Andrew M. Simons

Coming to America: multiple origins of New World geckos

Geckos in the Western Hemisphere provide an excellent model to study faunal assembly at a continental scale. We generated a time‐calibrated phylogeny, including exemplars of all New World gecko genera, to produce a biogeographical scenario for the New World geckos. Patterns of New World gecko origins are consistent with almost every biogeographical scenario utilized by a terrestrial vertebrate with different New World lineages showing evidence of vicariance, dispersal via temporary land bridge, overseas dispersal or anthropogenic introductions. We also recovered a strong relationship between clade age and species diversity, with older New World lineages having more species than more recently arrived lineages. Our data provide the first phylogenetic hypothesis for all New World geckos and highlight the intricate origins and ongoing organization of continental faunas. The phylogenetic and biogeographical hypotheses presented here provide an historical framework to further pursue research on the diversification and assembly of the New World herpetofauna.

Reconstructing the phylogenetic relationships of the earth's most diverse clade of freshwater fishes—order Cypriniformes (Actinopterygii: Ostariophysi): A case study using multiple nuclear loci and the mitochondrial genome

The order Cypriniformes is the most diverse clade of freshwater fishes and is natively distributed on all continents except South America, Australia, and Antarctica. Despite the diversity of the group and the fundamental importance of these species in both ecosystems and human culture, relatively little has been known about their relationships relative to their diversity. In recent years, with an international effort investigating the systematics of the group, more information as to their genealogical relationships has emerged and species discovery and their descriptions have increased. One of the more interesting aspects of this group has been a traditional lack of understanding of the relationships of the families, subfamilies, and other formally or informally identified groups. Historical studies have largely focused on smaller groups of species or genera. Because of the diversity of this group and previously published whole mitochondrial genome evidence for relationships of major clades in the order, this clade serves as an excellent group to investigate the congruence between relationships reconstructed for major clades with whole mitogenome data and those inferred from a series of nuclear gene sequences. As descent has resulted in only one tree of life, do the phylogenetic relationships of these major clades converge on similar topologies using the large number of available characters through this suite of nuclear genes and previously published mitochondrial genomes? In this study we examine the phylogenetic relationships of major clades of Cypriniformes using previously published mitogenomes and four putative single-copy nuclear genes of the same or closely related species. Combined nuclear gene sequences yielded 3810bp, approximately 26% of the bp found in a single mitogenome; however homoplasy in the nuclear genes was measurably less than that observed in mitochondrial sequences. Relationships of taxa and major clades derived from analyses of nuclear and mitochondrial sequences were nearly identical and both received high support values. While some differences of individual gene trees did exist for species, it is predicted that these differences will be minimized with increased taxon sampling in future analyses.

Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae)

The members of the cyprinid subfamily Danioninae form a diverse and scientifically important group of fishes, which includes the zebrafish, Danio rerio. The diversity of this assemblage has attracted much scientific interest but its monophyly and the relationships among its members are poorly understood. The phylogenetic relationships of the Danioninae are examined herein using sequence data from mitochondrial cytochrome b, mitochondrial cytochrome c oxidase I, nuclear opsin, and nuclear recombination activating gene 1. A combined data matrix of 4117 bp for 270 taxa was compiled and analyzed. The resulting topology supports some conclusions drawn by recent studies on the group and certain portions of the traditional classification, but our results also contradict key aspects of the traditional classification. The subfamily Danioninae is not monophyletic, with putative members scattered throughout Cyprinidae. Therefore, we restrict Danioninae to the monophyletic group that includes the following genera: Amblypharyngodon, Barilius, Cabdio, Chela, Chelaethiops, Danio, Danionella, Devario (including Inlecypris), Esomus, Horadandia, Laubuca, Leptocypris, Luciosoma, Malayochela, Microdevario, Microrasbora, Nematabramis, Neobola, Opsaridium, Opsarius, Paedocypris, Pectenocypris, Raiamas, Rasbora (including Boraras and Trigonostigma), Rasboroides, Salmostoma, Securicula, and Sundadanio. This Danioninae sensu stricto is divided into three major lineages, the tribes Chedrini, Danionini, and Rasborini, where Chedrini is sister to a Danionini-Rasborini clade. Each of these tribes is monophyletic, following the restriction of Danioninae. The tribe Chedrini includes a clade of exclusively African species and contains several genera of uncertain monophyly (Opsarius, Raiamas, Salmostoma). Within the tribe Rasborini, the species-rich genus Rasbora is rendered non-monophyletic by the placement of two monophyletic genera, Boraras and Trigonostigma, hence we synonymize those two genera with Rasbora. In the tribe Danionini, the miniature genus Danionella is recovered as the sister group of Danio, with D. nigrofasciatus sister to D. rerio.

Phylogeny and polyploidy: Resolving the classification of cyprinine fishes (Teleostei: Cypriniformes)

Cyprininae is the largest subfamily (>1300 species) of the family Cyprinidae and contains more polyploid species (∼400) than any other group of fishes. We examined the phylogenetic relationships of the Cyprininae based on extensive taxon, geographical, and genomic sampling of the taxa, using both mitochondrial and nuclear genes to address the phylogenetic challenges posed by polyploidy. Four datasets were analyzed in this study: two mitochondrial gene datasets (465 and 791 taxa, 5604bp), a mitogenome dataset (85 taxa, 14,771bp), and a cloned nuclear RAG1 dataset (97 taxa, 1497bp). Based on resulting trees, the subfamily Cyprininae was subdivided into 11 tribes: Probarbini (new; Probarbus+Catlocarpio), Labeonini Bleeker, 1859 (Labeo & allies), Torini Karaman, 1971 (Tor, Labeobarbus & allies), Smiliogastrini Bleeker, 1863 (Puntius, Enteromius & allies), Poropuntiini (Poropuntius & allies), Cyprinini Rafinesque, 1815 (Cyprinus & allies), Acrossocheilini (new; Acrossocheilus & allies), Spinibarbini (new; Spinibarbus), Schizothoracini McClelland, 1842 (Schizothorax & allies), Schizopygopsini Mirza, 1991 (Schizopygopsis & allies), and Barbini Bleeker, 1859 (Barbus & allies). Phylogenetic relationships within each tribe were discussed. Two or three distinct RAG1 lineages were identified for each of the following tribes Torini, Cyprinini, Spinibarbini, and Barbini, indicating their hybrid origin. The hexaploid African Labeobarbus & allies and Western Asian Capoeta are likely derived from two independent hybridization events between their respective maternal tetraploid ancestors and Cyprinion.

Inferring the Tree of Life of the order Cypriniformes, the earth's most diverse clade of freshwater fishes: Implications of varied taxon and character sampling

The phylogenetic relationships of species are fundamental to any biological investigation, including all evolutionary studies. Accurate inferences of sister group relationships provide the researcher with an historical framework within which the attributes or geographic origin of species (or supraspecific groups) evolved. Taken out of this phylogenetic context, interpretations of evolutionary processes or origins, geographic distributions, or speciation rates and mechanisms, are subject to nothing less than a biological experiment without controls. Cypriniformes is the most diverse clade of freshwater fishes with estimates of diversity of nearly 3,500 species. These fishes display an amazing array of morphological, ecological, behavioral, and geographic diversity and offer a tremendous opportunity to enhance our understanding of the biotic and abiotic factors associated with diversification and adaptation to environments. Given the nearly global distribution of these fishes, they serve as an important model group for a plethora of biological investigations, including indicator species for future cli- matic changes. The occurrence of the zebrafish, Danio rerio, in this order makes this clade a critical component in understanding and predicting the relationship between mutagenesis and phenotypic expressions in vertebrates, including humans. With the tremendous diversity in Cypriniformes, our understanding of their phylogenetic relationships has not proceeded at an acceptable rate, despite a plethora of morphological and more recent mo- lecular studies. Most studies are pre-Hennigian in origin or include relatively small numbers of taxa. Given that analyses of small numbers of taxa for molecular characters can be compromised by peculiarities of long-branch attraction and nodal-density effect, it is critical that significant progress in our understanding of the relationships of these important fishes occurs with increasing sampling of species to mitigate these potential problems. The recent Cypriniformes Tree of Life initiative is an effort to achieve this goal with morphological and molecular (mitochondrial and nuclear) data. In this early synthesis of our understanding of the phylogenetic relationships of these fishes, all types of data have contributed historically to improving our understanding, but not all analyses are complementary in taxon sampling, thus precluding direct understanding of the impact of taxon sampling on achieving accurate phylogenetic inferences. However, recent molecular studies do provide some insight and in some instances taxon sampling can be implicated as a variable that can influence sister group relationships. Other instances may also exist but without inclusion of more taxa for both mitochondrial and nuclear genes, one cannot distinguish between inferences being dictated by taxon sampling or the origins of the molecular data.

Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae)

The members of the cyprinid subfamily Gobioninae, commonly called gudgeons, form one of the most well-established assemblages in the family Cyprinidae. The subfamily is a species-rich group of fishes, these fishes display diverse life histories, appearances, and behavior. The phylogenetic relationships of Gobioninae are examined using sequence data from four loci: cytochrome b, cytochrome c oxidase I, opsin, and recombination activating gene 1. This investigation produced a data matrix of 4114 bp for 162 taxa that was analyzed using parsimony, maximum likelihood, and Bayesian inference methods. The phylogenies our analyses recovered corroborate recent studies on the group. The subfamily Gobioninae is monophyletic and composed of three major lineages. We find evidence for a Hemibarbus-Squalidus group, and the tribes Gobionini and Sarcocheilichthyini, with the Hemibarbus-Squalidus group sister to a clade of Gobionini-Sarcocheilichthyini. The Hemibarbus-Squalidus group includes those two genera; the tribe Sarcocheilichthyini includes Coreius, Coreoleuciscus, Gnathopogon, Gobiocypris, Ladislavia, Paracanthobrama, Pseudorasbora, Pseudopungtungia, Pungtungia, Rhinogobio, and Sarcocheilichthys; the tribe Gobionini includes Abbottina, Biwia, Gobio, Gobiobotia, Huigobio, Microphysogobio, Platysmacheilus, Pseudogobio, Romanogobio, Saurogobio, and Xenophysogobio. The monotypic Acanthogobio is placed into the synonymy of Gobio. We tentatively assign Belligobio to the Hemibarbus-Squalidus group and Mesogobio to Gobionini; Paraleucogobio and Parasqualidus remain incertae sedis. Based on the topologies presented, the evolution of swim bladder specializations, a distinctive feature among cyprinids, has occurred more than once within the subfamily.

Species limits and phylogeography of North American cricket frogs (Acris: Hylidae).

Cricket frogs are widely distributed across the eastern United States and two species, the northern cricket frog (Acris crepitans) and the southern cricket frog (A. gryllus) are currently recognized. We generated a phylogenetic hypothesis for Acris using fragments of nuclear and mitochondrial genes in separate and combined phylogenetic analyses. We also used distance methods and fixation indices to evaluate species limits within the genus and the validity of currently recognized subspecies of A. crepitans. The distributions of existing A. crepitans subspecies, defined by morphology and call types, do not match the distributions of evolutionary lineages recovered using our genetic data. We discuss a scenario of call evolution to explain this disparity. We also recovered distinct phylogeographic groups within A. crepitans and A. gryllus that are congruent with other codistributed taxa. Under a lineage-based species concept, we recognize Acris blanchardi as a distinct species. The importance of this revised taxonomy is discussed in light of the dramatic declines in A. blanchardi across the northern and western portions of its range.

The challenge of truly cryptic diversity: Diagnosis and description of a new madtom catfish (Ictaluridae: Noturus)

The Ozark madtom, Noturus albater, is distributed in upland streams in the upper White, Black, and St. Francis rivers of Missouri and Arkansas, USA. Fixed chromosomal and biochemical differences between populations in the upper White River and the Black and St. Francis rivers led earlier researchers to suggest that the Ozark madtom comprised two distinct species. The current study reviewed previous data, and examined osteology, pigmentation, morphometrics and DNA sequences from the mitochondrial cytochrome b gene and the nuclear Recombination Activating Gene 2. Sequence data were analysed using parsimony and Bayesian methods to construct a phylogenetic hypothesis of relationships within Noturus and examine relationships of populations of Ozark madtoms. Results of the molecular analyses were consistent with earlier chromosomal and biochemical studies. Morphology could not distinguish between populations from the upper White River and populations from the Black and St. Francis rivers. However, karyotypes, allozyme variation, and DNA sequences all provide diagnostic characters demonstrating the presence of two species consistent with the phylogenetic species concept. We describe the populations from the Black and St. Francis rivers as Noturus maydeni, a new cryptic species of madtom catfish.

Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America's open biomes

The gecko genus Phyllopezus occurs across South Americas open biomes: Cerrado, Seasonally Dry Tropical Forests (SDTF, including Caatinga), and Chaco. We generated a multi-gene dataset and estimated phylogenetic relationships among described Phyllopezus taxa and related species. We included exemplars from both described Phyllopezus pollicaris subspecies, P. p. pollicaris and P. p.przewalskii. Phylogenies from the concatenated data as well as species trees constructed from individual gene trees were largely congruent. All phylogeny reconstruction methods showed Bogertia lutzae as the sister species of Phyllopezus maranjonensis, rendering Phyllopezus paraphyletic. We synonymized the monotypic genus Bogertia with Phyllopezus to maintain a taxonomy that is isomorphic with phylogenetic history. We recovered multiple, deeply divergent, cryptic lineages within P. pollicaris. These cryptic lineages possessed mtDNA distances equivalent to distances among other gekkotan sister taxa. Described P. pollicaris subspecies are not reciprocally monophyletic and current subspecific taxonomy does not accurately reflect evolutionary relationships among cryptic lineages. We highlight the conservation significance of these results in light of the ongoing habitat loss in South Americas open biomes.

Phylogenetic Relationships of North American Cyprinids and Assessment of Homology of the Open Posterior Myodome

Phylogenetic analyses based on complete nucleotide sequences of mitochondrial 12S and 16S rRNA genes support the existence of three major clades within the North American phoxinins (Teleostei: Cyprinidae): the western clade, the creek chub clade and the open posterior myodome (OPM) clade. Analyses indicated strong support for the OPM clade including, among others, Mylocheilus, Pogonichthys, Tiaroga, and Rhinichthys. These latter taxa do not exhibit an OPM and previously have not been hypothesized to be related to members of the OPM clade. Parsimony analysis resolved relationships among basal members of the OPM clade and provided an opportunity to address homology of the OPM. Two hypotheses of homology of the OPM were included in analyses, with DNA sequence data allowing investigation of homology and evolution of the OPM. The OPM is best treated as a complex character exhibiting phylogenetic and ontogenetic variation. Previous attempts to simplify coding of the character do not result in hypotheses of homology that are congruent with phylogenetic hypotheses based on DNA sequence data.