PHYLOGENETIC INFERENCE OF NUPTIAL TRAIT EVOLUTION IN THE CONTEXT OF ASYMMETRICAL INTROGRESSION IN NORTH AMERICAN DARTERS (TELEOSTEI)

The little fishes that could: smaller fishes demonstrate slow body size evolution but faster speciation in the family Percidae

Body size affects numerous aspects of organismal biology and many factors have been invoked to explain body size distributions in a macroecological and macroevolutionary context. Body size in the freshwater fish family Percidae is strongly right-skewed (i.e. dominated by small sizes), with small body size potentially being associated with fast water habitats. We constructed a new species-level, multi-locus, time-calibrated phylogeny of Percidae, and used it to test for changes in the rate and pattern of maximum body size evolution. We also tested whether speciation rates varied as a function of body size. We found that Etheostomatinae evolved towards a smaller adaptive optimum in body size compared to the other subfamilies of Percidae, and that this shift was associated with a reduction in the rate of body size evolution. Speciation rates were associated with body size across percids, showing a peak around small to medium body size. Small body size appears to partially, but not fully, explain the diversity of small percids, as many darters fall well below the “optimum” body size. Reinforcement of selection for small body size via selection for novel morphologies or via sexual selection may help to fully explain the remarkable diversity of darter radiation.

Mimicry and mitonuclear discordance in nudibranchs: New insights from exon capture phylogenomics

Phylogenetic inference and species delimitation can be challenging in taxonomic groups that have recently radiated and where introgression produces conflicting gene trees, especially when species delimitation has traditionally relied on mitochondrial data and color pattern. Chromodoris, a genus of colorful and toxic nudibranch in the Indo-Pacific, has been shown to have extraordinary cryptic diversity and mimicry, and has recently radiated, ultimately complicating species delimitation. In these cases, additional genome-wide data can help improve phylogenetic resolution and provide important insights about evolutionary history. Here, we employ a transcriptome-based exon capture approach to resolve Chromodoris phylogeny with data from 2,925 exons and 1,630 genes, derived from 15 nudibranch transcriptomes. We show that some previously identified mimics instead show mitonuclear discordance, likely deriving from introgression or mitochondrial capture, but we confirm one "pure" mimic in Western Australia. Sister-species relationships and species-level entities were recovered with high support in both concatenated maximum likelihood (ML) and summary coalescent phylogenies, but the ML topologies were highly variable while the coalescent topologies were consistent across datasets. Our work also demonstrates the broad phylogenetic utility of 149 genes that were previously identified from eupulmonate gastropods. This study is one of the first to (a) demonstrate the efficacy of exon capture for recovering relationships among recently radiated invertebrate taxa, (b) employ genome-wide nuclear markers to test mimicry hypotheses in nudibranchs and (c) provide evidence for introgression and mitochondrial capture in nudibranchs.

Ecological and Genetic Divergences with Gene Flow of Two Sister Species (Leucomeris decora and Nouelia insignis) Driving by Climatic Transition in Southwest China

Understanding of the processes of divergence and speciation is a major task for biodiversity researches and may offer clearer insight into mechanisms generating biological diversity. Here, we employ an integrative approach to explore genetic and ecological differentiation of Leucomeris decora and Nouelia insignis distributed allopatrically along the two sides of the biogeographic boundary 'Tanaka Line' in Southwest China. We addressed these questions using ten low-copy nuclear genes and nine plastid DNA regions sequenced among individuals sampled from 28 populations across their geographic ranges in China. Phylogenetic, coalescent-based population genetic analyses, approximate Bayesian computation (ABC) framework and ecological niche models (ENMs) were conducted. We identified a closer phylogenetic relationship in maternal lineage of L. decora with N. insignis than that between L. decora and congeneric Leucomeris spectabilis. A deep divergence between the two species was observed and occurred at the boundary between later Pliocene and early Pleistocene. However, the evidence of significant chloroplast DNA gene flow was also detected between the marginal populations of L. decora and N. insignis. Niche models and statistical analyses showed significant ecological differentiation, and two nuclear loci among the ten nuclear genes may be under divergent selection. These integrative results imply that the role of climatic shift from Pliocene to Pleistocene may be the prominent factor for the divergence of L. decora and N. insignis, and population expansion after divergence may have given rise to chloroplast DNA introgression. The divergence was maintained by differential selection despite in the face of gene flow.

Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, that the impact of an individual calibration is the same when used alone or in unison with others. Thus, the most effective means of establishing the quality of fossil-based calibrations is through a priori evaluation of the intrinsic palaeontological, stratigraphic, geochronological and phylogenetic data. However, effort expended in establishing calibrations will not be rewarded unless they are implemented faithfully in divergence time analyses.

Phylogenetic relationships of Goneaperca and the evolution of parental care in darters (Teleostei: Percidae)

Inference of evolutionary relationships among closely related darter species (Teleostei: Percidae) has traditionally proven challenging due to a lack of sufficient numbers of informative morphological characters or reliance on mtDNA sequences. These factors have contributed to longstanding uncertainty of the monophyly of many described taxonomic groups. Although multi-locus data are now available for most darter species, uncertainty has persisted regarding the relationships of some major lineages. Here, we investigate the relationships of darters classified in Goneaperca, a clade of 46 species, many of which are characterized by distinct nuptial displays and male-only parental care. Previous phylogenetic analyses of morphological and molecular data have failed to provide strong resolution of relationships among major Goneaperca subclades, and especially the monophyly of Catonotus. We apply coalescent and phylogenetic analyses to a dataset that includes intraspecific sampling for nearly all species of Goneaperca for 13 nuclear genes. Our coalescent species tree analyses resolved a strongly supported sister relationship between Boleosoma and a monophyletic Catonotus. Ancestor state reconstructions using the posterior distribution of these newly inferred phylogenies support a single origin of male-only parental care in the most recent common ancestor of Boleosoma and Catonotus.

Speciation in Freshwater Fishes

The extraordinary species richness of freshwater fishes has attracted much research on mechanisms and modes of speciation. We here review research on speciation in freshwater fishes in light of speciation theory, and place this in a context of broad-scale diversity patterns in freshwater fishes. We discuss several major repeated themes in freshwater fish speciation and the speciation mechanisms they are frequently associated with. These include transitions between marine and freshwater habitats, transitions between discrete freshwater habitats, and ecological transitions within habitats, as well as speciation without distinct niche shifts. Major research directions in the years to come include understanding the transition from extrinsic environment-dependent to intrinsic reproductive isolation and its influences on species persistence and understanding the extrinsic and intrinsic constraints to speciation and how these relate to broad-scale diversification patterns through time.

Evidence for asymmetrical divergence-gene flow of nuclear loci, but not mitochondrial loci, between seabird sister species: blue-footed (Sula nebouxii) and Peruvian (S. variegata) boobies

Understanding the process of speciation requires understanding how gene flow influences divergence. Recent analyses indicate that divergence can take place despite gene flow and that the sex chromosomes can exhibit different levels of gene flow than autosomes and mitochondrial DNA. Using an eight marker dataset including autosomal, z-linked, and mitochondrial loci we tested the hypothesis that blue-footed (Sula nebouxii) and Peruvian (S. variegata) boobies diverged from their common ancestor with gene flow, paying specific attention to the differences in gene flow estimates from nuclear and mitochondrial markers. We found no gene flow at mitochondrial markers, but found evidence from the combined autosomal and z-linked dataset that blue-footed and Peruvian boobies experienced asymmetrical gene flow during or after their initial divergence, predominantly from Peruvian boobies into blue-footed boobies. This gene exchange may have occurred either sporadically between periods of allopatry, or regularly throughout the divergence process. Our results add to growing evidence that diverging species can remain distinct but exchange genes.