Kevin J. Roe

CHAPTER 17 – The Phylogenetic Utility of the Mitochondrial Cytochrome b Gene for Inferring Relationships among Actinopterygian Fishes

The objective of this chapter is to test the phylogenetic utility of the mitochondrial cytochrome b gene by analyzing the relationships of monophyletic Actinopterygii or ray-finned fishes at different hierarchic levels. Modern actinopterygians are the most diverse of all vertebrate groups and include more than 25,000 species. In order to assess the utility of the cytochrome b gene, actinopterygian fishes representing a diverse array of taxa and divergence times were selected. Facts and figures supporting phylogenetic hypothesis of actinopterygian fishes, including only the taxa, are examined based on morphological data from various sources. Although this chapter focuses on the cytochrome b gene, this study serves as a model for further studies that examines the utility of other genes. It lists the actinopterygian species examined in this study and their current classification. The mitochondrial cytochrome b gene sequences for the remaining 18 ray-finned fishes were retrieved from GenBank. The results of Cytochrome b sequence variation, base compositional bias, and amino acids differences are very important from the analytical point of view as is the assessment of the phylogenetic utility of the mitochondrial cytochrome b gene arrived at by examining taxonomic congruence between molecular- and morphological-based phylogenetic hypotheses.

Freshwater bivalve (Unioniformes) diversity, systematics, and evolution: status and future directions

Abstract Freshwater bivalves of the order Unioniformes represent the largest bivalve radiation in freshwater. The unioniform radiation is unique in the class Bivalvia because it has an obligate parasitic larval stage on the gills or fins of fish; it is divided into 6 families, 181 genera, and ∼800 species. These families are distributed across 6 of the 7 continents and represent the most endangered group of freshwater animals alive today. North American unioniform bivalves have been the subject of study and illustration since Martin Lister, 1686, and over the past 320 y, significant gains have been made in our understanding of the evolutionary history and systematics of these animals. Here, the current state of unioniform systematics and evolution is summarized, and suggestions for future research themes are proposed. Advancement in the areas of systematics and evolutionary relationships within the Unioniformes will require a resurgence of survey work and reevaluation of all taxa, especially outside of North America and Western Europe. This work will require collection of animals for shell morphology, comparative anatomy, and molecular analyses. Along with reexamination of described taxa, a renewed emphasis on the natural history, host-fish relationships, ecology, and physiology of these animals is needed. Traditional conchological and anatomical characters should be reevaluated, new character suites should be added, and new morphometric methods should be applied. The fossil record of freshwater bivalves should be carefully reviewed, and phylogenetic hypotheses including fossil taxa must be developed. We will have to expand our set of molecular tools to include or develop additional markers, such as single-copy nuclear genes and microsatellites. Examination of double uniparental inheritance of mitochondrial deoxyribonucleic acid (DNA) is providing new insights into the evolution of this order. Mitochondrial gene order differs among genera but is still to be explored. Expansion of our understanding of the evolutionary relationships and history of unioniform bivalves will provide a solid foundation to study the zoogeography of these rather sessile, obligate freshwater organisms. The unique natural history of unioniform bivalves provides a fertile area for testing and developing evolutionary theories, and, as our understanding of the systematics of these animals improves, a better understanding of the evolution of this expansive radiation in freshwater will develop.

Phylogeographic analysis of the threatened and endangered superconglutinate-producing mussels of the genus Lampsilis (Bivalvia: Unionidae)

Several species of freshwater unionid mussels in the genus Lampsilis exhibit a remarkable reproductive strategy. Female mussels of these species enclose their larvae in a minnow‐like lure, called a ‘superconglutinate’, to attract piscivorous fishes. When a fish attempts to ingest the superconglutinate the lure ruptures and the larvae are released to parasitize the fish. Of the four species of mussel which exhibit this strategy and are endemic to the Gulf Coast drainages of the southeastern United States, three are protected under the Endangered Species Act, and one is recognized as imperilled. Phylogenetic analysis of nucleotide sequences of the mitochondrial 16S ribosomal RNA and the first subunit of the cytochrome oxidase c genes was conducted on 18 individual specimens representing these four species and six outgroup taxa. Phylogenetic analyses of these data support the monophyly of the superconglutinate‐producing mussels, and indicates a strong geographical component to the data. The zoogeographic patterns of the four taxa included in the study are congruent with those seen in freshwater vertebrates, and are consistent with a vicariant pattern resulting from fluctuations in sea level during the Pleistocene. Despite the strong geographical structuring of the data, only one species, Lampsilis subangulata, was recovered as monophyletic. The authors attribute the lack of support for the monophyly of the remaining species to insufficient sequence variation and the recent origin of the ancestor of these taxa. Based on these data, any future captive breeding projects aimed at augmenting or re‐establishing populations should do so only from the appropriate source populations so as to maintain the genetic integrity of these nascent species.

Drawn to the dark side: A molecular phylogeny of freshwater shrimps (Crustacea: Decapoda: Caridea: Atyidae) reveals frequent cave invasions and challenges current taxonomic hypotheses

Atyid freshwater shrimps are globally distributed and form an important part of freshwater ecosystems, particularly in the tropics and subtropics. Despite their widespread distribution and ecological importance, their phylogenetic relationships are largely unresolved. Here we present the first comprehensive molecular phylogeny of the Atyidae investigating the evolutionary relationships among 32 of the 42 genera using mitochondrial and nuclear markers. Our data indicate that the established classification of the Atyidae is in need of substantial taxonomic revision at all taxonomic levels. We suggest a new suprageneric systematization of atyids and discuss problematic issues at the generic level, particularly in the most speciose genus, Caridina. Molecular clock based divergence time estimates for atyids vary widely, but invariably support the assumption that atyids are an ancient freshwater lineage with an origin in the mid-Cretaceous at the very latest. Atyid distribution patterns are the result of instances of both long-distance dispersal and vicariance, depending largely on the reproductive mode of taxa. From an evolutionary perspective, the high frequency of independent origin of both a complete (landlocked) freshwater life cycle and a cave-dwelling mode of life is remarkable and unparalleled among crustaceans.

Phylogenetic relationships of the genera of North American sunfishes and basses (Percoidei: Centrarchidae) as evidenced by the mitochondrial cytochrome b gene

Abstract The phylogenetic relationships of genera of the family Centrarchidae and its affinities to the Elassomatidae were examined using the mitochondrial DNA sequences of the cytochrome b gene. A total of 32 individuals representing 16 species from nine genera of centrarchids were sequenced. Outgroup were drawn from other perciform families including several families previously proposed to be closely related to the Centrarchidae. Phylogenetic analysis was conducted using the optimality criteria of maximum parsimony with two weighting schemes and using the maximum likelihood method. A priori and a posteriori alternative hypotheses of relationships within the Centrarchidae were investigated using the Shimodaira and Hasegawa Test. The results of all analyses support the monophyly of the Centrarchidae, although the interrelationships of centrarchid genera differed between analyses. Elassoma was never recovered as the sister taxon to the Centrarchidae; however, the sister relationship of these taxa could not be rejected. Additional data are required to unambiguously resolve relationships among centrarchid genera and determine the relationship of the Centrarchidae to other perciforms.

Development and characterization of sixteen microsatellite markers for the federally endangered species: Leptodea leptodon (Bivalvia: Unionidae) using paired-end Illumina shotgun sequencing

We isolated and characterized a total of 16 microsatellite loci in Leptodea leptodon. Loci were screened in 24 individuals from across the species current range in Missouri. The number of alleles per locus ranged from 3 to 17, observed heterozygosity ranged from 0.208 to 1.000, and the probability of identity values ranged from 0.014 to 0.67. These new loci will be used for conducting investigations into the genetic structure and diversity of extant populations of this federally endangered species.

A Mitochondrial DNA Perspective on the Molecular Systematics of the Sunfish Genus Lepomis (Actinopterygii: Centrarchidae)

Abstract Complete mitochondrial DNA cytochrome b gene sequences from 56 specimens representing all 12 species of Lepomis were used to examine phylogenetic relationships within the genus. Results supported the monophyly of Lepomis and all previously recognized subgenera, except Eupomotis, but there was no support for previously proposed relationships among subgenera. Seven species were recovered as monophyletic lineages, while five species (L. auritus, L. macrochirus, L. marginatus, L. miniatus, and L. symmetricus) were recovered as either poly- or paraphyletic or were placed as parts of unresolved polytomies with other species. Parametric bootstrapping tests rejected monophyly for only two of the five species (L. auritus and L. symmetricus). Without additional data, including increased geographic sampling and a comparable nuclear gene phylogeny, it is not possible to determine whether the failure to support monophyly for these two species reflects the presence of cryptic species or results from hybridization.

Identification of a fish host of the inflated heelsplitter Potamilus inflatus (Bivalvia: Unionidae) with a description of its glochidium

-A survey of the fishes of the Black Warrior River was undertaken to determine fish host(s) of the federally threatened inflated heelsplitter, Potamilus inflatus. Seven hundred-twenty individual fishes representing 30 species were examined; mussel glochidia were found on 10 individual fishes representing nine species. Potamilus inflatus glochidia were only found infesting one freshwater drum (Aplodinotus grunniens), which is concordant with previous findings for the genus Potamilus. The morphology of P inflatus glochidia is described and compared to P purpuratus.

The origin and phylogeny of Margaritiferidae (Bivalvia, Unionoida): a synthesis of molecular and fossil data

The family Margaritiferidae is a small but widely distributed group within the Unionoida, or freshwater mussels, whose taxonomy and systematics has been the subject of numerous publications. Despite several efforts, there is no consensus on which characters reliably diagnose this family. Herein, we present the results of a phylogenetic analysis of the most comprehensive data set for Margaritiferidae in terms of taxa and phylogenetic markers assembled to date, including eleven out of the twelve margaritiferid species currently considered valid. In addition, we review the fossil record of the family and attempt to integrate fossil and DNA sequence data to provide a diagnosis of Margaritiferidae, identify its origin and biogeographic patterns, and determine the systematic relationships of its constituent species and their taxonomic affinities. We assembled a molecular data set comprised of five markers: COI, 16S, 28S, 18S and histone 3 for a total of 59 specimens representing eleven species of Margaritifera. Our results indicate that the family Margaritiferidae is a monophyletic group comprised of the single genus Margaritifera, which includes the following 12 species: M. dahurica, M. margaritifera, M. monodonta, M. middendorffi, M. laevis, M. marrianae, M. hembeli, M. falcata, M. laosensis, M. auricularia and M. marocana plus the unstudied M. homsensis. Estimates of divergence times using fossil calibrations or mean substitution rates produced dramatically different results. Divergence estimates based on the fossil calibrations were 10 times higher than those obtained applying the mean substitution rates. The current distribution of the family implies dispersal across marine or brackish waters by their host fish, leaving a fossil record on four continents that dates to the Mesozoic. Margaritiferidae appear to be derived from putative ancestor in the Silesunionidae, with a likely origin in Asia. We suggest that Margaritiferidae had spread along the Tethys margins and crossed the Atlantic already in the Late Triassic or Early Jurassic. Further dispersal events, in the Late Cretaceous or Eocene, may be linked to salinity‐depleted coastal waters or freshwater layering.

Systematics and Zoogeography of the Rock Basses (Centrarchidae: Ambloplites)

Abstract This study examines the role that historical events have played in the diversification of members of the genus Ambloplites by estimating divergence times of clades within the genus. DNA sequences of the mitochondrial cytochrome b gene were used to develop phylogenetic hypotheses for Ambloplites using maximum parsimony and Bayesian methods. The timing of diversification within and between species of Ambloplites was estimated using nonparametric rate-smoothing and penalized likelihood methods calibrated by fossil dates. Monophyly of three of the four species was supported. The ages of the most recent common ancestors of species of Ambloplites estimated in this study confirm earlier estimates that in most instances, their origins occurred prior to the Pleistocene. A comparison of estimated divergence times of lineages to sea level fluctuations indicates a correspondence to extremely high or low sea stands throughout the Neogene Period. Populations of Ambloplites in the Ozarks and Ouachita highlands previously assigned to A. ariommus appear to have either been introgressed by A. rupestris or were misidentified as A. ariommus. Ambloplites rupestris displays low genetic divergence throughout its range and is consistent with a re-colonization of previously glaciated areas following the Pleistocene.