EVOLUTIONARY ORIGIN AND EARLY BIOGEOGRAPHY OF OTOPHYSAN FISHES (OSTARIOPHYSI: TELEOSTEI)

The biogeography of the mega‐diverse, freshwater, and globally distributed Otophysi has received considerable attention. This attraction largely stems from assumptions as to their ancient origin, the clade being almost exclusively freshwater, and their suitability as to explanations of trans‐oceanic distributions. Despite multiple hypotheses explaining present‐day distributions, problems remain, precluding more parsimonious explanations. Underlying previous hypotheses are alternative phylogenies for Otophysi, uncertainties as to temporal diversification and assumptions integral to various explanations. We reexamine the origin and early diversification of this clade based on a comprehensive time‐calibrated, molecular‐based phylogenetic analysis and event‐based approaches for ancestral range inference of lineages. Our results do not corroborate current phylogenetic classifications of otophysans. We demonstrate Siluriformes are never sister to Gymnotiformes and Characiformes are most likely nonmonophyletic. Divergence time estimates specify a split between Cypriniformes and Characiphysi with the fragmentation of Pangea. The early diversification of characiphysans either predated, or was contemporary with, the separation of Africa and South America, and involved a combination of within‐ and between‐continental divergence events for these lineages. The intercontinental diversification of siluroids and characoids postdated major intercontinental tectonic fragmentations (<90 Mya). Post‐tectonic drift dispersal events are hypothesized to account for their current distribution patterns.     

TESTING HYPOTHESES OF NEURAL EVOLUTION IN GYMNOTIFORM ELECTRIC FISHES USING PHYLOGENETIC CHARACTER DATA

In this paper, we propose a method to test alternative hypotheses of phenotypic evolution. The method compares patterns observed in phylogenetic character data with patterns expected by explicit models of evolutionary process. Observed patterns of character-state diversity are assessed from four properties of character-state change derived from a phylogenetic analysis: the sequence and correlation of transformations on a cladogram and the spatial and functional localization of these transformations to parts of an organism. Patterns expressed in terms of the localization of transformations are compared with the expectations of null models that the number of transformations is proportional to measures of size or complexity. Deviations from the values expected by the null models are then compared with qualitative expectations of the models. The method is applied to characters in the nervous system of gymnotiform electric fishes. Patterns in the diversity of 63 reconstructed character-state changes are compared with the expectations of 10 published models of neural evolution. A total of 63 expectations are reviewed, of which 33 (52%) are found to be consistent with the gymnotiform neural data. In general, the models reviewed are not successful at making global predictions, in part because they have been cast in excessively general terms. The data support the conclusion that evolution in the nervous system of gymnotiforms has involved a mosaic of processes, each operating differentially on functional and developmental systems and at different spatial and temporal scales. The results also indicate that more refined models are required, each making more explicit predictions.     

TESTING FOR ANCIENT ADAPTIVE RADIATIONS IN NEOTROPICAL CICHLID FISHES

Most contemporary studies of adaptive radiation focus on relatively recent and geographically restricted clades. It is less clear whether diversification of ancient clades spanning entire continents is consistent with adaptive radiation. We used novel fossil calibrations to generate a chronogram of Neotropical cichlid fishes and to test whether patterns of lineage and morphological diversification are congruent with hypothesized adaptive radiations in South and Central America. We found that diversification in the Neotropical cichlid clade and the highly diverse tribe Geophagini was consistent with diversity‐dependent, early bursts of divergence followed by decreased rates of lineage accumulation. South American Geophagini underwent early rapid differentiation in body shape, expanding into novel morphological space characterized by elongate‐bodied predators. Divergence in head shape attributes associated with trophic specialization evolved under strong adaptive constraints in all Neotropical cichlid clades. The South American Cichlasomatini followed patterns consistent with constant rates of morphological divergence. Although morphological diversification in South American Heroini was limited, Eocene invasion of Central American habitats was followed by convergent diversification mirroring variation observed in Geophagini. Diversification in Neotropical cichlids was influenced by the early adaptive radiation of Geophagini, which potentially limited differentiation in other cichlid clades.     

CHLOROPLAST DNA EVOLUTION AND PHYLOGENETIC RELATIONSHIPS IN CLARKIA SECT. PERIPETASMA (ONAGRACEAE)

Restriction-site analysis of chloroplast DNA in Clarkia sect. Peripetasma (Onagraceae) was done to test previously proposed phylogenetic models. One hundred nineteen restriction-site mutations were identified among the nine species using 29 restriction enzymes, and these were used to construct rooted most parsimonious trees (Wagner and Dollo). A chloroplast DNA evolutionary clock could not be statistically rejected. Branch points of this tree were statistically tested by Felsenstein's bootstrap method. This tree 1) provided an unambiguous and detailed genealogical history for the section, 2) verified a previous partial phylogenetic model for the section based on gene duplications and differential silencing, 3) provided details of the phylogenetic model not inferred or expected based on morphology and reproductive isolation, and 4) indicated that morphology evolves at markedly different rates within and between lineages in the section.     

CORRELATED EVOLUTION OF BEAK MORPHOLOGY AND SONG IN THE NEOTROPICAL WOODCREEPER RADIATION

Mating signals may diversify as a byproduct of morphological adaptation to different foraging niches, potentially driving speciation. Although many studies have focused on the direct influence of ecological and sexual selection on signal divergence, the role of indirect mechanisms remains poorly understood. Using phenotypic and molecular datasets, we explored the interplay between morphological and vocal evolution in an avian radiation characterized by dramatic beak variation, the Neotropical woodcreepers (Dendrocolaptinae). We found evidence of a trade-off between the rate of repetition of song syllables and frequency bandwidth: slow paced songs had either narrow or wide frequency bandwidths, and bandwidth decreased as song pace increased. This bounded phenotypic space for song structure supports the hypothesis that passerine birds face a motor constraint during song production. Diversification of acoustic characters within this bounded space was correlated with diversification of beak morphology. In particular, species with larger beaks produced slower songs with narrower frequency bandwidths, suggesting that ecological selection on beak morphology influences the diversification of woodcreeper songs. Because songs in turn mediate mate choice and species recognition in birds, these results indicate a broader role for ecology in avian diversification.     

A PHYLOGENETIC ANALYSIS OF BODY SIZE EVOLUTION AND BIOGEOGRAPHY IN CHUCKWALLAS (SAUROMALUS) AND OTHER IGUANINES

The evolution of body size was reconstructed in chuckwallas (genus Sauromalus), large herbivorous lizards of southwest North America, using a phylogeny derived from sequence variation in the mitochondrial cytochrome b gene. The body mass of two endemic island species (S. hispidus and S. varius) is typically fivefold larger than mainland species. We tested the hypothesis that large body size has evolved on these islands in response to local ecological conditions against the alternative hypothesis that large size is simply retained from large iguanine ancestors. The most parsimonious tree topology depicts the insular gigantic Sauromalus as monophyletic, having diverged from a common ancestor on the Baja California peninsula after the radiation of smaller bodied clades. In a robustness analysis of this topology, we found general support for this tree over alternative topologies representing minimum evolution hypotheses that imply large body size is retained from large iguanine ancestors. The most parsimonious reconstruction of body size evolution implies a change from large to small size after the Sauromalus ancestor diverged from Iguana, and one reversal back to large size within Sauromalus. The large size increase in the gigantic clade contrasts with evolutionary stasis of small body size (for an iguanine) in mainland populations. The gigantic species show 3–4% total sequence divergence from S. obesus populations on the nearby Baja California peninsula, and mainland populations of S. obesus obesus show similar levels of divergence from each other. An analysis of character transitions and comparative behavior implicates predation, and its relaxation on isolated islands, as a strong selective force in Sauromalus. Patterns of genetic differentiation in Sauromalus and biogeographic implications are discussed.     

THE OCCURRENCE,EVOLUTION, AND PHYLOGENETIC SIGNIFICANCE OF PARENCHYMA IN COLEOCHAETE BRÉB. (CHLOROPHYTA)

Thalli of four species of the charophycean green alga Coleochaete Bréb.; C. irregularis, C. soluta, C. orbicularis, and C. scutata, were examined using light and electron microscopy. The parenchymatous nature of the plant bodies of C. orbicularis and C. scutata became apparent when the degree of cellular association in these species was compared with that of parenchymatous land plant tissues, the pseudoparenchymatous thalli of C. soluta, and the branched filaments of C. irregularis. Coleochaete soluta was shown to be morphologically and phylogenetically transitional between the more primitive branched filamentous species (C. irregularis) and the more advanced discoid species (C. orbicularis and C. scutata). The branching patterns observed in C. soluta suggested a possible pathway for the evolutionary development of land plant parenchyma from branched, filamentous charophycean green algae.     

鳇亚科棒花鱼属鱼类的分类与系统发育关系

逗亚科棒花鱼属鱼类的分类与系统发育关系尚未解决。研究选择线粒体Cyt b基因和核基因RAG1、MLH3及MSH6作为分子标记, 重建了棒花鱼属鱼类的系统发育关系, 并结合形态证据对该属鱼类进行了分类厘定。结果表明: 棒花鱼与钝吻棒花鱼是单系种。拉林棒花鱼与辽宁棒花鱼是并系种, 一起形成单系群。拉林棒花鱼+辽宁棒花鱼一起嵌套在小鳔逗属鱼类内部, 钝吻棒花鱼嵌套在片唇逗属鱼类内部。拉林棒花鱼+辽宁棒花鱼+钝吻棒花鱼+片唇逗属+胡逗属+小鳔逗属+琵琶逗属鱼类组成单系群, 它们一起与棒花鱼形成姊妹群关系。可量性状与可数性状均不能区分拉林棒花鱼和辽宁棒花鱼。结合系统发育关系与形态证据, 棒花鱼属鱼类的分类厘定如下: 棒花鱼属鱼类包括棒花鱼和平江棒花鱼(未取样); 辽宁棒花鱼是拉林棒花鱼的同物异名, 后者的分类位置有待进一步校订; 钝吻棒花鱼校订为钝吻片唇逗。     

鳇亚科似鳇属鱼类的物种界定和系统发育关系

逗亚科似逗属鱼类的物种界定保持争议, 系统发育关系尚待解决。研究取样似逗属鱼类所有种, 使用核基因多位点序列重建似逗属鱼类的系统发育关系, 运用分子的物种界定方法并结合形态特征分析厘定我国似逗属鱼类的分类。贝叶斯系统发育树结果表明: 桂林似逗与平江似逗是单系种; 似逗与扁嘴似逗是多系种, 前者包括五个谱系A至E, 后者包括两个谱系A与B。POFAD距离分析和Structurama分析的结果表明似逗和扁嘴似逗的每个谱系是独立遗传种群, BP & P分析结果强烈支持它们是不同种。*Beast物种树结果揭示: 扁嘴似逗谱系B位于似逗属鱼类的基部位置; 似逗谱系A与B是姊妹群关系, 似逗谱系C是扁嘴似逗谱系A的姊妹群, 它们一起与桂林似逗形成姊妹群关系; 似逗谱系D与E是姊妹群关系, 它们一起是平江似逗的姊妹群。结合形态证据, 对我国似逗属鱼类分类厘定如下: 限定严格意义似逗包括似逗谱系A+B; 恢复长吻似逗(Pseudogobio longirostris Mori, 1934)给予似逗谱系C分类名; 似逗谱系D与E是隐存种, 桂林似逗与平江似逗是有效种。     

东亚似鮈类鱼类的起源和演化

本文采用分支扩散法和分支离散法两种生物地理学方法分析了似　类的起源和演化。结果说明似类于第三纪末起源于中国北方的原始类,逐步向南扩散。在其物种分化过程中可能存在南北两个分化中心。     

CORRELATED EVOLUTION OF SEXUAL DIMORPHISM AND MALE DIMORPHISM IN A CLADE OF NEOTROPICAL HARVESTMEN

Secondary sexual traits increase male fitness, but may be maladaptive in females, generating intralocus sexual conflict that is ameliorated through sexual dimorphism. Sexual selection on males may also lead some males to avoid expenditure on secondary sexual traits and achieve copulations using alternative reproductive tactics (ARTs). Secondary sexual traits can increase or decrease fitness in males, depending on which ART they employ, generating intralocus tactical conflict that can be ameliorated through male dimorphism. Due to the evolutionary forces acting against intralocus sexual and tactical conflicts, male dimorphism could coevolve with sexual dimorphism, a hypothesis that we tested by investigating these dimorphisms across 48 harvestman species. Using three independently derived phylogenies, we consistently found that the evolution of sexual dimorphism was correlated with that of male dimorphism, and suggest that the major force behind this relationship is the similarity between selection against intralocus sexual conflict and selection against intralocus tactical conflict. We also found that transitions in male dimorphism were more likely in the presence of sexual dimorphism, indicating that if a sexually selected trait arises on an autosome and is expressed in both sexes, its suppression in females probably evolves earlier than its suppression in small males that adopt ARTs.     

THE EVOLUTION OF DIAPAUSE IN THE KILLIFISH FAMILY RIVULIDAE (ATHERINOMORPHA,CYPRINODONTIFORMES): A MOLECULAR PHYLOGENETIC AND BIOGEOGRAPHIC PERSPECTIVE

Phylogenetic relationships within the family Rivulidae (order Cyprinodontiformes) are investigated using 1972 aligned base pairs of mitochondrial DNA (mtDNA) for samples representing 66 species. Genes analyzed include those encoding the 12S ribosomal RNA; transfer RNAs for valine, glutamine, methionine, tryptophan, alanine, asparagine, cysteine, and tyrosine; complete NADH dehydrogenase subunit II; and part of cytochrome oxidase I. Parsimony analysis of the aligned mtDNA sequences results in a single most parsimonious tree. The phylogeny reveals two independent origins of developmental diapause within the family Rivulidae. It is unlikely that diapause evolved de novo in each group, suggesting that the presence or absence of diapause is the result of developmental switches between alternative stabilized pathways. Phylogeny of the family Rivulidae shows high concordance with predictions derived from the geological history of South America and Central America. Basal lineages in the rivulid phylogeny are distributed primarily on geologically old areas, whereas more nested lineages occur in geologically younger areas. However, there is little concordance between the molecular phylogeny and currently available morphological hypotheses and existing taxonomies. Based on the mtDNA phylogeny, the genera Pterolebias, Rivulus, Pituna, and Plesiolebias are considered nonmonophyletic and warrant taxonomic reassessment.     

PATTERNS OF GENOME SIZE EVOLUTION IN TETRAODONTIFORM FISHES

Abstract We used flow cytometry to measure genome size in 15 species from seven families and subfamilies of tetraodontiform fishes. Previous studies have found that smooth pufferfishes (Tetraodontidae) have the smallest genome of any vertebrate measured to date (0.7–1.0 picograms diploid). We found that spiny pufferfishes (Diodontidae, sister group to the smooth puffers) possess a genome that is about two times larger (1.6–1.8 pg). Mola mola, a member of the sister group to Diodontidae and Tetraodontidae, also has a relatively large genome (1.7 pg). Parsimony analysis of this pattern indicates that the plesiomorphic condition for Molidae (Diodontidae, Tetraodontidae) is a genome size of 1.6–1.8 pg, and that tiny genome size is a derived character unique to smooth puffers. However, an alternative explanation is that the ancestor of Tetraodontidae acquired a heritable tendency toward decreasing genome size, such as a new or modified deletion mechanism, and genome size in all of the tetraodontid lineages has been decreasing in parallel since the split from Diodontidae. Small genome size (1.1–1.3 pg) also appears to have evolved independently in some members of Balistoidea (triggerfishes and filefishes) within Tetraodontiformes.     

PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION IN XIPHOPHORUS FISHES

Hybridization is increasingly being recognized as a widespread process, even between ecologically and behaviorally divergent animal species. Determining phylogenetic relationships in the presence of hybridization remains a major challenge for evolutionary biologists, but advances in sequencing technology and phylogenetic techniques are beginning to address these challenges. Here we reconstruct evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by remarkable morphological diversity and behavioral barriers to interspecific mating. Past attempts to reconstruct phylogenetic relationships within Xiphophorus have produced conflicting results. Because many of the 26 species in the genus are interfertile, these conflicts are likely due to hybridization. Using genomic data, we resolve a high‐confidence species tree of Xiphophorus that accounts for both incomplete lineage sorting and hybridization. Our results allow us to reexamine a long‐standing controversy about the evolution of the sexually selected sword in Xiphophorus, and demonstrate that hybridization has been strikingly widespread in the evolutionary history of this genus.