Phylogenomic resolution of lampreys reveals the recent evolution of an ancient vertebrate lineage.

Jawless vertebrates once dominated Palaeozoic waters, but just two lineages have persisted to the present day: lampreys and hagfishes. Living lampreys are a relatively small clade, with just over 50 species described, but knowledge of their evolutionary relationships has always been based on either a few mitochondrial genes or a small number of taxa. Biogeographers have noted the disjunct antitropical distribution of living lamprey families.

Phylogeography of the Mesa Silverside fish (Woolman, 1894) throughout the Mexican Plateau.

Background: Understanding the processes that influence distribution of organisms is a major goal in evolutionary biology. Speciation in freshwater fishes is mainly associated with the "island-like" model of evolution, in which the formation of land barriers between different hydrographic basins interrupts gene flow and promotes isolation. Freshwater fish therefore provide an excellent model system for macro- and micro-evolutionary studies.

Life in the fastlane? A comparative analysis of gene expression profiles across annual, semi-annual, and non-annual killifishes (Cyprinodontiformes: Nothobranchiidae).

The Turquoise Killifish is an important vertebrate for the study of aging and age-related diseases due to its short lifespan. Within Nothobranchiidae, species possess annual, semi-annual, or non-annual life-histories. We took a comparative approach and examined gene expression profiles (QuantSeq) from 62 individuals from eleven nothobranchid species that span three life-histories.

Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements.

Poeciliids (Cyprinodontiformes: Poeciliidae), commonly known as livebearers, are popular fishes in the aquarium trade (e.g., guppies, mollies, swordtails) that are widely distributed in the Americas, with 274 valid species in 27 genera.

Investigating the utility of Anchored Hybrid Enrichment data to investigate the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes.

The Killifishes (Cyprinodontiformes) are a diverse and well-known group of fishes that contains sixteen families inclusive of Anablepidae, Aphaniidae Aplocheilidae, Cubanichthyidae, Cyprinodontidae, Fluviphylacidae, Fundulidae, Goodeidae, Nothobranchiidae, Orestiidae, Pantanodontidae, Poeciliidae, Procatopodidae, Profundulidae, Rivulidae, and Valenciidae and more than 1,200 species that are globally distributed in tropical and temperate, freshwater and estuarine habitats. The evolutionary relationships among the families within the group, based on different molecular and morphological data sets, have remained uncertain. Therefore, the objective of this study was to use a targeted approach, anchored hybrid enrichment, to investigate the phylogenetic relationships among the families within the Cyprindontiformes.

Genomic data support the taxonomic validity of Middle American livebearers Poeciliopsis gracilis and Poeciliopsis pleurospilus (Cyprinodontiformes: Poeciliidae).

Poeciliopsis (Cyprinodontiformes: Poeciliidae) is a genus comprised of 25 species of freshwater fishes. Several well-known taxonomic uncertainties exist within the genus, especially in relation to the taxonomic status of Poeciliopsis pleurospilus and P. gracilis.

Molecular systematics of the Awaous banana complex (River gobies; Teleostei: Oxudercidae).

Diadromous fishes can exhibit interesting evolutionary and population-level patterns given their use of freshwater and marine environments as part of their life histories. The River goby genus Awaous are prominent members of riverine ichthyofaunas and occur throughout Atlantic and Pacific slopes of the Americas from the southern United States to Ecuador and Brazil. Here we study the widespread and polymorphic Awaous banana complex to assess phylogeographic patterns and test previous hypotheses that all populations of this species in the Americas belong to the same species.

Genetic differentiation among populations of the blackfin goodea Goodea atripinnis (Cyprinodontiformes: Goodeidae): implications for its evolutionary history.

Central Mexico is characterized by a complex topography that is the result of historic and contemporary tectonic and climatic factors. These events have influenced the evolutionary history of numerous freshwater fishes in the region. Nonetheless, recent studies have shown that life-history traits and ecological characteristics of species may influence dispersal capabilities and the degree of genetic connectivity.

Distribution and current conservation status of the Mexican Goodeidae (Actinopterygii, Cyprinodontiformes).

The current distribution and abundance of the 40 species of Goodeidae fishes known from Mexico are described, and a total of 84 Evolutionarily Significant Units (ESUs) is designated within these species. Two species and four ESUs are likely extinct with no captive populations, and three species and eight ESUs are probably extinct in the wild but have at least one captive population in Mexico, the United States, or Europe. Of the 35 extant species, the analyses indicate that nine should be considered as critically endangered, 14 as endangered, nine as vulnerable, and only three as least concern.

Assessing phylogenetic information to reveal uncertainty in historical data: An example using Goodeinae (Teleostei: Cyprinodontiformes: Goodeidae).

A major emerging challenge to resolution of a stable phylogenetic Tree of Life has been incongruent inference among studies. Given the increasing ubiquity of incongruent studies, analyzing the predicted phylogenetic utility and quantitative evidence regarding contributions toward resolution of commonly-used markers in historical studies over the last decade represents an important, yet neglected, component of phylogenetics. Here we examine the phylogenetic utility of two sets of commonly-used legacy markers for understanding the evolutionary relationships among goodeines, a group of viviparous freshwater fishes endemic to central Mexico.

Disentangling the drivers of diversification in an imperiled group of freshwater fishes (Cyprinodontiformes: Goodeidae).

Background: One of the most perplexing questions in evolutionary biology is why some lineages diversify into many species, and others do not. In many cases, ecological opportunity has played an important role, leading to diversification along trophic or habitat-based axes. The Goodeidae (Teleostomi: Cyprinodontiformes) are a family of freshwater fishes with two subfamilies: Goodeinae (42 species, viviparous, heterogeneous habitats, Mesa Central of Mexico) and Empetrichthyinae (4 species, oviparous, homogeneous habitats, Great Basin of the United States).

Evolving in the highlands: the case of the Neotropical Lerma live-bearing Poeciliopsis infans (Woolman, 1894) (Cyprinodontiformes: Poeciliidae) in Central Mexico.

Background: Volcanic and tectonic activities in conjunction with Quaternary climate are the main events that shaped the geographical distribution of genetic variation of many lineages. Poeciliopsis infans is the only poeciliid species that was able to colonize the temperate highlands of central Mexico. We inferred the phylogenetic relationships, biogeographic history, and historical demography in the widespread Neotropical species P.

Let's jump in: A phylogenetic study of the great basin springfishes and poolfishes, Crenichthys and Empetrichthys (Cyprinodontiformes: Goodeidae).

North America's Great Basin has long been of interest to biologists due to its high level of organismal endemicity throughout its endorheic watersheds. One example of such a group is the subfamily Empetricthyinae. In this paper, we analyzed the relationships of the Empetrichtyinae and assessed the validity of the subspecies designations given by Williams and Wilde within the group using concatenated phylogenetic tree estimation and species tree estimation.

Two new species of the genus Hubbs and Turner, 1939 (Teleostei, Goodeidae) from central-western Mexico.

The subfamily Goodeinae (Goodeidae) is one of the most representative and well-studied group of fishes from central Mexico, with around 18 genera and 40 species. Recent phylogenetic studies have documented a high degree of genetic diversity and divergences among populations, suggesting that the diversity of the group may be underestimated. The species Xenotoca eiseni has had several taxonomic changes since its description.

Taxonomy and systematics of the herichthyins (Cichlidae: Tribe Heroini), with the description of eight new Middle American Genera.

In recent years great strides have been made for improving our understanding of the evolutionary relationships among neotropical cichlids, particularly within the clade Heroini and its crown clade the herichthyins. Most phylogenetic studies have largely converged on congruent topologies for relationships among species and major lineages within the herichthyins. One major aspect missing from previous studies of these cichlids is a formal taxonomic revision, including the redefining of genera.

Black liquor and the hangover effect: fish assemblage recovery dynamics following a pulse disturbance.

Anthropogenic perturbations impact aquatic systems causing wide-ranging responses, from assemblage restructuring to assemblage recovery. Previous studies indicate the duration and intensity of disturbances play a role in the dynamics of assemblage recovery. In August 2011, the Pearl River, United States, was subjected to a weak black liquor spill from a paper mill which resulted in substantial loss of fish in a large stretch of the main channel.

Multi-locus fossil-calibrated phylogeny of Atheriniformes (Teleostei, Ovalentaria).

Phylogenetic relationships among families within the order Atheriniformes have been difficult to resolve on the basis of morphological evidence. Molecular studies so far have been fragmentary and based on a small number taxa and loci. In this study, we provide a new phylogenetic hypothesis based on sequence data collected for eight molecular markers for a representative sample of 103 atheriniform species, covering 2/3 of the genera in this order.

Do freshwater fishes diversify faster than marine fishes? A test using state-dependent diversification analyses and molecular phylogenetics of new world silversides (atherinopsidae).

Freshwater habitats make up only ∼0.01% of available aquatic habitat and yet harbor 40% of all fish species, whereas marine habitats comprise >99% of available aquatic habitat and have only 60% of fish species. One possible explanation for this pattern is that diversification rates are higher in freshwater habitats than in marine habitats.

It's a family matter: molecular phylogenetics of Atheriniformes and the polyphyly of the surf silversides (family: Notocheiridae).

Phylogenetic relationships among families of Atheriniformes have long been problematic. The affinities of one of the most enigmatic lineages, surf silversides (Notocheiridae), have proven particularly elusive due to this taxon's unique morphology and rarity in museum collections. In this study, we use mitochondrial and nuclear sequence data to generate a phylogeny for seven of the eight families of Atheriniformes.

Permanent genetic resources added to Molecular Ecology Resources Database 1 October 2010-30 November 2010.

This article documents the addition of 277 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Ascochyta rabiei, Cambarellus chapalanus, Chionodraco hamatus, Coptis omeiensis, Cynoscion nebulosus, Daphnia magna, Gerbillus nigeriae, Isurus oxyrinchus, Lates calcarifer, Metacarcinus magister, Oplegnathus fasciatus, Pachycondyla verenae, Phaethon lepturus, Pimelodus grosskopfii, Rotylenchulus reniformis, Scomberomorus niphonius, Sepia esculenta, Terapon jarbua, Teratosphaeria cryptica and Thunnus obesus. These loci were cross-tested on the following species: Austropotamobius italicus, Cambarellus montezumae, Cambarellus puer, Cambarellus shufeldtii, Cambarellus texanus, Chionodraco myersi, Chionodraco rastrospinosus, Coptis chinensis, Coptis chinensis var.

Phylogenetic relationships of the North American cyprinid subgenus Hydrophlox.

Notropis is one of the largest genera of North American fishes and is composed of a number of morphologically diagnosed subgroups; however, the validity of many has not been tested in a phylogenetic framework. One such subgroup is the subgenus Hydrophlox, which is composed of brilliantly colored species that engage in the symbiotic reproductive behavior of nest association. Although they have long been recognized as a cohesive group due to their nuptial coloration and fin tuberculation, very little is known about the relationships of species within Hydrophlox.

Molecular systematics of the enigmatic Middle American genus Vieja (Teleostei: Cichlidae).

The genus Vieja represents a group of heroine cichlids (Teleostei: Cichlidae) distributed on the Atlantic and Pacific slopes of North and Central America from southern Mexico to Panama. Sixteen species of Vieja are presently recognized; however, based on long-standing taxonomic problems, the genus itself appears to be weakly defined. A number of different generic designations have been proposed for members of Vieja, and recent systematic studies of heroine cichlids have not specifically addressed the validity of the grouping and have not included all species in the genus.

Discordant molecular and morphological evolution in buffalofishes (Actinopterygii: Catostomidae).

Buffalofishes (Genus Ictiobus) are large, robust-bodied suckers adapted to large rivers and lakes of North America. Currently recognized species are readily diagnosed by morphological characters, and the group is known from fossils dating back to the Miocene. However, sympatrically occurring species in the Mississippi River Basin are known to hybridize in nature and in the laboratory.