John S. Sparks

Phylogeny and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae)

Family level molecular phylogenetic analyses of cichlid fishes have generally suffered from a limited number of characters and/or poor taxonomic sampling across one or more major geographic assemblage, and therefore have not provided a robust test of early intrafamilial diversification. Herein we use both nuclear and mitochondrial nucleotide characters and direct optimization to reconstruct a phylogeny for cichlid fishes. Representatives of major cichlid lineages across all geographic assemblages are included, as well as nearly twice the number of characters as any prior family‐level study. In a strict consensus of 81 equally most‐parsimonious hypotheses, based on the simultaneous analysis of 2222 aligned nucleotide characters from two mitochondrial and two nuclear genes, four major subfamilial lineages are recovered with strong support. Etroplinae, endemic to Madagascar (Paretroplus) and southern Asia (Etroplus), is recovered as the sister taxon to the remainder of Cichlidae. Although the South Asian cichlids are monophyletic, the Malagasy plus South Asian lineages are not. The remaining Malagasy lineage, Ptychochrominae, is monophyletic and is recovered as the sister group to a clade comprising the African and Neotropical cichlids. The African (Pseudocrenilabrinae) and Neotropical (Cichlinae) lineages are each monophyletic in this reconstruction. The use of multiple molecular markers, from both mitochondrial and nuclear genes, results in a phylogeny that in general exhibits strong support, notably for early diversification events within Cichlidae. Results further indicate that Labroidei is not monophyletic, and that the sister group to Cichlidae may comprise a large and diverse assemblage of percomorph lineages. This hypothesis may at least partly explain why morphological studies that have attempted to place Cichlidae within Percomorpha, or that have tested cichlid monophyly using only “labroid” lineages, have met with only limited success.

Molecular phylogeny and biogeography of the Malagasy and South Asian cichlids (Teleostei: Perciformes: Cichlidae)

Phylogenetic relationships of the Malagasy and South Asian cichlids are investigated using nucleotide characters from two mitochondrial genes, a 544 bp region of the large ribosomal subunit (16S) and a 649 bp region of cytochrome c oxidase subunit I (COI). This is the first molecular analysis to include a thorough taxonomic sampling of all Malagasy-South Asian genera, and a near complete taxonomic inventory of all valid species. Parsimony analysis of the combined data set (1193 aligned nucleotide positions) results in a single, completely resolved phylogenetic hypothesis. Results of this analysis, and that based on more comprehensive taxonomic sampling across Cichlidae for 16S alone (554 bp for 73 taxa), indicate that the Malagasy cichlids are paraphyletic, whereas the Malagasy and South Asian cichlids comprise a monophyletic group. In both analyses, the African and Neotropical assemblages are monophyletic. The Malagasy-South Asian cichlids are not recovered as plesiomorphic members of the family in either analysis. Two major clades are recovered within the Malagasy-South Asian assemblage and given subfamilial rank, Etroplinae, comprising Paretroplus (Madagascar) and Etroplus (southern India and Sri Lanka), and Ptychochrominae, comprising Ptychochromis, Ptychochromoides, and Oxylapia, all endemic Malagasy genera. Placement of the endemic Malagasy genus Paratilapia is equivocal depending on the gene fragment(s) analyzed. Inter- and intrageneric relationships within Ptychochrominae and Etroplinae are presented and discussed. The hypothesis of relationships for Cichlidae based on nucleotide characters from 16S alone, arguably the most comprehensive and broadly sampled data set across all major geographic assemblages to date, is congruent with prevailing hypotheses regarding the sequence of Gondwanan fragmentation and a vicariance scenario to explain the current distribution of cichlid fishes.

Phylogeny, taxonomy, and evolution of Neotropical cichlids (Teleostei: Cichlidae: Cichlinae)

Despite recent progress on the higher‐level relationships of Cichlidae and its Indian, Malagasy, and Greater Antillean components, conflict and uncertainty remain within the species‐rich African, South American, and Middle American assemblages. Herein, we combine morphological and nucleotide characters from the mitochondrial large ribosomal subunit, cytochrome c oxidase subunit I, NADH dehydrogenase four, and cytochrome b genes and from the nuclear histone H3, recombination activating gene two, Tmo‐4C4, Tmo‐M27, and ribosomal S7 loci to analyse relationships within the Neotropical cichlid subfamily Cichlinae. The simultaneous analysis of 6309 characters for 90 terminals, including representatives of all major cichlid lineages and all Neotropical genera, resulted in the first well‐supported and resolved generic‐level phylogeny for Neotropical cichlids. The Neotropical subfamily Cichlinae was recovered as monophyletic and partitioned into seven tribes: Astronotini, Chaetobranchini, Cichlasomatini, Cichlini, Geophagini, Heroini, and Retroculini. Chaetobranchini + Geophagini (including the “crenicichlines”) was resolved as the sister group of Heroini + Cichlasomatini (including Acaronia). The monogeneric Astronotini was recovered as the sister group of these four tribes. Finally, a clade composed of Cichlini + Retroculini was resolved as the sister group to all other cichlines. The analysis included the recently described †Proterocara argentina, the oldest known cichlid fossil (Eocene), which was placed in an apical position within Geophagini, further supporting a Gondwanan origin for Cichlidae. These phylogenetic results were used as the basis for generating a monophyletic cichline taxonomy.

Freshwater Fishes, Dispersal Ability, and Nonevidence: “Gondwana Life Rafts” to the Rescue

Biogeography, as a topic for discourse or discussion, is in some ways like religion: both topics lend themselves to ever more complicated treatment in the abstract, which is apt to border even on the miraculous, but whichis apt to crumble in confrontation with concrete facts of life. Nelson and Platnick (1981:375) Having failed to dissect these concepts (center of origin, vicariance) to their core, contemporary zoogeographers founder in a self-created morass of chance hops; great capacities for, or mysterious means of, dispersal; rare accidents of over-sea transportation; small probabilities that with time become certainties; and other pseudo-explanations.

Conserving Madagascar's Freshwater Biodiversity

Abstract The island nation of Madagascar, an international conservation priority, is now also recognized as a global hotspot for freshwater biodiversity. Three emerging characteristics of Madagascars threatened freshwater biota deserve increased attention from the scientific and conservation communities. First, species richness is not low, as was once assumed for both the freshwater fishes and the invertebrates. Second, many species are restricted to a specific region or even to single river basins. Often these species are also limited to streams or rivers draining primary forest habitat. Finally, many of the islands freshwater fishes are basal taxa, having diverged earlier than any other extant members of their clade. As such, these taxa assume disproportional phylogenetic importance. In the face of ongoing environmental threats, links among microendemism, forest stream specialization, and basal phylogenetic position highlight the importance and vulnerability of these species and provide a powerful incentive for immediate conservation action.

The Covert World of Fish Biofluorescence: A Phylogenetically Widespread and Phenotypically Variable Phenomenon

The discovery of fluorescent proteins has revolutionized experimental biology. Whereas the majority of fluorescent proteins have been identified from cnidarians, recently several fluorescent proteins have been isolated across the animal tree of life. Here we show that biofluorescence is not only phylogenetically widespread, but is also phenotypically variable across both cartilaginous and bony fishes, highlighting its evolutionary history and the possibility for discovery of numerous novel fluorescent proteins. Fish biofluorescence is especially common and morphologically variable in cryptically patterned coral-reef lineages. We identified 16 orders, 50 families, 105 genera, and more than 180 species of biofluorescent fishes. We have also reconstructed our current understanding of the phylogenetic distribution of biofluorescence for ray-finned fishes. The presence of yellow long-pass intraocular filters in many biofluorescent fish lineages and the substantive color vision capabilities of coral-reef fishes suggest that they are capable of detecting fluoresced light. We present species-specific emission patterns among closely related species, indicating that biofluorescence potentially functions in intraspecific communication and evidence that fluorescence can be used for camouflage. This research provides insight into the distribution, evolution, and phenotypic variability of biofluorescence in marine lineages and examines the role this variation may play.

Temporal Patterns of Diversification across Global Cichlid Biodiversity (Acanthomorpha: Cichlidae)

The contrasting distribution of species diversity across the major lineages of cichlids makes them an ideal group for investigating macroevolutionary processes. In this study, we investigate whether different rates of diversification may explain the disparity in species richness across cichlid lineages globally. We present the most taxonomically robust time-calibrated hypothesis of cichlid evolutionary relationships to date. We then utilize this temporal framework to investigate whether both species-rich and depauperate lineages are associated with rapid shifts in diversification rates and if exceptional species richness can be explained by clade age alone. A single significant rapid rate shift increase is detected within the evolutionary history of the African subfamily Pseudocrenilabrinae, which includes the haplochromins of the East African Great Lakes. Several lineages from the subfamilies Pseudocrenilabrinae (Australotilapiini, Oreochromini) and Cichlinae (Heroini) exhibit exceptional species richness given their clade age, a net rate of diversification, and relative rates of extinction, indicating that clade age alone is not a sufficient explanation for their increased diversity. Our results indicate that the Neotropical Cichlinae includes lineages that have not experienced a significant rapid burst in diversification when compared to certain African lineages (rift lake). Neotropical cichlids have remained comparatively understudied with regard to macroevolutionary patterns relative to African lineages, and our results indicate that of Neotropical lineages, the tribe Heroini may have an elevated rate of diversification in contrast to other Neotropical cichlids. These findings provide insight into our understanding of the diversification patterns across taxonomically disparate lineages in this diverse clade of freshwater fishes and one of the most species-rich families of vertebrates.

The First Record of a Trans-Oceanic Sister-Group Relationship between Obligate Vertebrate Troglobites

We show using the most complete phylogeny of one of the most species-rich orders of vertebrates (Gobiiformes), and calibrations from the rich fossil record of teleost fishes, that the genus Typhleotris, endemic to subterranean karst habitats in southwestern Madagascar, is the sister group to Milyeringa, endemic to similar subterranean systems in northwestern Australia. Both groups are eyeless, and our phylogenetic and biogeographic results show that these obligate cave fishes now found on opposite ends of the Indian Ocean (separated by nearly 7,000 km) are each others closest relatives and owe their origins to the break up of the southern supercontinent, Gondwana, at the end of the Cretaceous period. Trans-oceanic sister-group relationships are otherwise unknown between blind, cave-adapted vertebrates and our results provide an extraordinary case of Gondwanan vicariance.

A Clade of Non-Sexually Dimorphic Ponyfishes (Teleostei: Perciformes: Leiognathidae): Phylogeny, Taxonomy, and Description of a New Species

Abstract A phylogeny was generated for Leiognathidae, commonly known as ponyfishes, using nucleotide characters from two mitochondrial genes. Results indicate that Leiognathidae comprises two major clades, one consisting of species that exhibit internally sexually dimorphic light-organ systems (LOS), and the Leiognathus equulus species complex, whose members exhibit neither internal nor external sexual dimorphism of the LOS. Species with internally sexually dimorphic LOS generally also exhibit associated male-specific external modifications in the form of transparent patches on the margin of the opercle, the midlateral flank, or behind the pectoral fin axil. The L. equulus species complex is the sister group to all other leiognathids, and a new species, L. robustus, recovered within this clade is described herein. Results demonstrate that Leiognathus is paraphyletic, whereas Gazza and Secutor are each monophyletic and are nested within the sexually dimorphic clade. The morphology of the LOS of non-sexually dimorphic leiognathids is compared to the more common sexually dimorphic state, and differences in these systems are discussed and illustrated. In the context of a family-level phylogeny, we can trace the evolution of the leiognathid LOS from a “simple” non-sexually dimorphic circumesophageal light organ to a complex and species-specific luminescence system involving not only major structural modifications of the light organ itself but also numerous associated tissues.

Evolution of the light organ system in ponyfishes (Teleostei: Leiognathidae)

Members of the leiognathid subfamily Gazzinae, comprising approximately two‐thirds of ponyfish species, are sexually dimorphic with regard to features of the light organ system (LOS). In Gazzinae, the circumesophageal light organ (LO) of males is enlarged and varies in shape compared with similarly sized conspecific females. In association with male species‐specific translucent external patches on the head and flank, these sexually dimorphic LO features are hypothesized to be correlated with species‐specific luminescence displays. Anatomical differences in LO shape, volume, and orientation, and its association with the gas bladder and other internal structures that function in light emission, are compared to observations of luminescence displays for every major lineage within Leiognathidae. We reconstruct the character evolution of both internal and external morphological features of the LOS to investigate the evolution of LO sexual dimorphism and morphology. Both internal and external sexual dimorphism in the ponyfish LOs were recovered as most likely to have evolved in the common ancestor of Leiognathidae, and likelihood‐based correlation analyses indicate that the evolution of internal and external dimorphism in males is statistically correlated. Magnetic resonance imaging technology was applied to examine the unique internal LOs of ponyfishes in situ, which provides a new metric (LO index) for comparison of LO structure across lineages. J. Morphol. 2011.