Ocean origin, with a relatively early and continued isolation of Peru from other regions. Dispersal of the dusky dolphin into the Atlantic is correlated with the history of anchovy populations, including multiple migrations from New Zealand to South Africa. Additionally, the cooling of the Eastern Equatorial Pacific led to the divergence of anchovy populations, which in turn explains the north-south equatorial transgression of L. obliquidens and the subsequent divergence of L. obscurus in the Southern Hemisphere. CONCLUSION: Overall, our study fails to support the west-wind drift hypothesis. Instead, our data indicate that changes in primary productivity and related abundance of prey played a key role in shaping the phylogeography of the dusky dolphin, with periods of ocean change coincident with important events in the history of this temperate dolphin species. Moderate, short-term changes in sea surface temperatures and current systems have a powerful effect on anchovy populations; thus, it is not infeasible that repeated fluctuations in anchovy populations continue to play an important role in the history of coastal dolphin populations.

Multi-locus phylogeny of dolphins in the subfamily Lissodelphininae: character synergy improves phylogenetic resolution.

BACKGROUND: Dolphins of the genus Lagenorhynchus are anti-tropically distributed in temperate to cool waters. Phylogenetic analyses of cytochrome b sequences have suggested that the genus is polyphyletic; however, many relationships were poorly resolved. In this study, we present a combined-analysis phylogenetic hypothesis for Lagenorhynchus and members of the subfamily Lissodelphininae, which is derived from two nuclear and two mitochondrial data sets and the addition of 34 individuals representing 9 species. In addition, we characterize with parsimony and Bayesian analyses the phylogenetic utility and interaction of characters with statistical measures, including the utility of highly consistent (non-homoplasious) characters as a conservative measure of phylogenetic robustness. We also explore the effects of removing sources of character conflict on phylogenetic resolution. RESULTS: Overall, our study provides strong support for the monophyly of the subfamily Lissodelphininae and the polyphyly of the genus Lagenorhynchus. In addition, the simultaneous parsimony analysis resolved and/or improved resolution for 12 nodes including: (1) L. albirostris, L. acutus; (2) L. obscurus and L. obliquidens; and (3) L. cruciger and L. australis. In addition, the Bayesian analysis supported the monophyly of the Cephalorhynchus, and resolved ambiguities regarding the relationship of L. australis/L. cruciger to other members of the genus Lagenorhynchus. The frequency of highly consistent characters varied among data partitions, but the rate of evolution was consistent within data partitions. Although the control region was the greatest source of character conflict, removal of this data partition impeded phylogenetic resolution. CONCLUSION: The simultaneous analysis approach produced a more robust phylogenetic hypothesis for Lagenorhynchus than previous studies, thus supporting a phylogenetic approach employing multiple data partitions that vary in overall rate of evolution. Even in cases where there was apparent conflict among characters, our data suggest a synergistic interaction in the simultaneous analysis, and speak against a priori exclusion of data because of potential conflicts, primarily because phylogenetic results can be less robust. For example, the removal of the control region, the putative source of character conflict, produced spurious results with inconsistencies among and within topologies from parsimony and Bayesian analyses.