Costa 2012 Oligocene killifishes from southern France: relationships, taxonomic position, and evidence of internal fertilization Abstract Phylogenetic relationships of five species of Prolebias from the Oligocene of southern France (P. aymardi, P. cephalotes, P. delphinensis, P. meridionalis, and P. stenoura) were examined under an analysis comprising 36 terminal taxa, representing all the main lineages of the order Cyprinodontiformes. It indicated Prolebias as a polyphyletic group, supporting Prolebias stenoura, the type species of the genus, as a valenciid monotypic lineage. Prolebias aymardi and P. delphinensis comprise a new valenciid genus, Francolebias, gen. nov., diagnosed by a unique morphology of pelvic bone, anterior proximal radials of the dorsal fin and anal fins, and hemal spines in putative males. The apomorphic specialized morphology of the anal fin and adjacent vertebrae is interpreted as evidence of an internal fertilization reproductive mode. Prolebias meridionalis is designated as the type species of a new monotypic cyprinodontid genus, Eurolebias, gen. nov., hypothesized to be the sister group to a clade comprising all other cyprinodontids, which is diagnosed by the apomorphic morphology of jaws, parhypural, and absence of parietals. Close relationships between P. cephalotes, P. egeranus from the lower Miocene of Czech Republic, and recent species of the poeciliid genus Pantanodon are corroborated on the basis of the apomorphic morphology of the dentary, pharyngobranchials, pelvic bone, and pelvic-fin rays, justifying the transference of those two species to the latter genus. The present study indicates that the European Oligocene fauna of cyprinodontiform fishes was greatly diversified when compared to its present poor fauna, comprising lineages now extinct or restricted to other continents. Costa 2018 Pantanodontidae (Teleostei, Cyprinodontiformes), the sister group to all other cyprinodontoid killifishes as inferred by molecular data Pantanodon, containing two African extant species and four European fossil species, for a long time had an uncertain position among the Cyprinodontiformes due to its peculiar morphology. In the last decades, Pantanodon has been considered closely related to African lamp-eyes of the Procatopodinae clade, which is contained in the Poeciliidae, a teleost fish family with a broad geographical distribution in Africa and the Americas. However, recent molecular studies have challenged the monophyly of the Poeciliidae, but the position of Pantanodon remained uncertain. We analysed one mitochondrial (COI) and five nuclear loci (GLYT1, MYH6, SH3PX3, RAG1, ENC1), a total of 5,083 bp, for 27 cyprinodontiform taxa and 6 outgroups, obtaining a well-supported phylogeny, in which the monophyly of Poeciliidae, as supported by morphological data is refuted. Pantanodon stuhlmanni, the type species of the genus, is recovered as the most basal cyprinodontoid lineage and other African taxa formerly placed in Poeciliidae are highly supported as more closely related to European non-poeciliid cyprinodontoid genera than to other taxa. Since the present tree topology is not compatible with the present classification of the Cyprinodontoidei, a new classification using available family group names is provided: Pantanodontidae is used for Pantanodon; Procatopodidae, for the African lamp-eye clade; and Fluviphylacidae, for the South American genus Fluviphylax. Poeciliidae is restricted to the American livebearers, hence restoring the classification generally used prior to 1981. Ghedotti 2000 Phylogenetic analysis and taxonomy of the poecilioid fishes Abstract Evidence from morphology is used to infer the phylogeny of the superfamily Poecilioidea using other cyprinodontoid fishes as outgroups. The three equally most parsimonious trees resulting from the phylogenetic analysis support the monophyly of the families Anablepidae and Poeciliidae with respect to each other, but the previous taxonomy within the Poeciliinae is not consistent with the resultant phylogenetic trees. The Poeciliidae is recognized with three subfamilies: the Aplocheilichthyinae containing solely Aplocheilichthys spilauchen, the Procatopodinae containing Fluviphylax (Fluviphylacini) and the African lamp-eyed killifishes (Procatopodini), and the Poeciliinae. The inferred hierarchical relationships of included suprageneric taxa are: ((Oxyzygonectinae, Anablepinae) (Aplocheilichthyinae ((Fluviphylacini, Procatopodini) (Alfarini (Priapellini (Gambusini (Heterandrini (Cnesterodontini (Girardini, Poeciliini))))))))). The tribe Alfarini is resurrected and a new tribe, the Priapellini, is described. Tomeurus gracilis is not the most basal poeciliine, and facultative viviparity in Tomeurus is not a plesiomorphic intermediate condition of viviparity retained from the common ancestor of poeciliines. Facultative viviparity in Tomeurus is the result of an evolutionary loss of obligate viviparity. Tomeurus gracilis is recognized as a member of the tribe Cnesterodontini. Lamprichthys tanganicus and Micropanchax pelagicus are not sister taxa, and the pelagic lacustrine habits of these two species are inferred to have evolved independently. Based on the principles of vicariance biogeography, the origin of the Poecilioidea is inferred to have occurred before the separation of Africa and South America. Full PDF Hrbek 2006 A phylogenetic and biogeographic perspective on the evolution of poeciliid fishes Abstract Phylogenetic relationships of members of the subfamily Poeciliinae (Cyprinodontiformes) are investigated to test alternate hypotheses of diversification resulting from the assembly of the Central America and the Caribbean from the Cretaceous period onwards. We use 4333 aligned base pairs of mitochondrial DNA and 1549 aligned base pairs of nuclear DNA from 55 samples representing 48 ingroup and seven outgroup species to test this hypothesis. Mitochondrial genes analyzed include those encoding the 12S and 16S ribosomal RNAs; transfer RNAs coding for valine, leucine, isoleucine, glutamine, methionine, tryptophan, alanine, asparagine, cysteine and tyrosine; and complete cytochrome b and NADH dehydrogenase subunit I and II; nuclear gene analyzed included the third exon of the recombination activation gene 1 (RAG1). Analyses of combined mtDNA and nuclear DNA data sets result in a well-supported phylogenetic hypothesis. This hypothesis is in conflict with the classical taxonomic assignment of genera into tribes and phylogenetic hypotheses based on the taxonomy; however, the molecular hypothesis defines nine clades that are geographically restricted and consistent with the geological evolution of Central America and the Caribbean. Our analyses support multiple colonization events of Middle America followed by a mix of vicariance and dispersal events. Moritz 2015 Multigene phylogeny of cyprinodontiform fishes suggests continental radiations and a rogue taxon position of Pantanodon We studied phylogenetic relationships among major clades in the tooth carps (Cyprinodontiformes) based on a concatenated DNA sequence alignment of two mitochondrial and three nuclear gene segments, totalling 2553 bp, in 66 ingroup terminals. The inferred tree supports monophyly of the major tooth carp subgroups, aplocheiloids and cyprinodontoids, and of several aplocheiloid subclades corresponding to the well-established families (Aplocheilidae, Nothobranchiidae, Rivulidae), each of which is restricted to major continental settings (India-Madagascar, Africa, South America). Contrary to previous molecular studies, our tree supports a sister-group relationship of the aplocheilids and nothobranchiids, rather than a nothobranchiid-rivulid clade. Within cyprinodontoids, the phylogeny matched more closely continent-scale distribution than current classification, suggesting that the delimitation of the families Cyprinodontidae, Poeciliidae, and Valenciidae is in need of revision. The East African Pantanodon stuhlmanni did not show close relationships with any other taxon in our analysis, suggesting that the phylogenetic position and classification of this rogue taxon is in need of further study. Reydon 2019 Species as natural entities, instrumental units and ranked taxa: new perspectives on the grouping and ranking problems This paper addresses the two problems that together constitute the species problem: the grouping problem (the question: on what basis should organisms be allocated to groups that are candidate species?) and the ranking problem (the question: on what basis should such groups be ranked as species?). We inquire what it means to say that species are real or that species are natural units, and argue for solutions to the grouping and ranking problems that allow us to be realists about species while at the same time avoiding the problems of a naive realism about species. In the account presented here, theoretical relevance is what constitutes the reality of species Alfaro 2018 Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary Brossard 2003

Campanella 2015 Multi-locus fossil-calibrated phylogeny of Atheriniformes 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. The phylogeny is calibrated with six carefully chosen fossil taxa to provide an explicit timeframe for the diversification of this group. Our results support the subdivision of Atheriniformes into two suborders (Atherinopsoidei and Atherinoidei), the nesting of Notocheirinae within Atherinopsidae, and the monophyly of tribe Menidiini, among others. We propose taxonomic changes for Atherinopsoidei, but a few weakly supported nodes in our phylogeny suggests that further study is necessary to support a revised taxonomy of Atherinoidei. The time-calibrated phylogeny was used to infer ancestral habitat reconstructions to explain the current distribution of marine and freshwater taxa. Based on these results, the current distribution of Atheriniformes is likely due to widespread marine dispersal along the margins of continents, infrequent trans-oceanic dispersal, and repeated invasion of freshwater habitats. This conclusion is supported by post-Gondwanan divergence times among families within the order, and a high probability of a marine ancestral habitat. "Divergence times and their estimated 95% highest posterior density (HPD) intervals place the origin of this order in the Late Cretaceous (72.8 Ma). Subsequent divergence between Old World and New World taxa started in the Paleogene and all currently recognized families originated during the Eocene and Oligocene (50-23 Ma). " Costa2018a Synchronic historical patterns of species diversification in seasonal aplocheiloid killifishes of the semi-arid Brazilian Caatinga The Caatinga is the largest nucleus of seasonally dry tropical forests in South America, but little is known about the evolutionary history and biogeography of endemic organisms. Evolutionary diversification and distribution of terrestrial vertebrates endemic to the Caatinga have been explained by palaeogeographical Neogene episodes, mostly related to changes in the course of the São Francisco River, the largest river in the region. Our objective is to estimate the timing of divergence of two endemic groups of short-lived seasonal killifishes inhabiting all ecoregions of the Caatinga, testing the occurrence of synchronic events of spatial diversification in light of available data on regional palaeogeography. We performed independent time-calibrated phylogenetic molecular analyses for two clades of sympatric and geographically widespread seasonal killifishes endemic to the Caatinga, the Hypsolebias antenori group and the Cynolebias alpha-clade. Our results consistently indicate that species diversification took place synchronically in both groups, as well as it is contemporary to diversification of other organisms adapted to life in the semi-arid Caatinga, including lizards and small mammals. Both groups originated during the Miocene, but species diversification started between the Late Miocene and Early Pliocene, when global cooling probably favoured the expansion of semi-arid areas. Synchronic diversification patterns found are chronologically related to Tertiary palaeogeographical reorganizations associated to continental drift and to Quaternary climatic changes, corroborating the recent proposal that South American biodiversity has been continuously shaped between the Late Paleogene and Pleistocene. Costa 1998 Phylogeny and Classification of Rivulidae Revisited PHYLOGENY AND CLASSIFICATION OF RIVULIDAE REVISITED: ORIGIN AND EVOLUTION OF ANNUALISM AND MINIATURIZATION IN RIVULID FISHES (CYPRINODONTIFORMES: APLOCHEILOIDEI) Wilson J.E.M. Costa Abstract. Costa, W.J.E. Phylogeny and classification of Rivulidae revisited: Origin and evolution of annualism and miniaturization in rivulid fishes (Cyprinodontiformes: Aplocheiloidei). J . Comp. Biol. 3(1):33-92. Phylogenetic relationships of rivulids are reexamined. The analysis comprises 243 characters in 46 terminal rivulid taxa. A total of 15 3 rivulid species were studied. Characters are primarily morphological, but some ecological and behavioral traits are also included. Monophyly of the Rivulidae is corroborated by 23 synapomorphies involving morphology and size of lateral ethmoid, frontal, lacrimal, dermosphenotic, autopalatine, preopercle, maxilla, first vertebra, absence of first postcleithrum, contiguity of branchiostegal and opercular membranes, and reduction of latero-sensory system of head. Twenty-seven genera are recognized in a formal classification obtained from the strict consensus tree for the 16 equally most parsimonious cladograms (consistency index 0.64, retention index 0.83, rescaled consistency index 0.51), presenting the following topology: ((Leptolebias (Cynopoecilus + Campellolebias)) (Spectrolebias ((Nematolebias gen. n. + Simpsonichthys) (Austrolebias gen. n. (Megalebias gen. n. + Cynolebias))))) (Rivulus (((Gnatholebias gen. n. + Pterolebias) (Aphyolebias gen. n. (Neofundulus + Trigonectes) (Micromoema gen. n. (Moema + Renova)))) (Millerichthys ((Rachovia (Austrofundulus + Terranatos)) (Pituna (Papiliolebias (Plesiolebias (Maratecoara + Stenolebias)))))))). Nematolebias includes species previously placed in Simpsonichthys, and Austrolebias and Megalebias are erected to cover monophyletic species assemblages previously classified in Cynolebias. Pterolebias is restricted to only two species, the remaining being transferred to Aphyolebias, Gnatholebias, and .Micromoema. Rivulus stellifer is transferred to Rachovia. Papiliolebias is considered a genus independent fiom Plesiolebias. Monophyly of all proposed genera are supported. The hypothesis of annualism constituting a single evolutionary event within Rivulidae and lost in Rivulus is equally parsimonious to the hypothesis of annualism arising twice among rivulids. Apomorphic ecological and behavioral features are considered to be coadaptive acquisitions associated to annualism, as well as some morphological tendencies, such as deep body, anteriorly positioned dorsal fin and elaborate cephalic neuromast pattern. Annualism among rivulids is considered to have been achieved by the successive colonization of peripheral aquatic habitats. Four evolutionary events of miniaturization are hypothesized to have occurred along the rivulid evolution. The unique common occurrence of all known miniatures in a single area of endemism suggests that the phenomenon was favored in this area. Key Words: Cladistics; Rivulidae; Neotropical Fishes; Historical Ecology; Miniaturization; Ichthyology; Annual fishes Huang 2016 Complete Mitochondrial Reveals a New Phylogenetic Perspective on the Brackish Water Goby Mugilogobius Group The Mugilogobius group consists of brackish water gobionellines widely distributed in the IndoWest Pacific region. Complete mitochondrial genome and morphological evidence was collected to estimate their phylogenetic relationship and taxonomic status. A total of 11 genera were sampled, including Brachygobius, Calamiana, Hemigobius, Mugilogobius, Pandaka, Pseudogobiopsis, Pseudogobius, Redigobius, Rhinogobius, Stigmatogobius, and Wuhanlinigobius, five of which were sequenced for the first time. A morphological phylogenetic tree was also reconstructed based on 35 characters. The molecular phylogenetic trees reveal that the Mugilogobius group contains four major clades. The present study also reveals that the adult male mouth size and forked sensory papillae row d can be considered as synapomorphies, and that the head pores on inter-orbital, anterior oculoscapular, and preopercular regions can be regarded as derived features among the Mugilogobius group. Furthermore, the absence of posterior oculoscapular pores may provide a clue for understanding the evolutionary history of the Mugilogobius group Li 2017 Molecular systematics and phylogenetic analysis of the Asian endemic freshwater sleepers : Li, H., He, Y., Jiang, J., Liu, Z., Li, C., Molecular systematics and phylogenetic analysis of the Asian endemic freshwater sleepers (Gobiiformes: Odontobutidae), Molecular Phylogenetics and Evolution (2017), doi: https://doi.org/10.1016/j.ympev.2017.12.026 Abstract The Odontobutidae is a group of freshwater sleepers endemic to East and Southeast Asia. The composition of the Odontobutidae is controversial and the systematics position of some species (e.g. Philypnus chalmersi) remains unknown. Phylogenetic relationship among the odontobutids has never been really tested due to the lack of informative morphological characters, and that molecular data have not been collected in many species. Here, we sampled 41 specimens, representing all known genera of the Odontobutidae except the Laotian genus Terateleotris, in addition to a disputable odontobutid species, Philypnus chalmersi and 14 outgroups(six families). We collected sequence data of 4,434 single-copy nuclear coding loci using gene capture and Illumina sequencing. A robust phylogeny of the odontobutids and outgroups was built, confirming that the Odontobutidae is monophyletic and sister to the Rhyacichthyidae. We verified that Sineleotris, Neodontobutis and Philypnus chalmersi are members of the Odontobutidae based on the resulting phylogeny as well as patterns of pectoral girdle examined by X-ray microtomography. We proposed a new genus Microdous for Philypnus chalmersi based on the new morphological and molecular evidences. The family of the Odontobutidae can be divided into two clades: Microdous (=Philypnus) sister to a group consisting of Micropercops and Sineleotris, and Odontobutis sister to a group unifying Perccottus and Neodontobutis. Divergence time among the odontobutids was estimated based on 100 most clock-like loci and three fossil calibration points using BEAST. Ancestral range of the family was reconstructed using Reconstruct Ancestral States in Phylogenies (RASP) and BioGeoBEARS. The results suggest that the common ancestor of the odontobutids originated around 30.8 Ma (20.7 - 42.0 Ma, 95% HPDs) in South China. Orogeny, climatic change and river capture might account for diversification and current distribution of the odontobutids. Rosen 1969 THE STRUCTURE AND RELATIONSHIPS OF THE PARACANTHOPTERYGIAN FISHES The work reported here was begun as a combined neontological and paleontological investigation to test the limits and validity of the paracanthopterygian group. Sonnenberg 2010 Description of Callopanchax sidibei (Nothobranchiidae: Epiplateinae), a new species of killifish from southwestern Guinea, West Africa A new species of the annual killifish genus Callopanchax (Nothobranchiidae: Epiplateinae) is described from coastal Guinea, West Africa. It is distinguished from its congeners by morphological and colour pattern characters including up to three irregular and interrupted horizontal stripes on blue flanks in males. A preliminary DNA study indicates that it is closely related with C. occidentalis and C. toddi, which is supported by the following apomorphic characters compared to the more distantly related C. monroviae: a dark red or black postopercular blotch and an origin of the dorsal fin anterior to or above the first ray of the anal fin. The species first turned up in commercial imports of ornamental fish from Guinea. The local collectors, the Sidibe family, are acknowledged for sharing their knowledge on this species and their support to the second author during his collections by naming it Callopanchax sidibei, new species. Currently it is only known from the type locality and is endemic to Guinea. VDZ 1994 powelli With comments on the concept of Genus.