Gene trees versus species trees: reassessing life-history evolution in a freshwater fish radiation.

Mechanisms of speciation are best understood in the context of phylogenetic relationships and as such have often been inferred from single gene trees, typically those derived from mitochondrial DNA (mtDNA) markers. Recent studies, however, have noted the potential for phylogenetic discordance between gene trees and underlying species trees (e.g., due to stochastic lineage sorting, introgression, or selection). Here, we employ a variety of nuclear DNA loci to reassess evolutionary relationships within a recent freshwater fish radiation to reappraise modes of speciation. New Zealand's freshwater-limited Galaxias vulgaris complex is thought to have evolved from G. brevipinnis, a widespread migratory species that retains a plesiomorphic marine juvenile phase. A well-resolved tree, based on four mtDNA regions, previously suggested that marine migratory ability has been lost on 3 independent occasions in the evolution of this species flock (assuming that loss of diadromy is irreversible). Here, we use pseudogene (galaxiid Numt: 1801 bp), intron (S: 903 bp), and exon (RAG-1: 1427 bp) markers, together with mtDNA, to reevaluate this hypothesis of parallel evolution. Interestingly, partitioned Bayesian analysis of concatenated nuclear sequences (3141 bp) and concatenated nuclear and mtDNA (4770 bp) both recover phylogenies implying a single loss of diadromy, not three parallel losses as previously inferred from mtDNA alone. This phylogenetic result is reinforced by a multilocus analysis performed using Bayesian estimation of species trees (BEST) software that estimates the posterior distribution of species trees under a coalescent model. We discuss factors that might explain the apparently misleading phylogenetic inferences generated by mtDNA.

Contrasting mtDNA diversity and population structure in a direct-developing marine gastropod and its trematode parasites.

The comparative genetic structure of hosts and their parasites has important implications for their coevolution, but has been investigated in relatively few systems. In this study, we analysed the genetic structure and diversity of the New Zealand intertidal snail Zeacumantus subcarinatus (n = 330) and two of its trematode parasites, Maritrema novaezealandensis (n = 269) and Philophthalmus sp. (n = 246), using cytochrome c oxidase subunit I gene (COI) sequences. Snails and trematodes were examined from 11 collection sites representing three regions on the South Island of New Zealand. Zeacumantus subcarinatus displayed low genetic diversity per geographic locality, strong genetic structure following an isolation by distance pattern, and low migration rates at the scale of the study. In contrast, M. novaezealandensis possessed high genetic diversity, genetic homogeneity among collection sites and high migration rates. Genetic diversity and migration rates were typically lower for Philophthalmus sp. compared to M. novaezealandensis and it displayed weak to moderate genetic structure. The observed patterns likely result from the limited dispersal ability of the direct developing snail and the utilization of bird definitive hosts by the trematodes. In addition, snails may occasionally experience long-distance dispersal. Discrepancies between trematode species may result from differences in their effective population sizes and/or life history traits.

Geological dates and molecular rates: rapid divergence of rivers and their biotas.

We highlight a novel molecular clock calibration system based on geologically dated river reversal and river capture events. Changes in drainage pattern may effect vicariant isolation of freshwater taxa, and thus provide a predictive framework for associated phylogeographic study. As a case in point, New Zealand's Pelorus and Kaituna rivers became geologically isolated from the larger Wairau River system 70 to 130 kyr BP. We conducted mitochondrial DNA phylogeographic analyses of two unrelated freshwater-limited fish taxa native to these river systems (Gobiomorphus breviceps, n = 63; Galaxias divergens, n = 95). Phylogenetic analysis of combined control region and cytochrome b sequences yielded reciprocally monophyletic clades of Pelorus-Kaituna and Wairau haplotypes for each species. Calibrated rates of molecular change based on this freshwater vicariant event are substantially faster than traditionally accepted rates for fishes but consistent with other recent inferences based on geologically young calibration points. A survey of freshwater phylogeographic literature reveals numerous examples in which the ages of recent evolutionary events may have been substantially overestimated through the use of "accepted" calibrations. We recommend that--wherever possible--biologists should start to reassess the conclusions of such studies by using more appropriate molecular calibrations derived from recent geological events.

Speciation dynamics in the Australo-Papuan Meliphaga honeyeaters.

The Australo-Papuan Meliphaga honeyeaters have diversified over a wide range of habitats and elevational zones and are one of the few regionally known cryptic avian radiations. Using a combined 1580 bp of mitochondrial and nuclear DNA we investigate the species limits, systematic affinities and biogeographic history of Meliphaga. We also investigate the role of spatial sorting mechanisms, including altitudinal replacement and niche partitioning, as mechanisms underlying the adaptive radiation of this group. Phylogenetic analysis indicates that the genus Meliphaga comprises at least 16 species, three more than recognized in current classifications. The genus divides into two clades; the species-poor lewinii group, and the larger analoga group that has diversified into a wider range of vertical, vegetational and elevational niches. The basal division of each clade into an Australian and New Guinean assemblage was likely induced by the formation of the Arafura Sea during the early Pliocene ( approximately 4 MYA) with a single reinvasion of Australia by the open forest species M. gracilis during the early Pleistocene (1.2-1.5 MYA) via intermittent land bridges or island hopping. Most recent sister species were found to replace each other geographically within the same ecological and elevational zone conforming to the classical allopatric mode of speciation. In contrast, M. orientalis (650-1950 m) and M. analoga (0-1100 m) were found to replace each other altitudinally across ecological zones providing empirical support for altitudinal speciation as a mechanism of diversification in a montane avifauna. We find no evidence of sympatric speciation (co-existing sister lineages) and suggest that spatial segregation within the habitat (niche partitioning) is primarily a mechanism enabling more divergent species to coexist.

Molecular systematics of the South American caviomorph rodents: relationships among species and genera in the family Octodontidae.

Nucleotide sequences from mitochondrial (12S rRNA) and nuclear (growth hormone receptor) genes were used to investigate phylogenetic relationships among South American hystricognath rodents of the superfamily Octodontoidea, with special emphasis on the family Octodontidae. Relationships among most taxa were well resolved by a combined analysis of both genes, and the molecular phylogeny was used to address several long-standing phylogenetic problems. The family Abrocomidae was the most basal lineage within the superfamily Octodontoidea, sensu stricto, and the family Ctenomyidae was sister to the family Octodontidae, followed by a monophyletic group containing the families Myocastoridae and Echimyidae. A basic dichotomy was observed within the family Octodontidae. The Argentine desert specialists, Tympanoctomys and Octomys, grouped separate from Octodontomys, which was sister to a clade containing a monophyletic Octodon and a clade represented by species of Aconaemys and Spalacopus. Aconaemys was paraphyletic relative to Spalacopus. The phylogeny was used as an interpretive framework for an examination of variation in several non-molecular characters. The primitive diploid number for most of the octodontoids was determined to be between 46 and 56, and the primitive genome size 8.2 pg. Members of the Octodontidae appeared to be derived from an ancestral stock occupying lower elevations in scrub habitat. Furthermore, estimates of divergence time from the molecular data provided a temporal perspective for changes in plant communities, which demonstrated turnover and diversification in response to climatic and geologic events occurring in the Miocene through the Pleistocene.

Phylogenetic relationships, ecological correlates, and molecular evolution within the cavioidea (mammalia, rodentia).

A molecular phylogeny of the rodent superfamily Cavioidea was derived using two nuclear sequences (exon #10 of the growth hormone receptor gene and intron #1 of the transthyretin gene) and one mitochondrial gene (12S rRNA). A combined analysis produced a highly derived and well-supported phylogenetic hypothesis that differed from traditional taxonomy primarily in the placement of two taxa. Kerodon, traditionally included within the subfamily Caviinae with guinea pigs and its relatives, is placed sister to the family Hydrochaeridae and closely aligned with the subfamily Dolichotinae. Inclusion of Hydrochaeris within the Caviidae renders the familial classification paraphyletic. Our data further support the taxonomic separation of the families Agoutidae and Dasyproctidae. Both the molecular and traditional morphological interpretations are assessed in testing an ecological constraints hypothesis regarding social behaviors. Whereas traditional taxonomy is consistent with an environmental constraints explanation for social behavior, the molecular data suggest that phylogenetic effects may be a more important factor in the evolution of social behavior in this group. Although lineage-specific rate heterogeneity was identified in all three molecular data sets, no significant support was obtained for the metabolic rate hypothesis. However, both nuclear genes displayed patterns in accordance with the generation time hypothesis.